1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 33b1 August 15, 2006 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.6.32-573.7.1.el6.x86_64(x86_64)@kont Created on 2/10/16 at 22:30:43 by user: annesc Maximum number of ATOMS: 360720, and RESidues: 120240 Current HEAP size: 10240000, and STACK size: 10000000 RDTITL> * GENERATE PSF AND CHARMM COORDINATE SET FOR RDTITL> * HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * CHARMM> CHARMM> set name "helix_allh" Parameter: NAME <- ""helix_allh"" CHARMM> set output mini_@name ! this is the output : replace by any other complexe name ! Parameter: NAME -> ""helix_allh"" Parameter: OUTPUT <- "MINI_"helix_allh"" CHARMM> CHARMM> CHARMM> ! Read in Topology and Parameter files CHARMM> !_____________________________________ CHARMM> CHARMM> open unit 1 card read name "../lib/toph19_eef1.1.inp" VOPEN> Attempting to open::../lib/toph19_eef1.1.inp:: OPNLGU> Unit 1 opened for READONLY access to ../lib/toph19_eef1.1.inp CHARMM> read RTF card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 TITLE> * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL TITLE> * THIS DIFFERS FROM TOPH19_EEF1.INP IN: TITLE> * SCALED DOWN PARTIAL CHARGE DISTRIBUTIONS OF PSEUDO-IONIC AND TITLE> * POLAR SIDECHAINS, CTER, NTER TITLE> * INCLUDES (DE-)PROTONATED IONIC SIDECHAINS, PSEUDO-IONIC HIS AND AIB TITLE> * IN TYR CZ IS NOW TYPE CR TITLE> * THIS IS WORK IN PROGRESS. NO EXTENSIVE TESTS HAVE BEEN MADE. TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 card read name "../lib/param19_eef1.1.inp" VOPEN> Attempting to open::../lib/param19_eef1.1.inp:: OPNLGU> Unit 1 opened for READONLY access to ../lib/param19_eef1.1.inp CHARMM> read PARA card unit 1 PARAMETER FILE BEING READ FROM UNIT 1 TITLE> * - PARAMETER FILE PARAM19 * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 TITLE> * PARRDR> NOTE: atom type "CR " is removed from previous group PARRDR> NOTE: atom type "OC " is removed from previous group PARRDR> NOTE: atom type "OT " is removed from previous group PARRDR> NOTE: atom type "OH2 " is removed from previous group PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> CHARMM> CHARMM> ! Read in structure and psf file of the Bovine alpha lactalbumine 1f6r CHARMM> !_____________________________________________________________________ CHARMM> CHARMM> open read unit 9 card name ../lib/@name.psf Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../lib/helix_allh.psf:: OPNLGU> Unit 9 opened for READONLY access to ../lib/helix_allh.psf CHARMM> read psf card unit 9 MAINIO> Protein structure file being read from unit 9. TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: annesc TITLE> * PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared. PSFSUM> Summary of the structure file counters : Number of segments = 1 Number of residues = 31 Number of atoms = 297 Number of groups = 112 Number of bonds = 302 Number of angles = 429 Number of dihedrals = 172 Number of impropers = 143 Number of cross-terms = 0 Number of HB acceptors = 43 Number of HB donors = 52 Number of NB exclusions = 48 Total charge = -0.00000 CHARMM> close unit 9 VCLOSE: Closing unit 9 with status "KEEP" CHARMM> CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> ! write the pdb coordinates (+hydrogens) in the comp set CHARMM> !coor copy comp CHARMM> CHARMM> ! Specify non bonded interactions and fast energy routines CHARMM> !faster 5 CHARMM> CHARMM> NBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - CHARMM> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 0 atom pairs and 0 atom exclusions. There are 0 group pairs and 0 group exclusions. with mode 5 found 756 exclusions and 503 interactions(1-4) found 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21392 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES CHARMM> !adm jr., 5/08/91, suggested cutoff scheme CHARMM> CHARMM> energy NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21392 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21392 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 331280.27532 0.00000 132180.77795 ENER INTERN> 321.17001 198.53966 0.00000 10.05373 4.01000 ENER EXTERN> 330978.11223 -231.61030 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> ! some useful protein selection definitions CHARMM> ! to see CHARMM> stream ../lib/prot.def VOPEN> Attempting to open::../lib/prot.def:: OPNLGU> Unit 99 opened for READONLY access to ../lib/prot.def INPUT STREAM SWITCHING TO UNIT 99 RDTITL> * PROTEIN SELECTION DEFINITION RDTITL> * Parameter: IN1 <- "" CHARMM> CHARMM> define prot sele ( segid prot) end SELRPN> 297 atoms have been selected out of 297 CHARMM> define water sele ( segid solv) end SELRPN> 0 atoms have been selected out of 297 CHARMM> define nonh sele ( .not. hydrogen ) end SELRPN> 245 atoms have been selected out of 297 CHARMM> define trace sele ( type ca ) end SELRPN> 31 atoms have been selected out of 297 CHARMM> define back sele ( type n .or. type ca .or. type c ) end SELRPN> 93 atoms have been selected out of 297 CHARMM> define main sele ( type n .or. type ca .or. type c .or. type o) end SELRPN> 123 atoms have been selected out of 297 CHARMM> define side sele ( (.not. main) ) end SELRPN> 174 atoms have been selected out of 297 CHARMM> VCLOSE: Closing unit 99 with status "KEEP" RETURNING TO INPUT STREAM 5 CHARMM> CHARMM> !rms difference between initial and minimized structures CHARMM> open unit 11 write form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for WRITE access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *# JOBNAME: MINI_"helix_allh" RDTITL> *# RMS COORDINATE DEVIATIONS WITH MINIMIZATION STEP NO. RDTITL> *# STEP PROT PEPT WATER TRACE RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> !Energy variations during minimization CHARMM> open unit 12 write form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for WRITE access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *# JOBNAME: MINI_"helix_allh" RDTITL> *# ENERGY CONTRIBUTIONS WITH MINIMIZATION STEP NO. RDTITL> *# GRMS AND ENER ARE CALCULATED W/OUT HARMONIC RESTRAINTS RDTITL> * CHARMM> !*# STEP ENER ELEC VDW BOND ANGL DIHE IMPR UREY USER CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> !===================================================== CHARMM> ! Specify energy minimization inside command loop CHARMM> !===================================================== CHARMM> CHARMM> set 1 0 ! loop index (step count) Parameter: 1 <- "0" CHARMM> set 2 500 ! step increment (no. of minimization sd steps each pass) Parameter: 2 <- "500" CHARMM> set 7 100 ! step increment (no. of minimization conj steps each pass) Parameter: 7 <- "100" CHARMM> set 8 600 ! total nb of min. steps Parameter: 8 <- "600" CHARMM> set 3 12000 ! step limit Parameter: 3 <- "12000" CHARMM> set 4 800 ! coordinate dump frequency. Parameter: 4 <- "800" CHARMM> set 5 0 ! coordinate dump counter. Parameter: 5 <- "0" CHARMM> set 6 5 ! nprint Parameter: 6 <- "5" CHARMM> CHARMM> CHARMM> ! Initialize harmonic constraint potential. CHARMM> ! cons harm : hold atoms in place , Exponentiel harmonic constraints CHARMM> CONS HARM EXPOnent 2 FORCe 1 CSTRAN: Harmonic Restraints ABSOlute type as set number 1. Number of selected atoms: 297 Reference coordinates set to main coordinates. Mass weighting will NOT be used for new restraints. The force constant of 1.00000 will be used. An exponent of 2 will be used. The XYZ scale factors are: 1.00000 1.00000 1.00000 A total of 297 atoms are restrained. CHARMM> CHARMM> ! { very tight on backbone of pcna } CHARMM> SCALar CONSTraint SET 250. SELEct ( prot .AND. main ) END SELRPN> 123 atoms have been selected out of 297 CHARMM> CHARMM> ! { quite tight on sidechains of pcna } CHARMM> SCALar CONSTraint SET 200. SELEct ( prot .AND. side ) END SELRPN> 174 atoms have been selected out of 297 CHARMM> CHARMM> CHARMM> !SCALar CONSTraint SET 50. SELEct ( resname TIP3 ) END CHARMM> !SCALar CONSTraint SET 25. SELEct (side ) END CHARMM> CHARMM> ! to check CHARMM> SCAlar CONSTraint SHOW ( PROT LYS 1 HT1 ) 200.00 ( PROT LYS 1 HT2 ) 200.00 ( PROT LYS 1 N ) 250.00 ( PROT LYS 1 HT3 ) 200.00 ( PROT LYS 1 CA ) 250.00 ( PROT LYS 1 CB ) 200.00 ( PROT LYS 1 CG ) 200.00 ( PROT LYS 1 CD ) 200.00 ( PROT LYS 1 CE ) 200.00 ( PROT LYS 1 NZ ) 200.00 ( PROT LYS 1 HZ1 ) 200.00 ( PROT LYS 1 HZ2 ) 200.00 ( PROT LYS 1 HZ3 ) 200.00 ( PROT LYS 1 C ) 250.00 ( PROT LYS 1 O ) 250.00 ( PROT MET 2 N ) 250.00 ( PROT MET 2 H ) 200.00 ( PROT MET 2 CA ) 250.00 ( PROT MET 2 CB ) 200.00 ( PROT MET 2 CG ) 200.00 ( PROT MET 2 SD ) 200.00 ( PROT MET 2 CE ) 200.00 ( PROT MET 2 C ) 250.00 ( PROT MET 2 O ) 250.00 ( PROT LYS 3 N ) 250.00 ( PROT LYS 3 H ) 200.00 ( PROT LYS 3 CA ) 250.00 ( PROT LYS 3 CB ) 200.00 ( PROT LYS 3 CG ) 200.00 ( PROT LYS 3 CD ) 200.00 ( PROT LYS 3 CE ) 200.00 ( PROT LYS 3 NZ ) 200.00 ( PROT LYS 3 HZ1 ) 200.00 ( PROT LYS 3 HZ2 ) 200.00 ( PROT LYS 3 HZ3 ) 200.00 ( PROT LYS 3 C ) 250.00 ( PROT LYS 3 O ) 250.00 ( PROT ALA 4 N ) 250.00 ( PROT ALA 4 H ) 200.00 ( PROT ALA 4 CA ) 250.00 ( PROT ALA 4 CB ) 200.00 ( PROT ALA 4 C ) 250.00 ( PROT ALA 4 O ) 250.00 ( PROT VAL 5 N ) 250.00 ( PROT VAL 5 H ) 200.00 ( PROT VAL 5 CA ) 250.00 ( PROT VAL 5 CB ) 200.00 ( PROT VAL 5 CG1 ) 200.00 ( PROT VAL 5 CG2 ) 200.00 ( PROT VAL 5 C ) 250.00 ( PROT VAL 5 O ) 250.00 ( PROT MET 6 N ) 250.00 ( PROT MET 6 H ) 200.00 ( PROT MET 6 CA ) 250.00 ( PROT MET 6 CB ) 200.00 ( PROT MET 6 CG ) 200.00 ( PROT MET 6 SD ) 200.00 ( PROT MET 6 CE ) 200.00 ( PROT MET 6 C ) 250.00 ( PROT MET 6 O ) 250.00 ( PROT ILE 7 N ) 250.00 ( PROT ILE 7 H ) 200.00 ( PROT ILE 7 CA ) 250.00 ( PROT ILE 7 CB ) 200.00 ( PROT ILE 7 CG2 ) 200.00 ( PROT ILE 7 CG1 ) 200.00 ( PROT ILE 7 CD ) 200.00 ( PROT ILE 7 C ) 250.00 ( PROT ILE 7 O ) 250.00 ( PROT GLY 8 N ) 250.00 ( PROT GLY 8 H ) 200.00 ( PROT GLY 8 CA ) 250.00 ( PROT GLY 8 C ) 250.00 ( PROT GLY 8 O ) 250.00 ( PROT ALA 9 N ) 250.00 ( PROT ALA 9 H ) 200.00 ( PROT ALA 9 CA ) 250.00 ( PROT ALA 9 CB ) 200.00 ( PROT ALA 9 C ) 250.00 ( PROT ALA 9 O ) 250.00 ( PROT CYS 10 N ) 250.00 ( PROT CYS 10 H ) 200.00 ( PROT CYS 10 CA ) 250.00 ( PROT CYS 10 CB ) 200.00 ( PROT CYS 10 SG ) 200.00 ( PROT CYS 10 C ) 250.00 ( PROT CYS 10 O ) 250.00 ( PROT PHE 11 N ) 250.00 ( PROT PHE 11 H ) 200.00 ( PROT PHE 11 CA ) 250.00 ( PROT PHE 11 CB ) 200.00 ( PROT PHE 11 CG ) 200.00 ( PROT PHE 11 CD1 ) 200.00 ( PROT PHE 11 CD2 ) 200.00 ( PROT PHE 11 CE1 ) 200.00 ( PROT PHE 11 CE2 ) 200.00 ( PROT PHE 11 CZ ) 200.00 ( PROT PHE 11 C ) 250.00 ( PROT PHE 11 O ) 250.00 ( PROT LEU 12 N ) 250.00 ( PROT LEU 12 H ) 200.00 ( PROT LEU 12 CA ) 250.00 ( PROT LEU 12 CB ) 200.00 ( PROT LEU 12 CG ) 200.00 ( PROT LEU 12 CD1 ) 200.00 ( PROT LEU 12 CD2 ) 200.00 ( PROT LEU 12 C ) 250.00 ( PROT LEU 12 O ) 250.00 ( PROT ILE 13 N ) 250.00 ( PROT ILE 13 H ) 200.00 ( PROT ILE 13 CA ) 250.00 ( PROT ILE 13 CB ) 200.00 ( PROT ILE 13 CG2 ) 200.00 ( PROT ILE 13 CG1 ) 200.00 ( PROT ILE 13 CD ) 200.00 ( PROT ILE 13 C ) 250.00 ( PROT ILE 13 O ) 250.00 ( PROT ASH 14 N ) 250.00 ( PROT ASH 14 H ) 200.00 ( PROT ASH 14 CA ) 250.00 ( PROT ASH 14 CB ) 200.00 ( PROT ASH 14 CG ) 200.00 ( PROT ASH 14 OD1 ) 200.00 ( PROT ASH 14 OD2 ) 200.00 ( PROT ASH 14 HD2 ) 200.00 ( PROT ASH 14 C ) 250.00 ( PROT ASH 14 O ) 250.00 ( PROT PHE 15 N ) 250.00 ( PROT PHE 15 H ) 200.00 ( PROT PHE 15 CA ) 250.00 ( PROT PHE 15 CB ) 200.00 ( PROT PHE 15 CG ) 200.00 ( PROT PHE 15 CD1 ) 200.00 ( PROT PHE 15 CD2 ) 200.00 ( PROT PHE 15 CE1 ) 200.00 ( PROT PHE 15 CE2 ) 200.00 ( PROT PHE 15 CZ ) 200.00 ( PROT PHE 15 C ) 250.00 ( PROT PHE 15 O ) 250.00 ( PROT MET 16 N ) 250.00 ( PROT MET 16 H ) 200.00 ( PROT MET 16 CA ) 250.00 ( PROT MET 16 CB ) 200.00 ( PROT MET 16 CG ) 200.00 ( PROT MET 16 SD ) 200.00 ( PROT MET 16 CE ) 200.00 ( PROT MET 16 C ) 250.00 ( PROT MET 16 O ) 250.00 ( PROT PHE 17 N ) 250.00 ( PROT PHE 17 H ) 200.00 ( PROT PHE 17 CA ) 250.00 ( PROT PHE 17 CB ) 200.00 ( PROT PHE 17 CG ) 200.00 ( PROT PHE 17 CD1 ) 200.00 ( PROT PHE 17 CD2 ) 200.00 ( PROT PHE 17 CE1 ) 200.00 ( PROT PHE 17 CE2 ) 200.00 ( PROT PHE 17 CZ ) 200.00 ( PROT PHE 17 C ) 250.00 ( PROT PHE 17 O ) 250.00 ( PROT PHE 18 N ) 250.00 ( PROT PHE 18 H ) 200.00 ( PROT PHE 18 CA ) 250.00 ( PROT PHE 18 CB ) 200.00 ( PROT PHE 18 CG ) 200.00 ( PROT PHE 18 CD1 ) 200.00 ( PROT PHE 18 CD2 ) 200.00 ( PROT PHE 18 CE1 ) 200.00 ( PROT PHE 18 CE2 ) 200.00 ( PROT PHE 18 CZ ) 200.00 ( PROT PHE 18 C ) 250.00 ( PROT PHE 18 O ) 250.00 ( PROT GLU 19 N ) 250.00 ( PROT GLU 19 H ) 200.00 ( PROT GLU 19 CA ) 250.00 ( PROT GLU 19 CB ) 200.00 ( PROT GLU 19 CG ) 200.00 ( PROT GLU 19 CD ) 200.00 ( PROT GLU 19 OE1 ) 200.00 ( PROT GLU 19 OE2 ) 200.00 ( PROT GLU 19 C ) 250.00 ( PROT GLU 19 O ) 250.00 ( PROT SER 20 N ) 250.00 ( PROT SER 20 H ) 200.00 ( PROT SER 20 CA ) 250.00 ( PROT SER 20 CB ) 200.00 ( PROT SER 20 OG ) 200.00 ( PROT SER 20 HG ) 200.00 ( PROT SER 20 C ) 250.00 ( PROT SER 20 O ) 250.00 ( PROT THR 21 N ) 250.00 ( PROT THR 21 H ) 200.00 ( PROT THR 21 CA ) 250.00 ( PROT THR 21 CB ) 200.00 ( PROT THR 21 OG1 ) 200.00 ( PROT THR 21 HG1 ) 200.00 ( PROT THR 21 CG2 ) 200.00 ( PROT THR 21 C ) 250.00 ( PROT THR 21 O ) 250.00 ( PROT GLY 22 N ) 250.00 ( PROT GLY 22 H ) 200.00 ( PROT GLY 22 CA ) 250.00 ( PROT GLY 22 C ) 250.00 ( PROT GLY 22 O ) 250.00 ( PROT SER 23 N ) 250.00 ( PROT SER 23 H ) 200.00 ( PROT SER 23 CA ) 250.00 ( PROT SER 23 CB ) 200.00 ( PROT SER 23 OG ) 200.00 ( PROT SER 23 HG ) 200.00 ( PROT SER 23 C ) 250.00 ( PROT SER 23 O ) 250.00 ( PROT GLN 24 N ) 250.00 ( PROT GLN 24 H ) 200.00 ( PROT GLN 24 CA ) 250.00 ( PROT GLN 24 CB ) 200.00 ( PROT GLN 24 CG ) 200.00 ( PROT GLN 24 CD ) 200.00 ( PROT GLN 24 OE1 ) 200.00 ( PROT GLN 24 NE2 ) 200.00 ( PROT GLN 24 HE21 ) 200.00 ( PROT GLN 24 HE22 ) 200.00 ( PROT GLN 24 C ) 250.00 ( PROT GLN 24 O ) 250.00 ( PROT GLU 25 N ) 250.00 ( PROT GLU 25 H ) 200.00 ( PROT GLU 25 CA ) 250.00 ( PROT GLU 25 CB ) 200.00 ( PROT GLU 25 CG ) 200.00 ( PROT GLU 25 CD ) 200.00 ( PROT GLU 25 OE1 ) 200.00 ( PROT GLU 25 OE2 ) 200.00 ( PROT GLU 25 C ) 250.00 ( PROT GLU 25 O ) 250.00 ( PROT GLN 26 N ) 250.00 ( PROT GLN 26 H ) 200.00 ( PROT GLN 26 CA ) 250.00 ( PROT GLN 26 CB ) 200.00 ( PROT GLN 26 CG ) 200.00 ( PROT GLN 26 CD ) 200.00 ( PROT GLN 26 OE1 ) 200.00 ( PROT GLN 26 NE2 ) 200.00 ( PROT GLN 26 HE21 ) 200.00 ( PROT GLN 26 HE22 ) 200.00 ( PROT GLN 26 C ) 250.00 ( PROT GLN 26 O ) 250.00 ( PROT LYS 27 N ) 250.00 ( PROT LYS 27 H ) 200.00 ( PROT LYS 27 CA ) 250.00 ( PROT LYS 27 CB ) 200.00 ( PROT LYS 27 CG ) 200.00 ( PROT LYS 27 CD ) 200.00 ( PROT LYS 27 CE ) 200.00 ( PROT LYS 27 NZ ) 200.00 ( PROT LYS 27 HZ1 ) 200.00 ( PROT LYS 27 HZ2 ) 200.00 ( PROT LYS 27 HZ3 ) 200.00 ( PROT LYS 27 C ) 250.00 ( PROT LYS 27 O ) 250.00 ( PROT SER 28 N ) 250.00 ( PROT SER 28 H ) 200.00 ( PROT SER 28 CA ) 250.00 ( PROT SER 28 CB ) 200.00 ( PROT SER 28 OG ) 200.00 ( PROT SER 28 HG ) 200.00 ( PROT SER 28 C ) 250.00 ( PROT SER 28 O ) 250.00 ( PROT GLY 29 N ) 250.00 ( PROT GLY 29 H ) 200.00 ( PROT GLY 29 CA ) 250.00 ( PROT GLY 29 C ) 250.00 ( PROT GLY 29 O ) 250.00 ( PROT VAL 30 N ) 250.00 ( PROT VAL 30 H ) 200.00 ( PROT VAL 30 CA ) 250.00 ( PROT VAL 30 CB ) 200.00 ( PROT VAL 30 CG1 ) 200.00 ( PROT VAL 30 CG2 ) 200.00 ( PROT VAL 30 C ) 250.00 ( PROT VAL 30 O ) 250.00 ( PROT TRP 31 N ) 250.00 ( PROT TRP 31 H ) 200.00 ( PROT TRP 31 CA ) 250.00 ( PROT TRP 31 CB ) 200.00 ( PROT TRP 31 CG ) 200.00 ( PROT TRP 31 CD2 ) 200.00 ( PROT TRP 31 CE2 ) 200.00 ( PROT TRP 31 CE3 ) 200.00 ( PROT TRP 31 CD1 ) 200.00 ( PROT TRP 31 NE1 ) 200.00 ( PROT TRP 31 HE1 ) 200.00 ( PROT TRP 31 CZ2 ) 200.00 ( PROT TRP 31 CZ3 ) 200.00 ( PROT TRP 31 CH2 ) 200.00 ( PROT TRP 31 C ) 250.00 ( PROT TRP 31 OT1 ) 200.00 ( PROT TRP 31 OT2 ) 200.00 CHARMM> CHARMM> !stop ! OK CHARMM> CHARMM> !do @2 steps of steepest descent with constraints CHARMM> label mini CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21392 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21392 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- MINI> 0 331280.27532 0.00000 132180.77795 0.02000 MINI INTERN> 321.17001 198.53966 0.00000 10.05373 4.01000 MINI EXTERN> 330978.11223 -231.61030 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 3398.10756 327882.16775 61.14737 0.02074 MINI INTERN> 597.24324 268.27832 0.00000 10.43345 101.76159 MINI EXTERN> 1865.25991 -129.79448 0.00000 0.00000 0.00000 MINI CONSTR> 684.92553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21365 ATOM PAIRS WERE FOUND FOR ATOM LIST 748 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 2523.61393 874.49363 19.87520 0.00896 MINI INTERN> 134.66976 163.38463 0.00000 12.74600 32.80890 MINI EXTERN> 1113.71683 -125.29078 0.00000 0.00000 0.00000 MINI CONSTR> 1191.57860 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 2485.82292 37.79101 7.40613 0.00387 MINI INTERN> 127.85937 170.11055 0.00000 13.69680 42.35291 MINI EXTERN> 987.13984 -124.04195 0.00000 0.00000 0.00000 MINI CONSTR> 1268.70541 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21362 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 2481.14186 4.68106 4.25429 0.00167 MINI INTERN> 114.08112 164.97815 0.00000 13.58915 38.01401 MINI EXTERN> 1027.82953 -124.17571 0.00000 0.00000 0.00000 MINI CONSTR> 1246.82560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 2479.32187 1.81999 0.20331 0.00030 MINI INTERN> 117.21916 165.66467 0.00000 13.78836 39.57019 MINI EXTERN> 1012.06986 -124.26934 0.00000 0.00000 0.00000 MINI CONSTR> 1255.27896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 750 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 2479.27030 0.05156 0.21041 0.00013 MINI INTERN> 117.05071 165.24985 0.00000 13.94013 39.55515 MINI EXTERN> 1012.70810 -124.29933 0.00000 0.00000 0.00000 MINI CONSTR> 1255.06570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 2479.24318 0.02713 0.23218 0.00013 MINI INTERN> 116.83872 165.04926 0.00000 14.03889 39.49496 MINI EXTERN> 1013.12373 -124.30462 0.00000 0.00000 0.00000 MINI CONSTR> 1255.00222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 750 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 2479.22749 0.01569 0.26151 0.00014 MINI INTERN> 116.75680 164.89010 0.00000 14.11963 39.51094 MINI EXTERN> 1013.27745 -124.31298 0.00000 0.00000 0.00000 MINI CONSTR> 1254.98554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 2479.20850 0.01899 0.07631 0.00006 MINI INTERN> 116.66165 165.02480 0.00000 14.17069 39.56449 MINI EXTERN> 1012.16566 -124.29598 0.00000 0.00000 0.00000 MINI CONSTR> 1255.91718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 2479.20090 0.00760 0.14368 0.00006 MINI INTERN> 116.48522 164.91166 0.00000 14.22772 39.56854 MINI EXTERN> 1012.43779 -124.29519 0.00000 0.00000 0.00000 MINI CONSTR> 1255.86515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 2479.19533 0.00557 0.14355 0.00006 MINI INTERN> 116.42783 164.87147 0.00000 14.27383 39.57264 MINI EXTERN> 1012.37129 -124.29492 0.00000 0.00000 0.00000 MINI CONSTR> 1255.97319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 750 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 2479.19009 0.00524 0.03733 0.00003 MINI INTERN> 116.52500 164.81894 0.00000 14.31126 39.57738 MINI EXTERN> 1012.26297 -124.30438 0.00000 0.00000 0.00000 MINI CONSTR> 1255.99891 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 2479.18710 0.00298 0.04788 0.00003 MINI INTERN> 116.51456 164.77755 0.00000 14.34969 39.58120 MINI EXTERN> 1012.18910 -124.30693 0.00000 0.00000 0.00000 MINI CONSTR> 1256.08194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 750 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 2479.18536 0.00174 0.05498 0.00003 MINI INTERN> 116.48900 164.73097 0.00000 14.37815 39.58395 MINI EXTERN> 1012.21451 -124.30924 0.00000 0.00000 0.00000 MINI CONSTR> 1256.09802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 2479.18444 0.00093 0.07744 0.00003 MINI INTERN> 116.40335 164.67028 0.00000 14.39828 39.58456 MINI EXTERN> 1012.42218 -124.30946 0.00000 0.00000 0.00000 MINI CONSTR> 1256.01526 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 750 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 2479.18357 0.00086 0.06656 0.00003 MINI INTERN> 116.41424 164.65819 0.00000 14.41670 39.58731 MINI EXTERN> 1012.32306 -124.31088 0.00000 0.00000 0.00000 MINI CONSTR> 1256.09494 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 2479.18262 0.00095 0.02501 0.00001 MINI INTERN> 116.37019 164.68668 0.00000 14.42882 39.58637 MINI EXTERN> 1012.18441 -124.30568 0.00000 0.00000 0.00000 MINI CONSTR> 1256.23183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 2479.18232 0.00030 0.03227 0.00001 MINI INTERN> 116.38086 164.68993 0.00000 14.44136 39.58766 MINI EXTERN> 1012.07615 -124.30585 0.00000 0.00000 0.00000 MINI CONSTR> 1256.31221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 2479.18207 0.00025 0.02851 0.00002 MINI INTERN> 116.34593 164.66398 0.00000 14.45068 39.58762 MINI EXTERN> 1012.16527 -124.30604 0.00000 0.00000 0.00000 MINI CONSTR> 1256.27464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 97 2479.18194 0.00014 0.00955 0.00001 STPD INTERN> 116.36357 164.65145 0.00000 14.45400 39.58914 STPD EXTERN> 1012.16536 -124.30823 0.00000 0.00000 0.00000 STPD CONSTR> 1256.26664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21364 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 750 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 2479.18194 0.00014 0.00955 0.00000 MINI INTERN> 116.36357 164.65145 0.00000 14.45400 39.58914 MINI EXTERN> 1012.16536 -124.30823 0.00000 0.00000 0.00000 MINI CONSTR> 1256.26664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 3 2479.18153 0.00041 0.00245 0.02000 CONJ INTERN> 116.31883 164.60683 0.00000 14.49401 39.59231 CONJ EXTERN> 1012.12485 -124.30908 0.00000 0.00000 0.00000 CONJ CONSTR> 1256.35378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 130.00 ( PROT LYS 1 HT2 ) 130.00 ( PROT LYS 1 N ) 162.50 ( PROT LYS 1 HT3 ) 130.00 ( PROT LYS 1 CA ) 162.50 ( PROT LYS 1 CB ) 130.00 ( PROT LYS 1 CG ) 130.00 ( PROT LYS 1 CD ) 130.00 ( PROT LYS 1 CE ) 130.00 ( PROT LYS 1 NZ ) 130.00 ( PROT LYS 1 HZ1 ) 130.00 ( PROT LYS 1 HZ2 ) 130.00 ( PROT LYS 1 HZ3 ) 130.00 ( PROT LYS 1 C ) 162.50 ( PROT LYS 1 O ) 162.50 ( PROT MET 2 N ) 162.50 ( PROT MET 2 H ) 130.00 ( PROT MET 2 CA ) 162.50 ( PROT MET 2 CB ) 130.00 ( PROT MET 2 CG ) 130.00 ( PROT MET 2 SD ) 130.00 ( PROT MET 2 CE ) 130.00 ( PROT MET 2 C ) 162.50 ( PROT MET 2 O ) 162.50 ( PROT LYS 3 N ) 162.50 ( PROT LYS 3 H ) 130.00 ( PROT LYS 3 CA ) 162.50 ( PROT LYS 3 CB ) 130.00 ( PROT LYS 3 CG ) 130.00 ( PROT LYS 3 CD ) 130.00 ( PROT LYS 3 CE ) 130.00 ( PROT LYS 3 NZ ) 130.00 ( PROT LYS 3 HZ1 ) 130.00 ( PROT LYS 3 HZ2 ) 130.00 ( PROT LYS 3 HZ3 ) 130.00 ( PROT LYS 3 C ) 162.50 ( PROT LYS 3 O ) 162.50 ( PROT ALA 4 N ) 162.50 ( PROT ALA 4 H ) 130.00 ( PROT ALA 4 CA ) 162.50 ( PROT ALA 4 CB ) 130.00 ( PROT ALA 4 C ) 162.50 ( PROT ALA 4 O ) 162.50 ( PROT VAL 5 N ) 162.50 ( PROT VAL 5 H ) 130.00 ( PROT VAL 5 CA ) 162.50 ( PROT VAL 5 CB ) 130.00 ( PROT VAL 5 CG1 ) 130.00 ( PROT VAL 5 CG2 ) 130.00 ( PROT VAL 5 C ) 162.50 ( PROT VAL 5 O ) 162.50 ( PROT MET 6 N ) 162.50 ( PROT MET 6 H ) 130.00 ( PROT MET 6 CA ) 162.50 ( PROT MET 6 CB ) 130.00 ( PROT MET 6 CG ) 130.00 ( PROT MET 6 SD ) 130.00 ( PROT MET 6 CE ) 130.00 ( PROT MET 6 C ) 162.50 ( PROT MET 6 O ) 162.50 ( PROT ILE 7 N ) 162.50 ( PROT ILE 7 H ) 130.00 ( PROT ILE 7 CA ) 162.50 ( PROT ILE 7 CB ) 130.00 ( PROT ILE 7 CG2 ) 130.00 ( PROT ILE 7 CG1 ) 130.00 ( PROT ILE 7 CD ) 130.00 ( PROT ILE 7 C ) 162.50 ( PROT ILE 7 O ) 162.50 ( PROT GLY 8 N ) 162.50 ( PROT GLY 8 H ) 130.00 ( PROT GLY 8 CA ) 162.50 ( PROT GLY 8 C ) 162.50 ( PROT GLY 8 O ) 162.50 ( PROT ALA 9 N ) 162.50 ( PROT ALA 9 H ) 130.00 ( PROT ALA 9 CA ) 162.50 ( PROT ALA 9 CB ) 130.00 ( PROT ALA 9 C ) 162.50 ( PROT ALA 9 O ) 162.50 ( PROT CYS 10 N ) 162.50 ( PROT CYS 10 H ) 130.00 ( PROT CYS 10 CA ) 162.50 ( PROT CYS 10 CB ) 130.00 ( PROT CYS 10 SG ) 130.00 ( PROT CYS 10 C ) 162.50 ( PROT CYS 10 O ) 162.50 ( PROT PHE 11 N ) 162.50 ( PROT PHE 11 H ) 130.00 ( PROT PHE 11 CA ) 162.50 ( PROT PHE 11 CB ) 130.00 ( PROT PHE 11 CG ) 130.00 ( PROT PHE 11 CD1 ) 130.00 ( PROT PHE 11 CD2 ) 130.00 ( PROT PHE 11 CE1 ) 130.00 ( PROT PHE 11 CE2 ) 130.00 ( PROT PHE 11 CZ ) 130.00 ( PROT PHE 11 C ) 162.50 ( PROT PHE 11 O ) 162.50 ( PROT LEU 12 N ) 162.50 ( PROT LEU 12 H ) 130.00 ( PROT LEU 12 CA ) 162.50 ( PROT LEU 12 CB ) 130.00 ( PROT LEU 12 CG ) 130.00 ( PROT LEU 12 CD1 ) 130.00 ( PROT LEU 12 CD2 ) 130.00 ( PROT LEU 12 C ) 162.50 ( PROT LEU 12 O ) 162.50 ( PROT ILE 13 N ) 162.50 ( PROT ILE 13 H ) 130.00 ( PROT ILE 13 CA ) 162.50 ( PROT ILE 13 CB ) 130.00 ( PROT ILE 13 CG2 ) 130.00 ( PROT ILE 13 CG1 ) 130.00 ( PROT ILE 13 CD ) 130.00 ( PROT ILE 13 C ) 162.50 ( PROT ILE 13 O ) 162.50 ( PROT ASH 14 N ) 162.50 ( PROT ASH 14 H ) 130.00 ( PROT ASH 14 CA ) 162.50 ( PROT ASH 14 CB ) 130.00 ( PROT ASH 14 CG ) 130.00 ( PROT ASH 14 OD1 ) 130.00 ( PROT ASH 14 OD2 ) 130.00 ( PROT ASH 14 HD2 ) 130.00 ( PROT ASH 14 C ) 162.50 ( PROT ASH 14 O ) 162.50 ( PROT PHE 15 N ) 162.50 ( PROT PHE 15 H ) 130.00 ( PROT PHE 15 CA ) 162.50 ( PROT PHE 15 CB ) 130.00 ( PROT PHE 15 CG ) 130.00 ( PROT PHE 15 CD1 ) 130.00 ( PROT PHE 15 CD2 ) 130.00 ( PROT PHE 15 CE1 ) 130.00 ( PROT PHE 15 CE2 ) 130.00 ( PROT PHE 15 CZ ) 130.00 ( PROT PHE 15 C ) 162.50 ( PROT PHE 15 O ) 162.50 ( PROT MET 16 N ) 162.50 ( PROT MET 16 H ) 130.00 ( PROT MET 16 CA ) 162.50 ( PROT MET 16 CB ) 130.00 ( PROT MET 16 CG ) 130.00 ( PROT MET 16 SD ) 130.00 ( PROT MET 16 CE ) 130.00 ( PROT MET 16 C ) 162.50 ( PROT MET 16 O ) 162.50 ( PROT PHE 17 N ) 162.50 ( PROT PHE 17 H ) 130.00 ( PROT PHE 17 CA ) 162.50 ( PROT PHE 17 CB ) 130.00 ( PROT PHE 17 CG ) 130.00 ( PROT PHE 17 CD1 ) 130.00 ( PROT PHE 17 CD2 ) 130.00 ( PROT PHE 17 CE1 ) 130.00 ( PROT PHE 17 CE2 ) 130.00 ( PROT PHE 17 CZ ) 130.00 ( PROT PHE 17 C ) 162.50 ( PROT PHE 17 O ) 162.50 ( PROT PHE 18 N ) 162.50 ( PROT PHE 18 H ) 130.00 ( PROT PHE 18 CA ) 162.50 ( PROT PHE 18 CB ) 130.00 ( PROT PHE 18 CG ) 130.00 ( PROT PHE 18 CD1 ) 130.00 ( PROT PHE 18 CD2 ) 130.00 ( PROT PHE 18 CE1 ) 130.00 ( PROT PHE 18 CE2 ) 130.00 ( PROT PHE 18 CZ ) 130.00 ( PROT PHE 18 C ) 162.50 ( PROT PHE 18 O ) 162.50 ( PROT GLU 19 N ) 162.50 ( PROT GLU 19 H ) 130.00 ( PROT GLU 19 CA ) 162.50 ( PROT GLU 19 CB ) 130.00 ( PROT GLU 19 CG ) 130.00 ( PROT GLU 19 CD ) 130.00 ( PROT GLU 19 OE1 ) 130.00 ( PROT GLU 19 OE2 ) 130.00 ( PROT GLU 19 C ) 162.50 ( PROT GLU 19 O ) 162.50 ( PROT SER 20 N ) 162.50 ( PROT SER 20 H ) 130.00 ( PROT SER 20 CA ) 162.50 ( PROT SER 20 CB ) 130.00 ( PROT SER 20 OG ) 130.00 ( PROT SER 20 HG ) 130.00 ( PROT SER 20 C ) 162.50 ( PROT SER 20 O ) 162.50 ( PROT THR 21 N ) 162.50 ( PROT THR 21 H ) 130.00 ( PROT THR 21 CA ) 162.50 ( PROT THR 21 CB ) 130.00 ( PROT THR 21 OG1 ) 130.00 ( PROT THR 21 HG1 ) 130.00 ( PROT THR 21 CG2 ) 130.00 ( PROT THR 21 C ) 162.50 ( PROT THR 21 O ) 162.50 ( PROT GLY 22 N ) 162.50 ( PROT GLY 22 H ) 130.00 ( PROT GLY 22 CA ) 162.50 ( PROT GLY 22 C ) 162.50 ( PROT GLY 22 O ) 162.50 ( PROT SER 23 N ) 162.50 ( PROT SER 23 H ) 130.00 ( PROT SER 23 CA ) 162.50 ( PROT SER 23 CB ) 130.00 ( PROT SER 23 OG ) 130.00 ( PROT SER 23 HG ) 130.00 ( PROT SER 23 C ) 162.50 ( PROT SER 23 O ) 162.50 ( PROT GLN 24 N ) 162.50 ( PROT GLN 24 H ) 130.00 ( PROT GLN 24 CA ) 162.50 ( PROT GLN 24 CB ) 130.00 ( PROT GLN 24 CG ) 130.00 ( PROT GLN 24 CD ) 130.00 ( PROT GLN 24 OE1 ) 130.00 ( PROT GLN 24 NE2 ) 130.00 ( PROT GLN 24 HE21 ) 130.00 ( PROT GLN 24 HE22 ) 130.00 ( PROT GLN 24 C ) 162.50 ( PROT GLN 24 O ) 162.50 ( PROT GLU 25 N ) 162.50 ( PROT GLU 25 H ) 130.00 ( PROT GLU 25 CA ) 162.50 ( PROT GLU 25 CB ) 130.00 ( PROT GLU 25 CG ) 130.00 ( PROT GLU 25 CD ) 130.00 ( PROT GLU 25 OE1 ) 130.00 ( PROT GLU 25 OE2 ) 130.00 ( PROT GLU 25 C ) 162.50 ( PROT GLU 25 O ) 162.50 ( PROT GLN 26 N ) 162.50 ( PROT GLN 26 H ) 130.00 ( PROT GLN 26 CA ) 162.50 ( PROT GLN 26 CB ) 130.00 ( PROT GLN 26 CG ) 130.00 ( PROT GLN 26 CD ) 130.00 ( PROT GLN 26 OE1 ) 130.00 ( PROT GLN 26 NE2 ) 130.00 ( PROT GLN 26 HE21 ) 130.00 ( PROT GLN 26 HE22 ) 130.00 ( PROT GLN 26 C ) 162.50 ( PROT GLN 26 O ) 162.50 ( PROT LYS 27 N ) 162.50 ( PROT LYS 27 H ) 130.00 ( PROT LYS 27 CA ) 162.50 ( PROT LYS 27 CB ) 130.00 ( PROT LYS 27 CG ) 130.00 ( PROT LYS 27 CD ) 130.00 ( PROT LYS 27 CE ) 130.00 ( PROT LYS 27 NZ ) 130.00 ( PROT LYS 27 HZ1 ) 130.00 ( PROT LYS 27 HZ2 ) 130.00 ( PROT LYS 27 HZ3 ) 130.00 ( PROT LYS 27 C ) 162.50 ( PROT LYS 27 O ) 162.50 ( PROT SER 28 N ) 162.50 ( PROT SER 28 H ) 130.00 ( PROT SER 28 CA ) 162.50 ( PROT SER 28 CB ) 130.00 ( PROT SER 28 OG ) 130.00 ( PROT SER 28 HG ) 130.00 ( PROT SER 28 C ) 162.50 ( PROT SER 28 O ) 162.50 ( PROT GLY 29 N ) 162.50 ( PROT GLY 29 H ) 130.00 ( PROT GLY 29 CA ) 162.50 ( PROT GLY 29 C ) 162.50 ( PROT GLY 29 O ) 162.50 ( PROT VAL 30 N ) 162.50 ( PROT VAL 30 H ) 130.00 ( PROT VAL 30 CA ) 162.50 ( PROT VAL 30 CB ) 130.00 ( PROT VAL 30 CG1 ) 130.00 ( PROT VAL 30 CG2 ) 130.00 ( PROT VAL 30 C ) 162.50 ( PROT VAL 30 O ) 162.50 ( PROT TRP 31 N ) 162.50 ( PROT TRP 31 H ) 130.00 ( PROT TRP 31 CA ) 162.50 ( PROT TRP 31 CB ) 130.00 ( PROT TRP 31 CG ) 130.00 ( PROT TRP 31 CD2 ) 130.00 ( PROT TRP 31 CE2 ) 130.00 ( PROT TRP 31 CE3 ) 130.00 ( PROT TRP 31 CD1 ) 130.00 ( PROT TRP 31 NE1 ) 130.00 ( PROT TRP 31 HE1 ) 130.00 ( PROT TRP 31 CZ2 ) 130.00 ( PROT TRP 31 CZ3 ) 130.00 ( PROT TRP 31 CH2 ) 130.00 ( PROT TRP 31 C ) 162.50 ( PROT TRP 31 OT1 ) 130.00 ( PROT TRP 31 OT2 ) 130.00 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63250 7.23086 -13.22163 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS -0.00169 -0.00144 0.00171 ROTATION MATRIX 1.000000 -0.000024 -0.000063 0.000024 1.000000 0.000052 0.000063 -0.000052 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 5.9124 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.141092 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1411" Parameter: A <- "0.1411" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51751 7.24756 -13.42798 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01072 0.00799 -0.01238 ROTATION MATRIX 0.999945 0.007357 0.007481 -0.007297 0.999941 -0.008003 -0.007540 0.007948 0.999940 AXIS OF ROTATION IS -0.605166 -0.569853 0.555915 ANGLE IS 0.76 TOTAL SQUARE DIFF IS 0.0434 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.037407 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1411" RDCMND substituted energy or value "?RMS" to " 0.0374" Parameter: A <- "0.1411 0.0374" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *600 0.1411 0.0374 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 1256.35" Parameter: H <- "1256.35" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 1222.82775 1256.35378 34.79049 ENER INTERN> 116.31883 164.60683 0.00000 14.49401 39.59231 ENER EXTERN> 1012.12485 -124.30908 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 1222.83" Parameter: B <- "1222.83" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -124.31" Parameter: C <- "-124.31" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 1012.12" Parameter: C <- " 887.81" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 887.81" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 116.32" Parameter: D <- "116.32" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 164.61" Parameter: D <- " 280.93" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 14.49" Parameter: D <- " 295.42" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 39.59" Parameter: D <- " 335.01" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 335.01" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 600 ENER= 1222.83 GRMS= 34.79 ELEC= -124.31 VDW= 1012.12 RDTITL> *EXTERNAL= 887.81 INTERNAL= 335.01 USER= 0.00 HARM= 1256.35 RDTITL> *BOND= 116.32 ANGL= 164.61 DIHE= 14.49 IMPR= 39.59 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21364 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21364 ATOM PAIRS WERE FOUND FOR ATOM LIST 750 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 2157.72473 -934.89698 14.86835 0.02000 MINI INTERN> 116.31883 164.60683 0.00000 14.49401 39.59231 MINI EXTERN> 1012.12485 -124.30908 0.00000 0.00000 0.00000 MINI CONSTR> 934.89698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 2042.03941 115.68532 16.43944 0.00864 MINI INTERN> 102.39357 174.58558 0.00000 17.47212 31.54208 MINI EXTERN> 830.70188 -125.70328 0.00000 0.00000 0.00000 MINI CONSTR> 1011.04745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21343 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1992.64213 49.39728 1.39272 0.00156 MINI INTERN> 100.42009 162.94556 0.00000 16.91214 33.74221 MINI EXTERN> 784.95372 -121.80326 0.00000 0.00000 0.00000 MINI CONSTR> 1015.47166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1990.59764 2.04450 0.57118 0.00067 MINI INTERN> 99.96853 162.24778 0.00000 17.16108 34.18489 MINI EXTERN> 778.46374 -121.88312 0.00000 0.00000 0.00000 MINI CONSTR> 1020.45473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21344 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1990.33733 0.26031 0.29984 0.00029 MINI INTERN> 98.84059 161.41102 0.00000 17.48610 33.74280 MINI EXTERN> 781.36682 -121.97879 0.00000 0.00000 0.00000 MINI CONSTR> 1019.46880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1990.29261 0.04471 0.50599 0.00030 MINI INTERN> 99.33144 161.32296 0.00000 17.71165 33.67037 MINI EXTERN> 779.72939 -121.86700 0.00000 0.00000 0.00000 MINI CONSTR> 1020.39381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21344 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1990.22457 0.06805 0.15989 0.00013 MINI INTERN> 99.01324 160.89547 0.00000 17.85076 33.91918 MINI EXTERN> 779.29610 -121.96080 0.00000 0.00000 0.00000 MINI CONSTR> 1021.21063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1990.20284 0.02173 0.23083 0.00013 MINI INTERN> 98.52155 160.66571 0.00000 17.98500 33.94777 MINI EXTERN> 779.80367 -122.03425 0.00000 0.00000 0.00000 MINI CONSTR> 1021.31339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21344 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1990.18262 0.02022 0.06802 0.00006 MINI INTERN> 98.65786 160.59037 0.00000 18.08195 33.82864 MINI EXTERN> 779.75002 -121.97393 0.00000 0.00000 0.00000 MINI CONSTR> 1021.24772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 1990.17339 0.00923 0.06329 0.00006 MINI INTERN> 98.59143 160.49354 0.00000 18.16223 33.82182 MINI EXTERN> 779.69627 -121.97664 0.00000 0.00000 0.00000 MINI CONSTR> 1021.38474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21344 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 1990.16920 0.00419 0.12023 0.00006 MINI INTERN> 98.21495 160.45980 0.00000 18.22498 33.80999 MINI EXTERN> 780.13886 -122.03655 0.00000 0.00000 0.00000 MINI CONSTR> 1021.35717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 1990.16607 0.00313 0.10309 0.00006 MINI INTERN> 98.50853 160.34017 0.00000 18.26720 33.79666 MINI EXTERN> 779.71977 -121.96970 0.00000 0.00000 0.00000 MINI CONSTR> 1021.50346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21344 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 1990.16320 0.00287 0.04312 0.00003 MINI INTERN> 98.51567 160.30691 0.00000 18.30171 33.86340 MINI EXTERN> 779.35737 -121.98435 0.00000 0.00000 0.00000 MINI CONSTR> 1021.80250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 1990.16246 0.00074 0.05588 0.00003 MINI INTERN> 98.51369 160.26043 0.00000 18.32534 33.86147 MINI EXTERN> 779.34875 -121.98034 0.00000 0.00000 0.00000 MINI CONSTR> 1021.83311 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21344 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 1990.16193 0.00054 0.05338 0.00003 MINI INTERN> 98.39176 160.26135 0.00000 18.34520 33.86845 MINI EXTERN> 779.43481 -122.00457 0.00000 0.00000 0.00000 MINI CONSTR> 1021.86493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 1990.16130 0.00062 0.01800 0.00001 MINI INTERN> 98.41352 160.25324 0.00000 18.35920 33.83814 MINI EXTERN> 779.47303 -121.99476 0.00000 0.00000 0.00000 MINI CONSTR> 1021.81893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 77 1990.16121 0.00009 0.00852 0.00001 STPD INTERN> 98.41266 160.25253 0.00000 18.36274 33.85038 STPD EXTERN> 779.40778 -121.99686 0.00000 0.00000 0.00000 STPD CONSTR> 1021.87198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21344 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21344 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1990.16121 0.00009 0.00852 0.00000 MINI INTERN> 98.41266 160.25253 0.00000 18.36274 33.85038 MINI EXTERN> 779.40778 -121.99686 0.00000 0.00000 0.00000 MINI CONSTR> 1021.87198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 3 1990.16092 0.00029 0.00139 0.02000 CONJ INTERN> 98.37777 160.20905 0.00000 18.39862 33.84705 CONJ EXTERN> 779.39712 -121.99925 0.00000 0.00000 0.00000 CONJ CONSTR> 1021.93056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "1200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 84.500 ( PROT LYS 1 HT2 ) 84.500 ( PROT LYS 1 N ) 105.63 ( PROT LYS 1 HT3 ) 84.500 ( PROT LYS 1 CA ) 105.63 ( PROT LYS 1 CB ) 84.500 ( PROT LYS 1 CG ) 84.500 ( PROT LYS 1 CD ) 84.500 ( PROT LYS 1 CE ) 84.500 ( PROT LYS 1 NZ ) 84.500 ( PROT LYS 1 HZ1 ) 84.500 ( PROT LYS 1 HZ2 ) 84.500 ( PROT LYS 1 HZ3 ) 84.500 ( PROT LYS 1 C ) 105.63 ( PROT LYS 1 O ) 105.63 ( PROT MET 2 N ) 105.63 ( PROT MET 2 H ) 84.500 ( PROT MET 2 CA ) 105.63 ( PROT MET 2 CB ) 84.500 ( PROT MET 2 CG ) 84.500 ( PROT MET 2 SD ) 84.500 ( PROT MET 2 CE ) 84.500 ( PROT MET 2 C ) 105.63 ( PROT MET 2 O ) 105.63 ( PROT LYS 3 N ) 105.63 ( PROT LYS 3 H ) 84.500 ( PROT LYS 3 CA ) 105.63 ( PROT LYS 3 CB ) 84.500 ( PROT LYS 3 CG ) 84.500 ( PROT LYS 3 CD ) 84.500 ( PROT LYS 3 CE ) 84.500 ( PROT LYS 3 NZ ) 84.500 ( PROT LYS 3 HZ1 ) 84.500 ( PROT LYS 3 HZ2 ) 84.500 ( PROT LYS 3 HZ3 ) 84.500 ( PROT LYS 3 C ) 105.63 ( PROT LYS 3 O ) 105.63 ( PROT ALA 4 N ) 105.63 ( PROT ALA 4 H ) 84.500 ( PROT ALA 4 CA ) 105.63 ( PROT ALA 4 CB ) 84.500 ( PROT ALA 4 C ) 105.63 ( PROT ALA 4 O ) 105.63 ( PROT VAL 5 N ) 105.63 ( PROT VAL 5 H ) 84.500 ( PROT VAL 5 CA ) 105.63 ( PROT VAL 5 CB ) 84.500 ( PROT VAL 5 CG1 ) 84.500 ( PROT VAL 5 CG2 ) 84.500 ( PROT VAL 5 C ) 105.63 ( PROT VAL 5 O ) 105.63 ( PROT MET 6 N ) 105.63 ( PROT MET 6 H ) 84.500 ( PROT MET 6 CA ) 105.63 ( PROT MET 6 CB ) 84.500 ( PROT MET 6 CG ) 84.500 ( PROT MET 6 SD ) 84.500 ( PROT MET 6 CE ) 84.500 ( PROT MET 6 C ) 105.63 ( PROT MET 6 O ) 105.63 ( PROT ILE 7 N ) 105.63 ( PROT ILE 7 H ) 84.500 ( PROT ILE 7 CA ) 105.63 ( PROT ILE 7 CB ) 84.500 ( PROT ILE 7 CG2 ) 84.500 ( PROT ILE 7 CG1 ) 84.500 ( PROT ILE 7 CD ) 84.500 ( PROT ILE 7 C ) 105.63 ( PROT ILE 7 O ) 105.63 ( PROT GLY 8 N ) 105.63 ( PROT GLY 8 H ) 84.500 ( PROT GLY 8 CA ) 105.63 ( PROT GLY 8 C ) 105.63 ( PROT GLY 8 O ) 105.63 ( PROT ALA 9 N ) 105.63 ( PROT ALA 9 H ) 84.500 ( PROT ALA 9 CA ) 105.63 ( PROT ALA 9 CB ) 84.500 ( PROT ALA 9 C ) 105.63 ( PROT ALA 9 O ) 105.63 ( PROT CYS 10 N ) 105.63 ( PROT CYS 10 H ) 84.500 ( PROT CYS 10 CA ) 105.63 ( PROT CYS 10 CB ) 84.500 ( PROT CYS 10 SG ) 84.500 ( PROT CYS 10 C ) 105.63 ( PROT CYS 10 O ) 105.63 ( PROT PHE 11 N ) 105.63 ( PROT PHE 11 H ) 84.500 ( PROT PHE 11 CA ) 105.63 ( PROT PHE 11 CB ) 84.500 ( PROT PHE 11 CG ) 84.500 ( PROT PHE 11 CD1 ) 84.500 ( PROT PHE 11 CD2 ) 84.500 ( PROT PHE 11 CE1 ) 84.500 ( PROT PHE 11 CE2 ) 84.500 ( PROT PHE 11 CZ ) 84.500 ( PROT PHE 11 C ) 105.63 ( PROT PHE 11 O ) 105.63 ( PROT LEU 12 N ) 105.63 ( PROT LEU 12 H ) 84.500 ( PROT LEU 12 CA ) 105.63 ( PROT LEU 12 CB ) 84.500 ( PROT LEU 12 CG ) 84.500 ( PROT LEU 12 CD1 ) 84.500 ( PROT LEU 12 CD2 ) 84.500 ( PROT LEU 12 C ) 105.63 ( PROT LEU 12 O ) 105.63 ( PROT ILE 13 N ) 105.63 ( PROT ILE 13 H ) 84.500 ( PROT ILE 13 CA ) 105.63 ( PROT ILE 13 CB ) 84.500 ( PROT ILE 13 CG2 ) 84.500 ( PROT ILE 13 CG1 ) 84.500 ( PROT ILE 13 CD ) 84.500 ( PROT ILE 13 C ) 105.63 ( PROT ILE 13 O ) 105.63 ( PROT ASH 14 N ) 105.63 ( PROT ASH 14 H ) 84.500 ( PROT ASH 14 CA ) 105.63 ( PROT ASH 14 CB ) 84.500 ( PROT ASH 14 CG ) 84.500 ( PROT ASH 14 OD1 ) 84.500 ( PROT ASH 14 OD2 ) 84.500 ( PROT ASH 14 HD2 ) 84.500 ( PROT ASH 14 C ) 105.63 ( PROT ASH 14 O ) 105.63 ( PROT PHE 15 N ) 105.63 ( PROT PHE 15 H ) 84.500 ( PROT PHE 15 CA ) 105.63 ( PROT PHE 15 CB ) 84.500 ( PROT PHE 15 CG ) 84.500 ( PROT PHE 15 CD1 ) 84.500 ( PROT PHE 15 CD2 ) 84.500 ( PROT PHE 15 CE1 ) 84.500 ( PROT PHE 15 CE2 ) 84.500 ( PROT PHE 15 CZ ) 84.500 ( PROT PHE 15 C ) 105.63 ( PROT PHE 15 O ) 105.63 ( PROT MET 16 N ) 105.63 ( PROT MET 16 H ) 84.500 ( PROT MET 16 CA ) 105.63 ( PROT MET 16 CB ) 84.500 ( PROT MET 16 CG ) 84.500 ( PROT MET 16 SD ) 84.500 ( PROT MET 16 CE ) 84.500 ( PROT MET 16 C ) 105.63 ( PROT MET 16 O ) 105.63 ( PROT PHE 17 N ) 105.63 ( PROT PHE 17 H ) 84.500 ( PROT PHE 17 CA ) 105.63 ( PROT PHE 17 CB ) 84.500 ( PROT PHE 17 CG ) 84.500 ( PROT PHE 17 CD1 ) 84.500 ( PROT PHE 17 CD2 ) 84.500 ( PROT PHE 17 CE1 ) 84.500 ( PROT PHE 17 CE2 ) 84.500 ( PROT PHE 17 CZ ) 84.500 ( PROT PHE 17 C ) 105.63 ( PROT PHE 17 O ) 105.63 ( PROT PHE 18 N ) 105.63 ( PROT PHE 18 H ) 84.500 ( PROT PHE 18 CA ) 105.63 ( PROT PHE 18 CB ) 84.500 ( PROT PHE 18 CG ) 84.500 ( PROT PHE 18 CD1 ) 84.500 ( PROT PHE 18 CD2 ) 84.500 ( PROT PHE 18 CE1 ) 84.500 ( PROT PHE 18 CE2 ) 84.500 ( PROT PHE 18 CZ ) 84.500 ( PROT PHE 18 C ) 105.63 ( PROT PHE 18 O ) 105.63 ( PROT GLU 19 N ) 105.63 ( PROT GLU 19 H ) 84.500 ( PROT GLU 19 CA ) 105.63 ( PROT GLU 19 CB ) 84.500 ( PROT GLU 19 CG ) 84.500 ( PROT GLU 19 CD ) 84.500 ( PROT GLU 19 OE1 ) 84.500 ( PROT GLU 19 OE2 ) 84.500 ( PROT GLU 19 C ) 105.63 ( PROT GLU 19 O ) 105.63 ( PROT SER 20 N ) 105.63 ( PROT SER 20 H ) 84.500 ( PROT SER 20 CA ) 105.63 ( PROT SER 20 CB ) 84.500 ( PROT SER 20 OG ) 84.500 ( PROT SER 20 HG ) 84.500 ( PROT SER 20 C ) 105.63 ( PROT SER 20 O ) 105.63 ( PROT THR 21 N ) 105.63 ( PROT THR 21 H ) 84.500 ( PROT THR 21 CA ) 105.63 ( PROT THR 21 CB ) 84.500 ( PROT THR 21 OG1 ) 84.500 ( PROT THR 21 HG1 ) 84.500 ( PROT THR 21 CG2 ) 84.500 ( PROT THR 21 C ) 105.63 ( PROT THR 21 O ) 105.63 ( PROT GLY 22 N ) 105.63 ( PROT GLY 22 H ) 84.500 ( PROT GLY 22 CA ) 105.63 ( PROT GLY 22 C ) 105.63 ( PROT GLY 22 O ) 105.63 ( PROT SER 23 N ) 105.63 ( PROT SER 23 H ) 84.500 ( PROT SER 23 CA ) 105.63 ( PROT SER 23 CB ) 84.500 ( PROT SER 23 OG ) 84.500 ( PROT SER 23 HG ) 84.500 ( PROT SER 23 C ) 105.63 ( PROT SER 23 O ) 105.63 ( PROT GLN 24 N ) 105.63 ( PROT GLN 24 H ) 84.500 ( PROT GLN 24 CA ) 105.63 ( PROT GLN 24 CB ) 84.500 ( PROT GLN 24 CG ) 84.500 ( PROT GLN 24 CD ) 84.500 ( PROT GLN 24 OE1 ) 84.500 ( PROT GLN 24 NE2 ) 84.500 ( PROT GLN 24 HE21 ) 84.500 ( PROT GLN 24 HE22 ) 84.500 ( PROT GLN 24 C ) 105.63 ( PROT GLN 24 O ) 105.63 ( PROT GLU 25 N ) 105.63 ( PROT GLU 25 H ) 84.500 ( PROT GLU 25 CA ) 105.63 ( PROT GLU 25 CB ) 84.500 ( PROT GLU 25 CG ) 84.500 ( PROT GLU 25 CD ) 84.500 ( PROT GLU 25 OE1 ) 84.500 ( PROT GLU 25 OE2 ) 84.500 ( PROT GLU 25 C ) 105.63 ( PROT GLU 25 O ) 105.63 ( PROT GLN 26 N ) 105.63 ( PROT GLN 26 H ) 84.500 ( PROT GLN 26 CA ) 105.63 ( PROT GLN 26 CB ) 84.500 ( PROT GLN 26 CG ) 84.500 ( PROT GLN 26 CD ) 84.500 ( PROT GLN 26 OE1 ) 84.500 ( PROT GLN 26 NE2 ) 84.500 ( PROT GLN 26 HE21 ) 84.500 ( PROT GLN 26 HE22 ) 84.500 ( PROT GLN 26 C ) 105.63 ( PROT GLN 26 O ) 105.63 ( PROT LYS 27 N ) 105.63 ( PROT LYS 27 H ) 84.500 ( PROT LYS 27 CA ) 105.63 ( PROT LYS 27 CB ) 84.500 ( PROT LYS 27 CG ) 84.500 ( PROT LYS 27 CD ) 84.500 ( PROT LYS 27 CE ) 84.500 ( PROT LYS 27 NZ ) 84.500 ( PROT LYS 27 HZ1 ) 84.500 ( PROT LYS 27 HZ2 ) 84.500 ( PROT LYS 27 HZ3 ) 84.500 ( PROT LYS 27 C ) 105.63 ( PROT LYS 27 O ) 105.63 ( PROT SER 28 N ) 105.63 ( PROT SER 28 H ) 84.500 ( PROT SER 28 CA ) 105.63 ( PROT SER 28 CB ) 84.500 ( PROT SER 28 OG ) 84.500 ( PROT SER 28 HG ) 84.500 ( PROT SER 28 C ) 105.63 ( PROT SER 28 O ) 105.63 ( PROT GLY 29 N ) 105.63 ( PROT GLY 29 H ) 84.500 ( PROT GLY 29 CA ) 105.63 ( PROT GLY 29 C ) 105.63 ( PROT GLY 29 O ) 105.63 ( PROT VAL 30 N ) 105.63 ( PROT VAL 30 H ) 84.500 ( PROT VAL 30 CA ) 105.63 ( PROT VAL 30 CB ) 84.500 ( PROT VAL 30 CG1 ) 84.500 ( PROT VAL 30 CG2 ) 84.500 ( PROT VAL 30 C ) 105.63 ( PROT VAL 30 O ) 105.63 ( PROT TRP 31 N ) 105.63 ( PROT TRP 31 H ) 84.500 ( PROT TRP 31 CA ) 105.63 ( PROT TRP 31 CB ) 84.500 ( PROT TRP 31 CG ) 84.500 ( PROT TRP 31 CD2 ) 84.500 ( PROT TRP 31 CE2 ) 84.500 ( PROT TRP 31 CE3 ) 84.500 ( PROT TRP 31 CD1 ) 84.500 ( PROT TRP 31 NE1 ) 84.500 ( PROT TRP 31 HE1 ) 84.500 ( PROT TRP 31 CZ2 ) 84.500 ( PROT TRP 31 CZ3 ) 84.500 ( PROT TRP 31 CH2 ) 84.500 ( PROT TRP 31 C ) 105.63 ( PROT TRP 31 OT1 ) 84.500 ( PROT TRP 31 OT2 ) 84.500 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63253 7.23084 -13.22171 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS -0.00173 -0.00142 0.00179 ROTATION MATRIX 1.000000 -0.000025 -0.000076 0.000025 1.000000 0.000060 0.000076 -0.000060 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 7.3791 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.157624 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1576" Parameter: A <- "0.1576" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51640 7.24750 -13.42608 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01183 0.00805 -0.01428 ROTATION MATRIX 0.999918 0.008948 0.009134 -0.008859 0.999914 -0.009721 -0.009220 0.009639 0.999911 AXIS OF ROTATION IS -0.603572 -0.572242 0.555194 ANGLE IS 0.92 TOTAL SQUARE DIFF IS 0.0709 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.047807 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1576" RDCMND substituted energy or value "?RMS" to " 0.0478" Parameter: A <- "0.1576 0.0478" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *1200 0.1576 0.0478 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 1021.93" Parameter: H <- "1021.93" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 968.23036 1021.93056 25.33538 ENER INTERN> 98.37777 160.20905 0.00000 18.39862 33.84705 ENER EXTERN> 779.39712 -121.99925 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 968.23" Parameter: B <- "968.23" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -122.00" Parameter: C <- "-122.00" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 779.40" Parameter: C <- " 657.40" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 657.40" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 98.38" Parameter: D <- "98.38" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 160.21" Parameter: D <- " 258.59" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 18.40" Parameter: D <- " 276.99" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 33.85" Parameter: D <- " 310.84" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 310.84" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 1200 ENER= 968.23 GRMS= 25.34 ELEC= -122.00 VDW= 779.40 RDTITL> *EXTERNAL= 657.40 INTERNAL= 310.84 USER= 0.00 HARM= 1021.93 RDTITL> *BOND= 98.38 ANGL= 160.21 DIHE= 18.40 IMPR= 33.85 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "1200" VOPEN> Attempting to open::../pdb/mini_helix_allh_1200.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_1200.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 1200 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 1200 ENER= 968.23 GRMS= 25.34 ELEC= -122.00 VDW= 779.40 RDTITL> *EXTERNAL= 657.40 INTERNAL= 310.84 USER= 0.00 HARM= 1021.93 RDTITL> *BOND= 98.38 ANGL= 160.21 DIHE= 18.40 IMPR= 33.85 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "1200" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_1200.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_1200.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 1200 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 1200 ENER= 968.23 GRMS= 25.34 ELEC= -122.00 VDW= 779.40 RDTITL> *EXTERNAL= 657.40 INTERNAL= 310.84 USER= 0.00 HARM= 1021.93 RDTITL> *BOND= 98.38 ANGL= 160.21 DIHE= 18.40 IMPR= 33.85 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 1200 0.1576 0.0478 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "1200" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21344 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21344 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1744.96237 -776.73201 11.10536 0.02000 MINI INTERN> 98.37777 160.20905 0.00000 18.39862 33.84705 MINI EXTERN> 779.39712 -121.99925 0.00000 0.00000 0.00000 MINI CONSTR> 776.73201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1654.33350 90.62888 18.29261 0.00864 MINI INTERN> 166.00833 155.32421 0.00000 21.42264 26.09388 MINI EXTERN> 571.82861 -113.28697 0.00000 0.00000 0.00000 MINI CONSTR> 826.94280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21333 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1603.69803 50.63546 7.04636 0.00373 MINI INTERN> 75.71961 163.95793 0.00000 21.33662 28.61254 MINI EXTERN> 609.61901 -123.34648 0.00000 0.00000 0.00000 MINI CONSTR> 827.79881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1594.46505 9.23298 2.46881 0.00161 MINI INTERN> 86.63526 157.15330 0.00000 21.88270 27.02687 MINI EXTERN> 598.05791 -121.67146 0.00000 0.00000 0.00000 MINI CONSTR> 825.38046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21335 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1592.92913 1.53592 0.91390 0.00070 MINI INTERN> 84.85636 157.44397 0.00000 21.98991 28.03731 MINI EXTERN> 591.63171 -121.71492 0.00000 0.00000 0.00000 MINI CONSTR> 830.68480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1592.67855 0.25058 0.37489 0.00030 MINI INTERN> 84.65945 156.37901 0.00000 22.07296 27.08481 MINI EXTERN> 595.40078 -121.73056 0.00000 0.00000 0.00000 MINI CONSTR> 828.81209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21334 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1592.63548 0.04308 0.24496 0.00013 MINI INTERN> 85.04850 156.35850 0.00000 22.15136 27.36979 MINI EXTERN> 593.22135 -121.69619 0.00000 0.00000 0.00000 MINI CONSTR> 830.18216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1592.62040 0.01508 0.05582 0.00006 MINI INTERN> 84.47673 156.31397 0.00000 22.19855 27.29189 MINI EXTERN> 594.00798 -121.75875 0.00000 0.00000 0.00000 MINI CONSTR> 830.09003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21333 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1592.61816 0.00224 0.10800 0.00006 MINI INTERN> 84.54196 156.26650 0.00000 22.23834 27.28150 MINI EXTERN> 593.78703 -121.75228 0.00000 0.00000 0.00000 MINI CONSTR> 830.25512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 1592.61551 0.00265 0.02838 0.00003 MINI INTERN> 84.42678 156.25059 0.00000 22.26047 27.32519 MINI EXTERN> 593.71046 -121.76098 0.00000 0.00000 0.00000 MINI CONSTR> 830.40300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21333 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 1592.61506 0.00046 0.03940 0.00003 MINI INTERN> 84.34988 156.23459 0.00000 22.27722 27.32192 MINI EXTERN> 593.77434 -121.76648 0.00000 0.00000 0.00000 MINI CONSTR> 830.42358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 1592.61461 0.00044 0.01759 0.00001 MINI INTERN> 84.37828 156.20806 0.00000 22.28803 27.30633 MINI EXTERN> 593.76973 -121.76467 0.00000 0.00000 0.00000 MINI CONSTR> 830.42885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 57 1592.61454 0.00008 0.00694 0.00001 STPD INTERN> 84.39084 156.20487 0.00000 22.29040 27.31106 STPD EXTERN> 593.73613 -121.76364 0.00000 0.00000 0.00000 STPD CONSTR> 830.44488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21333 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21333 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1592.61454 0.00008 0.00694 0.00000 MINI INTERN> 84.39084 156.20487 0.00000 22.29040 27.31106 MINI EXTERN> 593.73613 -121.76364 0.00000 0.00000 0.00000 MINI CONSTR> 830.44488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 3 1592.61433 0.00021 0.00220 0.02000 CONJ INTERN> 84.36852 156.17794 0.00000 22.31450 27.30680 CONJ EXTERN> 593.72194 -121.76542 0.00000 0.00000 0.00000 CONJ CONSTR> 830.49005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "1800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 54.925 ( PROT LYS 1 HT2 ) 54.925 ( PROT LYS 1 N ) 68.656 ( PROT LYS 1 HT3 ) 54.925 ( PROT LYS 1 CA ) 68.656 ( PROT LYS 1 CB ) 54.925 ( PROT LYS 1 CG ) 54.925 ( PROT LYS 1 CD ) 54.925 ( PROT LYS 1 CE ) 54.925 ( PROT LYS 1 NZ ) 54.925 ( PROT LYS 1 HZ1 ) 54.925 ( PROT LYS 1 HZ2 ) 54.925 ( PROT LYS 1 HZ3 ) 54.925 ( PROT LYS 1 C ) 68.656 ( PROT LYS 1 O ) 68.656 ( PROT MET 2 N ) 68.656 ( PROT MET 2 H ) 54.925 ( PROT MET 2 CA ) 68.656 ( PROT MET 2 CB ) 54.925 ( PROT MET 2 CG ) 54.925 ( PROT MET 2 SD ) 54.925 ( PROT MET 2 CE ) 54.925 ( PROT MET 2 C ) 68.656 ( PROT MET 2 O ) 68.656 ( PROT LYS 3 N ) 68.656 ( PROT LYS 3 H ) 54.925 ( PROT LYS 3 CA ) 68.656 ( PROT LYS 3 CB ) 54.925 ( PROT LYS 3 CG ) 54.925 ( PROT LYS 3 CD ) 54.925 ( PROT LYS 3 CE ) 54.925 ( PROT LYS 3 NZ ) 54.925 ( PROT LYS 3 HZ1 ) 54.925 ( PROT LYS 3 HZ2 ) 54.925 ( PROT LYS 3 HZ3 ) 54.925 ( PROT LYS 3 C ) 68.656 ( PROT LYS 3 O ) 68.656 ( PROT ALA 4 N ) 68.656 ( PROT ALA 4 H ) 54.925 ( PROT ALA 4 CA ) 68.656 ( PROT ALA 4 CB ) 54.925 ( PROT ALA 4 C ) 68.656 ( PROT ALA 4 O ) 68.656 ( PROT VAL 5 N ) 68.656 ( PROT VAL 5 H ) 54.925 ( PROT VAL 5 CA ) 68.656 ( PROT VAL 5 CB ) 54.925 ( PROT VAL 5 CG1 ) 54.925 ( PROT VAL 5 CG2 ) 54.925 ( PROT VAL 5 C ) 68.656 ( PROT VAL 5 O ) 68.656 ( PROT MET 6 N ) 68.656 ( PROT MET 6 H ) 54.925 ( PROT MET 6 CA ) 68.656 ( PROT MET 6 CB ) 54.925 ( PROT MET 6 CG ) 54.925 ( PROT MET 6 SD ) 54.925 ( PROT MET 6 CE ) 54.925 ( PROT MET 6 C ) 68.656 ( PROT MET 6 O ) 68.656 ( PROT ILE 7 N ) 68.656 ( PROT ILE 7 H ) 54.925 ( PROT ILE 7 CA ) 68.656 ( PROT ILE 7 CB ) 54.925 ( PROT ILE 7 CG2 ) 54.925 ( PROT ILE 7 CG1 ) 54.925 ( PROT ILE 7 CD ) 54.925 ( PROT ILE 7 C ) 68.656 ( PROT ILE 7 O ) 68.656 ( PROT GLY 8 N ) 68.656 ( PROT GLY 8 H ) 54.925 ( PROT GLY 8 CA ) 68.656 ( PROT GLY 8 C ) 68.656 ( PROT GLY 8 O ) 68.656 ( PROT ALA 9 N ) 68.656 ( PROT ALA 9 H ) 54.925 ( PROT ALA 9 CA ) 68.656 ( PROT ALA 9 CB ) 54.925 ( PROT ALA 9 C ) 68.656 ( PROT ALA 9 O ) 68.656 ( PROT CYS 10 N ) 68.656 ( PROT CYS 10 H ) 54.925 ( PROT CYS 10 CA ) 68.656 ( PROT CYS 10 CB ) 54.925 ( PROT CYS 10 SG ) 54.925 ( PROT CYS 10 C ) 68.656 ( PROT CYS 10 O ) 68.656 ( PROT PHE 11 N ) 68.656 ( PROT PHE 11 H ) 54.925 ( PROT PHE 11 CA ) 68.656 ( PROT PHE 11 CB ) 54.925 ( PROT PHE 11 CG ) 54.925 ( PROT PHE 11 CD1 ) 54.925 ( PROT PHE 11 CD2 ) 54.925 ( PROT PHE 11 CE1 ) 54.925 ( PROT PHE 11 CE2 ) 54.925 ( PROT PHE 11 CZ ) 54.925 ( PROT PHE 11 C ) 68.656 ( PROT PHE 11 O ) 68.656 ( PROT LEU 12 N ) 68.656 ( PROT LEU 12 H ) 54.925 ( PROT LEU 12 CA ) 68.656 ( PROT LEU 12 CB ) 54.925 ( PROT LEU 12 CG ) 54.925 ( PROT LEU 12 CD1 ) 54.925 ( PROT LEU 12 CD2 ) 54.925 ( PROT LEU 12 C ) 68.656 ( PROT LEU 12 O ) 68.656 ( PROT ILE 13 N ) 68.656 ( PROT ILE 13 H ) 54.925 ( PROT ILE 13 CA ) 68.656 ( PROT ILE 13 CB ) 54.925 ( PROT ILE 13 CG2 ) 54.925 ( PROT ILE 13 CG1 ) 54.925 ( PROT ILE 13 CD ) 54.925 ( PROT ILE 13 C ) 68.656 ( PROT ILE 13 O ) 68.656 ( PROT ASH 14 N ) 68.656 ( PROT ASH 14 H ) 54.925 ( PROT ASH 14 CA ) 68.656 ( PROT ASH 14 CB ) 54.925 ( PROT ASH 14 CG ) 54.925 ( PROT ASH 14 OD1 ) 54.925 ( PROT ASH 14 OD2 ) 54.925 ( PROT ASH 14 HD2 ) 54.925 ( PROT ASH 14 C ) 68.656 ( PROT ASH 14 O ) 68.656 ( PROT PHE 15 N ) 68.656 ( PROT PHE 15 H ) 54.925 ( PROT PHE 15 CA ) 68.656 ( PROT PHE 15 CB ) 54.925 ( PROT PHE 15 CG ) 54.925 ( PROT PHE 15 CD1 ) 54.925 ( PROT PHE 15 CD2 ) 54.925 ( PROT PHE 15 CE1 ) 54.925 ( PROT PHE 15 CE2 ) 54.925 ( PROT PHE 15 CZ ) 54.925 ( PROT PHE 15 C ) 68.656 ( PROT PHE 15 O ) 68.656 ( PROT MET 16 N ) 68.656 ( PROT MET 16 H ) 54.925 ( PROT MET 16 CA ) 68.656 ( PROT MET 16 CB ) 54.925 ( PROT MET 16 CG ) 54.925 ( PROT MET 16 SD ) 54.925 ( PROT MET 16 CE ) 54.925 ( PROT MET 16 C ) 68.656 ( PROT MET 16 O ) 68.656 ( PROT PHE 17 N ) 68.656 ( PROT PHE 17 H ) 54.925 ( PROT PHE 17 CA ) 68.656 ( PROT PHE 17 CB ) 54.925 ( PROT PHE 17 CG ) 54.925 ( PROT PHE 17 CD1 ) 54.925 ( PROT PHE 17 CD2 ) 54.925 ( PROT PHE 17 CE1 ) 54.925 ( PROT PHE 17 CE2 ) 54.925 ( PROT PHE 17 CZ ) 54.925 ( PROT PHE 17 C ) 68.656 ( PROT PHE 17 O ) 68.656 ( PROT PHE 18 N ) 68.656 ( PROT PHE 18 H ) 54.925 ( PROT PHE 18 CA ) 68.656 ( PROT PHE 18 CB ) 54.925 ( PROT PHE 18 CG ) 54.925 ( PROT PHE 18 CD1 ) 54.925 ( PROT PHE 18 CD2 ) 54.925 ( PROT PHE 18 CE1 ) 54.925 ( PROT PHE 18 CE2 ) 54.925 ( PROT PHE 18 CZ ) 54.925 ( PROT PHE 18 C ) 68.656 ( PROT PHE 18 O ) 68.656 ( PROT GLU 19 N ) 68.656 ( PROT GLU 19 H ) 54.925 ( PROT GLU 19 CA ) 68.656 ( PROT GLU 19 CB ) 54.925 ( PROT GLU 19 CG ) 54.925 ( PROT GLU 19 CD ) 54.925 ( PROT GLU 19 OE1 ) 54.925 ( PROT GLU 19 OE2 ) 54.925 ( PROT GLU 19 C ) 68.656 ( PROT GLU 19 O ) 68.656 ( PROT SER 20 N ) 68.656 ( PROT SER 20 H ) 54.925 ( PROT SER 20 CA ) 68.656 ( PROT SER 20 CB ) 54.925 ( PROT SER 20 OG ) 54.925 ( PROT SER 20 HG ) 54.925 ( PROT SER 20 C ) 68.656 ( PROT SER 20 O ) 68.656 ( PROT THR 21 N ) 68.656 ( PROT THR 21 H ) 54.925 ( PROT THR 21 CA ) 68.656 ( PROT THR 21 CB ) 54.925 ( PROT THR 21 OG1 ) 54.925 ( PROT THR 21 HG1 ) 54.925 ( PROT THR 21 CG2 ) 54.925 ( PROT THR 21 C ) 68.656 ( PROT THR 21 O ) 68.656 ( PROT GLY 22 N ) 68.656 ( PROT GLY 22 H ) 54.925 ( PROT GLY 22 CA ) 68.656 ( PROT GLY 22 C ) 68.656 ( PROT GLY 22 O ) 68.656 ( PROT SER 23 N ) 68.656 ( PROT SER 23 H ) 54.925 ( PROT SER 23 CA ) 68.656 ( PROT SER 23 CB ) 54.925 ( PROT SER 23 OG ) 54.925 ( PROT SER 23 HG ) 54.925 ( PROT SER 23 C ) 68.656 ( PROT SER 23 O ) 68.656 ( PROT GLN 24 N ) 68.656 ( PROT GLN 24 H ) 54.925 ( PROT GLN 24 CA ) 68.656 ( PROT GLN 24 CB ) 54.925 ( PROT GLN 24 CG ) 54.925 ( PROT GLN 24 CD ) 54.925 ( PROT GLN 24 OE1 ) 54.925 ( PROT GLN 24 NE2 ) 54.925 ( PROT GLN 24 HE21 ) 54.925 ( PROT GLN 24 HE22 ) 54.925 ( PROT GLN 24 C ) 68.656 ( PROT GLN 24 O ) 68.656 ( PROT GLU 25 N ) 68.656 ( PROT GLU 25 H ) 54.925 ( PROT GLU 25 CA ) 68.656 ( PROT GLU 25 CB ) 54.925 ( PROT GLU 25 CG ) 54.925 ( PROT GLU 25 CD ) 54.925 ( PROT GLU 25 OE1 ) 54.925 ( PROT GLU 25 OE2 ) 54.925 ( PROT GLU 25 C ) 68.656 ( PROT GLU 25 O ) 68.656 ( PROT GLN 26 N ) 68.656 ( PROT GLN 26 H ) 54.925 ( PROT GLN 26 CA ) 68.656 ( PROT GLN 26 CB ) 54.925 ( PROT GLN 26 CG ) 54.925 ( PROT GLN 26 CD ) 54.925 ( PROT GLN 26 OE1 ) 54.925 ( PROT GLN 26 NE2 ) 54.925 ( PROT GLN 26 HE21 ) 54.925 ( PROT GLN 26 HE22 ) 54.925 ( PROT GLN 26 C ) 68.656 ( PROT GLN 26 O ) 68.656 ( PROT LYS 27 N ) 68.656 ( PROT LYS 27 H ) 54.925 ( PROT LYS 27 CA ) 68.656 ( PROT LYS 27 CB ) 54.925 ( PROT LYS 27 CG ) 54.925 ( PROT LYS 27 CD ) 54.925 ( PROT LYS 27 CE ) 54.925 ( PROT LYS 27 NZ ) 54.925 ( PROT LYS 27 HZ1 ) 54.925 ( PROT LYS 27 HZ2 ) 54.925 ( PROT LYS 27 HZ3 ) 54.925 ( PROT LYS 27 C ) 68.656 ( PROT LYS 27 O ) 68.656 ( PROT SER 28 N ) 68.656 ( PROT SER 28 H ) 54.925 ( PROT SER 28 CA ) 68.656 ( PROT SER 28 CB ) 54.925 ( PROT SER 28 OG ) 54.925 ( PROT SER 28 HG ) 54.925 ( PROT SER 28 C ) 68.656 ( PROT SER 28 O ) 68.656 ( PROT GLY 29 N ) 68.656 ( PROT GLY 29 H ) 54.925 ( PROT GLY 29 CA ) 68.656 ( PROT GLY 29 C ) 68.656 ( PROT GLY 29 O ) 68.656 ( PROT VAL 30 N ) 68.656 ( PROT VAL 30 H ) 54.925 ( PROT VAL 30 CA ) 68.656 ( PROT VAL 30 CB ) 54.925 ( PROT VAL 30 CG1 ) 54.925 ( PROT VAL 30 CG2 ) 54.925 ( PROT VAL 30 C ) 68.656 ( PROT VAL 30 O ) 68.656 ( PROT TRP 31 N ) 68.656 ( PROT TRP 31 H ) 54.925 ( PROT TRP 31 CA ) 68.656 ( PROT TRP 31 CB ) 54.925 ( PROT TRP 31 CG ) 54.925 ( PROT TRP 31 CD2 ) 54.925 ( PROT TRP 31 CE2 ) 54.925 ( PROT TRP 31 CE3 ) 54.925 ( PROT TRP 31 CD1 ) 54.925 ( PROT TRP 31 NE1 ) 54.925 ( PROT TRP 31 HE1 ) 54.925 ( PROT TRP 31 CZ2 ) 54.925 ( PROT TRP 31 CZ3 ) 54.925 ( PROT TRP 31 CH2 ) 54.925 ( PROT TRP 31 C ) 68.656 ( PROT TRP 31 OT1 ) 54.925 ( PROT TRP 31 OT2 ) 54.925 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63248 7.23073 -13.22173 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS -0.00168 -0.00131 0.00181 ROTATION MATRIX 1.000000 -0.000029 -0.000095 0.000029 1.000000 0.000074 0.000095 -0.000074 1.000000 AXIS OF ROTATION IS 0.600268 0.764458 -0.235124 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 9.2096 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.176093 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1761" Parameter: A <- "0.1761" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51546 7.24772 -13.42391 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01277 0.00783 -0.01644 ROTATION MATRIX 0.999886 0.010553 0.010812 -0.010429 0.999880 -0.011455 -0.010931 0.011341 0.999876 AXIS OF ROTATION IS -0.602271 -0.574444 0.554332 ANGLE IS 1.08 CENTER OF ROTATION 13.791637 7.102370-13.293683 SHIFT IS -0.021304 TOTAL SQUARE DIFF IS 0.1092 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.059361 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1761" RDCMND substituted energy or value "?RMS" to " 0.0594" Parameter: A <- "0.1761 0.0594" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *1800 0.1761 0.0594 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 830.49" Parameter: H <- "830.49" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 762.12428 830.49005 18.43239 ENER INTERN> 84.36852 156.17794 0.00000 22.31450 27.30680 ENER EXTERN> 593.72194 -121.76542 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 762.12" Parameter: B <- "762.12" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -121.77" Parameter: C <- "-121.77" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 593.72" Parameter: C <- " 471.95" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 471.95" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 84.37" Parameter: D <- "84.37" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 156.18" Parameter: D <- " 240.55" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 22.31" Parameter: D <- " 262.86" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 27.31" Parameter: D <- " 290.17" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 290.17" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 1800 ENER= 762.12 GRMS= 18.43 ELEC= -121.77 VDW= 593.72 RDTITL> *EXTERNAL= 471.95 INTERNAL= 290.17 USER= 0.00 HARM= 830.49 RDTITL> *BOND= 84.37 ANGL= 156.18 DIHE= 22.31 IMPR= 27.31 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21333 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21333 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1402.99047 -640.86619 8.22123 0.02000 MINI INTERN> 84.36852 156.17794 0.00000 22.31450 27.30680 MINI EXTERN> 593.72194 -121.76542 0.00000 0.00000 0.00000 MINI CONSTR> 640.86619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1337.16784 65.82263 17.55787 0.00864 MINI INTERN> 158.63484 146.62289 0.00000 24.78840 21.13000 MINI EXTERN> 418.87942 -112.37267 0.00000 0.00000 0.00000 MINI CONSTR> 679.48496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21319 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1286.63096 50.53687 7.05478 0.00373 MINI INTERN> 60.46380 161.00211 0.00000 26.01036 22.32255 MINI EXTERN> 471.06495 -125.86521 0.00000 0.00000 0.00000 MINI CONSTR> 671.63240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1274.07807 12.55289 2.08934 0.00161 MINI INTERN> 76.90608 153.42777 0.00000 25.78195 21.61461 MINI EXTERN> 444.31236 -122.28137 0.00000 0.00000 0.00000 MINI CONSTR> 674.31668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21317 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1271.67985 2.39822 2.63078 0.00167 MINI INTERN> 76.34124 152.86701 0.00000 25.84474 21.54519 MINI EXTERN> 441.54253 -122.58007 0.00000 0.00000 0.00000 MINI CONSTR> 676.11921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1269.64625 2.03360 0.64945 0.00072 MINI INTERN> 71.88696 150.78574 0.00000 26.13881 21.37080 MINI EXTERN> 447.27684 -123.38284 0.00000 0.00000 0.00000 MINI CONSTR> 675.56994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21314 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1269.18017 0.46608 0.29786 0.00031 MINI INTERN> 71.95444 150.53124 0.00000 26.13801 21.33111 MINI EXTERN> 445.72884 -123.38634 0.00000 0.00000 0.00000 MINI CONSTR> 676.88287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1269.03884 0.14133 0.54245 0.00032 MINI INTERN> 72.02377 150.30867 0.00000 26.15043 21.31102 MINI EXTERN> 444.76204 -123.38942 0.00000 0.00000 0.00000 MINI CONSTR> 677.87231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21313 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1268.94388 0.09496 0.14677 0.00014 MINI INTERN> 71.36142 149.86912 0.00000 26.22787 21.29045 MINI EXTERN> 445.69509 -123.50495 0.00000 0.00000 0.00000 MINI CONSTR> 678.00487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 1268.92129 0.02259 0.17059 0.00014 MINI INTERN> 71.21276 149.71082 0.00000 26.25395 21.28309 MINI EXTERN> 445.64695 -123.52707 0.00000 0.00000 0.00000 MINI CONSTR> 678.34079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21313 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 1268.91042 0.01087 0.07998 0.00006 MINI INTERN> 71.32675 149.66691 0.00000 26.25114 21.27110 MINI EXTERN> 445.29355 -123.50279 0.00000 0.00000 0.00000 MINI CONSTR> 678.60376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 1268.90670 0.00372 0.02534 0.00003 MINI INTERN> 71.22605 149.61498 0.00000 26.26664 21.27504 MINI EXTERN> 445.33081 -123.51705 0.00000 0.00000 0.00000 MINI CONSTR> 678.71024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21313 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 1268.90550 0.00120 0.04144 0.00003 MINI INTERN> 71.17845 149.58185 0.00000 26.27709 21.27756 MINI EXTERN> 445.29929 -123.52200 0.00000 0.00000 0.00000 MINI CONSTR> 678.81325 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 1268.90511 0.00040 0.04716 0.00003 MINI INTERN> 71.15774 149.56294 0.00000 26.28360 21.27901 MINI EXTERN> 445.26621 -123.52313 0.00000 0.00000 0.00000 MINI CONSTR> 678.87873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 68 1268.90464 0.00046 0.00742 0.00001 STPD INTERN> 71.17233 149.53848 0.00000 26.28393 21.27085 STPD EXTERN> 445.27450 -123.51876 0.00000 0.00000 0.00000 STPD CONSTR> 678.88331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21313 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21313 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1268.90464 0.00046 0.00742 0.00000 MINI INTERN> 71.17233 149.53848 0.00000 26.28393 21.27085 MINI EXTERN> 445.27450 -123.51876 0.00000 0.00000 0.00000 MINI CONSTR> 678.88331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 2 1268.90444 0.00021 0.00394 0.02000 CONJ INTERN> 71.14468 149.50728 0.00000 26.29416 21.27076 CONJ EXTERN> 445.24310 -123.52009 0.00000 0.00000 0.00000 CONJ CONSTR> 678.96455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "2400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 35.701 ( PROT LYS 1 HT2 ) 35.701 ( PROT LYS 1 N ) 44.627 ( PROT LYS 1 HT3 ) 35.701 ( PROT LYS 1 CA ) 44.627 ( PROT LYS 1 CB ) 35.701 ( PROT LYS 1 CG ) 35.701 ( PROT LYS 1 CD ) 35.701 ( PROT LYS 1 CE ) 35.701 ( PROT LYS 1 NZ ) 35.701 ( PROT LYS 1 HZ1 ) 35.701 ( PROT LYS 1 HZ2 ) 35.701 ( PROT LYS 1 HZ3 ) 35.701 ( PROT LYS 1 C ) 44.627 ( PROT LYS 1 O ) 44.627 ( PROT MET 2 N ) 44.627 ( PROT MET 2 H ) 35.701 ( PROT MET 2 CA ) 44.627 ( PROT MET 2 CB ) 35.701 ( PROT MET 2 CG ) 35.701 ( PROT MET 2 SD ) 35.701 ( PROT MET 2 CE ) 35.701 ( PROT MET 2 C ) 44.627 ( PROT MET 2 O ) 44.627 ( PROT LYS 3 N ) 44.627 ( PROT LYS 3 H ) 35.701 ( PROT LYS 3 CA ) 44.627 ( PROT LYS 3 CB ) 35.701 ( PROT LYS 3 CG ) 35.701 ( PROT LYS 3 CD ) 35.701 ( PROT LYS 3 CE ) 35.701 ( PROT LYS 3 NZ ) 35.701 ( PROT LYS 3 HZ1 ) 35.701 ( PROT LYS 3 HZ2 ) 35.701 ( PROT LYS 3 HZ3 ) 35.701 ( PROT LYS 3 C ) 44.627 ( PROT LYS 3 O ) 44.627 ( PROT ALA 4 N ) 44.627 ( PROT ALA 4 H ) 35.701 ( PROT ALA 4 CA ) 44.627 ( PROT ALA 4 CB ) 35.701 ( PROT ALA 4 C ) 44.627 ( PROT ALA 4 O ) 44.627 ( PROT VAL 5 N ) 44.627 ( PROT VAL 5 H ) 35.701 ( PROT VAL 5 CA ) 44.627 ( PROT VAL 5 CB ) 35.701 ( PROT VAL 5 CG1 ) 35.701 ( PROT VAL 5 CG2 ) 35.701 ( PROT VAL 5 C ) 44.627 ( PROT VAL 5 O ) 44.627 ( PROT MET 6 N ) 44.627 ( PROT MET 6 H ) 35.701 ( PROT MET 6 CA ) 44.627 ( PROT MET 6 CB ) 35.701 ( PROT MET 6 CG ) 35.701 ( PROT MET 6 SD ) 35.701 ( PROT MET 6 CE ) 35.701 ( PROT MET 6 C ) 44.627 ( PROT MET 6 O ) 44.627 ( PROT ILE 7 N ) 44.627 ( PROT ILE 7 H ) 35.701 ( PROT ILE 7 CA ) 44.627 ( PROT ILE 7 CB ) 35.701 ( PROT ILE 7 CG2 ) 35.701 ( PROT ILE 7 CG1 ) 35.701 ( PROT ILE 7 CD ) 35.701 ( PROT ILE 7 C ) 44.627 ( PROT ILE 7 O ) 44.627 ( PROT GLY 8 N ) 44.627 ( PROT GLY 8 H ) 35.701 ( PROT GLY 8 CA ) 44.627 ( PROT GLY 8 C ) 44.627 ( PROT GLY 8 O ) 44.627 ( PROT ALA 9 N ) 44.627 ( PROT ALA 9 H ) 35.701 ( PROT ALA 9 CA ) 44.627 ( PROT ALA 9 CB ) 35.701 ( PROT ALA 9 C ) 44.627 ( PROT ALA 9 O ) 44.627 ( PROT CYS 10 N ) 44.627 ( PROT CYS 10 H ) 35.701 ( PROT CYS 10 CA ) 44.627 ( PROT CYS 10 CB ) 35.701 ( PROT CYS 10 SG ) 35.701 ( PROT CYS 10 C ) 44.627 ( PROT CYS 10 O ) 44.627 ( PROT PHE 11 N ) 44.627 ( PROT PHE 11 H ) 35.701 ( PROT PHE 11 CA ) 44.627 ( PROT PHE 11 CB ) 35.701 ( PROT PHE 11 CG ) 35.701 ( PROT PHE 11 CD1 ) 35.701 ( PROT PHE 11 CD2 ) 35.701 ( PROT PHE 11 CE1 ) 35.701 ( PROT PHE 11 CE2 ) 35.701 ( PROT PHE 11 CZ ) 35.701 ( PROT PHE 11 C ) 44.627 ( PROT PHE 11 O ) 44.627 ( PROT LEU 12 N ) 44.627 ( PROT LEU 12 H ) 35.701 ( PROT LEU 12 CA ) 44.627 ( PROT LEU 12 CB ) 35.701 ( PROT LEU 12 CG ) 35.701 ( PROT LEU 12 CD1 ) 35.701 ( PROT LEU 12 CD2 ) 35.701 ( PROT LEU 12 C ) 44.627 ( PROT LEU 12 O ) 44.627 ( PROT ILE 13 N ) 44.627 ( PROT ILE 13 H ) 35.701 ( PROT ILE 13 CA ) 44.627 ( PROT ILE 13 CB ) 35.701 ( PROT ILE 13 CG2 ) 35.701 ( PROT ILE 13 CG1 ) 35.701 ( PROT ILE 13 CD ) 35.701 ( PROT ILE 13 C ) 44.627 ( PROT ILE 13 O ) 44.627 ( PROT ASH 14 N ) 44.627 ( PROT ASH 14 H ) 35.701 ( PROT ASH 14 CA ) 44.627 ( PROT ASH 14 CB ) 35.701 ( PROT ASH 14 CG ) 35.701 ( PROT ASH 14 OD1 ) 35.701 ( PROT ASH 14 OD2 ) 35.701 ( PROT ASH 14 HD2 ) 35.701 ( PROT ASH 14 C ) 44.627 ( PROT ASH 14 O ) 44.627 ( PROT PHE 15 N ) 44.627 ( PROT PHE 15 H ) 35.701 ( PROT PHE 15 CA ) 44.627 ( PROT PHE 15 CB ) 35.701 ( PROT PHE 15 CG ) 35.701 ( PROT PHE 15 CD1 ) 35.701 ( PROT PHE 15 CD2 ) 35.701 ( PROT PHE 15 CE1 ) 35.701 ( PROT PHE 15 CE2 ) 35.701 ( PROT PHE 15 CZ ) 35.701 ( PROT PHE 15 C ) 44.627 ( PROT PHE 15 O ) 44.627 ( PROT MET 16 N ) 44.627 ( PROT MET 16 H ) 35.701 ( PROT MET 16 CA ) 44.627 ( PROT MET 16 CB ) 35.701 ( PROT MET 16 CG ) 35.701 ( PROT MET 16 SD ) 35.701 ( PROT MET 16 CE ) 35.701 ( PROT MET 16 C ) 44.627 ( PROT MET 16 O ) 44.627 ( PROT PHE 17 N ) 44.627 ( PROT PHE 17 H ) 35.701 ( PROT PHE 17 CA ) 44.627 ( PROT PHE 17 CB ) 35.701 ( PROT PHE 17 CG ) 35.701 ( PROT PHE 17 CD1 ) 35.701 ( PROT PHE 17 CD2 ) 35.701 ( PROT PHE 17 CE1 ) 35.701 ( PROT PHE 17 CE2 ) 35.701 ( PROT PHE 17 CZ ) 35.701 ( PROT PHE 17 C ) 44.627 ( PROT PHE 17 O ) 44.627 ( PROT PHE 18 N ) 44.627 ( PROT PHE 18 H ) 35.701 ( PROT PHE 18 CA ) 44.627 ( PROT PHE 18 CB ) 35.701 ( PROT PHE 18 CG ) 35.701 ( PROT PHE 18 CD1 ) 35.701 ( PROT PHE 18 CD2 ) 35.701 ( PROT PHE 18 CE1 ) 35.701 ( PROT PHE 18 CE2 ) 35.701 ( PROT PHE 18 CZ ) 35.701 ( PROT PHE 18 C ) 44.627 ( PROT PHE 18 O ) 44.627 ( PROT GLU 19 N ) 44.627 ( PROT GLU 19 H ) 35.701 ( PROT GLU 19 CA ) 44.627 ( PROT GLU 19 CB ) 35.701 ( PROT GLU 19 CG ) 35.701 ( PROT GLU 19 CD ) 35.701 ( PROT GLU 19 OE1 ) 35.701 ( PROT GLU 19 OE2 ) 35.701 ( PROT GLU 19 C ) 44.627 ( PROT GLU 19 O ) 44.627 ( PROT SER 20 N ) 44.627 ( PROT SER 20 H ) 35.701 ( PROT SER 20 CA ) 44.627 ( PROT SER 20 CB ) 35.701 ( PROT SER 20 OG ) 35.701 ( PROT SER 20 HG ) 35.701 ( PROT SER 20 C ) 44.627 ( PROT SER 20 O ) 44.627 ( PROT THR 21 N ) 44.627 ( PROT THR 21 H ) 35.701 ( PROT THR 21 CA ) 44.627 ( PROT THR 21 CB ) 35.701 ( PROT THR 21 OG1 ) 35.701 ( PROT THR 21 HG1 ) 35.701 ( PROT THR 21 CG2 ) 35.701 ( PROT THR 21 C ) 44.627 ( PROT THR 21 O ) 44.627 ( PROT GLY 22 N ) 44.627 ( PROT GLY 22 H ) 35.701 ( PROT GLY 22 CA ) 44.627 ( PROT GLY 22 C ) 44.627 ( PROT GLY 22 O ) 44.627 ( PROT SER 23 N ) 44.627 ( PROT SER 23 H ) 35.701 ( PROT SER 23 CA ) 44.627 ( PROT SER 23 CB ) 35.701 ( PROT SER 23 OG ) 35.701 ( PROT SER 23 HG ) 35.701 ( PROT SER 23 C ) 44.627 ( PROT SER 23 O ) 44.627 ( PROT GLN 24 N ) 44.627 ( PROT GLN 24 H ) 35.701 ( PROT GLN 24 CA ) 44.627 ( PROT GLN 24 CB ) 35.701 ( PROT GLN 24 CG ) 35.701 ( PROT GLN 24 CD ) 35.701 ( PROT GLN 24 OE1 ) 35.701 ( PROT GLN 24 NE2 ) 35.701 ( PROT GLN 24 HE21 ) 35.701 ( PROT GLN 24 HE22 ) 35.701 ( PROT GLN 24 C ) 44.627 ( PROT GLN 24 O ) 44.627 ( PROT GLU 25 N ) 44.627 ( PROT GLU 25 H ) 35.701 ( PROT GLU 25 CA ) 44.627 ( PROT GLU 25 CB ) 35.701 ( PROT GLU 25 CG ) 35.701 ( PROT GLU 25 CD ) 35.701 ( PROT GLU 25 OE1 ) 35.701 ( PROT GLU 25 OE2 ) 35.701 ( PROT GLU 25 C ) 44.627 ( PROT GLU 25 O ) 44.627 ( PROT GLN 26 N ) 44.627 ( PROT GLN 26 H ) 35.701 ( PROT GLN 26 CA ) 44.627 ( PROT GLN 26 CB ) 35.701 ( PROT GLN 26 CG ) 35.701 ( PROT GLN 26 CD ) 35.701 ( PROT GLN 26 OE1 ) 35.701 ( PROT GLN 26 NE2 ) 35.701 ( PROT GLN 26 HE21 ) 35.701 ( PROT GLN 26 HE22 ) 35.701 ( PROT GLN 26 C ) 44.627 ( PROT GLN 26 O ) 44.627 ( PROT LYS 27 N ) 44.627 ( PROT LYS 27 H ) 35.701 ( PROT LYS 27 CA ) 44.627 ( PROT LYS 27 CB ) 35.701 ( PROT LYS 27 CG ) 35.701 ( PROT LYS 27 CD ) 35.701 ( PROT LYS 27 CE ) 35.701 ( PROT LYS 27 NZ ) 35.701 ( PROT LYS 27 HZ1 ) 35.701 ( PROT LYS 27 HZ2 ) 35.701 ( PROT LYS 27 HZ3 ) 35.701 ( PROT LYS 27 C ) 44.627 ( PROT LYS 27 O ) 44.627 ( PROT SER 28 N ) 44.627 ( PROT SER 28 H ) 35.701 ( PROT SER 28 CA ) 44.627 ( PROT SER 28 CB ) 35.701 ( PROT SER 28 OG ) 35.701 ( PROT SER 28 HG ) 35.701 ( PROT SER 28 C ) 44.627 ( PROT SER 28 O ) 44.627 ( PROT GLY 29 N ) 44.627 ( PROT GLY 29 H ) 35.701 ( PROT GLY 29 CA ) 44.627 ( PROT GLY 29 C ) 44.627 ( PROT GLY 29 O ) 44.627 ( PROT VAL 30 N ) 44.627 ( PROT VAL 30 H ) 35.701 ( PROT VAL 30 CA ) 44.627 ( PROT VAL 30 CB ) 35.701 ( PROT VAL 30 CG1 ) 35.701 ( PROT VAL 30 CG2 ) 35.701 ( PROT VAL 30 C ) 44.627 ( PROT VAL 30 O ) 44.627 ( PROT TRP 31 N ) 44.627 ( PROT TRP 31 H ) 35.701 ( PROT TRP 31 CA ) 44.627 ( PROT TRP 31 CB ) 35.701 ( PROT TRP 31 CG ) 35.701 ( PROT TRP 31 CD2 ) 35.701 ( PROT TRP 31 CE2 ) 35.701 ( PROT TRP 31 CE3 ) 35.701 ( PROT TRP 31 CD1 ) 35.701 ( PROT TRP 31 NE1 ) 35.701 ( PROT TRP 31 HE1 ) 35.701 ( PROT TRP 31 CZ2 ) 35.701 ( PROT TRP 31 CZ3 ) 35.701 ( PROT TRP 31 CH2 ) 35.701 ( PROT TRP 31 C ) 44.627 ( PROT TRP 31 OT1 ) 35.701 ( PROT TRP 31 OT2 ) 35.701 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63231 7.23053 -13.22167 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS -0.00151 -0.00110 0.00176 ROTATION MATRIX 1.000000 -0.000041 -0.000126 0.000041 1.000000 0.000102 0.000126 -0.000102 1.000000 AXIS OF ROTATION IS 0.610536 0.753371 -0.244290 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 11.5686 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.197361 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1974" Parameter: A <- "0.1974" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51464 7.24798 -13.42133 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01358 0.00757 -0.01903 ROTATION MATRIX 0.999847 0.012210 0.012541 -0.012043 0.999840 -0.013247 -0.012701 0.013094 0.999834 AXIS OF ROTATION IS -0.601279 -0.576174 0.553612 ANGLE IS 1.26 CENTER OF ROTATION 13.830554 7.072819-13.281346 SHIFT IS -0.023060 TOTAL SQUARE DIFF IS 0.1582 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.071437 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1974" RDCMND substituted energy or value "?RMS" to " 0.0714" Parameter: A <- "0.1974 0.0714" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *2400 0.1974 0.0714 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 678.96" Parameter: H <- "678.96" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 589.93989 678.96455 13.44624 ENER INTERN> 71.14468 149.50728 0.00000 26.29416 21.27076 ENER EXTERN> 445.24310 -123.52009 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 589.94" Parameter: B <- "589.94" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -123.52" Parameter: C <- "-123.52" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 445.24" Parameter: C <- " 321.72" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 321.72" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 71.14" Parameter: D <- "71.14" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 149.51" Parameter: D <- " 220.65" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 26.29" Parameter: D <- " 246.94" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 21.27" Parameter: D <- " 268.21" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 268.21" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 2400 ENER= 589.94 GRMS= 13.45 ELEC= -123.52 VDW= 445.24 RDTITL> *EXTERNAL= 321.72 INTERNAL= 268.21 USER= 0.00 HARM= 678.96 RDTITL> *BOND= 71.14 ANGL= 149.51 DIHE= 26.29 IMPR= 21.27 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "2400" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_2400.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_2400.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 2400 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 2400 ENER= 589.94 GRMS= 13.45 ELEC= -123.52 VDW= 445.24 RDTITL> *EXTERNAL= 321.72 INTERNAL= 268.21 USER= 0.00 HARM= 678.96 RDTITL> *BOND= 71.14 ANGL= 149.51 DIHE= 26.29 IMPR= 21.27 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "2400" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_2400.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_2400.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 2400 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 2400 ENER= 589.94 GRMS= 13.45 ELEC= -123.52 VDW= 445.24 RDTITL> *EXTERNAL= 321.72 INTERNAL= 268.21 USER= 0.00 HARM= 678.96 RDTITL> *BOND= 71.14 ANGL= 149.51 DIHE= 26.29 IMPR= 21.27 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 2400 0.1974 0.0714 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "2400" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21313 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21313 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1118.86878 -528.92889 6.05980 0.02000 MINI INTERN> 71.14468 149.50728 0.00000 26.29416 21.27076 MINI EXTERN> 445.24310 -123.52009 0.00000 0.00000 0.00000 MINI CONSTR> 528.92889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1073.74219 45.12659 16.37138 0.00864 MINI INTERN> 129.04890 139.76061 0.00000 28.62113 16.64583 MINI EXTERN> 319.68320 -117.19509 0.00000 0.00000 0.00000 MINI CONSTR> 557.17761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21299 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1024.42291 49.31928 5.77678 0.00373 MINI INTERN> 58.25009 149.07253 0.00000 30.86963 17.85822 MINI EXTERN> 339.21015 -126.40678 0.00000 0.00000 0.00000 MINI CONSTR> 555.56907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1011.55997 12.86294 1.40624 0.00161 MINI INTERN> 60.82421 143.42550 0.00000 30.35068 17.13413 MINI EXTERN> 329.57859 -125.47609 0.00000 0.00000 0.00000 MINI CONSTR> 555.72296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21295 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1007.21037 4.34960 2.33394 0.00167 MINI INTERN> 58.04863 142.03127 0.00000 30.43138 17.01770 MINI EXTERN> 328.87874 -126.28972 0.00000 0.00000 0.00000 MINI CONSTR> 557.09237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1004.60158 2.60879 0.73022 0.00072 MINI INTERN> 57.96296 140.63931 0.00000 30.68371 17.18480 MINI EXTERN> 325.67811 -126.26553 0.00000 0.00000 0.00000 MINI CONSTR> 558.71821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21296 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1003.51601 1.08557 0.50906 0.00075 MINI INTERN> 57.90293 139.55597 0.00000 30.73488 17.17265 MINI EXTERN> 324.56916 -126.32529 0.00000 0.00000 0.00000 MINI CONSTR> 559.90571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1003.05549 0.46052 1.07388 0.00078 MINI INTERN> 58.04724 138.97675 0.00000 30.80961 17.26674 MINI EXTERN> 323.08496 -126.37865 0.00000 0.00000 0.00000 MINI CONSTR> 561.24884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21293 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1002.63620 0.41929 0.28967 0.00034 MINI INTERN> 57.17974 138.44199 0.00000 30.79632 17.14799 MINI EXTERN> 323.87292 -126.50997 0.00000 0.00000 0.00000 MINI CONSTR> 561.70722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 1002.52887 0.10733 0.58760 0.00035 MINI INTERN> 55.79289 138.68915 0.00000 30.80644 17.14865 MINI EXTERN> 324.59769 -126.80955 0.00000 0.00000 0.00000 MINI CONSTR> 562.30360 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21293 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 1002.46064 0.06823 0.52856 0.00036 MINI INTERN> 56.19565 138.26240 0.00000 30.81353 17.13274 MINI EXTERN> 324.11727 -126.74658 0.00000 0.00000 0.00000 MINI CONSTR> 562.68564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 1002.38569 0.07496 0.19390 0.00016 MINI INTERN> 56.54765 138.13723 0.00000 30.84243 17.20155 MINI EXTERN> 323.23815 -126.69373 0.00000 0.00000 0.00000 MINI CONSTR> 563.11242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21294 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 1002.36207 0.02361 0.06546 0.00007 MINI INTERN> 56.59701 137.93535 0.00000 30.84257 17.18300 MINI EXTERN> 323.19316 -126.68055 0.00000 0.00000 0.00000 MINI CONSTR> 563.29153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 1002.35253 0.00954 0.05177 0.00007 MINI INTERN> 56.55431 137.88686 0.00000 30.84514 17.18442 MINI EXTERN> 323.13388 -126.69683 0.00000 0.00000 0.00000 MINI CONSTR> 563.44475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21294 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 1002.34768 0.00486 0.10979 0.00007 MINI INTERN> 56.37991 137.88527 0.00000 30.84567 17.18295 MINI EXTERN> 323.21304 -126.73705 0.00000 0.00000 0.00000 MINI CONSTR> 563.57789 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 1002.34529 0.00239 0.12623 0.00007 MINI INTERN> 56.77603 137.67748 0.00000 30.84834 17.18106 MINI EXTERN> 322.85999 -126.66424 0.00000 0.00000 0.00000 MINI CONSTR> 563.66663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21294 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 1002.34140 0.00389 0.03537 0.00003 MINI INTERN> 56.51213 137.80465 0.00000 30.84936 17.19148 MINI EXTERN> 322.96487 -126.72865 0.00000 0.00000 0.00000 MINI CONSTR> 563.74756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 1002.34053 0.00087 0.04961 0.00003 MINI INTERN> 56.39069 137.84575 0.00000 30.84918 17.19389 MINI EXTERN> 323.02180 -126.75868 0.00000 0.00000 0.00000 MINI CONSTR> 563.79791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21294 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 1002.33955 0.00098 0.01293 0.00001 MINI INTERN> 56.46858 137.78417 0.00000 30.84878 17.19044 MINI EXTERN> 322.96542 -126.74457 0.00000 0.00000 0.00000 MINI CONSTR> 563.82674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 1002.33906 0.00049 0.01110 0.00002 MINI INTERN> 56.45882 137.77994 0.00000 30.84851 17.19082 MINI EXTERN> 322.95334 -126.75132 0.00000 0.00000 0.00000 MINI CONSTR> 563.85894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21294 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 1002.33879 0.00028 0.02350 0.00002 MINI INTERN> 56.43783 137.78118 0.00000 30.84793 17.19037 MINI EXTERN> 322.95717 -126.75969 0.00000 0.00000 0.00000 MINI CONSTR> 563.88400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 103 1002.33861 0.00017 0.00855 0.00001 STPD INTERN> 56.45818 137.77077 0.00000 30.84798 17.19103 STPD EXTERN> 322.93426 -126.75757 0.00000 0.00000 0.00000 STPD CONSTR> 563.89396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21294 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21294 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1002.33861 0.00017 0.00855 0.00000 MINI INTERN> 56.45818 137.77077 0.00000 30.84798 17.19103 MINI EXTERN> 322.93426 -126.75757 0.00000 0.00000 0.00000 MINI CONSTR> 563.89396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 3 1002.33792 0.00069 0.00366 0.02000 CONJ INTERN> 56.45445 137.74424 0.00000 30.84560 17.19191 CONJ EXTERN> 322.86985 -126.78179 0.00000 0.00000 0.00000 CONJ CONSTR> 564.01367 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "3000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 23.206 ( PROT LYS 1 HT2 ) 23.206 ( PROT LYS 1 N ) 29.007 ( PROT LYS 1 HT3 ) 23.206 ( PROT LYS 1 CA ) 29.007 ( PROT LYS 1 CB ) 23.206 ( PROT LYS 1 CG ) 23.206 ( PROT LYS 1 CD ) 23.206 ( PROT LYS 1 CE ) 23.206 ( PROT LYS 1 NZ ) 23.206 ( PROT LYS 1 HZ1 ) 23.206 ( PROT LYS 1 HZ2 ) 23.206 ( PROT LYS 1 HZ3 ) 23.206 ( PROT LYS 1 C ) 29.007 ( PROT LYS 1 O ) 29.007 ( PROT MET 2 N ) 29.007 ( PROT MET 2 H ) 23.206 ( PROT MET 2 CA ) 29.007 ( PROT MET 2 CB ) 23.206 ( PROT MET 2 CG ) 23.206 ( PROT MET 2 SD ) 23.206 ( PROT MET 2 CE ) 23.206 ( PROT MET 2 C ) 29.007 ( PROT MET 2 O ) 29.007 ( PROT LYS 3 N ) 29.007 ( PROT LYS 3 H ) 23.206 ( PROT LYS 3 CA ) 29.007 ( PROT LYS 3 CB ) 23.206 ( PROT LYS 3 CG ) 23.206 ( PROT LYS 3 CD ) 23.206 ( PROT LYS 3 CE ) 23.206 ( PROT LYS 3 NZ ) 23.206 ( PROT LYS 3 HZ1 ) 23.206 ( PROT LYS 3 HZ2 ) 23.206 ( PROT LYS 3 HZ3 ) 23.206 ( PROT LYS 3 C ) 29.007 ( PROT LYS 3 O ) 29.007 ( PROT ALA 4 N ) 29.007 ( PROT ALA 4 H ) 23.206 ( PROT ALA 4 CA ) 29.007 ( PROT ALA 4 CB ) 23.206 ( PROT ALA 4 C ) 29.007 ( PROT ALA 4 O ) 29.007 ( PROT VAL 5 N ) 29.007 ( PROT VAL 5 H ) 23.206 ( PROT VAL 5 CA ) 29.007 ( PROT VAL 5 CB ) 23.206 ( PROT VAL 5 CG1 ) 23.206 ( PROT VAL 5 CG2 ) 23.206 ( PROT VAL 5 C ) 29.007 ( PROT VAL 5 O ) 29.007 ( PROT MET 6 N ) 29.007 ( PROT MET 6 H ) 23.206 ( PROT MET 6 CA ) 29.007 ( PROT MET 6 CB ) 23.206 ( PROT MET 6 CG ) 23.206 ( PROT MET 6 SD ) 23.206 ( PROT MET 6 CE ) 23.206 ( PROT MET 6 C ) 29.007 ( PROT MET 6 O ) 29.007 ( PROT ILE 7 N ) 29.007 ( PROT ILE 7 H ) 23.206 ( PROT ILE 7 CA ) 29.007 ( PROT ILE 7 CB ) 23.206 ( PROT ILE 7 CG2 ) 23.206 ( PROT ILE 7 CG1 ) 23.206 ( PROT ILE 7 CD ) 23.206 ( PROT ILE 7 C ) 29.007 ( PROT ILE 7 O ) 29.007 ( PROT GLY 8 N ) 29.007 ( PROT GLY 8 H ) 23.206 ( PROT GLY 8 CA ) 29.007 ( PROT GLY 8 C ) 29.007 ( PROT GLY 8 O ) 29.007 ( PROT ALA 9 N ) 29.007 ( PROT ALA 9 H ) 23.206 ( PROT ALA 9 CA ) 29.007 ( PROT ALA 9 CB ) 23.206 ( PROT ALA 9 C ) 29.007 ( PROT ALA 9 O ) 29.007 ( PROT CYS 10 N ) 29.007 ( PROT CYS 10 H ) 23.206 ( PROT CYS 10 CA ) 29.007 ( PROT CYS 10 CB ) 23.206 ( PROT CYS 10 SG ) 23.206 ( PROT CYS 10 C ) 29.007 ( PROT CYS 10 O ) 29.007 ( PROT PHE 11 N ) 29.007 ( PROT PHE 11 H ) 23.206 ( PROT PHE 11 CA ) 29.007 ( PROT PHE 11 CB ) 23.206 ( PROT PHE 11 CG ) 23.206 ( PROT PHE 11 CD1 ) 23.206 ( PROT PHE 11 CD2 ) 23.206 ( PROT PHE 11 CE1 ) 23.206 ( PROT PHE 11 CE2 ) 23.206 ( PROT PHE 11 CZ ) 23.206 ( PROT PHE 11 C ) 29.007 ( PROT PHE 11 O ) 29.007 ( PROT LEU 12 N ) 29.007 ( PROT LEU 12 H ) 23.206 ( PROT LEU 12 CA ) 29.007 ( PROT LEU 12 CB ) 23.206 ( PROT LEU 12 CG ) 23.206 ( PROT LEU 12 CD1 ) 23.206 ( PROT LEU 12 CD2 ) 23.206 ( PROT LEU 12 C ) 29.007 ( PROT LEU 12 O ) 29.007 ( PROT ILE 13 N ) 29.007 ( PROT ILE 13 H ) 23.206 ( PROT ILE 13 CA ) 29.007 ( PROT ILE 13 CB ) 23.206 ( PROT ILE 13 CG2 ) 23.206 ( PROT ILE 13 CG1 ) 23.206 ( PROT ILE 13 CD ) 23.206 ( PROT ILE 13 C ) 29.007 ( PROT ILE 13 O ) 29.007 ( PROT ASH 14 N ) 29.007 ( PROT ASH 14 H ) 23.206 ( PROT ASH 14 CA ) 29.007 ( PROT ASH 14 CB ) 23.206 ( PROT ASH 14 CG ) 23.206 ( PROT ASH 14 OD1 ) 23.206 ( PROT ASH 14 OD2 ) 23.206 ( PROT ASH 14 HD2 ) 23.206 ( PROT ASH 14 C ) 29.007 ( PROT ASH 14 O ) 29.007 ( PROT PHE 15 N ) 29.007 ( PROT PHE 15 H ) 23.206 ( PROT PHE 15 CA ) 29.007 ( PROT PHE 15 CB ) 23.206 ( PROT PHE 15 CG ) 23.206 ( PROT PHE 15 CD1 ) 23.206 ( PROT PHE 15 CD2 ) 23.206 ( PROT PHE 15 CE1 ) 23.206 ( PROT PHE 15 CE2 ) 23.206 ( PROT PHE 15 CZ ) 23.206 ( PROT PHE 15 C ) 29.007 ( PROT PHE 15 O ) 29.007 ( PROT MET 16 N ) 29.007 ( PROT MET 16 H ) 23.206 ( PROT MET 16 CA ) 29.007 ( PROT MET 16 CB ) 23.206 ( PROT MET 16 CG ) 23.206 ( PROT MET 16 SD ) 23.206 ( PROT MET 16 CE ) 23.206 ( PROT MET 16 C ) 29.007 ( PROT MET 16 O ) 29.007 ( PROT PHE 17 N ) 29.007 ( PROT PHE 17 H ) 23.206 ( PROT PHE 17 CA ) 29.007 ( PROT PHE 17 CB ) 23.206 ( PROT PHE 17 CG ) 23.206 ( PROT PHE 17 CD1 ) 23.206 ( PROT PHE 17 CD2 ) 23.206 ( PROT PHE 17 CE1 ) 23.206 ( PROT PHE 17 CE2 ) 23.206 ( PROT PHE 17 CZ ) 23.206 ( PROT PHE 17 C ) 29.007 ( PROT PHE 17 O ) 29.007 ( PROT PHE 18 N ) 29.007 ( PROT PHE 18 H ) 23.206 ( PROT PHE 18 CA ) 29.007 ( PROT PHE 18 CB ) 23.206 ( PROT PHE 18 CG ) 23.206 ( PROT PHE 18 CD1 ) 23.206 ( PROT PHE 18 CD2 ) 23.206 ( PROT PHE 18 CE1 ) 23.206 ( PROT PHE 18 CE2 ) 23.206 ( PROT PHE 18 CZ ) 23.206 ( PROT PHE 18 C ) 29.007 ( PROT PHE 18 O ) 29.007 ( PROT GLU 19 N ) 29.007 ( PROT GLU 19 H ) 23.206 ( PROT GLU 19 CA ) 29.007 ( PROT GLU 19 CB ) 23.206 ( PROT GLU 19 CG ) 23.206 ( PROT GLU 19 CD ) 23.206 ( PROT GLU 19 OE1 ) 23.206 ( PROT GLU 19 OE2 ) 23.206 ( PROT GLU 19 C ) 29.007 ( PROT GLU 19 O ) 29.007 ( PROT SER 20 N ) 29.007 ( PROT SER 20 H ) 23.206 ( PROT SER 20 CA ) 29.007 ( PROT SER 20 CB ) 23.206 ( PROT SER 20 OG ) 23.206 ( PROT SER 20 HG ) 23.206 ( PROT SER 20 C ) 29.007 ( PROT SER 20 O ) 29.007 ( PROT THR 21 N ) 29.007 ( PROT THR 21 H ) 23.206 ( PROT THR 21 CA ) 29.007 ( PROT THR 21 CB ) 23.206 ( PROT THR 21 OG1 ) 23.206 ( PROT THR 21 HG1 ) 23.206 ( PROT THR 21 CG2 ) 23.206 ( PROT THR 21 C ) 29.007 ( PROT THR 21 O ) 29.007 ( PROT GLY 22 N ) 29.007 ( PROT GLY 22 H ) 23.206 ( PROT GLY 22 CA ) 29.007 ( PROT GLY 22 C ) 29.007 ( PROT GLY 22 O ) 29.007 ( PROT SER 23 N ) 29.007 ( PROT SER 23 H ) 23.206 ( PROT SER 23 CA ) 29.007 ( PROT SER 23 CB ) 23.206 ( PROT SER 23 OG ) 23.206 ( PROT SER 23 HG ) 23.206 ( PROT SER 23 C ) 29.007 ( PROT SER 23 O ) 29.007 ( PROT GLN 24 N ) 29.007 ( PROT GLN 24 H ) 23.206 ( PROT GLN 24 CA ) 29.007 ( PROT GLN 24 CB ) 23.206 ( PROT GLN 24 CG ) 23.206 ( PROT GLN 24 CD ) 23.206 ( PROT GLN 24 OE1 ) 23.206 ( PROT GLN 24 NE2 ) 23.206 ( PROT GLN 24 HE21 ) 23.206 ( PROT GLN 24 HE22 ) 23.206 ( PROT GLN 24 C ) 29.007 ( PROT GLN 24 O ) 29.007 ( PROT GLU 25 N ) 29.007 ( PROT GLU 25 H ) 23.206 ( PROT GLU 25 CA ) 29.007 ( PROT GLU 25 CB ) 23.206 ( PROT GLU 25 CG ) 23.206 ( PROT GLU 25 CD ) 23.206 ( PROT GLU 25 OE1 ) 23.206 ( PROT GLU 25 OE2 ) 23.206 ( PROT GLU 25 C ) 29.007 ( PROT GLU 25 O ) 29.007 ( PROT GLN 26 N ) 29.007 ( PROT GLN 26 H ) 23.206 ( PROT GLN 26 CA ) 29.007 ( PROT GLN 26 CB ) 23.206 ( PROT GLN 26 CG ) 23.206 ( PROT GLN 26 CD ) 23.206 ( PROT GLN 26 OE1 ) 23.206 ( PROT GLN 26 NE2 ) 23.206 ( PROT GLN 26 HE21 ) 23.206 ( PROT GLN 26 HE22 ) 23.206 ( PROT GLN 26 C ) 29.007 ( PROT GLN 26 O ) 29.007 ( PROT LYS 27 N ) 29.007 ( PROT LYS 27 H ) 23.206 ( PROT LYS 27 CA ) 29.007 ( PROT LYS 27 CB ) 23.206 ( PROT LYS 27 CG ) 23.206 ( PROT LYS 27 CD ) 23.206 ( PROT LYS 27 CE ) 23.206 ( PROT LYS 27 NZ ) 23.206 ( PROT LYS 27 HZ1 ) 23.206 ( PROT LYS 27 HZ2 ) 23.206 ( PROT LYS 27 HZ3 ) 23.206 ( PROT LYS 27 C ) 29.007 ( PROT LYS 27 O ) 29.007 ( PROT SER 28 N ) 29.007 ( PROT SER 28 H ) 23.206 ( PROT SER 28 CA ) 29.007 ( PROT SER 28 CB ) 23.206 ( PROT SER 28 OG ) 23.206 ( PROT SER 28 HG ) 23.206 ( PROT SER 28 C ) 29.007 ( PROT SER 28 O ) 29.007 ( PROT GLY 29 N ) 29.007 ( PROT GLY 29 H ) 23.206 ( PROT GLY 29 CA ) 29.007 ( PROT GLY 29 C ) 29.007 ( PROT GLY 29 O ) 29.007 ( PROT VAL 30 N ) 29.007 ( PROT VAL 30 H ) 23.206 ( PROT VAL 30 CA ) 29.007 ( PROT VAL 30 CB ) 23.206 ( PROT VAL 30 CG1 ) 23.206 ( PROT VAL 30 CG2 ) 23.206 ( PROT VAL 30 C ) 29.007 ( PROT VAL 30 O ) 29.007 ( PROT TRP 31 N ) 29.007 ( PROT TRP 31 H ) 23.206 ( PROT TRP 31 CA ) 29.007 ( PROT TRP 31 CB ) 23.206 ( PROT TRP 31 CG ) 23.206 ( PROT TRP 31 CD2 ) 23.206 ( PROT TRP 31 CE2 ) 23.206 ( PROT TRP 31 CE3 ) 23.206 ( PROT TRP 31 CD1 ) 23.206 ( PROT TRP 31 NE1 ) 23.206 ( PROT TRP 31 HE1 ) 23.206 ( PROT TRP 31 CZ2 ) 23.206 ( PROT TRP 31 CZ3 ) 23.206 ( PROT TRP 31 CH2 ) 23.206 ( PROT TRP 31 C ) 29.007 ( PROT TRP 31 OT1 ) 23.206 ( PROT TRP 31 OT2 ) 23.206 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63201 7.23023 -13.22153 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS -0.00121 -0.00080 0.00161 ROTATION MATRIX 1.000000 -0.000056 -0.000166 0.000056 1.000000 0.000140 0.000166 -0.000140 1.000000 AXIS OF ROTATION IS 0.623550 0.740570 -0.250482 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 14.7530 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.222876 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2229" Parameter: A <- "0.2229" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51400 7.24778 -13.41834 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01423 0.00777 -0.02201 ROTATION MATRIX 0.999803 0.013835 0.014221 -0.013621 0.999795 -0.014995 -0.014426 0.014799 0.999786 AXIS OF ROTATION IS -0.600439 -0.577330 0.553321 ANGLE IS 1.42 CENTER OF ROTATION 13.860069 7.036198-13.286344 SHIFT IS -0.025207 TOTAL SQUARE DIFF IS 0.2176 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.083772 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2229" RDCMND substituted energy or value "?RMS" to " 0.0838" Parameter: A <- "0.2229 0.0838" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *3000 0.2229 0.0838 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 564.01" Parameter: H <- "564.01" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 438.32426 564.01367 9.89225 ENER INTERN> 56.45445 137.74424 0.00000 30.84560 17.19191 ENER EXTERN> 322.86985 -126.78179 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 438.32" Parameter: B <- "438.32" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -126.78" Parameter: C <- "-126.78" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 322.87" Parameter: C <- " 196.09" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 196.09" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 56.45" Parameter: D <- "56.45" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 137.74" Parameter: D <- " 194.19" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 30.85" Parameter: D <- " 225.04" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 17.19" Parameter: D <- " 242.23" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 242.23" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 3000 ENER= 438.32 GRMS= 9.89 ELEC= -126.78 VDW= 322.87 RDTITL> *EXTERNAL= 196.09 INTERNAL= 242.23 USER= 0.00 HARM= 564.01 RDTITL> *BOND= 56.45 ANGL= 137.74 DIHE= 30.85 IMPR= 17.19 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21294 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21294 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 877.94600 -439.62174 4.45649 0.02000 MINI INTERN> 56.45445 137.74424 0.00000 30.84560 17.19191 MINI EXTERN> 322.86985 -126.78179 0.00000 0.00000 0.00000 MINI CONSTR> 439.62174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 843.30690 34.63910 12.93788 0.00864 MINI INTERN> 69.65260 132.01177 0.00000 33.86722 14.34450 MINI EXTERN> 259.22432 -127.02333 0.00000 0.00000 0.00000 MINI CONSTR> 461.22981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21279 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 804.72855 38.57834 4.22055 0.00373 MINI INTERN> 48.42967 135.20667 0.00000 35.43570 15.99102 MINI EXTERN> 230.21867 -128.19456 0.00000 0.00000 0.00000 MINI CONSTR> 467.64139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 794.39930 10.32925 1.51821 0.00161 MINI INTERN> 45.57716 129.68672 0.00000 35.53118 15.48872 MINI EXTERN> 230.37786 -128.65697 0.00000 0.00000 0.00000 MINI CONSTR> 466.39463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 788.93678 5.46253 1.25150 0.00167 MINI INTERN> 44.71727 127.58903 0.00000 35.72662 15.61858 MINI EXTERN> 226.93188 -128.89516 0.00000 0.00000 0.00000 MINI CONSTR> 467.24855 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 786.04813 2.88865 2.57507 0.00173 MINI INTERN> 44.71306 125.49605 0.00000 35.80888 15.60209 MINI EXTERN> 225.54767 -129.10824 0.00000 0.00000 0.00000 MINI CONSTR> 467.98862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 783.35231 2.69582 0.70079 0.00075 MINI INTERN> 42.90209 125.92588 0.00000 35.94617 15.87240 MINI EXTERN> 223.11867 -129.42192 0.00000 0.00000 0.00000 MINI CONSTR> 469.00901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 781.91937 1.43294 0.54213 0.00078 MINI INTERN> 42.61290 125.15813 0.00000 35.98140 15.90657 MINI EXTERN> 222.09086 -129.55557 0.00000 0.00000 0.00000 MINI CONSTR> 469.72508 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21269 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 781.03904 0.88033 1.07879 0.00080 MINI INTERN> 42.11140 125.10176 0.00000 36.02721 16.00834 MINI EXTERN> 220.96907 -129.78084 0.00000 0.00000 0.00000 MINI CONSTR> 470.60210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 780.62905 0.40999 1.44289 0.00083 MINI INTERN> 42.00007 124.82043 0.00000 36.02150 16.00352 MINI EXTERN> 220.60546 -129.89750 0.00000 0.00000 0.00000 MINI CONSTR> 471.07557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 780.31204 0.31700 1.42246 0.00087 MINI INTERN> 41.77931 124.70339 0.00000 36.02380 16.02717 MINI EXTERN> 220.25785 -129.96675 0.00000 0.00000 0.00000 MINI CONSTR> 471.48727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 779.79972 0.51232 0.35827 0.00037 MINI INTERN> 42.19211 123.65693 0.00000 35.96355 15.93017 MINI EXTERN> 220.18813 -129.90058 0.00000 0.00000 0.00000 MINI CONSTR> 471.76943 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 779.68324 0.11648 0.61150 0.00039 MINI INTERN> 42.13128 123.55325 0.00000 35.94239 15.92207 MINI EXTERN> 220.05553 -129.99771 0.00000 0.00000 0.00000 MINI CONSTR> 472.07643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 779.54292 0.14032 0.17130 0.00017 MINI INTERN> 41.93648 123.68283 0.00000 35.94337 15.95285 MINI EXTERN> 219.70522 -130.04616 0.00000 0.00000 0.00000 MINI CONSTR> 472.36833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21269 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 779.47279 0.07013 0.14528 0.00017 MINI INTERN> 41.92272 123.60881 0.00000 35.92689 15.94776 MINI EXTERN> 219.55907 -130.08500 0.00000 0.00000 0.00000 MINI CONSTR> 472.59255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 779.42205 0.05074 0.25474 0.00018 MINI INTERN> 41.81411 123.65604 0.00000 35.91328 15.95538 MINI EXTERN> 219.39850 -130.15359 0.00000 0.00000 0.00000 MINI CONSTR> 472.83834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 779.38691 0.03514 0.26714 0.00019 MINI INTERN> 41.75923 123.65406 0.00000 35.90066 15.95788 MINI EXTERN> 219.27295 -130.18634 0.00000 0.00000 0.00000 MINI CONSTR> 473.02848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 779.35970 0.02721 0.31290 0.00019 MINI INTERN> 41.76410 123.63122 0.00000 35.88239 15.95184 MINI EXTERN> 219.15939 -130.23903 0.00000 0.00000 0.00000 MINI CONSTR> 473.20978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 779.33733 0.02237 0.29078 0.00020 MINI INTERN> 41.73909 123.59344 0.00000 35.86911 15.94699 MINI EXTERN> 219.07900 -130.24055 0.00000 0.00000 0.00000 MINI CONSTR> 473.35025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 779.30821 0.02912 0.10316 0.00009 MINI INTERN> 42.00674 123.31999 0.00000 35.83672 15.90187 MINI EXTERN> 219.03860 -130.24036 0.00000 0.00000 0.00000 MINI CONSTR> 473.44465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 779.29400 0.01421 0.09379 0.00009 MINI INTERN> 42.01496 123.30349 0.00000 35.82303 15.89615 MINI EXTERN> 218.96124 -130.26807 0.00000 0.00000 0.00000 MINI CONSTR> 473.56320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 779.28047 0.01353 0.08915 0.00009 MINI INTERN> 42.00544 123.29549 0.00000 35.80961 15.89177 MINI EXTERN> 218.88057 -130.29141 0.00000 0.00000 0.00000 MINI CONSTR> 473.68899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 779.27116 0.00931 0.13289 0.00010 MINI INTERN> 42.06932 123.23755 0.00000 35.79295 15.87877 MINI EXTERN> 218.81315 -130.31410 0.00000 0.00000 0.00000 MINI CONSTR> 473.79351 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 779.26317 0.00799 0.17758 0.00010 MINI INTERN> 42.05185 123.23254 0.00000 35.78226 15.87535 MINI EXTERN> 218.74232 -130.32121 0.00000 0.00000 0.00000 MINI CONSTR> 473.90005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 779.25528 0.00789 0.17286 0.00010 MINI INTERN> 42.04651 123.23292 0.00000 35.77289 15.87225 MINI EXTERN> 218.68429 -130.33947 0.00000 0.00000 0.00000 MINI CONSTR> 473.98590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 779.24696 0.00832 0.14863 0.00011 MINI INTERN> 42.11551 123.18396 0.00000 35.75808 15.85993 MINI EXTERN> 218.62671 -130.36707 0.00000 0.00000 0.00000 MINI CONSTR> 474.06983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 779.23639 0.01057 0.05009 0.00005 MINI INTERN> 41.94776 123.31725 0.00000 35.75870 15.87806 MINI EXTERN> 218.56478 -130.40326 0.00000 0.00000 0.00000 MINI CONSTR> 474.17309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 779.23365 0.00274 0.16387 0.00012 MINI INTERN> 42.13159 123.15760 0.00000 35.73747 15.84881 MINI EXTERN> 218.51025 -130.39458 0.00000 0.00000 0.00000 MINI CONSTR> 474.24251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 779.22381 0.00984 0.06263 0.00005 MINI INTERN> 41.93924 123.31459 0.00000 35.74077 15.87074 MINI EXTERN> 218.45651 -130.43558 0.00000 0.00000 0.00000 MINI CONSTR> 474.33755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 779.21852 0.00529 0.05250 0.00005 MINI INTERN> 41.95002 123.30328 0.00000 35.73247 15.86571 MINI EXTERN> 218.41198 -130.44938 0.00000 0.00000 0.00000 MINI CONSTR> 474.40443 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 779.21337 0.00514 0.05661 0.00005 MINI INTERN> 41.94554 123.30614 0.00000 35.72484 15.86262 MINI EXTERN> 218.36469 -130.46674 0.00000 0.00000 0.00000 MINI CONSTR> 474.47627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 779.20853 0.00484 0.06376 0.00006 MINI INTERN> 41.94144 123.30375 0.00000 35.71740 15.85890 MINI EXTERN> 218.31796 -130.47763 0.00000 0.00000 0.00000 MINI CONSTR> 474.54671 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 779.20444 0.00408 0.08395 0.00006 MINI INTERN> 41.92565 123.32026 0.00000 35.71133 15.85787 MINI EXTERN> 218.27461 -130.49906 0.00000 0.00000 0.00000 MINI CONSTR> 474.61379 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 779.20030 0.00414 0.08695 0.00006 MINI INTERN> 41.91473 123.32199 0.00000 35.70525 15.85513 MINI EXTERN> 218.23208 -130.50673 0.00000 0.00000 0.00000 MINI CONSTR> 474.67785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 779.19656 0.00375 0.10236 0.00006 MINI INTERN> 41.92868 123.31692 0.00000 35.69790 15.85043 MINI EXTERN> 218.19093 -130.52637 0.00000 0.00000 0.00000 MINI CONSTR> 474.73808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 779.19262 0.00394 0.08960 0.00006 MINI INTERN> 41.91564 123.31773 0.00000 35.69272 15.84785 MINI EXTERN> 218.15204 -130.52961 0.00000 0.00000 0.00000 MINI CONSTR> 474.79625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 779.18955 0.00307 0.11693 0.00007 MINI INTERN> 41.93402 123.31149 0.00000 35.68552 15.84279 MINI EXTERN> 218.11241 -130.55025 0.00000 0.00000 0.00000 MINI CONSTR> 474.85357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 779.18618 0.00336 0.11054 0.00007 MINI INTERN> 41.93710 123.30691 0.00000 35.68012 15.83903 MINI EXTERN> 218.07764 -130.55883 0.00000 0.00000 0.00000 MINI CONSTR> 474.90421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 779.18320 0.00299 0.11843 0.00007 MINI INTERN> 41.93403 123.29285 0.00000 35.67491 15.83453 MINI EXTERN> 218.03984 -130.55100 0.00000 0.00000 0.00000 MINI CONSTR> 474.95806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 779.17993 0.00327 0.10801 0.00007 MINI INTERN> 41.90958 123.32303 0.00000 35.67123 15.83533 MINI EXTERN> 218.00566 -130.57736 0.00000 0.00000 0.00000 MINI CONSTR> 475.01246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 779.17529 0.00463 0.03616 0.00003 MINI INTERN> 42.04113 123.20981 0.00000 35.65803 15.81436 MINI EXTERN> 217.96744 -130.56621 0.00000 0.00000 0.00000 MINI CONSTR> 475.05073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 779.17429 0.00100 0.11266 0.00008 MINI INTERN> 41.90165 123.32169 0.00000 35.66181 15.82903 MINI EXTERN> 217.93585 -130.59004 0.00000 0.00000 0.00000 MINI CONSTR> 475.11431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 779.16960 0.00469 0.04268 0.00003 MINI INTERN> 42.05424 123.19575 0.00000 35.64738 15.80560 MINI EXTERN> 217.89669 -130.58155 0.00000 0.00000 0.00000 MINI CONSTR> 475.15149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 779.16709 0.00251 0.03823 0.00004 MINI INTERN> 42.05068 123.19924 0.00000 35.64340 15.80313 MINI EXTERN> 217.86633 -130.59176 0.00000 0.00000 0.00000 MINI CONSTR> 475.19607 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 779.16468 0.00241 0.03944 0.00004 MINI INTERN> 42.05604 123.19253 0.00000 35.63885 15.79913 MINI EXTERN> 217.83495 -130.59738 0.00000 0.00000 0.00000 MINI CONSTR> 475.24056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 779.16215 0.00252 0.03775 0.00004 MINI INTERN> 42.05189 123.19639 0.00000 35.63478 15.79643 MINI EXTERN> 217.80275 -130.60772 0.00000 0.00000 0.00000 MINI CONSTR> 475.28763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 779.16011 0.00205 0.05681 0.00004 MINI INTERN> 42.07875 123.17065 0.00000 35.62900 15.78940 MINI EXTERN> 217.77010 -130.60846 0.00000 0.00000 0.00000 MINI CONSTR> 475.33067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 779.15809 0.00201 0.06610 0.00004 MINI INTERN> 42.08061 123.17333 0.00000 35.62512 15.78656 MINI EXTERN> 217.74151 -130.62119 0.00000 0.00000 0.00000 MINI CONSTR> 475.37216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 779.15620 0.00190 0.07071 0.00004 MINI INTERN> 42.08462 123.16936 0.00000 35.62136 15.78314 MINI EXTERN> 217.71408 -130.62748 0.00000 0.00000 0.00000 MINI CONSTR> 475.41111 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 779.15416 0.00204 0.06214 0.00004 MINI INTERN> 42.09019 123.15796 0.00000 35.61756 15.77895 MINI EXTERN> 217.68638 -130.62628 0.00000 0.00000 0.00000 MINI CONSTR> 475.44938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 779.15250 0.00166 0.08026 0.00005 MINI INTERN> 42.09027 123.16376 0.00000 35.61407 15.77650 MINI EXTERN> 217.65892 -130.64047 0.00000 0.00000 0.00000 MINI CONSTR> 475.48944 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 779.15066 0.00183 0.07396 0.00005 MINI INTERN> 42.09185 123.16029 0.00000 35.61089 15.77345 MINI EXTERN> 217.63409 -130.64458 0.00000 0.00000 0.00000 MINI CONSTR> 475.52468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 779.14879 0.00188 0.06703 0.00005 MINI INTERN> 42.10036 123.14644 0.00000 35.60709 15.76886 MINI EXTERN> 217.60687 -130.64268 0.00000 0.00000 0.00000 MINI CONSTR> 475.56183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 779.14648 0.00231 0.02388 0.00002 MINI INTERN> 42.02181 123.21093 0.00000 35.60893 15.77610 MINI EXTERN> 217.58512 -130.65967 0.00000 0.00000 0.00000 MINI CONSTR> 475.60326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 779.14556 0.00092 0.07523 0.00005 MINI INTERN> 42.11152 123.13500 0.00000 35.60018 15.76155 MINI EXTERN> 217.55482 -130.65203 0.00000 0.00000 0.00000 MINI CONSTR> 475.63453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 779.14313 0.00243 0.02565 0.00002 MINI INTERN> 42.01977 123.20998 0.00000 35.60291 15.77035 MINI EXTERN> 217.53368 -130.67025 0.00000 0.00000 0.00000 MINI CONSTR> 475.67668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 779.14174 0.00139 0.02185 0.00002 MINI INTERN> 42.02727 123.20327 0.00000 35.59995 15.76693 MINI EXTERN> 217.51211 -130.67406 0.00000 0.00000 0.00000 MINI CONSTR> 475.70628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 779.14019 0.00154 0.02149 0.00002 MINI INTERN> 42.02968 123.20070 0.00000 35.59696 15.76379 MINI EXTERN> 217.48767 -130.67926 0.00000 0.00000 0.00000 MINI CONSTR> 475.74066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 779.13868 0.00151 0.03168 0.00003 MINI INTERN> 42.01210 123.21390 0.00000 35.59506 15.76291 MINI EXTERN> 217.46238 -130.68653 0.00000 0.00000 0.00000 MINI CONSTR> 475.77884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 779.13733 0.00135 0.02067 0.00003 MINI INTERN> 42.03163 123.19618 0.00000 35.59154 15.75794 MINI EXTERN> 217.44125 -130.68721 0.00000 0.00000 0.00000 MINI CONSTR> 475.80602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 779.13598 0.00136 0.03999 0.00003 MINI INTERN> 42.00790 123.21335 0.00000 35.59010 15.75773 MINI EXTERN> 217.41644 -130.69377 0.00000 0.00000 0.00000 MINI CONSTR> 475.84422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 779.13465 0.00132 0.03007 0.00003 MINI INTERN> 42.01923 123.20360 0.00000 35.58714 15.75389 MINI EXTERN> 217.39567 -130.69679 0.00000 0.00000 0.00000 MINI CONSTR> 475.87193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 779.13348 0.00117 0.04135 0.00003 MINI INTERN> 42.00290 123.21789 0.00000 35.58567 15.75337 MINI EXTERN> 217.37393 -130.70514 0.00000 0.00000 0.00000 MINI CONSTR> 475.90486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 779.13210 0.00138 0.03369 0.00003 MINI INTERN> 42.01856 123.20155 0.00000 35.58231 15.74851 MINI EXTERN> 217.35123 -130.70448 0.00000 0.00000 0.00000 MINI CONSTR> 475.93442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 779.13114 0.00096 0.05011 0.00003 MINI INTERN> 42.00815 123.20811 0.00000 35.58076 15.74721 MINI EXTERN> 217.33091 -130.70796 0.00000 0.00000 0.00000 MINI CONSTR> 475.96396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 779.12995 0.00119 0.04689 0.00003 MINI INTERN> 41.99862 123.21753 0.00000 35.57914 15.74606 MINI EXTERN> 217.31058 -130.71581 0.00000 0.00000 0.00000 MINI CONSTR> 475.99384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 779.12890 0.00105 0.05953 0.00003 MINI INTERN> 42.00535 123.21481 0.00000 35.57631 15.74288 MINI EXTERN> 217.29028 -130.72406 0.00000 0.00000 0.00000 MINI CONSTR> 476.02333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 779.12779 0.00111 0.05431 0.00004 MINI INTERN> 42.00423 123.21394 0.00000 35.57438 15.74059 MINI EXTERN> 217.27151 -130.72654 0.00000 0.00000 0.00000 MINI CONSTR> 476.04967 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 779.12668 0.00111 0.05122 0.00004 MINI INTERN> 41.99630 123.21535 0.00000 35.57279 15.73869 MINI EXTERN> 217.25071 -130.72571 0.00000 0.00000 0.00000 MINI CONSTR> 476.07855 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 779.12533 0.00135 0.01833 0.00002 MINI INTERN> 42.05271 123.16823 0.00000 35.56750 15.72957 MINI EXTERN> 217.23121 -130.72237 0.00000 0.00000 0.00000 MINI CONSTR> 476.09849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 779.12468 0.00065 0.05609 0.00004 MINI INTERN> 41.99206 123.21798 0.00000 35.56916 15.73448 MINI EXTERN> 217.21078 -130.73329 0.00000 0.00000 0.00000 MINI CONSTR> 476.13351 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 779.12322 0.00146 0.01942 0.00002 MINI INTERN> 42.05574 123.16314 0.00000 35.56323 15.72418 MINI EXTERN> 217.19127 -130.72797 0.00000 0.00000 0.00000 MINI CONSTR> 476.15363 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 779.12232 0.00090 0.01726 0.00002 MINI INTERN> 42.05200 123.16546 0.00000 35.56172 15.72252 MINI EXTERN> 217.17467 -130.73149 0.00000 0.00000 0.00000 MINI CONSTR> 476.17746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 779.12188 0.00045 0.06547 0.00004 MINI INTERN> 41.98524 123.21745 0.00000 35.56339 15.72768 MINI EXTERN> 217.15683 -130.74148 0.00000 0.00000 0.00000 MINI CONSTR> 476.21277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 779.12035 0.00153 0.02239 0.00002 MINI INTERN> 42.06053 123.15525 0.00000 35.55720 15.71645 MINI EXTERN> 217.13584 -130.73579 0.00000 0.00000 0.00000 MINI CONSTR> 476.23088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 779.11951 0.00084 0.01724 0.00002 MINI INTERN> 42.05296 123.16113 0.00000 35.55610 15.71543 MINI EXTERN> 217.12008 -130.73970 0.00000 0.00000 0.00000 MINI CONSTR> 476.25351 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 779.11860 0.00091 0.01761 0.00002 MINI INTERN> 42.05386 123.15884 0.00000 35.55424 15.71298 MINI EXTERN> 217.10195 -130.74184 0.00000 0.00000 0.00000 MINI CONSTR> 476.27856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 779.11772 0.00088 0.01778 0.00002 MINI INTERN> 42.05459 123.15728 0.00000 35.55245 15.71065 MINI EXTERN> 217.08437 -130.74458 0.00000 0.00000 0.00000 MINI CONSTR> 476.30296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 779.11682 0.00091 0.02946 0.00002 MINI INTERN> 42.06720 123.14401 0.00000 35.54968 15.70641 MINI EXTERN> 217.06383 -130.74419 0.00000 0.00000 0.00000 MINI CONSTR> 476.32988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 779.11598 0.00083 0.02459 0.00002 MINI INTERN> 42.06330 123.14656 0.00000 35.54832 15.70484 MINI EXTERN> 217.04791 -130.74756 0.00000 0.00000 0.00000 MINI CONSTR> 476.35262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 779.11517 0.00082 0.02734 0.00002 MINI INTERN> 42.06702 123.14300 0.00000 35.54640 15.70223 MINI EXTERN> 217.03081 -130.75045 0.00000 0.00000 0.00000 MINI CONSTR> 476.37615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 779.11436 0.00081 0.02927 0.00002 MINI INTERN> 42.06736 123.14008 0.00000 35.54470 15.69986 MINI EXTERN> 217.01368 -130.75114 0.00000 0.00000 0.00000 MINI CONSTR> 476.39982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 779.11365 0.00071 0.03838 0.00003 MINI INTERN> 42.07366 123.13598 0.00000 35.54269 15.69715 MINI EXTERN> 216.99722 -130.75540 0.00000 0.00000 0.00000 MINI CONSTR> 476.42235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 779.11289 0.00076 0.03895 0.00003 MINI INTERN> 42.07811 123.12938 0.00000 35.54080 15.69433 MINI EXTERN> 216.98101 -130.75534 0.00000 0.00000 0.00000 MINI CONSTR> 476.44461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 779.11216 0.00073 0.04550 0.00003 MINI INTERN> 42.07345 123.12894 0.00000 35.53945 15.69244 MINI EXTERN> 216.96354 -130.75439 0.00000 0.00000 0.00000 MINI CONSTR> 476.46873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 779.11138 0.00078 0.03941 0.00003 MINI INTERN> 42.07803 123.12630 0.00000 35.53768 15.69010 MINI EXTERN> 216.94875 -130.75883 0.00000 0.00000 0.00000 MINI CONSTR> 476.48936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 779.11065 0.00073 0.04961 0.00003 MINI INTERN> 42.07721 123.12297 0.00000 35.53602 15.68761 MINI EXTERN> 216.92931 -130.75767 0.00000 0.00000 0.00000 MINI CONSTR> 476.51520 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 779.10990 0.00076 0.04293 0.00003 MINI INTERN> 42.08067 123.12055 0.00000 35.53437 15.68541 MINI EXTERN> 216.91491 -130.76129 0.00000 0.00000 0.00000 MINI CONSTR> 476.53529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 779.10892 0.00098 0.01492 0.00001 MINI INTERN> 42.03693 123.15787 0.00000 35.53566 15.68889 MINI EXTERN> 216.89924 -130.77041 0.00000 0.00000 0.00000 MINI CONSTR> 476.56074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 779.10848 0.00044 0.04649 0.00003 MINI INTERN> 42.08366 123.11520 0.00000 35.53116 15.68087 MINI EXTERN> 216.88219 -130.76428 0.00000 0.00000 0.00000 MINI CONSTR> 476.57969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 779.10748 0.00100 0.01604 0.00001 MINI INTERN> 42.03378 123.15750 0.00000 35.53284 15.68509 MINI EXTERN> 216.86716 -130.77410 0.00000 0.00000 0.00000 MINI CONSTR> 476.60521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 779.10686 0.00062 0.01435 0.00001 MINI INTERN> 42.03669 123.15408 0.00000 35.53138 15.68299 MINI EXTERN> 216.85332 -130.77544 0.00000 0.00000 0.00000 MINI CONSTR> 476.62384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 779.10662 0.00024 0.05947 0.00004 MINI INTERN> 42.07363 123.11648 0.00000 35.52752 15.67593 MINI EXTERN> 216.83623 -130.76665 0.00000 0.00000 0.00000 MINI CONSTR> 476.64349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 779.10550 0.00112 0.01681 0.00002 MINI INTERN> 42.03166 123.15575 0.00000 35.52879 15.67957 MINI EXTERN> 216.82199 -130.77959 0.00000 0.00000 0.00000 MINI CONSTR> 476.66733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 779.10491 0.00059 0.01441 0.00002 MINI INTERN> 42.03480 123.15155 0.00000 35.52738 15.67746 MINI EXTERN> 216.80865 -130.78011 0.00000 0.00000 0.00000 MINI CONSTR> 476.68517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 779.10425 0.00066 0.01365 0.00002 MINI INTERN> 42.03592 123.14889 0.00000 35.52590 15.67534 MINI EXTERN> 216.79345 -130.78116 0.00000 0.00000 0.00000 MINI CONSTR> 476.70591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 779.10360 0.00065 0.01477 0.00002 MINI INTERN> 42.03285 123.15009 0.00000 35.52470 15.67376 MINI EXTERN> 216.77816 -130.78305 0.00000 0.00000 0.00000 MINI CONSTR> 476.72709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 779.10296 0.00064 0.02440 0.00002 MINI INTERN> 42.02243 123.15856 0.00000 35.52384 15.67301 MINI EXTERN> 216.76172 -130.78728 0.00000 0.00000 0.00000 MINI CONSTR> 476.75067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 779.10236 0.00060 0.02011 0.00002 MINI INTERN> 42.02518 123.15440 0.00000 35.52245 15.67092 MINI EXTERN> 216.74810 -130.78747 0.00000 0.00000 0.00000 MINI CONSTR> 476.76879 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 779.10176 0.00060 0.02234 0.00002 MINI INTERN> 42.02236 123.15445 0.00000 35.52131 15.66932 MINI EXTERN> 216.73338 -130.78801 0.00000 0.00000 0.00000 MINI CONSTR> 476.78895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 779.10119 0.00057 0.02364 0.00002 MINI INTERN> 42.01997 123.15571 0.00000 35.52020 15.66789 MINI EXTERN> 216.71921 -130.79009 0.00000 0.00000 0.00000 MINI CONSTR> 476.80830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 779.10119 0.00057 0.02364 0.00002 STPD INTERN> 42.01997 123.15571 0.00000 35.52020 15.66789 STPD EXTERN> 216.71921 -130.79009 0.00000 0.00000 0.00000 STPD CONSTR> 476.80830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21271 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21271 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 779.10119 0.00057 0.02364 0.00000 MINI INTERN> 42.01997 123.15571 0.00000 35.52020 15.66789 MINI EXTERN> 216.71921 -130.79009 0.00000 0.00000 0.00000 MINI CONSTR> 476.80830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 779.06867 0.03253 0.08193 0.01482 MINI INTERN> 41.69029 122.94886 0.00000 35.40222 15.56485 MINI EXTERN> 214.92190 -130.75456 0.00000 0.00000 0.00000 MINI CONSTR> 479.29512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 779.06325 0.00542 0.05850 0.00557 MINI INTERN> 41.71879 122.88310 0.00000 35.39289 15.54810 MINI EXTERN> 214.69651 -130.74127 0.00000 0.00000 0.00000 MINI CONSTR> 479.56513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 779.06042 0.00283 0.03579 0.00275 MINI INTERN> 41.70689 122.94815 0.00000 35.36208 15.51088 MINI EXTERN> 214.77906 -130.73863 0.00000 0.00000 0.00000 MINI CONSTR> 479.49199 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 779.05936 0.00106 0.02536 0.00134 MINI INTERN> 41.75192 122.97112 0.00000 35.35545 15.50028 MINI EXTERN> 214.77234 -130.73628 0.00000 0.00000 0.00000 MINI CONSTR> 479.44454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 779.05878 0.00058 0.02353 0.00088 MINI INTERN> 41.76871 122.97311 0.00000 35.35256 15.50381 MINI EXTERN> 214.73205 -130.73546 0.00000 0.00000 0.00000 MINI CONSTR> 479.46399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 779.05824 0.00054 0.02049 0.00125 MINI INTERN> 41.75896 122.93959 0.00000 35.35595 15.49827 MINI EXTERN> 214.74551 -130.74648 0.00000 0.00000 0.00000 MINI CONSTR> 479.50642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 779.05770 0.00055 0.02278 0.00166 MINI INTERN> 41.74615 122.93666 0.00000 35.35918 15.51014 MINI EXTERN> 214.69979 -130.74523 0.00000 0.00000 0.00000 MINI CONSTR> 479.55101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 779.05699 0.00071 0.02339 0.00232 MINI INTERN> 41.73889 122.91707 0.00000 35.36704 15.51282 MINI EXTERN> 214.71304 -130.73901 0.00000 0.00000 0.00000 MINI CONSTR> 479.54715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 779.05636 0.00062 0.01872 0.00202 MINI INTERN> 41.74021 122.93820 0.00000 35.36792 15.51119 MINI EXTERN> 214.75441 -130.72530 0.00000 0.00000 0.00000 MINI CONSTR> 479.46974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 779.05605 0.00031 0.01422 0.00098 MINI INTERN> 41.75901 122.96107 0.00000 35.36879 15.50780 MINI EXTERN> 214.79476 -130.72338 0.00000 0.00000 0.00000 MINI CONSTR> 479.38799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 779.05588 0.00017 0.01009 0.00069 MINI INTERN> 41.75857 122.97225 0.00000 35.36683 15.50605 MINI EXTERN> 214.83358 -130.72017 0.00000 0.00000 0.00000 MINI CONSTR> 479.33876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 58 779.05580 0.00008 0.00886 0.02000 CONJ INTERN> 41.75890 122.97769 0.00000 35.36429 15.50926 CONJ EXTERN> 214.82055 -130.71535 0.00000 0.00000 0.00000 CONJ CONSTR> 479.34046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "3600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 15.084 ( PROT LYS 1 HT2 ) 15.084 ( PROT LYS 1 N ) 18.855 ( PROT LYS 1 HT3 ) 15.084 ( PROT LYS 1 CA ) 18.855 ( PROT LYS 1 CB ) 15.084 ( PROT LYS 1 CG ) 15.084 ( PROT LYS 1 CD ) 15.084 ( PROT LYS 1 CE ) 15.084 ( PROT LYS 1 NZ ) 15.084 ( PROT LYS 1 HZ1 ) 15.084 ( PROT LYS 1 HZ2 ) 15.084 ( PROT LYS 1 HZ3 ) 15.084 ( PROT LYS 1 C ) 18.855 ( PROT LYS 1 O ) 18.855 ( PROT MET 2 N ) 18.855 ( PROT MET 2 H ) 15.084 ( PROT MET 2 CA ) 18.855 ( PROT MET 2 CB ) 15.084 ( PROT MET 2 CG ) 15.084 ( PROT MET 2 SD ) 15.084 ( PROT MET 2 CE ) 15.084 ( PROT MET 2 C ) 18.855 ( PROT MET 2 O ) 18.855 ( PROT LYS 3 N ) 18.855 ( PROT LYS 3 H ) 15.084 ( PROT LYS 3 CA ) 18.855 ( PROT LYS 3 CB ) 15.084 ( PROT LYS 3 CG ) 15.084 ( PROT LYS 3 CD ) 15.084 ( PROT LYS 3 CE ) 15.084 ( PROT LYS 3 NZ ) 15.084 ( PROT LYS 3 HZ1 ) 15.084 ( PROT LYS 3 HZ2 ) 15.084 ( PROT LYS 3 HZ3 ) 15.084 ( PROT LYS 3 C ) 18.855 ( PROT LYS 3 O ) 18.855 ( PROT ALA 4 N ) 18.855 ( PROT ALA 4 H ) 15.084 ( PROT ALA 4 CA ) 18.855 ( PROT ALA 4 CB ) 15.084 ( PROT ALA 4 C ) 18.855 ( PROT ALA 4 O ) 18.855 ( PROT VAL 5 N ) 18.855 ( PROT VAL 5 H ) 15.084 ( PROT VAL 5 CA ) 18.855 ( PROT VAL 5 CB ) 15.084 ( PROT VAL 5 CG1 ) 15.084 ( PROT VAL 5 CG2 ) 15.084 ( PROT VAL 5 C ) 18.855 ( PROT VAL 5 O ) 18.855 ( PROT MET 6 N ) 18.855 ( PROT MET 6 H ) 15.084 ( PROT MET 6 CA ) 18.855 ( PROT MET 6 CB ) 15.084 ( PROT MET 6 CG ) 15.084 ( PROT MET 6 SD ) 15.084 ( PROT MET 6 CE ) 15.084 ( PROT MET 6 C ) 18.855 ( PROT MET 6 O ) 18.855 ( PROT ILE 7 N ) 18.855 ( PROT ILE 7 H ) 15.084 ( PROT ILE 7 CA ) 18.855 ( PROT ILE 7 CB ) 15.084 ( PROT ILE 7 CG2 ) 15.084 ( PROT ILE 7 CG1 ) 15.084 ( PROT ILE 7 CD ) 15.084 ( PROT ILE 7 C ) 18.855 ( PROT ILE 7 O ) 18.855 ( PROT GLY 8 N ) 18.855 ( PROT GLY 8 H ) 15.084 ( PROT GLY 8 CA ) 18.855 ( PROT GLY 8 C ) 18.855 ( PROT GLY 8 O ) 18.855 ( PROT ALA 9 N ) 18.855 ( PROT ALA 9 H ) 15.084 ( PROT ALA 9 CA ) 18.855 ( PROT ALA 9 CB ) 15.084 ( PROT ALA 9 C ) 18.855 ( PROT ALA 9 O ) 18.855 ( PROT CYS 10 N ) 18.855 ( PROT CYS 10 H ) 15.084 ( PROT CYS 10 CA ) 18.855 ( PROT CYS 10 CB ) 15.084 ( PROT CYS 10 SG ) 15.084 ( PROT CYS 10 C ) 18.855 ( PROT CYS 10 O ) 18.855 ( PROT PHE 11 N ) 18.855 ( PROT PHE 11 H ) 15.084 ( PROT PHE 11 CA ) 18.855 ( PROT PHE 11 CB ) 15.084 ( PROT PHE 11 CG ) 15.084 ( PROT PHE 11 CD1 ) 15.084 ( PROT PHE 11 CD2 ) 15.084 ( PROT PHE 11 CE1 ) 15.084 ( PROT PHE 11 CE2 ) 15.084 ( PROT PHE 11 CZ ) 15.084 ( PROT PHE 11 C ) 18.855 ( PROT PHE 11 O ) 18.855 ( PROT LEU 12 N ) 18.855 ( PROT LEU 12 H ) 15.084 ( PROT LEU 12 CA ) 18.855 ( PROT LEU 12 CB ) 15.084 ( PROT LEU 12 CG ) 15.084 ( PROT LEU 12 CD1 ) 15.084 ( PROT LEU 12 CD2 ) 15.084 ( PROT LEU 12 C ) 18.855 ( PROT LEU 12 O ) 18.855 ( PROT ILE 13 N ) 18.855 ( PROT ILE 13 H ) 15.084 ( PROT ILE 13 CA ) 18.855 ( PROT ILE 13 CB ) 15.084 ( PROT ILE 13 CG2 ) 15.084 ( PROT ILE 13 CG1 ) 15.084 ( PROT ILE 13 CD ) 15.084 ( PROT ILE 13 C ) 18.855 ( PROT ILE 13 O ) 18.855 ( PROT ASH 14 N ) 18.855 ( PROT ASH 14 H ) 15.084 ( PROT ASH 14 CA ) 18.855 ( PROT ASH 14 CB ) 15.084 ( PROT ASH 14 CG ) 15.084 ( PROT ASH 14 OD1 ) 15.084 ( PROT ASH 14 OD2 ) 15.084 ( PROT ASH 14 HD2 ) 15.084 ( PROT ASH 14 C ) 18.855 ( PROT ASH 14 O ) 18.855 ( PROT PHE 15 N ) 18.855 ( PROT PHE 15 H ) 15.084 ( PROT PHE 15 CA ) 18.855 ( PROT PHE 15 CB ) 15.084 ( PROT PHE 15 CG ) 15.084 ( PROT PHE 15 CD1 ) 15.084 ( PROT PHE 15 CD2 ) 15.084 ( PROT PHE 15 CE1 ) 15.084 ( PROT PHE 15 CE2 ) 15.084 ( PROT PHE 15 CZ ) 15.084 ( PROT PHE 15 C ) 18.855 ( PROT PHE 15 O ) 18.855 ( PROT MET 16 N ) 18.855 ( PROT MET 16 H ) 15.084 ( PROT MET 16 CA ) 18.855 ( PROT MET 16 CB ) 15.084 ( PROT MET 16 CG ) 15.084 ( PROT MET 16 SD ) 15.084 ( PROT MET 16 CE ) 15.084 ( PROT MET 16 C ) 18.855 ( PROT MET 16 O ) 18.855 ( PROT PHE 17 N ) 18.855 ( PROT PHE 17 H ) 15.084 ( PROT PHE 17 CA ) 18.855 ( PROT PHE 17 CB ) 15.084 ( PROT PHE 17 CG ) 15.084 ( PROT PHE 17 CD1 ) 15.084 ( PROT PHE 17 CD2 ) 15.084 ( PROT PHE 17 CE1 ) 15.084 ( PROT PHE 17 CE2 ) 15.084 ( PROT PHE 17 CZ ) 15.084 ( PROT PHE 17 C ) 18.855 ( PROT PHE 17 O ) 18.855 ( PROT PHE 18 N ) 18.855 ( PROT PHE 18 H ) 15.084 ( PROT PHE 18 CA ) 18.855 ( PROT PHE 18 CB ) 15.084 ( PROT PHE 18 CG ) 15.084 ( PROT PHE 18 CD1 ) 15.084 ( PROT PHE 18 CD2 ) 15.084 ( PROT PHE 18 CE1 ) 15.084 ( PROT PHE 18 CE2 ) 15.084 ( PROT PHE 18 CZ ) 15.084 ( PROT PHE 18 C ) 18.855 ( PROT PHE 18 O ) 18.855 ( PROT GLU 19 N ) 18.855 ( PROT GLU 19 H ) 15.084 ( PROT GLU 19 CA ) 18.855 ( PROT GLU 19 CB ) 15.084 ( PROT GLU 19 CG ) 15.084 ( PROT GLU 19 CD ) 15.084 ( PROT GLU 19 OE1 ) 15.084 ( PROT GLU 19 OE2 ) 15.084 ( PROT GLU 19 C ) 18.855 ( PROT GLU 19 O ) 18.855 ( PROT SER 20 N ) 18.855 ( PROT SER 20 H ) 15.084 ( PROT SER 20 CA ) 18.855 ( PROT SER 20 CB ) 15.084 ( PROT SER 20 OG ) 15.084 ( PROT SER 20 HG ) 15.084 ( PROT SER 20 C ) 18.855 ( PROT SER 20 O ) 18.855 ( PROT THR 21 N ) 18.855 ( PROT THR 21 H ) 15.084 ( PROT THR 21 CA ) 18.855 ( PROT THR 21 CB ) 15.084 ( PROT THR 21 OG1 ) 15.084 ( PROT THR 21 HG1 ) 15.084 ( PROT THR 21 CG2 ) 15.084 ( PROT THR 21 C ) 18.855 ( PROT THR 21 O ) 18.855 ( PROT GLY 22 N ) 18.855 ( PROT GLY 22 H ) 15.084 ( PROT GLY 22 CA ) 18.855 ( PROT GLY 22 C ) 18.855 ( PROT GLY 22 O ) 18.855 ( PROT SER 23 N ) 18.855 ( PROT SER 23 H ) 15.084 ( PROT SER 23 CA ) 18.855 ( PROT SER 23 CB ) 15.084 ( PROT SER 23 OG ) 15.084 ( PROT SER 23 HG ) 15.084 ( PROT SER 23 C ) 18.855 ( PROT SER 23 O ) 18.855 ( PROT GLN 24 N ) 18.855 ( PROT GLN 24 H ) 15.084 ( PROT GLN 24 CA ) 18.855 ( PROT GLN 24 CB ) 15.084 ( PROT GLN 24 CG ) 15.084 ( PROT GLN 24 CD ) 15.084 ( PROT GLN 24 OE1 ) 15.084 ( PROT GLN 24 NE2 ) 15.084 ( PROT GLN 24 HE21 ) 15.084 ( PROT GLN 24 HE22 ) 15.084 ( PROT GLN 24 C ) 18.855 ( PROT GLN 24 O ) 18.855 ( PROT GLU 25 N ) 18.855 ( PROT GLU 25 H ) 15.084 ( PROT GLU 25 CA ) 18.855 ( PROT GLU 25 CB ) 15.084 ( PROT GLU 25 CG ) 15.084 ( PROT GLU 25 CD ) 15.084 ( PROT GLU 25 OE1 ) 15.084 ( PROT GLU 25 OE2 ) 15.084 ( PROT GLU 25 C ) 18.855 ( PROT GLU 25 O ) 18.855 ( PROT GLN 26 N ) 18.855 ( PROT GLN 26 H ) 15.084 ( PROT GLN 26 CA ) 18.855 ( PROT GLN 26 CB ) 15.084 ( PROT GLN 26 CG ) 15.084 ( PROT GLN 26 CD ) 15.084 ( PROT GLN 26 OE1 ) 15.084 ( PROT GLN 26 NE2 ) 15.084 ( PROT GLN 26 HE21 ) 15.084 ( PROT GLN 26 HE22 ) 15.084 ( PROT GLN 26 C ) 18.855 ( PROT GLN 26 O ) 18.855 ( PROT LYS 27 N ) 18.855 ( PROT LYS 27 H ) 15.084 ( PROT LYS 27 CA ) 18.855 ( PROT LYS 27 CB ) 15.084 ( PROT LYS 27 CG ) 15.084 ( PROT LYS 27 CD ) 15.084 ( PROT LYS 27 CE ) 15.084 ( PROT LYS 27 NZ ) 15.084 ( PROT LYS 27 HZ1 ) 15.084 ( PROT LYS 27 HZ2 ) 15.084 ( PROT LYS 27 HZ3 ) 15.084 ( PROT LYS 27 C ) 18.855 ( PROT LYS 27 O ) 18.855 ( PROT SER 28 N ) 18.855 ( PROT SER 28 H ) 15.084 ( PROT SER 28 CA ) 18.855 ( PROT SER 28 CB ) 15.084 ( PROT SER 28 OG ) 15.084 ( PROT SER 28 HG ) 15.084 ( PROT SER 28 C ) 18.855 ( PROT SER 28 O ) 18.855 ( PROT GLY 29 N ) 18.855 ( PROT GLY 29 H ) 15.084 ( PROT GLY 29 CA ) 18.855 ( PROT GLY 29 C ) 18.855 ( PROT GLY 29 O ) 18.855 ( PROT VAL 30 N ) 18.855 ( PROT VAL 30 H ) 15.084 ( PROT VAL 30 CA ) 18.855 ( PROT VAL 30 CB ) 15.084 ( PROT VAL 30 CG1 ) 15.084 ( PROT VAL 30 CG2 ) 15.084 ( PROT VAL 30 C ) 18.855 ( PROT VAL 30 O ) 18.855 ( PROT TRP 31 N ) 18.855 ( PROT TRP 31 H ) 15.084 ( PROT TRP 31 CA ) 18.855 ( PROT TRP 31 CB ) 15.084 ( PROT TRP 31 CG ) 15.084 ( PROT TRP 31 CD2 ) 15.084 ( PROT TRP 31 CE2 ) 15.084 ( PROT TRP 31 CE3 ) 15.084 ( PROT TRP 31 CD1 ) 15.084 ( PROT TRP 31 NE1 ) 15.084 ( PROT TRP 31 HE1 ) 15.084 ( PROT TRP 31 CZ2 ) 15.084 ( PROT TRP 31 CZ3 ) 15.084 ( PROT TRP 31 CH2 ) 15.084 ( PROT TRP 31 C ) 18.855 ( PROT TRP 31 OT1 ) 15.084 ( PROT TRP 31 OT2 ) 15.084 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63173 7.22967 -13.22136 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS -0.00093 -0.00024 0.00144 ROTATION MATRIX 1.000000 -0.000088 -0.000229 0.000088 1.000000 0.000204 0.000229 -0.000204 1.000000 AXIS OF ROTATION IS 0.639012 0.718377 -0.274953 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 19.1226 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.253743 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2537" Parameter: A <- "0.2537" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51325 7.24783 -13.41588 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01498 0.00772 -0.02448 ROTATION MATRIX 0.999776 0.014738 0.015187 -0.014495 0.999767 -0.015975 -0.015418 0.015751 0.999757 AXIS OF ROTATION IS -0.599802 -0.578613 0.552671 ANGLE IS 1.52 CENTER OF ROTATION 13.894887 7.009552-13.275558 SHIFT IS -0.026981 TOTAL SQUARE DIFF IS 0.2961 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.097738 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2537" RDCMND substituted energy or value "?RMS" to " 0.0977" Parameter: A <- "0.2537 0.0977" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *3600 0.2537 0.0977 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 479.34" Parameter: H <- "479.34" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 299.71534 479.34046 7.38698 ENER INTERN> 41.75890 122.97769 0.00000 35.36429 15.50926 ENER EXTERN> 214.82055 -130.71535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 299.72" Parameter: B <- "299.72" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -130.72" Parameter: C <- "-130.72" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 214.82" Parameter: C <- " 84.10" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 84.10" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 41.76" Parameter: D <- "41.76" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 122.98" Parameter: D <- " 164.74" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 35.36" Parameter: D <- " 200.10" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 15.51" Parameter: D <- " 215.61" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 215.61" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 3600 ENER= 299.72 GRMS= 7.39 ELEC= -130.72 VDW= 214.82 RDTITL> *EXTERNAL= 84.10 INTERNAL= 215.61 USER= 0.00 HARM= 479.34 RDTITL> *BOND= 41.76 ANGL= 122.98 DIHE= 35.36 IMPR= 15.51 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "3600" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_3600.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_3600.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 3600 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 3600 ENER= 299.72 GRMS= 7.39 ELEC= -130.72 VDW= 214.82 RDTITL> *EXTERNAL= 84.10 INTERNAL= 215.61 USER= 0.00 HARM= 479.34 RDTITL> *BOND= 41.76 ANGL= 122.98 DIHE= 35.36 IMPR= 15.51 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "3600" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_3600.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_3600.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 3600 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 3600 ENER= 299.72 GRMS= 7.39 ELEC= -130.72 VDW= 214.82 RDTITL> *EXTERNAL= 84.10 INTERNAL= 215.61 USER= 0.00 HARM= 479.34 RDTITL> *BOND= 41.76 ANGL= 122.98 DIHE= 35.36 IMPR= 15.51 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 3600 0.2537 0.0977 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "3600" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21271 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21272 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 665.36046 -365.64512 3.23594 0.02000 MINI INTERN> 41.75890 122.97769 0.00000 35.36429 15.50926 MINI EXTERN> 214.82055 -130.71535 0.00000 0.00000 0.00000 MINI CONSTR> 365.64512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 627.16141 38.19905 2.77277 0.00360 MINI INTERN> 36.86504 125.22707 0.00000 39.91772 15.43638 MINI EXTERN> 145.34113 -129.33404 0.00000 0.00000 0.00000 MINI CONSTR> 393.70811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21262 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 615.24275 11.91866 1.51022 0.00156 MINI INTERN> 33.42817 117.48991 0.00000 39.70246 15.28067 MINI EXTERN> 145.24494 -130.29217 0.00000 0.00000 0.00000 MINI CONSTR> 394.38878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 608.38737 6.85538 1.64072 0.00161 MINI INTERN> 33.06521 115.38428 0.00000 40.04421 15.55937 MINI EXTERN> 138.72555 -130.24311 0.00000 0.00000 0.00000 MINI CONSTR> 395.85186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21260 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 603.66294 4.72442 1.67872 0.00167 MINI INTERN> 32.16250 113.91976 0.00000 40.22990 15.64618 MINI EXTERN> 135.43549 -130.27145 0.00000 0.00000 0.00000 MINI CONSTR> 396.54056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 600.85331 2.80964 2.51606 0.00173 MINI INTERN> 33.24740 112.73857 0.00000 40.19076 15.83927 MINI EXTERN> 131.87213 -130.17775 0.00000 0.00000 0.00000 MINI CONSTR> 397.14293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21262 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 598.56296 2.29034 3.10796 0.00180 MINI INTERN> 33.36748 111.97411 0.00000 40.24412 15.87547 MINI EXTERN> 129.74207 -130.18664 0.00000 0.00000 0.00000 MINI CONSTR> 397.54635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 596.62426 1.93870 2.83120 0.00186 MINI INTERN> 33.25844 111.09811 0.00000 40.22092 15.83007 MINI EXTERN> 128.59583 -130.12240 0.00000 0.00000 0.00000 MINI CONSTR> 397.74329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21260 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 594.00657 2.61769 0.98464 0.00080 MINI INTERN> 29.29898 110.55507 0.00000 40.57568 15.27913 MINI EXTERN> 131.16265 -130.32010 0.00000 0.00000 0.00000 MINI CONSTR> 397.45515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 592.81138 1.19519 0.76737 0.00083 MINI INTERN> 29.23885 110.19798 0.00000 40.52182 15.26937 MINI EXTERN> 130.13743 -130.27794 0.00000 0.00000 0.00000 MINI CONSTR> 397.72387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21259 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 592.05652 0.75486 1.28331 0.00087 MINI INTERN> 29.14770 109.71791 0.00000 40.51776 15.14045 MINI EXTERN> 129.85230 -130.23467 0.00000 0.00000 0.00000 MINI CONSTR> 397.91509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 591.46055 0.59597 1.47011 0.00090 MINI INTERN> 28.81552 109.58196 0.00000 40.49261 15.06578 MINI EXTERN> 129.58482 -130.21552 0.00000 0.00000 0.00000 MINI CONSTR> 398.13538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21258 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 590.93460 0.52595 1.37077 0.00093 MINI INTERN> 28.62479 109.43704 0.00000 40.46489 15.01696 MINI EXTERN> 129.20271 -130.18562 0.00000 0.00000 0.00000 MINI CONSTR> 398.37383 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 590.21303 0.72157 0.41121 0.00040 MINI INTERN> 28.91924 109.55103 0.00000 40.30096 15.18195 MINI EXTERN> 127.52870 -130.12367 0.00000 0.00000 0.00000 MINI CONSTR> 398.85482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21262 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 589.90556 0.30747 0.31409 0.00042 MINI INTERN> 28.89425 109.34208 0.00000 40.25655 15.12562 MINI EXTERN> 127.27740 -130.06648 0.00000 0.00000 0.00000 MINI CONSTR> 399.07615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 589.65418 0.25138 0.62576 0.00043 MINI INTERN> 28.84397 109.39483 0.00000 40.18889 15.12863 MINI EXTERN> 126.70338 -130.02763 0.00000 0.00000 0.00000 MINI CONSTR> 399.42211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21262 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 589.43318 0.22100 0.66721 0.00045 MINI INTERN> 28.61476 109.38197 0.00000 40.14938 15.08196 MINI EXTERN> 126.49367 -129.98746 0.00000 0.00000 0.00000 MINI CONSTR> 399.69890 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 589.27813 0.15505 0.75485 0.00046 MINI INTERN> 28.66005 109.24812 0.00000 40.09954 15.04459 MINI EXTERN> 126.18644 -129.92343 0.00000 0.00000 0.00000 MINI CONSTR> 399.96283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21263 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 589.13552 0.14261 0.69866 0.00048 MINI INTERN> 28.57887 109.19271 0.00000 40.05092 15.01383 MINI EXTERN> 125.97933 -129.87375 0.00000 0.00000 0.00000 MINI CONSTR> 400.19362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 588.94104 0.19447 0.22467 0.00021 MINI INTERN> 28.74884 108.64185 0.00000 40.00168 14.89315 MINI EXTERN> 126.04090 -129.74686 0.00000 0.00000 0.00000 MINI CONSTR> 400.36149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21263 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 588.84923 0.09181 0.17600 0.00022 MINI INTERN> 28.65841 108.63441 0.00000 39.96608 14.87190 MINI EXTERN> 125.85547 -129.70477 0.00000 0.00000 0.00000 MINI CONSTR> 400.56773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 588.76008 0.08916 0.30558 0.00022 MINI INTERN> 28.73202 108.43508 0.00000 39.91258 14.82087 MINI EXTERN> 125.66625 -129.61634 0.00000 0.00000 0.00000 MINI CONSTR> 400.80962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21263 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 588.68382 0.07626 0.26228 0.00023 MINI INTERN> 28.63755 108.42860 0.00000 39.87596 14.79875 MINI EXTERN> 125.49715 -129.57106 0.00000 0.00000 0.00000 MINI CONSTR> 401.01688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 588.62654 0.05727 0.34422 0.00024 MINI INTERN> 28.66403 108.30988 0.00000 39.83595 14.76439 MINI EXTERN> 125.33604 -129.49918 0.00000 0.00000 0.00000 MINI CONSTR> 401.21543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21263 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 588.57472 0.05182 0.41631 0.00025 MINI INTERN> 28.59679 108.28507 0.00000 39.79799 14.73893 MINI EXTERN> 125.19934 -129.45412 0.00000 0.00000 0.00000 MINI CONSTR> 401.41073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 588.52148 0.05324 0.36669 0.00026 MINI INTERN> 28.56939 108.22229 0.00000 39.76649 14.71477 MINI EXTERN> 125.05661 -129.39314 0.00000 0.00000 0.00000 MINI CONSTR> 401.58506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21263 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 588.45455 0.06693 0.12058 0.00011 MINI INTERN> 28.35882 108.40543 0.00000 39.74075 14.72944 MINI EXTERN> 124.79833 -129.37392 0.00000 0.00000 0.00000 MINI CONSTR> 401.79569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 588.43306 0.02150 0.39775 0.00028 MINI INTERN> 28.55355 108.10213 0.00000 39.69341 14.67037 MINI EXTERN> 124.74169 -129.27499 0.00000 0.00000 0.00000 MINI CONSTR> 401.94690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21262 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 588.36876 0.06429 0.13126 0.00012 MINI INTERN> 28.27101 108.34236 0.00000 39.67516 14.68963 MINI EXTERN> 124.50006 -129.26312 0.00000 0.00000 0.00000 MINI CONSTR> 402.15366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 588.33575 0.03301 0.10465 0.00012 MINI INTERN> 28.27261 108.27820 0.00000 39.64638 14.66932 MINI EXTERN> 124.39045 -129.21233 0.00000 0.00000 0.00000 MINI CONSTR> 402.29112 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21262 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 588.30196 0.03379 0.16833 0.00013 MINI INTERN> 28.18451 108.30388 0.00000 39.61863 14.65815 MINI EXTERN> 124.23439 -129.16435 0.00000 0.00000 0.00000 MINI CONSTR> 402.46675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 588.26998 0.03198 0.13199 0.00013 MINI INTERN> 28.18677 108.23559 0.00000 39.58930 14.63703 MINI EXTERN> 124.12958 -129.11256 0.00000 0.00000 0.00000 MINI CONSTR> 402.60428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21261 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 588.24337 0.02661 0.16457 0.00014 MINI INTERN> 28.14685 108.22248 0.00000 39.56411 14.62385 MINI EXTERN> 124.01043 -129.06814 0.00000 0.00000 0.00000 MINI CONSTR> 402.74378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 588.22104 0.02233 0.21110 0.00014 MINI INTERN> 28.09779 108.22694 0.00000 39.54185 14.61415 MINI EXTERN> 123.89279 -129.02765 0.00000 0.00000 0.00000 MINI CONSTR> 402.87518 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21261 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 588.19778 0.02326 0.22548 0.00015 MINI INTERN> 28.07627 108.19996 0.00000 39.51864 14.60217 MINI EXTERN> 123.76911 -128.97424 0.00000 0.00000 0.00000 MINI CONSTR> 403.00587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 588.17601 0.02178 0.24780 0.00015 MINI INTERN> 28.04710 108.18196 0.00000 39.49505 14.58885 MINI EXTERN> 123.67562 -128.93957 0.00000 0.00000 0.00000 MINI CONSTR> 403.12701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21262 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 588.15459 0.02142 0.23302 0.00016 MINI INTERN> 28.04386 108.13433 0.00000 39.47391 14.57621 MINI EXTERN> 123.56784 -128.88177 0.00000 0.00000 0.00000 MINI CONSTR> 403.24022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 588.12853 0.02606 0.07892 0.00007 MINI INTERN> 28.12365 107.98229 0.00000 39.44733 14.54864 MINI EXTERN> 123.52864 -128.82689 0.00000 0.00000 0.00000 MINI CONSTR> 403.32487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21263 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 588.11743 0.01111 0.24564 0.00017 MINI INTERN> 27.99412 108.10191 0.00000 39.43356 14.55542 MINI EXTERN> 123.38172 -128.80673 0.00000 0.00000 0.00000 MINI CONSTR> 403.45743 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 588.08960 0.02783 0.07665 0.00007 MINI INTERN> 28.08276 107.92841 0.00000 39.40551 14.52553 MINI EXTERN> 123.33783 -128.73878 0.00000 0.00000 0.00000 MINI CONSTR> 403.54834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21264 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 588.08291 0.00668 0.27140 0.00019 MINI INTERN> 27.92922 108.07049 0.00000 39.39540 14.53395 MINI EXTERN> 123.21146 -128.72765 0.00000 0.00000 0.00000 MINI CONSTR> 403.67004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 588.05690 0.02601 0.09821 0.00008 MINI INTERN> 28.05653 107.86646 0.00000 39.36742 14.50337 MINI EXTERN> 123.17349 -128.65648 0.00000 0.00000 0.00000 MINI CONSTR> 403.74610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21264 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 588.04267 0.01423 0.08570 0.00008 MINI INTERN> 28.03366 107.85361 0.00000 39.35245 14.49611 MINI EXTERN> 123.09498 -128.62132 0.00000 0.00000 0.00000 MINI CONSTR> 403.83319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 588.02879 0.01388 0.09098 0.00009 MINI INTERN> 28.01158 107.83670 0.00000 39.33634 14.48748 MINI EXTERN> 123.02308 -128.58722 0.00000 0.00000 0.00000 MINI CONSTR> 403.92082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21265 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 588.01614 0.01265 0.09738 0.00009 MINI INTERN> 27.99862 107.81219 0.00000 39.32118 14.47889 MINI EXTERN> 122.95370 -128.55134 0.00000 0.00000 0.00000 MINI CONSTR> 404.00290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 588.00399 0.01215 0.10652 0.00009 MINI INTERN> 27.98868 107.78620 0.00000 39.30637 14.47061 MINI EXTERN> 122.88202 -128.51428 0.00000 0.00000 0.00000 MINI CONSTR> 404.08439 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21265 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 587.99353 0.01046 0.14205 0.00010 MINI INTERN> 27.97754 107.76052 0.00000 39.29141 14.46152 MINI EXTERN> 122.82423 -128.48256 0.00000 0.00000 0.00000 MINI CONSTR> 404.16087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 587.98310 0.01043 0.15233 0.00010 MINI INTERN> 27.97259 107.73157 0.00000 39.27820 14.45396 MINI EXTERN> 122.75513 -128.44416 0.00000 0.00000 0.00000 MINI CONSTR> 404.23581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21266 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 587.97314 0.00995 0.16024 0.00010 MINI INTERN> 27.94985 107.72279 0.00000 39.26565 14.44734 MINI EXTERN> 122.70137 -128.41964 0.00000 0.00000 0.00000 MINI CONSTR> 404.30579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 587.96352 0.00962 0.15966 0.00011 MINI INTERN> 27.93678 107.70669 0.00000 39.25490 14.44229 MINI EXTERN> 122.63149 -128.38340 0.00000 0.00000 0.00000 MINI CONSTR> 404.37477 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21266 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 587.95433 0.00918 0.15964 0.00011 MINI INTERN> 27.91204 107.70504 0.00000 39.24356 14.43663 MINI EXTERN> 122.58455 -128.36605 0.00000 0.00000 0.00000 MINI CONSTR> 404.43857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 587.94286 0.01148 0.05043 0.00005 MINI INTERN> 27.85821 107.74759 0.00000 39.23757 14.43936 MINI EXTERN> 122.50099 -128.34549 0.00000 0.00000 0.00000 MINI CONSTR> 404.50464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21266 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 587.93882 0.00404 0.18764 0.00012 MINI INTERN> 27.88510 107.68053 0.00000 39.22278 14.42573 MINI EXTERN> 122.47820 -128.31511 0.00000 0.00000 0.00000 MINI CONSTR> 404.56158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 587.92644 0.01237 0.05605 0.00005 MINI INTERN> 27.82901 107.72534 0.00000 39.21744 14.42921 MINI EXTERN> 122.38850 -128.29140 0.00000 0.00000 0.00000 MINI CONSTR> 404.62834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21266 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 587.91963 0.00681 0.04778 0.00005 MINI INTERN> 27.82274 107.70849 0.00000 39.20873 14.42402 MINI EXTERN> 122.34589 -128.26850 0.00000 0.00000 0.00000 MINI CONSTR> 404.67826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 587.91260 0.00704 0.04757 0.00006 MINI INTERN> 27.81139 107.69606 0.00000 39.19998 14.41930 MINI EXTERN> 122.29625 -128.24323 0.00000 0.00000 0.00000 MINI CONSTR> 404.73285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21267 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 587.90593 0.00667 0.04757 0.00006 MINI INTERN> 27.80047 107.68508 0.00000 39.19164 14.41480 MINI EXTERN> 122.24881 -128.22013 0.00000 0.00000 0.00000 MINI CONSTR> 404.78526 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 587.89939 0.00654 0.08012 0.00006 MINI INTERN> 27.77933 107.68607 0.00000 39.18349 14.41170 MINI EXTERN> 122.18728 -128.19409 0.00000 0.00000 0.00000 MINI CONSTR> 404.84560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21266 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 587.89337 0.00602 0.06785 0.00006 MINI INTERN> 27.77397 107.67168 0.00000 39.17591 14.40701 MINI EXTERN> 122.14877 -128.17485 0.00000 0.00000 0.00000 MINI CONSTR> 404.89089 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 587.88831 0.00506 0.09512 0.00006 MINI INTERN> 27.75924 107.66640 0.00000 39.16927 14.40384 MINI EXTERN> 122.09847 -128.14931 0.00000 0.00000 0.00000 MINI CONSTR> 404.94039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21267 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 587.88318 0.00513 0.09975 0.00007 MINI INTERN> 27.75147 107.66133 0.00000 39.16254 14.40037 MINI EXTERN> 122.05741 -128.13458 0.00000 0.00000 0.00000 MINI CONSTR> 404.98464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 587.87836 0.00482 0.10900 0.00007 MINI INTERN> 27.74113 107.64785 0.00000 39.15642 14.39644 MINI EXTERN> 122.01509 -128.10735 0.00000 0.00000 0.00000 MINI CONSTR> 405.02877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21267 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 587.87364 0.00472 0.10532 0.00007 MINI INTERN> 27.73768 107.64082 0.00000 39.15034 14.39286 MINI EXTERN> 121.98180 -128.09693 0.00000 0.00000 0.00000 MINI CONSTR> 405.06707 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 587.86926 0.00438 0.11065 0.00007 MINI INTERN> 27.72732 107.62460 0.00000 39.14501 14.38888 MINI EXTERN> 121.94350 -128.06743 0.00000 0.00000 0.00000 MINI CONSTR> 405.10739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21267 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 587.86493 0.00433 0.10459 0.00008 MINI INTERN> 27.72115 107.62242 0.00000 39.13972 14.38625 MINI EXTERN> 121.90514 -128.05544 0.00000 0.00000 0.00000 MINI CONSTR> 405.14569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 587.85922 0.00571 0.03470 0.00003 MINI INTERN> 27.72531 107.58290 0.00000 39.13343 14.37858 MINI EXTERN> 121.89570 -128.03322 0.00000 0.00000 0.00000 MINI CONSTR> 405.17652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21267 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 587.85716 0.00206 0.12067 0.00008 MINI INTERN> 27.70368 107.60663 0.00000 39.13014 14.37971 MINI EXTERN> 121.83128 -128.01646 0.00000 0.00000 0.00000 MINI CONSTR> 405.22219 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 587.85137 0.00580 0.03972 0.00004 MINI INTERN> 27.71185 107.56269 0.00000 39.12386 14.37149 MINI EXTERN> 121.82961 -127.99710 0.00000 0.00000 0.00000 MINI CONSTR> 405.24897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21267 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 587.85023 0.00113 0.12639 0.00009 MINI INTERN> 27.68751 107.59561 0.00000 39.12190 14.37382 MINI EXTERN> 121.76683 -127.98539 0.00000 0.00000 0.00000 MINI CONSTR> 405.28995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 587.84422 0.00602 0.04432 0.00004 MINI INTERN> 27.69914 107.54457 0.00000 39.11540 14.36481 MINI EXTERN> 121.76618 -127.96309 0.00000 0.00000 0.00000 MINI CONSTR> 405.31720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 587.84129 0.00293 0.03013 0.00004 MINI INTERN> 27.68874 107.54561 0.00000 39.11282 14.36319 MINI EXTERN> 121.73599 -127.95020 0.00000 0.00000 0.00000 MINI CONSTR> 405.34514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 587.83830 0.00299 0.05889 0.00004 MINI INTERN> 27.68722 107.52611 0.00000 39.10844 14.35849 MINI EXTERN> 121.71135 -127.93034 0.00000 0.00000 0.00000 MINI CONSTR> 405.37702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 587.83546 0.00284 0.04564 0.00004 MINI INTERN> 27.68015 107.52494 0.00000 39.10585 14.35647 MINI EXTERN> 121.68418 -127.91980 0.00000 0.00000 0.00000 MINI CONSTR> 405.40367 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 587.83266 0.00280 0.04603 0.00004 MINI INTERN> 27.67314 107.51820 0.00000 39.10300 14.35365 MINI EXTERN> 121.65634 -127.90400 0.00000 0.00000 0.00000 MINI CONSTR> 405.43232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 587.83047 0.00219 0.06537 0.00005 MINI INTERN> 27.67194 107.50708 0.00000 39.10000 14.35028 MINI EXTERN> 121.63579 -127.89195 0.00000 0.00000 0.00000 MINI CONSTR> 405.45732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 587.82825 0.00222 0.08054 0.00005 MINI INTERN> 27.66260 107.49985 0.00000 39.09780 14.34757 MINI EXTERN> 121.60908 -127.87281 0.00000 0.00000 0.00000 MINI CONSTR> 405.48415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 587.82599 0.00226 0.07131 0.00005 MINI INTERN> 27.65907 107.49476 0.00000 39.09572 14.34516 MINI EXTERN> 121.58903 -127.86365 0.00000 0.00000 0.00000 MINI CONSTR> 405.50591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 587.82398 0.00202 0.08048 0.00005 MINI INTERN> 27.65720 107.49692 0.00000 39.09377 14.34348 MINI EXTERN> 121.56379 -127.86017 0.00000 0.00000 0.00000 MINI CONSTR> 405.52899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 587.82137 0.00260 0.02514 0.00002 MINI INTERN> 27.64200 107.50561 0.00000 39.09337 14.34321 MINI EXTERN> 121.53299 -127.84694 0.00000 0.00000 0.00000 MINI CONSTR> 405.55113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 587.82024 0.00114 0.07884 0.00005 MINI INTERN> 27.64665 107.47995 0.00000 39.09042 14.33799 MINI EXTERN> 121.52820 -127.83293 0.00000 0.00000 0.00000 MINI CONSTR> 405.56996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 587.81744 0.00279 0.02579 0.00002 MINI INTERN> 27.63240 107.49661 0.00000 39.09025 14.33843 MINI EXTERN> 121.48898 -127.82416 0.00000 0.00000 0.00000 MINI CONSTR> 405.59494 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 587.81678 0.00066 0.08896 0.00006 MINI INTERN> 27.63429 107.46942 0.00000 39.08783 14.33324 MINI EXTERN> 121.48613 -127.80597 0.00000 0.00000 0.00000 MINI CONSTR> 405.61185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 587.81406 0.00272 0.03035 0.00003 MINI INTERN> 27.62316 107.48931 0.00000 39.08794 14.33408 MINI EXTERN> 121.44820 -127.80299 0.00000 0.00000 0.00000 MINI CONSTR> 405.63436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 587.81263 0.00143 0.02226 0.00003 MINI INTERN> 27.62154 107.48278 0.00000 39.08686 14.33180 MINI EXTERN> 121.43482 -127.79467 0.00000 0.00000 0.00000 MINI CONSTR> 405.64950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 587.81106 0.00157 0.03592 0.00003 MINI INTERN> 27.61503 107.48251 0.00000 39.08618 14.32989 MINI EXTERN> 121.41039 -127.78345 0.00000 0.00000 0.00000 MINI CONSTR> 405.67052 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 587.80964 0.00142 0.03055 0.00003 MINI INTERN> 27.61325 107.47764 0.00000 39.08531 14.32766 MINI EXTERN> 121.39535 -127.77585 0.00000 0.00000 0.00000 MINI CONSTR> 405.68628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21268 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 587.80833 0.00132 0.03303 0.00003 MINI INTERN> 27.60916 107.47464 0.00000 39.08476 14.32567 MINI EXTERN> 121.37752 -127.76625 0.00000 0.00000 0.00000 MINI CONSTR> 405.70283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 587.80693 0.00140 0.02907 0.00003 MINI INTERN> 27.60569 107.46986 0.00000 39.08418 14.32334 MINI EXTERN> 121.36134 -127.75674 0.00000 0.00000 0.00000 MINI CONSTR> 405.71926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21269 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 587.80582 0.00111 0.04560 0.00003 MINI INTERN> 27.60137 107.47064 0.00000 39.08398 14.32167 MINI EXTERN> 121.34054 -127.74880 0.00000 0.00000 0.00000 MINI CONSTR> 405.73641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 587.80466 0.00115 0.05308 0.00003 MINI INTERN> 27.59596 107.46565 0.00000 39.08378 14.31937 MINI EXTERN> 121.32431 -127.73672 0.00000 0.00000 0.00000 MINI CONSTR> 405.75231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 587.80356 0.00110 0.04914 0.00003 MINI INTERN> 27.59588 107.46461 0.00000 39.08346 14.31762 MINI EXTERN> 121.31011 -127.73350 0.00000 0.00000 0.00000 MINI CONSTR> 405.76539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 587.80258 0.00098 0.05544 0.00004 MINI INTERN> 27.59048 107.45733 0.00000 39.08340 14.31524 MINI EXTERN> 121.29747 -127.72020 0.00000 0.00000 0.00000 MINI CONSTR> 405.77886 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21269 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 587.80132 0.00127 0.01737 0.00002 MINI INTERN> 27.59283 107.44731 0.00000 39.08270 14.31253 MINI EXTERN> 121.29420 -127.71623 0.00000 0.00000 0.00000 MINI CONSTR> 405.78798 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 587.80076 0.00056 0.05595 0.00004 MINI INTERN> 27.58839 107.45691 0.00000 39.08339 14.31204 MINI EXTERN> 121.26827 -127.71195 0.00000 0.00000 0.00000 MINI CONSTR> 405.80371 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21269 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 587.79946 0.00129 0.01796 0.00002 MINI INTERN> 27.58770 107.44143 0.00000 39.08284 14.30868 MINI EXTERN> 121.26850 -127.70212 0.00000 0.00000 0.00000 MINI CONSTR> 405.81244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 587.79917 0.00029 0.06560 0.00004 MINI INTERN> 27.58038 107.44757 0.00000 39.08379 14.30800 MINI EXTERN> 121.24452 -127.69203 0.00000 0.00000 0.00000 MINI CONSTR> 405.82694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21269 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 587.79779 0.00139 0.01923 0.00002 MINI INTERN> 27.58284 107.43584 0.00000 39.08325 14.30491 MINI EXTERN> 121.24448 -127.68866 0.00000 0.00000 0.00000 MINI CONSTR> 405.83514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 587.79706 0.00072 0.01561 0.00002 MINI INTERN> 27.58011 107.43481 0.00000 39.08362 14.30343 MINI EXTERN> 121.23263 -127.68266 0.00000 0.00000 0.00000 MINI CONSTR> 405.84512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21269 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 587.79628 0.00078 0.02443 0.00002 MINI INTERN> 27.57854 107.42981 0.00000 39.08387 14.30109 MINI EXTERN> 121.22266 -127.67589 0.00000 0.00000 0.00000 MINI CONSTR> 405.85620 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 587.79557 0.00072 0.02070 0.00002 MINI INTERN> 27.57542 107.42850 0.00000 39.08439 14.29951 MINI EXTERN> 121.21063 -127.66912 0.00000 0.00000 0.00000 MINI CONSTR> 405.86624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 587.79492 0.00065 0.02259 0.00002 MINI INTERN> 27.57343 107.42588 0.00000 39.08483 14.29772 MINI EXTERN> 121.20083 -127.66334 0.00000 0.00000 0.00000 MINI CONSTR> 405.87558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 587.79492 0.00065 0.02259 0.00002 STPD INTERN> 27.57343 107.42588 0.00000 39.08483 14.29772 STPD EXTERN> 121.20083 -127.66334 0.00000 0.00000 0.00000 STPD CONSTR> 405.87558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21270 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 587.79492 0.00065 0.02259 0.00000 MINI INTERN> 27.57343 107.42588 0.00000 39.08483 14.29772 MINI EXTERN> 121.20083 -127.66334 0.00000 0.00000 0.00000 MINI CONSTR> 405.87558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 587.78147 0.01344 0.01520 0.00053 MINI INTERN> 27.47271 107.32594 0.00000 39.11012 14.23348 MINI EXTERN> 120.76439 -127.41953 0.00000 0.00000 0.00000 MINI CONSTR> 406.29437 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 587.78061 0.00087 0.01896 0.00212 MINI INTERN> 27.51153 107.40039 0.00000 39.12006 14.20638 MINI EXTERN> 120.82677 -127.43494 0.00000 0.00000 0.00000 MINI CONSTR> 406.15041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 587.77967 0.00094 0.01650 0.00242 MINI INTERN> 27.52298 107.39404 0.00000 39.15722 14.19053 MINI EXTERN> 120.82880 -127.44402 0.00000 0.00000 0.00000 MINI CONSTR> 406.13011 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 19 587.77938 0.00029 0.00931 0.02000 CONJ INTERN> 27.51487 107.37861 0.00000 39.16901 14.18139 CONJ EXTERN> 120.79693 -127.43423 0.00000 0.00000 0.00000 CONJ CONSTR> 406.17280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "4200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 9.8045 ( PROT LYS 1 HT2 ) 9.8045 ( PROT LYS 1 N ) 12.256 ( PROT LYS 1 HT3 ) 9.8045 ( PROT LYS 1 CA ) 12.256 ( PROT LYS 1 CB ) 9.8045 ( PROT LYS 1 CG ) 9.8045 ( PROT LYS 1 CD ) 9.8045 ( PROT LYS 1 CE ) 9.8045 ( PROT LYS 1 NZ ) 9.8045 ( PROT LYS 1 HZ1 ) 9.8045 ( PROT LYS 1 HZ2 ) 9.8045 ( PROT LYS 1 HZ3 ) 9.8045 ( PROT LYS 1 C ) 12.256 ( PROT LYS 1 O ) 12.256 ( PROT MET 2 N ) 12.256 ( PROT MET 2 H ) 9.8045 ( PROT MET 2 CA ) 12.256 ( PROT MET 2 CB ) 9.8045 ( PROT MET 2 CG ) 9.8045 ( PROT MET 2 SD ) 9.8045 ( PROT MET 2 CE ) 9.8045 ( PROT MET 2 C ) 12.256 ( PROT MET 2 O ) 12.256 ( PROT LYS 3 N ) 12.256 ( PROT LYS 3 H ) 9.8045 ( PROT LYS 3 CA ) 12.256 ( PROT LYS 3 CB ) 9.8045 ( PROT LYS 3 CG ) 9.8045 ( PROT LYS 3 CD ) 9.8045 ( PROT LYS 3 CE ) 9.8045 ( PROT LYS 3 NZ ) 9.8045 ( PROT LYS 3 HZ1 ) 9.8045 ( PROT LYS 3 HZ2 ) 9.8045 ( PROT LYS 3 HZ3 ) 9.8045 ( PROT LYS 3 C ) 12.256 ( PROT LYS 3 O ) 12.256 ( PROT ALA 4 N ) 12.256 ( PROT ALA 4 H ) 9.8045 ( PROT ALA 4 CA ) 12.256 ( PROT ALA 4 CB ) 9.8045 ( PROT ALA 4 C ) 12.256 ( PROT ALA 4 O ) 12.256 ( PROT VAL 5 N ) 12.256 ( PROT VAL 5 H ) 9.8045 ( PROT VAL 5 CA ) 12.256 ( PROT VAL 5 CB ) 9.8045 ( PROT VAL 5 CG1 ) 9.8045 ( PROT VAL 5 CG2 ) 9.8045 ( PROT VAL 5 C ) 12.256 ( PROT VAL 5 O ) 12.256 ( PROT MET 6 N ) 12.256 ( PROT MET 6 H ) 9.8045 ( PROT MET 6 CA ) 12.256 ( PROT MET 6 CB ) 9.8045 ( PROT MET 6 CG ) 9.8045 ( PROT MET 6 SD ) 9.8045 ( PROT MET 6 CE ) 9.8045 ( PROT MET 6 C ) 12.256 ( PROT MET 6 O ) 12.256 ( PROT ILE 7 N ) 12.256 ( PROT ILE 7 H ) 9.8045 ( PROT ILE 7 CA ) 12.256 ( PROT ILE 7 CB ) 9.8045 ( PROT ILE 7 CG2 ) 9.8045 ( PROT ILE 7 CG1 ) 9.8045 ( PROT ILE 7 CD ) 9.8045 ( PROT ILE 7 C ) 12.256 ( PROT ILE 7 O ) 12.256 ( PROT GLY 8 N ) 12.256 ( PROT GLY 8 H ) 9.8045 ( PROT GLY 8 CA ) 12.256 ( PROT GLY 8 C ) 12.256 ( PROT GLY 8 O ) 12.256 ( PROT ALA 9 N ) 12.256 ( PROT ALA 9 H ) 9.8045 ( PROT ALA 9 CA ) 12.256 ( PROT ALA 9 CB ) 9.8045 ( PROT ALA 9 C ) 12.256 ( PROT ALA 9 O ) 12.256 ( PROT CYS 10 N ) 12.256 ( PROT CYS 10 H ) 9.8045 ( PROT CYS 10 CA ) 12.256 ( PROT CYS 10 CB ) 9.8045 ( PROT CYS 10 SG ) 9.8045 ( PROT CYS 10 C ) 12.256 ( PROT CYS 10 O ) 12.256 ( PROT PHE 11 N ) 12.256 ( PROT PHE 11 H ) 9.8045 ( PROT PHE 11 CA ) 12.256 ( PROT PHE 11 CB ) 9.8045 ( PROT PHE 11 CG ) 9.8045 ( PROT PHE 11 CD1 ) 9.8045 ( PROT PHE 11 CD2 ) 9.8045 ( PROT PHE 11 CE1 ) 9.8045 ( PROT PHE 11 CE2 ) 9.8045 ( PROT PHE 11 CZ ) 9.8045 ( PROT PHE 11 C ) 12.256 ( PROT PHE 11 O ) 12.256 ( PROT LEU 12 N ) 12.256 ( PROT LEU 12 H ) 9.8045 ( PROT LEU 12 CA ) 12.256 ( PROT LEU 12 CB ) 9.8045 ( PROT LEU 12 CG ) 9.8045 ( PROT LEU 12 CD1 ) 9.8045 ( PROT LEU 12 CD2 ) 9.8045 ( PROT LEU 12 C ) 12.256 ( PROT LEU 12 O ) 12.256 ( PROT ILE 13 N ) 12.256 ( PROT ILE 13 H ) 9.8045 ( PROT ILE 13 CA ) 12.256 ( PROT ILE 13 CB ) 9.8045 ( PROT ILE 13 CG2 ) 9.8045 ( PROT ILE 13 CG1 ) 9.8045 ( PROT ILE 13 CD ) 9.8045 ( PROT ILE 13 C ) 12.256 ( PROT ILE 13 O ) 12.256 ( PROT ASH 14 N ) 12.256 ( PROT ASH 14 H ) 9.8045 ( PROT ASH 14 CA ) 12.256 ( PROT ASH 14 CB ) 9.8045 ( PROT ASH 14 CG ) 9.8045 ( PROT ASH 14 OD1 ) 9.8045 ( PROT ASH 14 OD2 ) 9.8045 ( PROT ASH 14 HD2 ) 9.8045 ( PROT ASH 14 C ) 12.256 ( PROT ASH 14 O ) 12.256 ( PROT PHE 15 N ) 12.256 ( PROT PHE 15 H ) 9.8045 ( PROT PHE 15 CA ) 12.256 ( PROT PHE 15 CB ) 9.8045 ( PROT PHE 15 CG ) 9.8045 ( PROT PHE 15 CD1 ) 9.8045 ( PROT PHE 15 CD2 ) 9.8045 ( PROT PHE 15 CE1 ) 9.8045 ( PROT PHE 15 CE2 ) 9.8045 ( PROT PHE 15 CZ ) 9.8045 ( PROT PHE 15 C ) 12.256 ( PROT PHE 15 O ) 12.256 ( PROT MET 16 N ) 12.256 ( PROT MET 16 H ) 9.8045 ( PROT MET 16 CA ) 12.256 ( PROT MET 16 CB ) 9.8045 ( PROT MET 16 CG ) 9.8045 ( PROT MET 16 SD ) 9.8045 ( PROT MET 16 CE ) 9.8045 ( PROT MET 16 C ) 12.256 ( PROT MET 16 O ) 12.256 ( PROT PHE 17 N ) 12.256 ( PROT PHE 17 H ) 9.8045 ( PROT PHE 17 CA ) 12.256 ( PROT PHE 17 CB ) 9.8045 ( PROT PHE 17 CG ) 9.8045 ( PROT PHE 17 CD1 ) 9.8045 ( PROT PHE 17 CD2 ) 9.8045 ( PROT PHE 17 CE1 ) 9.8045 ( PROT PHE 17 CE2 ) 9.8045 ( PROT PHE 17 CZ ) 9.8045 ( PROT PHE 17 C ) 12.256 ( PROT PHE 17 O ) 12.256 ( PROT PHE 18 N ) 12.256 ( PROT PHE 18 H ) 9.8045 ( PROT PHE 18 CA ) 12.256 ( PROT PHE 18 CB ) 9.8045 ( PROT PHE 18 CG ) 9.8045 ( PROT PHE 18 CD1 ) 9.8045 ( PROT PHE 18 CD2 ) 9.8045 ( PROT PHE 18 CE1 ) 9.8045 ( PROT PHE 18 CE2 ) 9.8045 ( PROT PHE 18 CZ ) 9.8045 ( PROT PHE 18 C ) 12.256 ( PROT PHE 18 O ) 12.256 ( PROT GLU 19 N ) 12.256 ( PROT GLU 19 H ) 9.8045 ( PROT GLU 19 CA ) 12.256 ( PROT GLU 19 CB ) 9.8045 ( PROT GLU 19 CG ) 9.8045 ( PROT GLU 19 CD ) 9.8045 ( PROT GLU 19 OE1 ) 9.8045 ( PROT GLU 19 OE2 ) 9.8045 ( PROT GLU 19 C ) 12.256 ( PROT GLU 19 O ) 12.256 ( PROT SER 20 N ) 12.256 ( PROT SER 20 H ) 9.8045 ( PROT SER 20 CA ) 12.256 ( PROT SER 20 CB ) 9.8045 ( PROT SER 20 OG ) 9.8045 ( PROT SER 20 HG ) 9.8045 ( PROT SER 20 C ) 12.256 ( PROT SER 20 O ) 12.256 ( PROT THR 21 N ) 12.256 ( PROT THR 21 H ) 9.8045 ( PROT THR 21 CA ) 12.256 ( PROT THR 21 CB ) 9.8045 ( PROT THR 21 OG1 ) 9.8045 ( PROT THR 21 HG1 ) 9.8045 ( PROT THR 21 CG2 ) 9.8045 ( PROT THR 21 C ) 12.256 ( PROT THR 21 O ) 12.256 ( PROT GLY 22 N ) 12.256 ( PROT GLY 22 H ) 9.8045 ( PROT GLY 22 CA ) 12.256 ( PROT GLY 22 C ) 12.256 ( PROT GLY 22 O ) 12.256 ( PROT SER 23 N ) 12.256 ( PROT SER 23 H ) 9.8045 ( PROT SER 23 CA ) 12.256 ( PROT SER 23 CB ) 9.8045 ( PROT SER 23 OG ) 9.8045 ( PROT SER 23 HG ) 9.8045 ( PROT SER 23 C ) 12.256 ( PROT SER 23 O ) 12.256 ( PROT GLN 24 N ) 12.256 ( PROT GLN 24 H ) 9.8045 ( PROT GLN 24 CA ) 12.256 ( PROT GLN 24 CB ) 9.8045 ( PROT GLN 24 CG ) 9.8045 ( PROT GLN 24 CD ) 9.8045 ( PROT GLN 24 OE1 ) 9.8045 ( PROT GLN 24 NE2 ) 9.8045 ( PROT GLN 24 HE21 ) 9.8045 ( PROT GLN 24 HE22 ) 9.8045 ( PROT GLN 24 C ) 12.256 ( PROT GLN 24 O ) 12.256 ( PROT GLU 25 N ) 12.256 ( PROT GLU 25 H ) 9.8045 ( PROT GLU 25 CA ) 12.256 ( PROT GLU 25 CB ) 9.8045 ( PROT GLU 25 CG ) 9.8045 ( PROT GLU 25 CD ) 9.8045 ( PROT GLU 25 OE1 ) 9.8045 ( PROT GLU 25 OE2 ) 9.8045 ( PROT GLU 25 C ) 12.256 ( PROT GLU 25 O ) 12.256 ( PROT GLN 26 N ) 12.256 ( PROT GLN 26 H ) 9.8045 ( PROT GLN 26 CA ) 12.256 ( PROT GLN 26 CB ) 9.8045 ( PROT GLN 26 CG ) 9.8045 ( PROT GLN 26 CD ) 9.8045 ( PROT GLN 26 OE1 ) 9.8045 ( PROT GLN 26 NE2 ) 9.8045 ( PROT GLN 26 HE21 ) 9.8045 ( PROT GLN 26 HE22 ) 9.8045 ( PROT GLN 26 C ) 12.256 ( PROT GLN 26 O ) 12.256 ( PROT LYS 27 N ) 12.256 ( PROT LYS 27 H ) 9.8045 ( PROT LYS 27 CA ) 12.256 ( PROT LYS 27 CB ) 9.8045 ( PROT LYS 27 CG ) 9.8045 ( PROT LYS 27 CD ) 9.8045 ( PROT LYS 27 CE ) 9.8045 ( PROT LYS 27 NZ ) 9.8045 ( PROT LYS 27 HZ1 ) 9.8045 ( PROT LYS 27 HZ2 ) 9.8045 ( PROT LYS 27 HZ3 ) 9.8045 ( PROT LYS 27 C ) 12.256 ( PROT LYS 27 O ) 12.256 ( PROT SER 28 N ) 12.256 ( PROT SER 28 H ) 9.8045 ( PROT SER 28 CA ) 12.256 ( PROT SER 28 CB ) 9.8045 ( PROT SER 28 OG ) 9.8045 ( PROT SER 28 HG ) 9.8045 ( PROT SER 28 C ) 12.256 ( PROT SER 28 O ) 12.256 ( PROT GLY 29 N ) 12.256 ( PROT GLY 29 H ) 9.8045 ( PROT GLY 29 CA ) 12.256 ( PROT GLY 29 C ) 12.256 ( PROT GLY 29 O ) 12.256 ( PROT VAL 30 N ) 12.256 ( PROT VAL 30 H ) 9.8045 ( PROT VAL 30 CA ) 12.256 ( PROT VAL 30 CB ) 9.8045 ( PROT VAL 30 CG1 ) 9.8045 ( PROT VAL 30 CG2 ) 9.8045 ( PROT VAL 30 C ) 12.256 ( PROT VAL 30 O ) 12.256 ( PROT TRP 31 N ) 12.256 ( PROT TRP 31 H ) 9.8045 ( PROT TRP 31 CA ) 12.256 ( PROT TRP 31 CB ) 9.8045 ( PROT TRP 31 CG ) 9.8045 ( PROT TRP 31 CD2 ) 9.8045 ( PROT TRP 31 CE2 ) 9.8045 ( PROT TRP 31 CE3 ) 9.8045 ( PROT TRP 31 CD1 ) 9.8045 ( PROT TRP 31 NE1 ) 9.8045 ( PROT TRP 31 HE1 ) 9.8045 ( PROT TRP 31 CZ2 ) 9.8045 ( PROT TRP 31 CZ3 ) 9.8045 ( PROT TRP 31 CH2 ) 9.8045 ( PROT TRP 31 C ) 12.256 ( PROT TRP 31 OT1 ) 9.8045 ( PROT TRP 31 OT2 ) 9.8045 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63139 7.22912 -13.22111 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS -0.00059 0.00031 0.00119 ROTATION MATRIX 1.000000 -0.000085 -0.000286 0.000085 1.000000 0.000254 0.000286 -0.000254 1.000000 AXIS OF ROTATION IS 0.648729 0.729292 -0.217447 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 24.6980 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.288372 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2884" Parameter: A <- "0.2884" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51367 7.24851 -13.41248 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01455 0.00704 -0.02787 ROTATION MATRIX 0.999767 0.014962 0.015570 -0.014708 0.999759 -0.016319 -0.015811 0.016086 0.999746 AXIS OF ROTATION IS -0.600185 -0.581215 0.549515 ANGLE IS 1.55 CENTER OF ROTATION 13.977591 6.928654-13.269701 SHIFT IS -0.028142 TOTAL SQUARE DIFF IS 0.4215 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.116608 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2884" RDCMND substituted energy or value "?RMS" to " 0.1166" Parameter: A <- "0.2884 0.1166" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *4200 0.2884 0.1166 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 406.17" Parameter: H <- "406.17" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 181.60658 406.17280 5.50869 ENER INTERN> 27.51487 107.37861 0.00000 39.16901 14.18139 ENER EXTERN> 120.79693 -127.43423 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 181.61" Parameter: B <- "181.61" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -127.43" Parameter: C <- "-127.43" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 120.80" Parameter: C <- " -6.63" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -6.63" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 27.51" Parameter: D <- "27.51" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 107.38" Parameter: D <- " 134.89" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 39.17" Parameter: D <- " 174.06" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 14.18" Parameter: D <- " 188.24" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 188.24" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 4200 ENER= 181.61 GRMS= 5.51 ELEC= -127.43 VDW= 120.80 RDTITL> *EXTERNAL= -6.63 INTERNAL= 188.24 USER= 0.00 HARM= 406.17 RDTITL> *BOND= 27.51 ANGL= 107.38 DIHE= 39.17 IMPR= 14.18 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21270 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21270 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 482.52931 -300.92273 2.32334 0.02000 MINI INTERN> 27.51487 107.37861 0.00000 39.16901 14.18139 MINI EXTERN> 120.79693 -127.43423 0.00000 0.00000 0.00000 MINI CONSTR> 300.92273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 458.76998 23.75932 2.00599 0.00360 MINI INTERN> 25.52438 106.07225 0.00000 43.08982 14.42300 MINI EXTERN> 69.44121 -124.25422 0.00000 0.00000 0.00000 MINI CONSTR> 324.47353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21242 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 452.06907 6.70091 1.23104 0.00156 MINI INTERN> 22.62462 102.54028 0.00000 43.23419 13.93982 MINI EXTERN> 67.85781 -124.34012 0.00000 0.00000 0.00000 MINI CONSTR> 326.21248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 448.49616 3.57292 2.70619 0.00161 MINI INTERN> 25.87456 98.81254 0.00000 43.59747 13.81294 MINI EXTERN> 62.56720 -123.36780 0.00000 0.00000 0.00000 MINI CONSTR> 327.19924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21239 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 445.84682 2.64933 3.12274 0.00167 MINI INTERN> 26.55037 97.36795 0.00000 43.78556 13.73593 MINI EXTERN> 59.74255 -122.99995 0.00000 0.00000 0.00000 MINI CONSTR> 327.66441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 443.62216 2.22467 2.93961 0.00173 MINI INTERN> 25.81315 96.90336 0.00000 43.89452 13.65483 MINI EXTERN> 58.49032 -122.96338 0.00000 0.00000 0.00000 MINI CONSTR> 327.82935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 441.67217 1.94999 3.04131 0.00180 MINI INTERN> 25.79001 96.18768 0.00000 43.97558 13.57122 MINI EXTERN> 57.09709 -122.83043 0.00000 0.00000 0.00000 MINI CONSTR> 327.88103 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 438.79151 2.88066 1.03064 0.00078 MINI INTERN> 18.97973 99.50722 0.00000 43.93135 13.62404 MINI EXTERN> 58.78643 -124.10703 0.00000 0.00000 0.00000 MINI CONSTR> 328.06977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 437.40155 1.38995 0.79806 0.00080 MINI INTERN> 19.21540 98.81976 0.00000 43.95633 13.55363 MINI EXTERN> 57.80701 -123.94262 0.00000 0.00000 0.00000 MINI CONSTR> 327.99204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 436.13558 1.26598 0.77491 0.00083 MINI INTERN> 19.07042 98.45944 0.00000 43.96423 13.48648 MINI EXTERN> 57.12604 -123.88100 0.00000 0.00000 0.00000 MINI CONSTR> 327.90997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 435.28304 0.85254 1.46897 0.00087 MINI INTERN> 17.96256 99.00620 0.00000 43.94502 13.44727 MINI EXTERN> 57.15660 -124.11028 0.00000 0.00000 0.00000 MINI CONSTR> 327.87567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 434.50461 0.77843 1.66076 0.00090 MINI INTERN> 17.67331 98.95544 0.00000 43.92741 13.39788 MINI EXTERN> 56.85279 -124.12385 0.00000 0.00000 0.00000 MINI CONSTR> 327.82164 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21230 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 433.84566 0.65895 1.56810 0.00093 MINI INTERN> 17.76782 98.65676 0.00000 43.89937 13.36216 MINI EXTERN> 56.42419 -124.04438 0.00000 0.00000 0.00000 MINI CONSTR> 327.77973 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 433.24979 0.59587 1.60635 0.00096 MINI INTERN> 17.69000 98.49145 0.00000 43.87455 13.31771 MINI EXTERN> 56.13099 -124.00415 0.00000 0.00000 0.00000 MINI CONSTR> 327.74924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21230 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 432.37671 0.87308 0.48044 0.00042 MINI INTERN> 20.02472 96.40023 0.00000 43.87211 13.22454 MINI EXTERN> 54.53268 -123.30562 0.00000 0.00000 0.00000 MINI CONSTR> 327.62805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 431.99112 0.38559 0.35076 0.00043 MINI INTERN> 19.67714 96.47378 0.00000 43.84913 13.19496 MINI EXTERN> 54.49463 -123.33491 0.00000 0.00000 0.00000 MINI CONSTR> 327.63638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21230 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 431.62155 0.36958 0.74562 0.00045 MINI INTERN> 20.47575 95.78535 0.00000 43.81332 13.14745 MINI EXTERN> 53.87187 -123.10040 0.00000 0.00000 0.00000 MINI CONSTR> 327.62820 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 431.30634 0.31520 0.74141 0.00046 MINI INTERN> 20.43153 95.67685 0.00000 43.77973 13.11848 MINI EXTERN> 53.70390 -123.06208 0.00000 0.00000 0.00000 MINI CONSTR> 327.65792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21231 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 431.04009 0.26625 0.80809 0.00048 MINI INTERN> 20.48669 95.52843 0.00000 43.73881 13.09401 MINI EXTERN> 53.49839 -123.00809 0.00000 0.00000 0.00000 MINI CONSTR> 327.70185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 430.83880 0.20129 0.91854 0.00050 MINI INTERN> 20.59882 95.36034 0.00000 43.70317 13.06968 MINI EXTERN> 53.30112 -122.94384 0.00000 0.00000 0.00000 MINI CONSTR> 327.74952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21232 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 430.65866 0.18014 0.85692 0.00052 MINI INTERN> 20.46523 95.33145 0.00000 43.68873 13.04165 MINI EXTERN> 53.26470 -122.92369 0.00000 0.00000 0.00000 MINI CONSTR> 327.79058 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 430.50215 0.15651 0.89279 0.00054 MINI INTERN> 20.44644 95.26325 0.00000 43.65407 13.02367 MINI EXTERN> 53.15339 -122.89151 0.00000 0.00000 0.00000 MINI CONSTR> 327.85284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21232 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 430.26043 0.24172 0.30295 0.00023 MINI INTERN> 19.09576 96.01556 0.00000 43.64152 13.00220 MINI EXTERN> 53.69198 -123.13140 0.00000 0.00000 0.00000 MINI CONSTR> 327.94481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 430.14242 0.11800 0.23124 0.00024 MINI INTERN> 19.18390 95.88232 0.00000 43.61264 12.98563 MINI EXTERN> 53.54958 -123.07509 0.00000 0.00000 0.00000 MINI CONSTR> 328.00343 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21231 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 430.03437 0.10806 0.22729 0.00025 MINI INTERN> 19.17769 95.80646 0.00000 43.58681 12.96534 MINI EXTERN> 53.46088 -123.03417 0.00000 0.00000 0.00000 MINI CONSTR> 328.07136 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 429.95918 0.07518 0.41150 0.00026 MINI INTERN> 18.99536 95.84718 0.00000 43.57500 12.93760 MINI EXTERN> 53.49084 -123.02657 0.00000 0.00000 0.00000 MINI CONSTR> 328.13977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21231 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 429.88866 0.07052 0.45402 0.00027 MINI INTERN> 18.95153 95.80384 0.00000 43.55723 12.91682 MINI EXTERN> 53.44750 -122.99436 0.00000 0.00000 0.00000 MINI CONSTR> 328.20611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 429.82912 0.05954 0.43259 0.00028 MINI INTERN> 18.97851 95.74256 0.00000 43.53059 12.90760 MINI EXTERN> 53.36250 -122.96117 0.00000 0.00000 0.00000 MINI CONSTR> 328.26852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21233 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 429.74996 0.07917 0.12689 0.00012 MINI INTERN> 19.34852 95.48967 0.00000 43.46623 12.92228 MINI EXTERN> 53.05069 -122.87401 0.00000 0.00000 0.00000 MINI CONSTR> 328.34657 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 429.73306 0.01690 0.45917 0.00030 MINI INTERN> 18.92045 95.66926 0.00000 43.49464 12.87796 MINI EXTERN> 53.28072 -122.90460 0.00000 0.00000 0.00000 MINI CONSTR> 328.39463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21234 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 429.66156 0.07150 0.15434 0.00013 MINI INTERN> 19.41220 95.37219 0.00000 43.40881 12.90598 MINI EXTERN> 52.88133 -122.80475 0.00000 0.00000 0.00000 MINI CONSTR> 328.48579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 429.62728 0.03428 0.12106 0.00013 MINI INTERN> 19.36646 95.35566 0.00000 43.39289 12.89382 MINI EXTERN> 52.85790 -122.78364 0.00000 0.00000 0.00000 MINI CONSTR> 328.54419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21235 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 429.59574 0.03154 0.11849 0.00014 MINI INTERN> 19.36973 95.31639 0.00000 43.36934 12.88516 MINI EXTERN> 52.79953 -122.75447 0.00000 0.00000 0.00000 MINI CONSTR> 328.61006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 429.57392 0.02182 0.21830 0.00014 MINI INTERN> 19.52215 95.21604 0.00000 43.32761 12.88836 MINI EXTERN> 52.64499 -122.70772 0.00000 0.00000 0.00000 MINI CONSTR> 328.68249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21235 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 429.55324 0.02068 0.24288 0.00015 MINI INTERN> 19.55922 95.16897 0.00000 43.30217 12.88375 MINI EXTERN> 52.57190 -122.67721 0.00000 0.00000 0.00000 MINI CONSTR> 328.74445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 429.53576 0.01748 0.23091 0.00015 MINI INTERN> 19.54021 95.15051 0.00000 43.28766 12.87640 MINI EXTERN> 52.54655 -122.65782 0.00000 0.00000 0.00000 MINI CONSTR> 328.79226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 429.51197 0.02379 0.06739 0.00007 MINI INTERN> 19.20328 95.26668 0.00000 43.31303 12.84458 MINI EXTERN> 52.73493 -122.67635 0.00000 0.00000 0.00000 MINI CONSTR> 328.82582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 429.50683 0.00514 0.24667 0.00017 MINI INTERN> 19.56164 95.09060 0.00000 43.24920 12.86658 MINI EXTERN> 52.45285 -122.61036 0.00000 0.00000 0.00000 MINI CONSTR> 328.89631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 429.48509 0.02174 0.08337 0.00007 MINI INTERN> 19.15009 95.23820 0.00000 43.28461 12.82919 MINI EXTERN> 52.69532 -122.63754 0.00000 0.00000 0.00000 MINI CONSTR> 328.92522 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 429.47455 0.01054 0.06597 0.00007 MINI INTERN> 19.17451 95.20632 0.00000 43.26610 12.82666 MINI EXTERN> 52.64563 -122.61499 0.00000 0.00000 0.00000 MINI CONSTR> 328.97031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 429.46460 0.00995 0.06305 0.00008 MINI INTERN> 19.17304 95.18454 0.00000 43.25003 12.82189 MINI EXTERN> 52.61267 -122.59428 0.00000 0.00000 0.00000 MINI CONSTR> 329.01670 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 429.45583 0.00876 0.07407 0.00008 MINI INTERN> 19.14826 95.17295 0.00000 43.23708 12.81543 MINI EXTERN> 52.59665 -122.57598 0.00000 0.00000 0.00000 MINI CONSTR> 329.06145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 429.45034 0.00549 0.12015 0.00008 MINI INTERN> 19.07805 95.18536 0.00000 43.23297 12.80610 MINI EXTERN> 52.61905 -122.56707 0.00000 0.00000 0.00000 MINI CONSTR> 329.09588 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 429.44411 0.00623 0.12769 0.00009 MINI INTERN> 19.06657 95.17229 0.00000 43.22076 12.80156 MINI EXTERN> 52.59977 -122.55083 0.00000 0.00000 0.00000 MINI CONSTR> 329.13400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 429.43816 0.00595 0.12957 0.00009 MINI INTERN> 19.06213 95.15543 0.00000 43.20728 12.79794 MINI EXTERN> 52.57486 -122.53165 0.00000 0.00000 0.00000 MINI CONSTR> 329.17218 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 429.43104 0.00713 0.04097 0.00004 MINI INTERN> 19.24611 95.06570 0.00000 43.17079 12.81056 MINI EXTERN> 52.41990 -122.49698 0.00000 0.00000 0.00000 MINI CONSTR> 329.21497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 429.42692 0.00411 0.03418 0.00004 MINI INTERN> 19.22904 95.05978 0.00000 43.16255 12.80676 MINI EXTERN> 52.41155 -122.48552 0.00000 0.00000 0.00000 MINI CONSTR> 329.24277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 429.42265 0.00428 0.03299 0.00004 MINI INTERN> 19.22671 95.04649 0.00000 43.15087 12.80408 MINI EXTERN> 52.38987 -122.47025 0.00000 0.00000 0.00000 MINI CONSTR> 329.27486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 429.41878 0.00387 0.05964 0.00004 MINI INTERN> 19.27586 95.01252 0.00000 43.13146 12.80566 MINI EXTERN> 52.33011 -122.44879 0.00000 0.00000 0.00000 MINI CONSTR> 329.31194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 429.41527 0.00350 0.04094 0.00004 MINI INTERN> 19.24725 95.01253 0.00000 43.12545 12.80115 MINI EXTERN> 52.33204 -122.43999 0.00000 0.00000 0.00000 MINI CONSTR> 329.33683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 429.41224 0.00304 0.05167 0.00005 MINI INTERN> 19.26287 94.99401 0.00000 43.11245 12.80060 MINI EXTERN> 52.30029 -122.42382 0.00000 0.00000 0.00000 MINI CONSTR> 329.36585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 429.40984 0.00240 0.07044 0.00005 MINI INTERN> 19.29065 94.97256 0.00000 43.09916 12.80104 MINI EXTERN> 52.26313 -122.40932 0.00000 0.00000 0.00000 MINI CONSTR> 329.39261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 429.40713 0.00272 0.07580 0.00005 MINI INTERN> 19.29020 94.96140 0.00000 43.08848 12.79945 MINI EXTERN> 52.24299 -122.39504 0.00000 0.00000 0.00000 MINI CONSTR> 329.41966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 429.40490 0.00223 0.08614 0.00005 MINI INTERN> 19.30295 94.94775 0.00000 43.07789 12.79851 MINI EXTERN> 52.21887 -122.38537 0.00000 0.00000 0.00000 MINI CONSTR> 329.44430 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 429.40271 0.00219 0.07911 0.00005 MINI INTERN> 19.29973 94.93913 0.00000 43.06992 12.79703 MINI EXTERN> 52.20594 -122.37371 0.00000 0.00000 0.00000 MINI CONSTR> 329.46466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 429.39971 0.00300 0.02433 0.00002 MINI INTERN> 19.19695 94.96988 0.00000 43.07522 12.78707 MINI EXTERN> 52.26394 -122.37316 0.00000 0.00000 0.00000 MINI CONSTR> 329.47981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 429.39876 0.00095 0.08856 0.00006 MINI INTERN> 19.30122 94.92184 0.00000 43.05246 12.79427 MINI EXTERN> 52.17482 -122.35420 0.00000 0.00000 0.00000 MINI CONSTR> 329.50835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 429.39588 0.00289 0.02764 0.00002 MINI INTERN> 19.18595 94.95688 0.00000 43.05979 12.78361 MINI EXTERN> 52.24225 -122.35337 0.00000 0.00000 0.00000 MINI CONSTR> 329.52077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 429.39429 0.00158 0.02160 0.00003 MINI INTERN> 19.19836 94.94524 0.00000 43.05099 12.78371 MINI EXTERN> 52.22088 -122.34361 0.00000 0.00000 0.00000 MINI CONSTR> 329.53872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 429.39256 0.00173 0.02169 0.00003 MINI INTERN> 19.19569 94.93803 0.00000 43.04305 12.78240 MINI EXTERN> 52.20849 -122.33347 0.00000 0.00000 0.00000 MINI CONSTR> 329.55837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 429.39097 0.00159 0.03793 0.00003 MINI INTERN> 19.16881 94.93990 0.00000 43.03824 12.77887 MINI EXTERN> 52.21399 -122.32580 0.00000 0.00000 0.00000 MINI CONSTR> 329.57697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 429.38945 0.00153 0.02550 0.00003 MINI INTERN> 19.18686 94.92649 0.00000 43.02865 12.77953 MINI EXTERN> 52.18902 -122.31590 0.00000 0.00000 0.00000 MINI CONSTR> 329.59479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 429.38802 0.00142 0.03079 0.00003 MINI INTERN> 19.17871 94.92190 0.00000 43.02190 12.77799 MINI EXTERN> 52.18161 -122.30632 0.00000 0.00000 0.00000 MINI CONSTR> 329.61224 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 429.38690 0.00112 0.04525 0.00003 MINI INTERN> 19.15892 94.92332 0.00000 43.01778 12.77535 MINI EXTERN> 52.18520 -122.30060 0.00000 0.00000 0.00000 MINI CONSTR> 329.62694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 429.38544 0.00146 0.02833 0.00003 MINI INTERN> 19.18139 94.90862 0.00000 43.00774 12.77648 MINI EXTERN> 52.15767 -122.29063 0.00000 0.00000 0.00000 MINI CONSTR> 329.64418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 429.38446 0.00098 0.04767 0.00003 MINI INTERN> 19.15681 94.91155 0.00000 43.00419 12.77356 MINI EXTERN> 52.16459 -122.28443 0.00000 0.00000 0.00000 MINI CONSTR> 329.65819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 429.38326 0.00120 0.05193 0.00003 MINI INTERN> 19.15606 94.90468 0.00000 42.99695 12.77255 MINI EXTERN> 52.15439 -122.27584 0.00000 0.00000 0.00000 MINI CONSTR> 329.67445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 429.38221 0.00105 0.05801 0.00004 MINI INTERN> 19.15232 94.89920 0.00000 42.99053 12.77142 MINI EXTERN> 52.14642 -122.26716 0.00000 0.00000 0.00000 MINI CONSTR> 329.68948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 429.38120 0.00101 0.05414 0.00004 MINI INTERN> 19.15384 94.89470 0.00000 42.98450 12.77106 MINI EXTERN> 52.13624 -122.26129 0.00000 0.00000 0.00000 MINI CONSTR> 329.70214 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 429.38012 0.00108 0.05479 0.00004 MINI INTERN> 19.15817 94.88603 0.00000 42.97701 12.77066 MINI EXTERN> 52.12287 -122.25181 0.00000 0.00000 0.00000 MINI CONSTR> 329.71719 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 429.37879 0.00133 0.01778 0.00002 MINI INTERN> 19.20658 94.86647 0.00000 42.96404 12.77496 MINI EXTERN> 52.07565 -122.24214 0.00000 0.00000 0.00000 MINI CONSTR> 329.73322 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 429.37841 0.00038 0.05995 0.00004 MINI INTERN> 19.15338 94.87906 0.00000 42.96595 12.76908 MINI EXTERN> 52.10959 -122.24028 0.00000 0.00000 0.00000 MINI CONSTR> 329.74163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 429.37757 0.00084 0.06658 0.00004 MINI INTERN> 19.15947 94.86927 0.00000 42.95855 12.76900 MINI EXTERN> 52.09462 -122.22898 0.00000 0.00000 0.00000 MINI CONSTR> 329.75565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 429.37615 0.00142 0.02132 0.00002 MINI INTERN> 19.20947 94.85206 0.00000 42.94546 12.77373 MINI EXTERN> 52.04636 -122.22197 0.00000 0.00000 0.00000 MINI CONSTR> 329.77105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 429.37543 0.00072 0.01461 0.00002 MINI INTERN> 19.20191 94.85032 0.00000 42.94175 12.77250 MINI EXTERN> 52.04582 -122.21709 0.00000 0.00000 0.00000 MINI CONSTR> 329.78023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 429.37461 0.00082 0.01560 0.00002 MINI INTERN> 19.20361 94.84567 0.00000 42.93547 12.77220 MINI EXTERN> 52.03590 -122.21068 0.00000 0.00000 0.00000 MINI CONSTR> 329.79244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 429.37389 0.00072 0.02890 0.00002 MINI INTERN> 19.21307 94.83919 0.00000 42.92782 12.77283 MINI EXTERN> 52.01855 -122.20317 0.00000 0.00000 0.00000 MINI CONSTR> 329.80560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 429.37313 0.00075 0.02003 0.00002 MINI INTERN> 19.20624 94.83757 0.00000 42.92374 12.77163 MINI EXTERN> 52.01787 -122.19891 0.00000 0.00000 0.00000 MINI CONSTR> 329.81499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 429.37254 0.00059 0.03224 0.00002 MINI INTERN> 19.21325 94.83211 0.00000 42.91709 12.77211 MINI EXTERN> 52.00324 -122.19171 0.00000 0.00000 0.00000 MINI CONSTR> 329.82644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 429.37191 0.00063 0.03612 0.00002 MINI INTERN> 19.21288 94.82983 0.00000 42.91201 12.77159 MINI EXTERN> 51.99774 -122.18839 0.00000 0.00000 0.00000 MINI CONSTR> 329.83625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 429.37133 0.00058 0.03710 0.00002 MINI INTERN> 19.21643 94.82521 0.00000 42.90654 12.77161 MINI EXTERN> 51.98807 -122.18240 0.00000 0.00000 0.00000 MINI CONSTR> 329.84587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 429.37076 0.00057 0.03859 0.00002 MINI INTERN> 19.21696 94.82101 0.00000 42.90143 12.77138 MINI EXTERN> 51.98019 -122.17554 0.00000 0.00000 0.00000 MINI CONSTR> 329.85534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 429.37019 0.00057 0.03709 0.00003 MINI INTERN> 19.21742 94.81854 0.00000 42.89685 12.77097 MINI EXTERN> 51.97526 -122.17255 0.00000 0.00000 0.00000 MINI CONSTR> 329.86371 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 429.36966 0.00054 0.04052 0.00003 MINI INTERN> 19.21129 94.81578 0.00000 42.89272 12.77012 MINI EXTERN> 51.97204 -122.16481 0.00000 0.00000 0.00000 MINI CONSTR> 329.87251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 429.36897 0.00069 0.01262 0.00001 MINI INTERN> 19.19721 94.81681 0.00000 42.89111 12.76802 MINI EXTERN> 51.98151 -122.16375 0.00000 0.00000 0.00000 MINI CONSTR> 329.87807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 429.36869 0.00028 0.04317 0.00003 MINI INTERN> 19.22140 94.80897 0.00000 42.88243 12.77029 MINI EXTERN> 51.95552 -122.15901 0.00000 0.00000 0.00000 MINI CONSTR> 329.88909 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21236 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 429.36826 0.00043 0.04997 0.00003 MINI INTERN> 19.21224 94.80667 0.00000 42.87893 12.76924 MINI EXTERN> 51.95426 -122.15018 0.00000 0.00000 0.00000 MINI CONSTR> 329.89709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 429.36779 0.00047 0.04863 0.00003 MINI INTERN> 19.22083 94.80199 0.00000 42.87323 12.76975 MINI EXTERN> 51.94278 -122.14628 0.00000 0.00000 0.00000 MINI CONSTR> 329.90549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 429.36701 0.00078 0.01435 0.00001 MINI INTERN> 19.19508 94.80695 0.00000 42.87325 12.76649 MINI EXTERN> 51.96126 -122.14612 0.00000 0.00000 0.00000 MINI CONSTR> 329.91010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 429.36659 0.00042 0.01149 0.00001 MINI INTERN> 19.19758 94.80421 0.00000 42.86889 12.76653 MINI EXTERN> 51.95417 -122.14197 0.00000 0.00000 0.00000 MINI CONSTR> 329.91718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 429.36616 0.00044 0.01201 0.00001 MINI INTERN> 19.19660 94.80220 0.00000 42.86471 12.76612 MINI EXTERN> 51.94993 -122.13791 0.00000 0.00000 0.00000 MINI CONSTR> 329.92450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 429.36572 0.00043 0.01959 0.00001 MINI INTERN> 19.19154 94.80101 0.00000 42.86080 12.76518 MINI EXTERN> 51.94924 -122.13404 0.00000 0.00000 0.00000 MINI CONSTR> 329.93199 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 429.36530 0.00042 0.01551 0.00002 MINI INTERN> 19.19423 94.79805 0.00000 42.85625 12.76524 MINI EXTERN> 51.94177 -122.12939 0.00000 0.00000 0.00000 MINI CONSTR> 329.93914 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 429.36492 0.00038 0.01762 0.00002 MINI INTERN> 19.19203 94.79676 0.00000 42.85248 12.76472 MINI EXTERN> 51.93902 -122.12586 0.00000 0.00000 0.00000 MINI CONSTR> 329.94577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 429.36454 0.00038 0.01865 0.00002 MINI INTERN> 19.19173 94.79515 0.00000 42.84843 12.76437 MINI EXTERN> 51.93505 -122.12264 0.00000 0.00000 0.00000 MINI CONSTR> 329.95244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 429.36421 0.00033 0.02490 0.00002 MINI INTERN> 19.18724 94.79416 0.00000 42.84504 12.76364 MINI EXTERN> 51.93389 -122.11848 0.00000 0.00000 0.00000 MINI CONSTR> 329.95872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 429.36385 0.00035 0.02822 0.00002 MINI INTERN> 19.18966 94.79214 0.00000 42.84064 12.76348 MINI EXTERN> 51.92874 -122.11615 0.00000 0.00000 0.00000 MINI CONSTR> 329.96534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 429.36352 0.00033 0.02886 0.00002 MINI INTERN> 19.18627 94.79142 0.00000 42.83729 12.76291 MINI EXTERN> 51.92685 -122.11245 0.00000 0.00000 0.00000 MINI CONSTR> 329.97124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 429.36318 0.00034 0.02762 0.00002 MINI INTERN> 19.18567 94.78941 0.00000 42.83352 12.76269 MINI EXTERN> 51.92225 -122.10764 0.00000 0.00000 0.00000 MINI CONSTR> 329.97728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 492 429.36299 0.00019 0.00995 0.00001 STPD INTERN> 19.20165 94.78503 0.00000 42.82993 12.76435 STPD EXTERN> 51.90816 -122.10643 0.00000 0.00000 0.00000 STPD CONSTR> 329.98029 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21237 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21237 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 429.36299 0.00019 0.00995 0.00000 MINI INTERN> 19.20165 94.78503 0.00000 42.82993 12.76435 MINI EXTERN> 51.90816 -122.10643 0.00000 0.00000 0.00000 MINI CONSTR> 329.98029 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 429.35124 0.01175 0.01633 0.00093 MINI INTERN> 19.18249 94.64576 0.00000 42.56599 12.74940 MINI EXTERN> 51.59495 -121.84007 0.00000 0.00000 0.00000 MINI CONSTR> 330.45272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 429.34989 0.00136 0.02965 0.00383 MINI INTERN> 19.21724 94.75012 0.00000 42.50613 12.71555 MINI EXTERN> 51.68100 -121.84929 0.00000 0.00000 0.00000 MINI CONSTR> 330.32913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 429.34459 0.00530 0.06761 0.01895 MINI INTERN> 19.27160 94.86419 0.00000 42.29741 12.72945 MINI EXTERN> 51.77281 -121.80300 0.00000 0.00000 0.00000 MINI CONSTR> 330.21212 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 429.33252 0.01207 0.07410 0.02689 MINI INTERN> 19.18937 95.03087 0.00000 41.96919 12.70415 MINI EXTERN> 51.24940 -121.50078 0.00000 0.00000 0.00000 MINI CONSTR> 330.69031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 429.32466 0.00785 0.06634 0.01969 MINI INTERN> 19.09801 94.99308 0.00000 41.74837 12.59925 MINI EXTERN> 51.17273 -121.28664 0.00000 0.00000 0.00000 MINI CONSTR> 330.99986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 429.31910 0.00556 0.06030 0.01307 MINI INTERN> 19.07350 95.07560 0.00000 41.57382 12.53862 MINI EXTERN> 51.15616 -121.09667 0.00000 0.00000 0.00000 MINI CONSTR> 330.99807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 429.31527 0.00384 0.05086 0.00919 MINI INTERN> 19.06386 95.16394 0.00000 41.44154 12.51375 MINI EXTERN> 51.29525 -121.00014 0.00000 0.00000 0.00000 MINI CONSTR> 330.83706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 429.31260 0.00267 0.04361 0.00686 MINI INTERN> 19.06142 95.32343 0.00000 41.33110 12.51337 MINI EXTERN> 51.26453 -120.92303 0.00000 0.00000 0.00000 MINI CONSTR> 330.74177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 429.31038 0.00222 0.04015 0.00629 MINI INTERN> 19.06155 95.34699 0.00000 41.27886 12.50500 MINI EXTERN> 51.26994 -120.89178 0.00000 0.00000 0.00000 MINI CONSTR> 330.73984 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 429.30847 0.00192 0.03630 0.00529 MINI INTERN> 19.04036 95.37014 0.00000 41.21991 12.51130 MINI EXTERN> 51.18736 -120.85400 0.00000 0.00000 0.00000 MINI CONSTR> 330.83340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 429.30693 0.00154 0.03394 0.00423 MINI INTERN> 19.03831 95.34192 0.00000 41.21409 12.51247 MINI EXTERN> 51.16156 -120.85613 0.00000 0.00000 0.00000 MINI CONSTR> 330.89471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 429.30562 0.00131 0.03195 0.00417 MINI INTERN> 19.03011 95.38846 0.00000 41.19018 12.51722 MINI EXTERN> 51.18361 -120.87664 0.00000 0.00000 0.00000 MINI CONSTR> 330.87268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 429.30429 0.00133 0.03432 0.00481 MINI INTERN> 19.04846 95.41415 0.00000 41.16821 12.54571 MINI EXTERN> 51.28042 -120.93619 0.00000 0.00000 0.00000 MINI CONSTR> 330.78352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 429.30259 0.00169 0.03672 0.00666 MINI INTERN> 19.07667 95.50416 0.00000 41.12816 12.56837 MINI EXTERN> 51.37093 -121.04102 0.00000 0.00000 0.00000 MINI CONSTR> 330.69532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 429.30060 0.00199 0.03903 0.00697 MINI INTERN> 19.09765 95.55664 0.00000 41.08353 12.58799 MINI EXTERN> 51.45975 -121.14122 0.00000 0.00000 0.00000 MINI CONSTR> 330.65626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 429.29869 0.00190 0.03813 0.00644 MINI INTERN> 19.11206 95.59277 0.00000 41.03593 12.59404 MINI EXTERN> 51.47919 -121.17517 0.00000 0.00000 0.00000 MINI CONSTR> 330.65986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 429.29684 0.00185 0.03654 0.00657 MINI INTERN> 19.11566 95.60349 0.00000 40.96947 12.59712 MINI EXTERN> 51.59569 -121.21989 0.00000 0.00000 0.00000 MINI CONSTR> 330.63531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 429.29539 0.00146 0.03306 0.00464 MINI INTERN> 19.13689 95.65367 0.00000 40.91708 12.58731 MINI EXTERN> 51.67998 -121.28611 0.00000 0.00000 0.00000 MINI CONSTR> 330.60655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 429.29412 0.00127 0.03038 0.00482 MINI INTERN> 19.13722 95.71043 0.00000 40.86319 12.57031 MINI EXTERN> 51.73871 -121.31770 0.00000 0.00000 0.00000 MINI CONSTR> 330.59197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 429.29291 0.00121 0.02972 0.00473 MINI INTERN> 19.12802 95.71936 0.00000 40.81253 12.55729 MINI EXTERN> 51.79181 -121.33223 0.00000 0.00000 0.00000 MINI CONSTR> 330.61613 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 429.29291 0.00121 0.02972 0.02000 CONJ INTERN> 19.12802 95.71936 0.00000 40.81253 12.55729 CONJ EXTERN> 51.79181 -121.33223 0.00000 0.00000 0.00000 CONJ CONSTR> 330.61613 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "4800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 6.3729 ( PROT LYS 1 HT2 ) 6.3729 ( PROT LYS 1 N ) 7.9661 ( PROT LYS 1 HT3 ) 6.3729 ( PROT LYS 1 CA ) 7.9661 ( PROT LYS 1 CB ) 6.3729 ( PROT LYS 1 CG ) 6.3729 ( PROT LYS 1 CD ) 6.3729 ( PROT LYS 1 CE ) 6.3729 ( PROT LYS 1 NZ ) 6.3729 ( PROT LYS 1 HZ1 ) 6.3729 ( PROT LYS 1 HZ2 ) 6.3729 ( PROT LYS 1 HZ3 ) 6.3729 ( PROT LYS 1 C ) 7.9661 ( PROT LYS 1 O ) 7.9661 ( PROT MET 2 N ) 7.9661 ( PROT MET 2 H ) 6.3729 ( PROT MET 2 CA ) 7.9661 ( PROT MET 2 CB ) 6.3729 ( PROT MET 2 CG ) 6.3729 ( PROT MET 2 SD ) 6.3729 ( PROT MET 2 CE ) 6.3729 ( PROT MET 2 C ) 7.9661 ( PROT MET 2 O ) 7.9661 ( PROT LYS 3 N ) 7.9661 ( PROT LYS 3 H ) 6.3729 ( PROT LYS 3 CA ) 7.9661 ( PROT LYS 3 CB ) 6.3729 ( PROT LYS 3 CG ) 6.3729 ( PROT LYS 3 CD ) 6.3729 ( PROT LYS 3 CE ) 6.3729 ( PROT LYS 3 NZ ) 6.3729 ( PROT LYS 3 HZ1 ) 6.3729 ( PROT LYS 3 HZ2 ) 6.3729 ( PROT LYS 3 HZ3 ) 6.3729 ( PROT LYS 3 C ) 7.9661 ( PROT LYS 3 O ) 7.9661 ( PROT ALA 4 N ) 7.9661 ( PROT ALA 4 H ) 6.3729 ( PROT ALA 4 CA ) 7.9661 ( PROT ALA 4 CB ) 6.3729 ( PROT ALA 4 C ) 7.9661 ( PROT ALA 4 O ) 7.9661 ( PROT VAL 5 N ) 7.9661 ( PROT VAL 5 H ) 6.3729 ( PROT VAL 5 CA ) 7.9661 ( PROT VAL 5 CB ) 6.3729 ( PROT VAL 5 CG1 ) 6.3729 ( PROT VAL 5 CG2 ) 6.3729 ( PROT VAL 5 C ) 7.9661 ( PROT VAL 5 O ) 7.9661 ( PROT MET 6 N ) 7.9661 ( PROT MET 6 H ) 6.3729 ( PROT MET 6 CA ) 7.9661 ( PROT MET 6 CB ) 6.3729 ( PROT MET 6 CG ) 6.3729 ( PROT MET 6 SD ) 6.3729 ( PROT MET 6 CE ) 6.3729 ( PROT MET 6 C ) 7.9661 ( PROT MET 6 O ) 7.9661 ( PROT ILE 7 N ) 7.9661 ( PROT ILE 7 H ) 6.3729 ( PROT ILE 7 CA ) 7.9661 ( PROT ILE 7 CB ) 6.3729 ( PROT ILE 7 CG2 ) 6.3729 ( PROT ILE 7 CG1 ) 6.3729 ( PROT ILE 7 CD ) 6.3729 ( PROT ILE 7 C ) 7.9661 ( PROT ILE 7 O ) 7.9661 ( PROT GLY 8 N ) 7.9661 ( PROT GLY 8 H ) 6.3729 ( PROT GLY 8 CA ) 7.9661 ( PROT GLY 8 C ) 7.9661 ( PROT GLY 8 O ) 7.9661 ( PROT ALA 9 N ) 7.9661 ( PROT ALA 9 H ) 6.3729 ( PROT ALA 9 CA ) 7.9661 ( PROT ALA 9 CB ) 6.3729 ( PROT ALA 9 C ) 7.9661 ( PROT ALA 9 O ) 7.9661 ( PROT CYS 10 N ) 7.9661 ( PROT CYS 10 H ) 6.3729 ( PROT CYS 10 CA ) 7.9661 ( PROT CYS 10 CB ) 6.3729 ( PROT CYS 10 SG ) 6.3729 ( PROT CYS 10 C ) 7.9661 ( PROT CYS 10 O ) 7.9661 ( PROT PHE 11 N ) 7.9661 ( PROT PHE 11 H ) 6.3729 ( PROT PHE 11 CA ) 7.9661 ( PROT PHE 11 CB ) 6.3729 ( PROT PHE 11 CG ) 6.3729 ( PROT PHE 11 CD1 ) 6.3729 ( PROT PHE 11 CD2 ) 6.3729 ( PROT PHE 11 CE1 ) 6.3729 ( PROT PHE 11 CE2 ) 6.3729 ( PROT PHE 11 CZ ) 6.3729 ( PROT PHE 11 C ) 7.9661 ( PROT PHE 11 O ) 7.9661 ( PROT LEU 12 N ) 7.9661 ( PROT LEU 12 H ) 6.3729 ( PROT LEU 12 CA ) 7.9661 ( PROT LEU 12 CB ) 6.3729 ( PROT LEU 12 CG ) 6.3729 ( PROT LEU 12 CD1 ) 6.3729 ( PROT LEU 12 CD2 ) 6.3729 ( PROT LEU 12 C ) 7.9661 ( PROT LEU 12 O ) 7.9661 ( PROT ILE 13 N ) 7.9661 ( PROT ILE 13 H ) 6.3729 ( PROT ILE 13 CA ) 7.9661 ( PROT ILE 13 CB ) 6.3729 ( PROT ILE 13 CG2 ) 6.3729 ( PROT ILE 13 CG1 ) 6.3729 ( PROT ILE 13 CD ) 6.3729 ( PROT ILE 13 C ) 7.9661 ( PROT ILE 13 O ) 7.9661 ( PROT ASH 14 N ) 7.9661 ( PROT ASH 14 H ) 6.3729 ( PROT ASH 14 CA ) 7.9661 ( PROT ASH 14 CB ) 6.3729 ( PROT ASH 14 CG ) 6.3729 ( PROT ASH 14 OD1 ) 6.3729 ( PROT ASH 14 OD2 ) 6.3729 ( PROT ASH 14 HD2 ) 6.3729 ( PROT ASH 14 C ) 7.9661 ( PROT ASH 14 O ) 7.9661 ( PROT PHE 15 N ) 7.9661 ( PROT PHE 15 H ) 6.3729 ( PROT PHE 15 CA ) 7.9661 ( PROT PHE 15 CB ) 6.3729 ( PROT PHE 15 CG ) 6.3729 ( PROT PHE 15 CD1 ) 6.3729 ( PROT PHE 15 CD2 ) 6.3729 ( PROT PHE 15 CE1 ) 6.3729 ( PROT PHE 15 CE2 ) 6.3729 ( PROT PHE 15 CZ ) 6.3729 ( PROT PHE 15 C ) 7.9661 ( PROT PHE 15 O ) 7.9661 ( PROT MET 16 N ) 7.9661 ( PROT MET 16 H ) 6.3729 ( PROT MET 16 CA ) 7.9661 ( PROT MET 16 CB ) 6.3729 ( PROT MET 16 CG ) 6.3729 ( PROT MET 16 SD ) 6.3729 ( PROT MET 16 CE ) 6.3729 ( PROT MET 16 C ) 7.9661 ( PROT MET 16 O ) 7.9661 ( PROT PHE 17 N ) 7.9661 ( PROT PHE 17 H ) 6.3729 ( PROT PHE 17 CA ) 7.9661 ( PROT PHE 17 CB ) 6.3729 ( PROT PHE 17 CG ) 6.3729 ( PROT PHE 17 CD1 ) 6.3729 ( PROT PHE 17 CD2 ) 6.3729 ( PROT PHE 17 CE1 ) 6.3729 ( PROT PHE 17 CE2 ) 6.3729 ( PROT PHE 17 CZ ) 6.3729 ( PROT PHE 17 C ) 7.9661 ( PROT PHE 17 O ) 7.9661 ( PROT PHE 18 N ) 7.9661 ( PROT PHE 18 H ) 6.3729 ( PROT PHE 18 CA ) 7.9661 ( PROT PHE 18 CB ) 6.3729 ( PROT PHE 18 CG ) 6.3729 ( PROT PHE 18 CD1 ) 6.3729 ( PROT PHE 18 CD2 ) 6.3729 ( PROT PHE 18 CE1 ) 6.3729 ( PROT PHE 18 CE2 ) 6.3729 ( PROT PHE 18 CZ ) 6.3729 ( PROT PHE 18 C ) 7.9661 ( PROT PHE 18 O ) 7.9661 ( PROT GLU 19 N ) 7.9661 ( PROT GLU 19 H ) 6.3729 ( PROT GLU 19 CA ) 7.9661 ( PROT GLU 19 CB ) 6.3729 ( PROT GLU 19 CG ) 6.3729 ( PROT GLU 19 CD ) 6.3729 ( PROT GLU 19 OE1 ) 6.3729 ( PROT GLU 19 OE2 ) 6.3729 ( PROT GLU 19 C ) 7.9661 ( PROT GLU 19 O ) 7.9661 ( PROT SER 20 N ) 7.9661 ( PROT SER 20 H ) 6.3729 ( PROT SER 20 CA ) 7.9661 ( PROT SER 20 CB ) 6.3729 ( PROT SER 20 OG ) 6.3729 ( PROT SER 20 HG ) 6.3729 ( PROT SER 20 C ) 7.9661 ( PROT SER 20 O ) 7.9661 ( PROT THR 21 N ) 7.9661 ( PROT THR 21 H ) 6.3729 ( PROT THR 21 CA ) 7.9661 ( PROT THR 21 CB ) 6.3729 ( PROT THR 21 OG1 ) 6.3729 ( PROT THR 21 HG1 ) 6.3729 ( PROT THR 21 CG2 ) 6.3729 ( PROT THR 21 C ) 7.9661 ( PROT THR 21 O ) 7.9661 ( PROT GLY 22 N ) 7.9661 ( PROT GLY 22 H ) 6.3729 ( PROT GLY 22 CA ) 7.9661 ( PROT GLY 22 C ) 7.9661 ( PROT GLY 22 O ) 7.9661 ( PROT SER 23 N ) 7.9661 ( PROT SER 23 H ) 6.3729 ( PROT SER 23 CA ) 7.9661 ( PROT SER 23 CB ) 6.3729 ( PROT SER 23 OG ) 6.3729 ( PROT SER 23 HG ) 6.3729 ( PROT SER 23 C ) 7.9661 ( PROT SER 23 O ) 7.9661 ( PROT GLN 24 N ) 7.9661 ( PROT GLN 24 H ) 6.3729 ( PROT GLN 24 CA ) 7.9661 ( PROT GLN 24 CB ) 6.3729 ( PROT GLN 24 CG ) 6.3729 ( PROT GLN 24 CD ) 6.3729 ( PROT GLN 24 OE1 ) 6.3729 ( PROT GLN 24 NE2 ) 6.3729 ( PROT GLN 24 HE21 ) 6.3729 ( PROT GLN 24 HE22 ) 6.3729 ( PROT GLN 24 C ) 7.9661 ( PROT GLN 24 O ) 7.9661 ( PROT GLU 25 N ) 7.9661 ( PROT GLU 25 H ) 6.3729 ( PROT GLU 25 CA ) 7.9661 ( PROT GLU 25 CB ) 6.3729 ( PROT GLU 25 CG ) 6.3729 ( PROT GLU 25 CD ) 6.3729 ( PROT GLU 25 OE1 ) 6.3729 ( PROT GLU 25 OE2 ) 6.3729 ( PROT GLU 25 C ) 7.9661 ( PROT GLU 25 O ) 7.9661 ( PROT GLN 26 N ) 7.9661 ( PROT GLN 26 H ) 6.3729 ( PROT GLN 26 CA ) 7.9661 ( PROT GLN 26 CB ) 6.3729 ( PROT GLN 26 CG ) 6.3729 ( PROT GLN 26 CD ) 6.3729 ( PROT GLN 26 OE1 ) 6.3729 ( PROT GLN 26 NE2 ) 6.3729 ( PROT GLN 26 HE21 ) 6.3729 ( PROT GLN 26 HE22 ) 6.3729 ( PROT GLN 26 C ) 7.9661 ( PROT GLN 26 O ) 7.9661 ( PROT LYS 27 N ) 7.9661 ( PROT LYS 27 H ) 6.3729 ( PROT LYS 27 CA ) 7.9661 ( PROT LYS 27 CB ) 6.3729 ( PROT LYS 27 CG ) 6.3729 ( PROT LYS 27 CD ) 6.3729 ( PROT LYS 27 CE ) 6.3729 ( PROT LYS 27 NZ ) 6.3729 ( PROT LYS 27 HZ1 ) 6.3729 ( PROT LYS 27 HZ2 ) 6.3729 ( PROT LYS 27 HZ3 ) 6.3729 ( PROT LYS 27 C ) 7.9661 ( PROT LYS 27 O ) 7.9661 ( PROT SER 28 N ) 7.9661 ( PROT SER 28 H ) 6.3729 ( PROT SER 28 CA ) 7.9661 ( PROT SER 28 CB ) 6.3729 ( PROT SER 28 OG ) 6.3729 ( PROT SER 28 HG ) 6.3729 ( PROT SER 28 C ) 7.9661 ( PROT SER 28 O ) 7.9661 ( PROT GLY 29 N ) 7.9661 ( PROT GLY 29 H ) 6.3729 ( PROT GLY 29 CA ) 7.9661 ( PROT GLY 29 C ) 7.9661 ( PROT GLY 29 O ) 7.9661 ( PROT VAL 30 N ) 7.9661 ( PROT VAL 30 H ) 6.3729 ( PROT VAL 30 CA ) 7.9661 ( PROT VAL 30 CB ) 6.3729 ( PROT VAL 30 CG1 ) 6.3729 ( PROT VAL 30 CG2 ) 6.3729 ( PROT VAL 30 C ) 7.9661 ( PROT VAL 30 O ) 7.9661 ( PROT TRP 31 N ) 7.9661 ( PROT TRP 31 H ) 6.3729 ( PROT TRP 31 CA ) 7.9661 ( PROT TRP 31 CB ) 6.3729 ( PROT TRP 31 CG ) 6.3729 ( PROT TRP 31 CD2 ) 6.3729 ( PROT TRP 31 CE2 ) 6.3729 ( PROT TRP 31 CE3 ) 6.3729 ( PROT TRP 31 CD1 ) 6.3729 ( PROT TRP 31 NE1 ) 6.3729 ( PROT TRP 31 HE1 ) 6.3729 ( PROT TRP 31 CZ2 ) 6.3729 ( PROT TRP 31 CZ3 ) 6.3729 ( PROT TRP 31 CH2 ) 6.3729 ( PROT TRP 31 C ) 7.9661 ( PROT TRP 31 OT1 ) 6.3729 ( PROT TRP 31 OT2 ) 6.3729 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63098 7.22892 -13.22076 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS -0.00017 0.00051 0.00085 ROTATION MATRIX 1.000000 -0.000097 -0.000327 0.000097 1.000000 0.000286 0.000327 -0.000286 1.000000 AXIS OF ROTATION IS 0.643194 0.734300 -0.217036 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 30.7692 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.321870 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3219" Parameter: A <- "0.3219" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51582 7.24872 -13.40970 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01241 0.00683 -0.03065 ROTATION MATRIX 0.999749 0.015525 0.016138 -0.015249 0.999738 -0.017043 -0.016398 0.016792 0.999725 AXIS OF ROTATION IS -0.602813 -0.579667 0.548272 ANGLE IS 1.61 CENTER OF ROTATION 14.021572 6.836228-13.315504 SHIFT IS -0.028245 TOTAL SQUARE DIFF IS 0.6041 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.139597 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3219" RDCMND substituted energy or value "?RMS" to " 0.1396" Parameter: A <- "0.3219 0.1396" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *4800 0.3219 0.1396 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 330.62" Parameter: H <- "330.62" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 98.67678 330.61613 4.01853 ENER INTERN> 19.12802 95.71936 0.00000 40.81253 12.55729 ENER EXTERN> 51.79181 -121.33223 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 98.68" Parameter: B <- "98.68" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -121.33" Parameter: C <- "-121.33" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 51.79" Parameter: C <- " -69.54" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -69.54" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 19.13" Parameter: D <- "19.13" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 95.72" Parameter: D <- " 114.85" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 40.81" Parameter: D <- " 155.66" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 12.56" Parameter: D <- " 168.22" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 168.22" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 4800 ENER= 98.68 GRMS= 4.02 ELEC= -121.33 VDW= 51.79 RDTITL> *EXTERNAL= -69.54 INTERNAL= 168.22 USER= 0.00 HARM= 330.62 RDTITL> *BOND= 19.13 ANGL= 95.72 DIHE= 40.81 IMPR= 12.56 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "4800" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_4800.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_4800.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 4800 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 4800 ENER= 98.68 GRMS= 4.02 ELEC= -121.33 VDW= 51.79 RDTITL> *EXTERNAL= -69.54 INTERNAL= 168.22 USER= 0.00 HARM= 330.62 RDTITL> *BOND= 19.13 ANGL= 95.72 DIHE= 40.81 IMPR= 12.56 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "4800" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_4800.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_4800.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 4800 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 4800 ENER= 98.68 GRMS= 4.02 ELEC= -121.33 VDW= 51.79 RDTITL> *EXTERNAL= -69.54 INTERNAL= 168.22 USER= 0.00 HARM= 330.62 RDTITL> *BOND= 19.13 ANGL= 95.72 DIHE= 40.81 IMPR= 12.56 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 4800 0.3219 0.1396 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "4800" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21237 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21234 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 339.55465 -240.87787 1.65790 0.02000 MINI INTERN> 19.12802 95.71936 0.00000 40.81253 12.55729 MINI EXTERN> 51.79181 -121.33223 0.00000 0.00000 0.00000 MINI CONSTR> 240.87787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 324.81503 14.73962 1.81441 0.00360 MINI INTERN> 17.68661 92.81733 0.00000 43.90989 12.75027 MINI EXTERN> 18.00438 -118.16825 0.00000 0.00000 0.00000 MINI CONSTR> 257.81480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21218 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 320.77072 4.04431 1.41535 0.00156 MINI INTERN> 16.71297 92.57298 0.00000 44.17851 12.41382 MINI EXTERN> 12.76401 -117.58334 0.00000 0.00000 0.00000 MINI CONSTR> 259.71179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 318.85225 1.91847 2.73141 0.00161 MINI INTERN> 15.25183 92.27897 0.00000 44.71239 12.15335 MINI EXTERN> 11.36016 -117.31019 0.00000 0.00000 0.00000 MINI CONSTR> 260.40574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21214 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 316.18085 2.67139 0.71765 0.00070 MINI INTERN> 15.85194 91.09703 0.00000 44.55211 12.26353 MINI EXTERN> 8.70961 -117.13524 0.00000 0.00000 0.00000 MINI CONSTR> 260.84188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 315.52416 0.65669 2.77418 0.00173 MINI INTERN> 14.00962 91.82164 0.00000 45.07524 11.93219 MINI EXTERN> 9.10589 -117.33667 0.00000 0.00000 0.00000 MINI CONSTR> 260.91626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21210 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 313.09592 2.42824 0.86944 0.00075 MINI INTERN> 16.16267 89.83555 0.00000 44.55689 12.13392 MINI EXTERN> 6.18775 -116.89472 0.00000 0.00000 0.00000 MINI CONSTR> 261.11386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 311.95788 1.13804 0.57205 0.00078 MINI INTERN> 15.39376 89.79064 0.00000 44.65331 12.02674 MINI EXTERN> 5.90150 -116.90167 0.00000 0.00000 0.00000 MINI CONSTR> 261.09361 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21207 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 310.73184 1.22604 1.15188 0.00080 MINI INTERN> 16.63303 88.79528 0.00000 44.46388 12.03328 MINI EXTERN> 4.40612 -116.68296 0.00000 0.00000 0.00000 MINI CONSTR> 261.08321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 309.65767 1.07417 0.73572 0.00083 MINI INTERN> 15.79917 88.82029 0.00000 44.52646 11.92945 MINI EXTERN> 4.29712 -116.71550 0.00000 0.00000 0.00000 MINI CONSTR> 261.00068 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 308.93780 0.71987 1.26611 0.00087 MINI INTERN> 16.73016 88.15756 0.00000 44.36272 11.93946 MINI EXTERN> 3.35536 -116.55900 0.00000 0.00000 0.00000 MINI CONSTR> 260.95154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 308.19096 0.74684 1.44209 0.00090 MINI INTERN> 17.05268 87.75348 0.00000 44.27749 11.90254 MINI EXTERN> 2.82548 -116.49753 0.00000 0.00000 0.00000 MINI CONSTR> 260.87683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21202 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 307.55275 0.63822 1.37724 0.00093 MINI INTERN> 16.86615 87.62198 0.00000 44.24011 11.86212 MINI EXTERN> 2.58488 -116.43870 0.00000 0.00000 0.00000 MINI CONSTR> 260.81620 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 306.69512 0.85763 0.42035 0.00040 MINI INTERN> 14.49256 88.47112 0.00000 44.48828 11.67117 MINI EXTERN> 3.53248 -116.65763 0.00000 0.00000 0.00000 MINI CONSTR> 260.69714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21203 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 306.48677 0.20835 1.47409 0.00100 MINI INTERN> 16.98405 87.22041 0.00000 44.10687 11.80274 MINI EXTERN> 2.01435 -116.35625 0.00000 0.00000 0.00000 MINI CONSTR> 260.71461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 305.66715 0.81962 0.46339 0.00043 MINI INTERN> 14.24781 88.24662 0.00000 44.39712 11.59017 MINI EXTERN> 3.18735 -116.60321 0.00000 0.00000 0.00000 MINI CONSTR> 260.60129 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21202 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 305.29512 0.37203 0.32927 0.00045 MINI INTERN> 14.53824 87.94659 0.00000 44.30363 11.58497 MINI EXTERN> 2.86713 -116.53011 0.00000 0.00000 0.00000 MINI CONSTR> 260.58466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 304.91832 0.37680 0.68048 0.00046 MINI INTERN> 13.82503 88.20411 0.00000 44.33984 11.50735 MINI EXTERN> 3.07620 -116.57876 0.00000 0.00000 0.00000 MINI CONSTR> 260.54454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21199 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 304.55586 0.36246 0.40588 0.00048 MINI INTERN> 14.22124 87.84568 0.00000 44.22111 11.51405 MINI EXTERN> 2.69909 -116.49339 0.00000 0.00000 0.00000 MINI CONSTR> 260.54808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 304.30895 0.24691 0.73446 0.00050 MINI INTERN> 13.69190 88.04970 0.00000 44.24080 11.45634 MINI EXTERN> 2.86322 -116.52728 0.00000 0.00000 0.00000 MINI CONSTR> 260.53426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21200 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 304.05769 0.25126 0.82151 0.00052 MINI INTERN> 13.54733 88.03775 0.00000 44.20160 11.42997 MINI EXTERN> 2.80301 -116.50342 0.00000 0.00000 0.00000 MINI CONSTR> 260.54145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 303.84207 0.21562 0.78798 0.00054 MINI INTERN> 13.59900 87.91014 0.00000 44.14625 11.41361 MINI EXTERN> 2.69829 -116.47880 0.00000 0.00000 0.00000 MINI CONSTR> 260.55358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21200 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 303.55541 0.28666 0.24109 0.00023 MINI INTERN> 14.76455 87.11930 0.00000 43.92297 11.47047 MINI EXTERN> 1.97271 -116.29714 0.00000 0.00000 0.00000 MINI CONSTR> 260.60254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 303.48226 0.07315 0.85501 0.00058 MINI INTERN> 13.51903 87.79905 0.00000 44.05723 11.37735 MINI EXTERN> 2.57299 -116.43845 0.00000 0.00000 0.00000 MINI CONSTR> 260.59507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21200 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 303.21461 0.26765 0.28823 0.00025 MINI INTERN> 14.90728 86.87834 0.00000 43.80176 11.44896 MINI EXTERN> 1.74103 -116.22283 0.00000 0.00000 0.00000 MINI CONSTR> 260.66009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 303.08746 0.12715 0.19053 0.00026 MINI INTERN> 14.65409 86.96441 0.00000 43.79472 11.42721 MINI EXTERN> 1.79509 -116.23002 0.00000 0.00000 0.00000 MINI CONSTR> 260.68196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21199 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 302.94458 0.14288 0.36113 0.00027 MINI INTERN> 15.05400 86.64809 0.00000 43.68659 11.42863 MINI EXTERN> 1.54500 -116.15019 0.00000 0.00000 0.00000 MINI CONSTR> 260.73246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 302.82525 0.11933 0.25130 0.00028 MINI INTERN> 14.84556 86.70658 0.00000 43.66994 11.40990 MINI EXTERN> 1.57643 -116.14829 0.00000 0.00000 0.00000 MINI CONSTR> 260.76514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21199 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 302.74079 0.08446 0.41920 0.00029 MINI INTERN> 15.14542 86.48081 0.00000 43.58825 11.41229 MINI EXTERN> 1.39672 -116.09310 0.00000 0.00000 0.00000 MINI CONSTR> 260.81040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 302.65811 0.08268 0.49178 0.00030 MINI INTERN> 15.17357 86.40120 0.00000 43.54338 11.40191 MINI EXTERN> 1.33260 -116.04862 0.00000 0.00000 0.00000 MINI CONSTR> 260.85408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21198 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 302.58200 0.07612 0.44859 0.00031 MINI INTERN> 15.18656 86.36712 0.00000 43.50361 11.40049 MINI EXTERN> 1.27486 -116.04210 0.00000 0.00000 0.00000 MINI CONSTR> 260.89146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 302.50621 0.07579 0.45234 0.00032 MINI INTERN> 15.18825 86.30189 0.00000 43.46389 11.38817 MINI EXTERN> 1.24559 -116.01652 0.00000 0.00000 0.00000 MINI CONSTR> 260.93493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21198 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 302.41538 0.09083 0.14237 0.00014 MINI INTERN> 14.40919 86.74026 0.00000 43.52562 11.35823 MINI EXTERN> 1.50898 -116.09087 0.00000 0.00000 0.00000 MINI CONSTR> 260.96397 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 302.36275 0.05263 0.11973 0.00014 MINI INTERN> 14.46608 86.66455 0.00000 43.48653 11.35388 MINI EXTERN> 1.45362 -116.06457 0.00000 0.00000 0.00000 MINI CONSTR> 261.00266 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21198 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 302.30890 0.05385 0.11555 0.00015 MINI INTERN> 14.46338 86.62916 0.00000 43.45096 11.34862 MINI EXTERN> 1.41410 -116.04427 0.00000 0.00000 0.00000 MINI CONSTR> 261.04695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 302.26330 0.04560 0.21303 0.00015 MINI INTERN> 14.26363 86.74130 0.00000 43.43786 11.34277 MINI EXTERN> 1.43592 -116.05115 0.00000 0.00000 0.00000 MINI CONSTR> 261.09298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21198 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 302.22353 0.03977 0.17258 0.00016 MINI INTERN> 14.30888 86.66861 0.00000 43.40407 11.33703 MINI EXTERN> 1.40142 -116.02630 0.00000 0.00000 0.00000 MINI CONSTR> 261.12983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 302.19225 0.03128 0.24298 0.00017 MINI INTERN> 14.21393 86.71025 0.00000 43.38698 11.33156 MINI EXTERN> 1.40163 -116.02139 0.00000 0.00000 0.00000 MINI CONSTR> 261.16929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 302.16267 0.02958 0.27388 0.00017 MINI INTERN> 14.17978 86.69934 0.00000 43.36267 11.32632 MINI EXTERN> 1.39669 -116.00857 0.00000 0.00000 0.00000 MINI CONSTR> 261.20645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 302.13437 0.02830 0.25891 0.00018 MINI INTERN> 14.19281 86.66333 0.00000 43.33764 11.32139 MINI EXTERN> 1.36663 -115.98965 0.00000 0.00000 0.00000 MINI CONSTR> 261.24222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 302.10110 0.03327 0.08685 0.00008 MINI INTERN> 14.54355 86.38931 0.00000 43.26952 11.32434 MINI EXTERN> 1.22479 -115.92878 0.00000 0.00000 0.00000 MINI CONSTR> 261.27838 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 302.08796 0.01314 0.28327 0.00019 MINI INTERN> 14.15189 86.63607 0.00000 43.29421 11.31218 MINI EXTERN> 1.34348 -115.96216 0.00000 0.00000 0.00000 MINI CONSTR> 261.31229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 302.06975 0.01821 0.33793 0.00020 MINI INTERN> 14.24845 86.54937 0.00000 43.25521 11.31352 MINI EXTERN> 1.29338 -115.93844 0.00000 0.00000 0.00000 MINI CONSTR> 261.34826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 302.03628 0.03347 0.09415 0.00009 MINI INTERN> 14.57404 86.29942 0.00000 43.19234 11.31727 MINI EXTERN> 1.14741 -115.87926 0.00000 0.00000 0.00000 MINI CONSTR> 261.38506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 302.02011 0.01617 0.07127 0.00009 MINI INTERN> 14.52200 86.31812 0.00000 43.17888 11.31493 MINI EXTERN> 1.14539 -115.87337 0.00000 0.00000 0.00000 MINI CONSTR> 261.41414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 302.00381 0.01630 0.12619 0.00009 MINI INTERN> 14.62996 86.22318 0.00000 43.14101 11.31477 MINI EXTERN> 1.08714 -115.84419 0.00000 0.00000 0.00000 MINI CONSTR> 261.45194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 301.98811 0.01570 0.08492 0.00010 MINI INTERN> 14.55488 86.25284 0.00000 43.12997 11.31117 MINI EXTERN> 1.09754 -115.84012 0.00000 0.00000 0.00000 MINI CONSTR> 261.48182 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 301.97517 0.01294 0.11398 0.00010 MINI INTERN> 14.60739 86.20023 0.00000 43.10227 11.31082 MINI EXTERN> 1.05929 -115.81974 0.00000 0.00000 0.00000 MINI CONSTR> 261.51491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 301.96463 0.01054 0.14758 0.00010 MINI INTERN> 14.65084 86.15435 0.00000 43.07730 11.31046 MINI EXTERN> 1.02864 -115.80200 0.00000 0.00000 0.00000 MINI CONSTR> 261.54503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 301.95441 0.01022 0.17795 0.00011 MINI INTERN> 14.65540 86.13323 0.00000 43.05825 11.30796 MINI EXTERN> 1.01049 -115.78663 0.00000 0.00000 0.00000 MINI CONSTR> 261.57570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 301.94452 0.00989 0.15902 0.00011 MINI INTERN> 14.66158 86.11795 0.00000 43.03993 11.30877 MINI EXTERN> 0.99127 -115.77647 0.00000 0.00000 0.00000 MINI CONSTR> 261.60149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 301.93198 0.01253 0.05193 0.00005 MINI INTERN> 14.44654 86.24987 0.00000 43.05024 11.30425 MINI EXTERN> 1.04796 -115.79211 0.00000 0.00000 0.00000 MINI CONSTR> 261.62523 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 301.92774 0.00424 0.17451 0.00012 MINI INTERN> 14.66647 86.08420 0.00000 43.00577 11.30643 MINI EXTERN> 0.96208 -115.75196 0.00000 0.00000 0.00000 MINI CONSTR> 261.65475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 301.91569 0.01205 0.05636 0.00005 MINI INTERN> 14.42917 86.23472 0.00000 43.01932 11.30263 MINI EXTERN> 1.02376 -115.77144 0.00000 0.00000 0.00000 MINI CONSTR> 261.67753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 301.90916 0.00653 0.04378 0.00005 MINI INTERN> 14.45454 86.20329 0.00000 43.00277 11.30181 MINI EXTERN> 1.00538 -115.75799 0.00000 0.00000 0.00000 MINI CONSTR> 261.69937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 301.90260 0.00656 0.04521 0.00006 MINI INTERN> 14.44545 86.19695 0.00000 42.98916 11.30104 MINI EXTERN> 0.99536 -115.74844 0.00000 0.00000 0.00000 MINI CONSTR> 261.72307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 301.89660 0.00601 0.07744 0.00006 MINI INTERN> 14.39567 86.22143 0.00000 42.97948 11.30052 MINI EXTERN> 0.99532 -115.74409 0.00000 0.00000 0.00000 MINI CONSTR> 261.74826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 301.89096 0.00564 0.06326 0.00006 MINI INTERN> 14.41930 86.19218 0.00000 42.96387 11.29992 MINI EXTERN> 0.97664 -115.73047 0.00000 0.00000 0.00000 MINI CONSTR> 261.76952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 301.88654 0.00441 0.08743 0.00006 MINI INTERN> 14.38187 86.20793 0.00000 42.95587 11.29898 MINI EXTERN> 0.97783 -115.72603 0.00000 0.00000 0.00000 MINI CONSTR> 261.79011 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 301.88088 0.00566 0.05405 0.00006 MINI INTERN> 14.42216 86.16801 0.00000 42.93761 11.29947 MINI EXTERN> 0.95294 -115.71096 0.00000 0.00000 0.00000 MINI CONSTR> 261.81165 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 301.87713 0.00375 0.09203 0.00007 MINI INTERN> 14.38087 86.19059 0.00000 42.92995 11.29947 MINI EXTERN> 0.95109 -115.70771 0.00000 0.00000 0.00000 MINI CONSTR> 261.83286 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 301.87324 0.00389 0.11378 0.00007 MINI INTERN> 14.37500 86.18423 0.00000 42.91666 11.30060 MINI EXTERN> 0.93565 -115.69399 0.00000 0.00000 0.00000 MINI CONSTR> 261.85508 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 301.86943 0.00381 0.10059 0.00007 MINI INTERN> 14.37453 86.17713 0.00000 42.90737 11.29990 MINI EXTERN> 0.92854 -115.68962 0.00000 0.00000 0.00000 MINI CONSTR> 261.87158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 301.86434 0.00509 0.03198 0.00003 MINI INTERN> 14.47260 86.08457 0.00000 42.88558 11.29735 MINI EXTERN> 0.90238 -115.66689 0.00000 0.00000 0.00000 MINI CONSTR> 261.88875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21198 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 301.86309 0.00125 0.12613 0.00008 MINI INTERN> 14.39344 86.13931 0.00000 42.88293 11.29993 MINI EXTERN> 0.90256 -115.66310 0.00000 0.00000 0.00000 MINI CONSTR> 261.90802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 301.85992 0.00318 0.11509 0.00008 MINI INTERN> 14.36782 86.15891 0.00000 42.87695 11.30071 MINI EXTERN> 0.89714 -115.66618 0.00000 0.00000 0.00000 MINI CONSTR> 261.92457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 301.85491 0.00501 0.03659 0.00003 MINI INTERN> 14.47969 86.04960 0.00000 42.85497 11.29655 MINI EXTERN> 0.87462 -115.64031 0.00000 0.00000 0.00000 MINI CONSTR> 261.93979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 301.85239 0.00252 0.02798 0.00004 MINI INTERN> 14.46529 86.05472 0.00000 42.84832 11.29726 MINI EXTERN> 0.86823 -115.63535 0.00000 0.00000 0.00000 MINI CONSTR> 261.95391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 301.84983 0.00256 0.04978 0.00004 MINI INTERN> 14.48904 86.02246 0.00000 42.83641 11.29581 MINI EXTERN> 0.85824 -115.62230 0.00000 0.00000 0.00000 MINI CONSTR> 261.97017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 301.84745 0.00238 0.04140 0.00004 MINI INTERN> 14.48148 86.02427 0.00000 42.82954 11.29654 MINI EXTERN> 0.85010 -115.61840 0.00000 0.00000 0.00000 MINI CONSTR> 261.98393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 301.84532 0.00213 0.04577 0.00004 MINI INTERN> 14.48505 86.01311 0.00000 42.82136 11.29651 MINI EXTERN> 0.84224 -115.61047 0.00000 0.00000 0.00000 MINI CONSTR> 261.99751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 301.84340 0.00192 0.06060 0.00004 MINI INTERN> 14.48939 85.99850 0.00000 42.81307 11.29607 MINI EXTERN> 0.83576 -115.60051 0.00000 0.00000 0.00000 MINI CONSTR> 262.01112 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 301.84149 0.00190 0.06370 0.00004 MINI INTERN> 14.49665 85.98836 0.00000 42.80539 11.29627 MINI EXTERN> 0.82639 -115.59543 0.00000 0.00000 0.00000 MINI CONSTR> 262.02385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 301.83969 0.00180 0.07041 0.00004 MINI INTERN> 14.48972 85.98331 0.00000 42.79883 11.29639 MINI EXTERN> 0.82137 -115.58652 0.00000 0.00000 0.00000 MINI CONSTR> 262.03659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 301.83790 0.00179 0.06581 0.00005 MINI INTERN> 14.49350 85.97870 0.00000 42.79252 11.29693 MINI EXTERN> 0.81234 -115.58412 0.00000 0.00000 0.00000 MINI CONSTR> 262.04803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 301.83573 0.00217 0.02269 0.00002 MINI INTERN> 14.44540 86.01484 0.00000 42.79200 11.29899 MINI EXTERN> 0.80990 -115.58475 0.00000 0.00000 0.00000 MINI CONSTR> 262.05934 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 301.83471 0.00101 0.06975 0.00005 MINI INTERN> 14.49410 85.96387 0.00000 42.78005 11.29730 MINI EXTERN> 0.79952 -115.57085 0.00000 0.00000 0.00000 MINI CONSTR> 262.07074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 301.83238 0.00234 0.02232 0.00002 MINI INTERN> 14.44359 86.00305 0.00000 42.77987 11.29946 MINI EXTERN> 0.79609 -115.57247 0.00000 0.00000 0.00000 MINI CONSTR> 262.08278 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 301.83170 0.00068 0.07759 0.00005 MINI INTERN> 14.49325 85.95167 0.00000 42.76887 11.29728 MINI EXTERN> 0.78804 -115.56041 0.00000 0.00000 0.00000 MINI CONSTR> 262.09299 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 301.82945 0.00224 0.02651 0.00002 MINI INTERN> 14.43868 85.99580 0.00000 42.76953 11.30016 MINI EXTERN> 0.78325 -115.56216 0.00000 0.00000 0.00000 MINI CONSTR> 262.10418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 301.82823 0.00122 0.02046 0.00002 MINI INTERN> 14.44372 85.98488 0.00000 42.76469 11.29991 MINI EXTERN> 0.77832 -115.55594 0.00000 0.00000 0.00000 MINI CONSTR> 262.11264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 301.82694 0.00130 0.02068 0.00002 MINI INTERN> 14.44306 85.97997 0.00000 42.76004 11.30014 MINI EXTERN> 0.77242 -115.55099 0.00000 0.00000 0.00000 MINI CONSTR> 262.12229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 301.82563 0.00130 0.03281 0.00003 MINI INTERN> 14.43296 85.98277 0.00000 42.75592 11.30090 MINI EXTERN> 0.76592 -115.54603 0.00000 0.00000 0.00000 MINI CONSTR> 262.13319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 301.82446 0.00117 0.02817 0.00003 MINI INTERN> 14.43642 85.97497 0.00000 42.75158 11.30092 MINI EXTERN> 0.76053 -115.54157 0.00000 0.00000 0.00000 MINI CONSTR> 262.14161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 301.82329 0.00117 0.02914 0.00003 MINI INTERN> 14.43542 85.96917 0.00000 42.74735 11.30111 MINI EXTERN> 0.75501 -115.53549 0.00000 0.00000 0.00000 MINI CONSTR> 262.15072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 301.82231 0.00097 0.04018 0.00003 MINI INTERN> 14.42971 85.97104 0.00000 42.74423 11.30171 MINI EXTERN> 0.74925 -115.53302 0.00000 0.00000 0.00000 MINI CONSTR> 262.15940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 301.82115 0.00116 0.03274 0.00003 MINI INTERN> 14.43379 85.95974 0.00000 42.73983 11.30159 MINI EXTERN> 0.74425 -115.52571 0.00000 0.00000 0.00000 MINI CONSTR> 262.16766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 301.82034 0.00081 0.04522 0.00003 MINI INTERN> 14.42827 85.95975 0.00000 42.73716 11.30194 MINI EXTERN> 0.73946 -115.52166 0.00000 0.00000 0.00000 MINI CONSTR> 262.17542 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 301.81941 0.00093 0.04736 0.00003 MINI INTERN> 14.43209 85.95515 0.00000 42.73377 11.30224 MINI EXTERN> 0.73396 -115.52062 0.00000 0.00000 0.00000 MINI CONSTR> 262.18283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 301.81849 0.00092 0.04779 0.00003 MINI INTERN> 14.42729 85.95072 0.00000 42.73093 11.30230 MINI EXTERN> 0.72978 -115.51301 0.00000 0.00000 0.00000 MINI CONSTR> 262.19048 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21196 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 301.81761 0.00088 0.04908 0.00003 MINI INTERN> 14.43127 85.94595 0.00000 42.72782 11.30257 MINI EXTERN> 0.72460 -115.51207 0.00000 0.00000 0.00000 MINI CONSTR> 262.19747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 301.81675 0.00086 0.04877 0.00004 MINI INTERN> 14.42632 85.94250 0.00000 42.72541 11.30265 MINI EXTERN> 0.72053 -115.50536 0.00000 0.00000 0.00000 MINI CONSTR> 262.20469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 301.81563 0.00112 0.01634 0.00002 MINI INTERN> 14.44630 85.91954 0.00000 42.72017 11.30233 MINI EXTERN> 0.71632 -115.49961 0.00000 0.00000 0.00000 MINI CONSTR> 262.21057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 301.81522 0.00040 0.05588 0.00004 MINI INTERN> 14.42427 85.93468 0.00000 42.72049 11.30302 MINI EXTERN> 0.71164 -115.49707 0.00000 0.00000 0.00000 MINI CONSTR> 262.21819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 301.81400 0.00122 0.01844 0.00002 MINI INTERN> 14.44667 85.90968 0.00000 42.71495 11.30279 MINI EXTERN> 0.70734 -115.49144 0.00000 0.00000 0.00000 MINI CONSTR> 262.22402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 301.81377 0.00023 0.06081 0.00004 MINI INTERN> 14.42825 85.92644 0.00000 42.71573 11.30358 MINI EXTERN> 0.70237 -115.49323 0.00000 0.00000 0.00000 MINI CONSTR> 262.23063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 301.81253 0.00124 0.02126 0.00002 MINI INTERN> 14.44722 85.90080 0.00000 42.71040 11.30329 MINI EXTERN> 0.69878 -115.48437 0.00000 0.00000 0.00000 MINI CONSTR> 262.23642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 301.81189 0.00064 0.01499 0.00002 MINI INTERN> 14.44335 85.90077 0.00000 42.70916 11.30363 MINI EXTERN> 0.69504 -115.48162 0.00000 0.00000 0.00000 MINI CONSTR> 262.24157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 301.81116 0.00073 0.02464 0.00002 MINI INTERN> 14.44747 85.89231 0.00000 42.70636 11.30381 MINI EXTERN> 0.69055 -115.47748 0.00000 0.00000 0.00000 MINI CONSTR> 262.24814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 301.81050 0.00066 0.02101 0.00002 MINI INTERN> 14.44464 85.89034 0.00000 42.70494 11.30409 MINI EXTERN> 0.68667 -115.47382 0.00000 0.00000 0.00000 MINI CONSTR> 262.25361 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 301.80987 0.00063 0.02267 0.00002 MINI INTERN> 14.44558 85.88605 0.00000 42.70314 11.30438 MINI EXTERN> 0.68264 -115.47095 0.00000 0.00000 0.00000 MINI CONSTR> 262.25903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 301.80987 0.00063 0.02267 0.00002 STPD INTERN> 14.44558 85.88605 0.00000 42.70314 11.30438 STPD EXTERN> 0.68264 -115.47095 0.00000 0.00000 0.00000 STPD CONSTR> 262.25903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21197 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21197 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 301.80987 0.00063 0.02267 0.00000 MINI INTERN> 14.44558 85.88605 0.00000 42.70314 11.30438 MINI EXTERN> 0.68264 -115.47095 0.00000 0.00000 0.00000 MINI CONSTR> 262.25903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 301.79165 0.01822 0.01267 0.00238 MINI INTERN> 14.41434 85.65860 0.00000 42.66555 11.32285 MINI EXTERN> 0.39826 -115.27746 0.00000 0.00000 0.00000 MINI CONSTR> 262.60950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 301.79030 0.00135 0.02560 0.00368 MINI INTERN> 14.40886 85.66556 0.00000 42.71466 11.31158 MINI EXTERN> 0.51516 -115.31047 0.00000 0.00000 0.00000 MINI CONSTR> 262.48496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 301.78882 0.00148 0.02394 0.00337 MINI INTERN> 14.43573 85.62739 0.00000 42.75578 11.32246 MINI EXTERN> 0.51987 -115.31573 0.00000 0.00000 0.00000 MINI CONSTR> 262.44332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 301.78800 0.00082 0.01543 0.00201 MINI INTERN> 14.40985 85.64173 0.00000 42.79292 11.32290 MINI EXTERN> 0.43028 -115.31355 0.00000 0.00000 0.00000 MINI CONSTR> 262.50387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 301.78758 0.00042 0.01327 0.00132 MINI INTERN> 14.41266 85.62735 0.00000 42.81697 11.32227 MINI EXTERN> 0.42023 -115.32509 0.00000 0.00000 0.00000 MINI CONSTR> 262.51320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 301.78700 0.00058 0.01767 0.00260 MINI INTERN> 14.41232 85.61065 0.00000 42.84619 11.32810 MINI EXTERN> 0.47993 -115.35643 0.00000 0.00000 0.00000 MINI CONSTR> 262.46625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 301.78648 0.00052 0.01157 0.00202 MINI INTERN> 14.40485 85.61239 0.00000 42.88561 11.32811 MINI EXTERN> 0.46202 -115.37138 0.00000 0.00000 0.00000 MINI CONSTR> 262.46489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 38 301.78630 0.00018 0.00995 0.02000 CONJ INTERN> 14.40877 85.59469 0.00000 42.90077 11.32855 CONJ EXTERN> 0.46131 -115.38280 0.00000 0.00000 0.00000 CONJ CONSTR> 262.47502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "5400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 4.1424 ( PROT LYS 1 HT2 ) 4.1424 ( PROT LYS 1 N ) 5.1780 ( PROT LYS 1 HT3 ) 4.1424 ( PROT LYS 1 CA ) 5.1780 ( PROT LYS 1 CB ) 4.1424 ( PROT LYS 1 CG ) 4.1424 ( PROT LYS 1 CD ) 4.1424 ( PROT LYS 1 CE ) 4.1424 ( PROT LYS 1 NZ ) 4.1424 ( PROT LYS 1 HZ1 ) 4.1424 ( PROT LYS 1 HZ2 ) 4.1424 ( PROT LYS 1 HZ3 ) 4.1424 ( PROT LYS 1 C ) 5.1780 ( PROT LYS 1 O ) 5.1780 ( PROT MET 2 N ) 5.1780 ( PROT MET 2 H ) 4.1424 ( PROT MET 2 CA ) 5.1780 ( PROT MET 2 CB ) 4.1424 ( PROT MET 2 CG ) 4.1424 ( PROT MET 2 SD ) 4.1424 ( PROT MET 2 CE ) 4.1424 ( PROT MET 2 C ) 5.1780 ( PROT MET 2 O ) 5.1780 ( PROT LYS 3 N ) 5.1780 ( PROT LYS 3 H ) 4.1424 ( PROT LYS 3 CA ) 5.1780 ( PROT LYS 3 CB ) 4.1424 ( PROT LYS 3 CG ) 4.1424 ( PROT LYS 3 CD ) 4.1424 ( PROT LYS 3 CE ) 4.1424 ( PROT LYS 3 NZ ) 4.1424 ( PROT LYS 3 HZ1 ) 4.1424 ( PROT LYS 3 HZ2 ) 4.1424 ( PROT LYS 3 HZ3 ) 4.1424 ( PROT LYS 3 C ) 5.1780 ( PROT LYS 3 O ) 5.1780 ( PROT ALA 4 N ) 5.1780 ( PROT ALA 4 H ) 4.1424 ( PROT ALA 4 CA ) 5.1780 ( PROT ALA 4 CB ) 4.1424 ( PROT ALA 4 C ) 5.1780 ( PROT ALA 4 O ) 5.1780 ( PROT VAL 5 N ) 5.1780 ( PROT VAL 5 H ) 4.1424 ( PROT VAL 5 CA ) 5.1780 ( PROT VAL 5 CB ) 4.1424 ( PROT VAL 5 CG1 ) 4.1424 ( PROT VAL 5 CG2 ) 4.1424 ( PROT VAL 5 C ) 5.1780 ( PROT VAL 5 O ) 5.1780 ( PROT MET 6 N ) 5.1780 ( PROT MET 6 H ) 4.1424 ( PROT MET 6 CA ) 5.1780 ( PROT MET 6 CB ) 4.1424 ( PROT MET 6 CG ) 4.1424 ( PROT MET 6 SD ) 4.1424 ( PROT MET 6 CE ) 4.1424 ( PROT MET 6 C ) 5.1780 ( PROT MET 6 O ) 5.1780 ( PROT ILE 7 N ) 5.1780 ( PROT ILE 7 H ) 4.1424 ( PROT ILE 7 CA ) 5.1780 ( PROT ILE 7 CB ) 4.1424 ( PROT ILE 7 CG2 ) 4.1424 ( PROT ILE 7 CG1 ) 4.1424 ( PROT ILE 7 CD ) 4.1424 ( PROT ILE 7 C ) 5.1780 ( PROT ILE 7 O ) 5.1780 ( PROT GLY 8 N ) 5.1780 ( PROT GLY 8 H ) 4.1424 ( PROT GLY 8 CA ) 5.1780 ( PROT GLY 8 C ) 5.1780 ( PROT GLY 8 O ) 5.1780 ( PROT ALA 9 N ) 5.1780 ( PROT ALA 9 H ) 4.1424 ( PROT ALA 9 CA ) 5.1780 ( PROT ALA 9 CB ) 4.1424 ( PROT ALA 9 C ) 5.1780 ( PROT ALA 9 O ) 5.1780 ( PROT CYS 10 N ) 5.1780 ( PROT CYS 10 H ) 4.1424 ( PROT CYS 10 CA ) 5.1780 ( PROT CYS 10 CB ) 4.1424 ( PROT CYS 10 SG ) 4.1424 ( PROT CYS 10 C ) 5.1780 ( PROT CYS 10 O ) 5.1780 ( PROT PHE 11 N ) 5.1780 ( PROT PHE 11 H ) 4.1424 ( PROT PHE 11 CA ) 5.1780 ( PROT PHE 11 CB ) 4.1424 ( PROT PHE 11 CG ) 4.1424 ( PROT PHE 11 CD1 ) 4.1424 ( PROT PHE 11 CD2 ) 4.1424 ( PROT PHE 11 CE1 ) 4.1424 ( PROT PHE 11 CE2 ) 4.1424 ( PROT PHE 11 CZ ) 4.1424 ( PROT PHE 11 C ) 5.1780 ( PROT PHE 11 O ) 5.1780 ( PROT LEU 12 N ) 5.1780 ( PROT LEU 12 H ) 4.1424 ( PROT LEU 12 CA ) 5.1780 ( PROT LEU 12 CB ) 4.1424 ( PROT LEU 12 CG ) 4.1424 ( PROT LEU 12 CD1 ) 4.1424 ( PROT LEU 12 CD2 ) 4.1424 ( PROT LEU 12 C ) 5.1780 ( PROT LEU 12 O ) 5.1780 ( PROT ILE 13 N ) 5.1780 ( PROT ILE 13 H ) 4.1424 ( PROT ILE 13 CA ) 5.1780 ( PROT ILE 13 CB ) 4.1424 ( PROT ILE 13 CG2 ) 4.1424 ( PROT ILE 13 CG1 ) 4.1424 ( PROT ILE 13 CD ) 4.1424 ( PROT ILE 13 C ) 5.1780 ( PROT ILE 13 O ) 5.1780 ( PROT ASH 14 N ) 5.1780 ( PROT ASH 14 H ) 4.1424 ( PROT ASH 14 CA ) 5.1780 ( PROT ASH 14 CB ) 4.1424 ( PROT ASH 14 CG ) 4.1424 ( PROT ASH 14 OD1 ) 4.1424 ( PROT ASH 14 OD2 ) 4.1424 ( PROT ASH 14 HD2 ) 4.1424 ( PROT ASH 14 C ) 5.1780 ( PROT ASH 14 O ) 5.1780 ( PROT PHE 15 N ) 5.1780 ( PROT PHE 15 H ) 4.1424 ( PROT PHE 15 CA ) 5.1780 ( PROT PHE 15 CB ) 4.1424 ( PROT PHE 15 CG ) 4.1424 ( PROT PHE 15 CD1 ) 4.1424 ( PROT PHE 15 CD2 ) 4.1424 ( PROT PHE 15 CE1 ) 4.1424 ( PROT PHE 15 CE2 ) 4.1424 ( PROT PHE 15 CZ ) 4.1424 ( PROT PHE 15 C ) 5.1780 ( PROT PHE 15 O ) 5.1780 ( PROT MET 16 N ) 5.1780 ( PROT MET 16 H ) 4.1424 ( PROT MET 16 CA ) 5.1780 ( PROT MET 16 CB ) 4.1424 ( PROT MET 16 CG ) 4.1424 ( PROT MET 16 SD ) 4.1424 ( PROT MET 16 CE ) 4.1424 ( PROT MET 16 C ) 5.1780 ( PROT MET 16 O ) 5.1780 ( PROT PHE 17 N ) 5.1780 ( PROT PHE 17 H ) 4.1424 ( PROT PHE 17 CA ) 5.1780 ( PROT PHE 17 CB ) 4.1424 ( PROT PHE 17 CG ) 4.1424 ( PROT PHE 17 CD1 ) 4.1424 ( PROT PHE 17 CD2 ) 4.1424 ( PROT PHE 17 CE1 ) 4.1424 ( PROT PHE 17 CE2 ) 4.1424 ( PROT PHE 17 CZ ) 4.1424 ( PROT PHE 17 C ) 5.1780 ( PROT PHE 17 O ) 5.1780 ( PROT PHE 18 N ) 5.1780 ( PROT PHE 18 H ) 4.1424 ( PROT PHE 18 CA ) 5.1780 ( PROT PHE 18 CB ) 4.1424 ( PROT PHE 18 CG ) 4.1424 ( PROT PHE 18 CD1 ) 4.1424 ( PROT PHE 18 CD2 ) 4.1424 ( PROT PHE 18 CE1 ) 4.1424 ( PROT PHE 18 CE2 ) 4.1424 ( PROT PHE 18 CZ ) 4.1424 ( PROT PHE 18 C ) 5.1780 ( PROT PHE 18 O ) 5.1780 ( PROT GLU 19 N ) 5.1780 ( PROT GLU 19 H ) 4.1424 ( PROT GLU 19 CA ) 5.1780 ( PROT GLU 19 CB ) 4.1424 ( PROT GLU 19 CG ) 4.1424 ( PROT GLU 19 CD ) 4.1424 ( PROT GLU 19 OE1 ) 4.1424 ( PROT GLU 19 OE2 ) 4.1424 ( PROT GLU 19 C ) 5.1780 ( PROT GLU 19 O ) 5.1780 ( PROT SER 20 N ) 5.1780 ( PROT SER 20 H ) 4.1424 ( PROT SER 20 CA ) 5.1780 ( PROT SER 20 CB ) 4.1424 ( PROT SER 20 OG ) 4.1424 ( PROT SER 20 HG ) 4.1424 ( PROT SER 20 C ) 5.1780 ( PROT SER 20 O ) 5.1780 ( PROT THR 21 N ) 5.1780 ( PROT THR 21 H ) 4.1424 ( PROT THR 21 CA ) 5.1780 ( PROT THR 21 CB ) 4.1424 ( PROT THR 21 OG1 ) 4.1424 ( PROT THR 21 HG1 ) 4.1424 ( PROT THR 21 CG2 ) 4.1424 ( PROT THR 21 C ) 5.1780 ( PROT THR 21 O ) 5.1780 ( PROT GLY 22 N ) 5.1780 ( PROT GLY 22 H ) 4.1424 ( PROT GLY 22 CA ) 5.1780 ( PROT GLY 22 C ) 5.1780 ( PROT GLY 22 O ) 5.1780 ( PROT SER 23 N ) 5.1780 ( PROT SER 23 H ) 4.1424 ( PROT SER 23 CA ) 5.1780 ( PROT SER 23 CB ) 4.1424 ( PROT SER 23 OG ) 4.1424 ( PROT SER 23 HG ) 4.1424 ( PROT SER 23 C ) 5.1780 ( PROT SER 23 O ) 5.1780 ( PROT GLN 24 N ) 5.1780 ( PROT GLN 24 H ) 4.1424 ( PROT GLN 24 CA ) 5.1780 ( PROT GLN 24 CB ) 4.1424 ( PROT GLN 24 CG ) 4.1424 ( PROT GLN 24 CD ) 4.1424 ( PROT GLN 24 OE1 ) 4.1424 ( PROT GLN 24 NE2 ) 4.1424 ( PROT GLN 24 HE21 ) 4.1424 ( PROT GLN 24 HE22 ) 4.1424 ( PROT GLN 24 C ) 5.1780 ( PROT GLN 24 O ) 5.1780 ( PROT GLU 25 N ) 5.1780 ( PROT GLU 25 H ) 4.1424 ( PROT GLU 25 CA ) 5.1780 ( PROT GLU 25 CB ) 4.1424 ( PROT GLU 25 CG ) 4.1424 ( PROT GLU 25 CD ) 4.1424 ( PROT GLU 25 OE1 ) 4.1424 ( PROT GLU 25 OE2 ) 4.1424 ( PROT GLU 25 C ) 5.1780 ( PROT GLU 25 O ) 5.1780 ( PROT GLN 26 N ) 5.1780 ( PROT GLN 26 H ) 4.1424 ( PROT GLN 26 CA ) 5.1780 ( PROT GLN 26 CB ) 4.1424 ( PROT GLN 26 CG ) 4.1424 ( PROT GLN 26 CD ) 4.1424 ( PROT GLN 26 OE1 ) 4.1424 ( PROT GLN 26 NE2 ) 4.1424 ( PROT GLN 26 HE21 ) 4.1424 ( PROT GLN 26 HE22 ) 4.1424 ( PROT GLN 26 C ) 5.1780 ( PROT GLN 26 O ) 5.1780 ( PROT LYS 27 N ) 5.1780 ( PROT LYS 27 H ) 4.1424 ( PROT LYS 27 CA ) 5.1780 ( PROT LYS 27 CB ) 4.1424 ( PROT LYS 27 CG ) 4.1424 ( PROT LYS 27 CD ) 4.1424 ( PROT LYS 27 CE ) 4.1424 ( PROT LYS 27 NZ ) 4.1424 ( PROT LYS 27 HZ1 ) 4.1424 ( PROT LYS 27 HZ2 ) 4.1424 ( PROT LYS 27 HZ3 ) 4.1424 ( PROT LYS 27 C ) 5.1780 ( PROT LYS 27 O ) 5.1780 ( PROT SER 28 N ) 5.1780 ( PROT SER 28 H ) 4.1424 ( PROT SER 28 CA ) 5.1780 ( PROT SER 28 CB ) 4.1424 ( PROT SER 28 OG ) 4.1424 ( PROT SER 28 HG ) 4.1424 ( PROT SER 28 C ) 5.1780 ( PROT SER 28 O ) 5.1780 ( PROT GLY 29 N ) 5.1780 ( PROT GLY 29 H ) 4.1424 ( PROT GLY 29 CA ) 5.1780 ( PROT GLY 29 C ) 5.1780 ( PROT GLY 29 O ) 5.1780 ( PROT VAL 30 N ) 5.1780 ( PROT VAL 30 H ) 4.1424 ( PROT VAL 30 CA ) 5.1780 ( PROT VAL 30 CB ) 4.1424 ( PROT VAL 30 CG1 ) 4.1424 ( PROT VAL 30 CG2 ) 4.1424 ( PROT VAL 30 C ) 5.1780 ( PROT VAL 30 O ) 5.1780 ( PROT TRP 31 N ) 5.1780 ( PROT TRP 31 H ) 4.1424 ( PROT TRP 31 CA ) 5.1780 ( PROT TRP 31 CB ) 4.1424 ( PROT TRP 31 CG ) 4.1424 ( PROT TRP 31 CD2 ) 4.1424 ( PROT TRP 31 CE2 ) 4.1424 ( PROT TRP 31 CE3 ) 4.1424 ( PROT TRP 31 CD1 ) 4.1424 ( PROT TRP 31 NE1 ) 4.1424 ( PROT TRP 31 HE1 ) 4.1424 ( PROT TRP 31 CZ2 ) 4.1424 ( PROT TRP 31 CZ3 ) 4.1424 ( PROT TRP 31 CH2 ) 4.1424 ( PROT TRP 31 C ) 5.1780 ( PROT TRP 31 OT1 ) 4.1424 ( PROT TRP 31 OT2 ) 4.1424 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63065 7.22865 -13.22041 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00015 0.00078 0.00049 ROTATION MATRIX 1.000000 -0.000125 -0.000374 0.000125 1.000000 0.000334 0.000374 -0.000334 1.000000 AXIS OF ROTATION IS 0.646724 0.723354 -0.241882 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 37.5225 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.355441 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3554" Parameter: A <- "0.3554" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.51799 7.24899 -13.40880 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01024 0.00656 -0.03155 ROTATION MATRIX 0.999714 0.016621 0.017188 -0.016304 0.999698 -0.018409 -0.017488 0.018124 0.999683 AXIS OF ROTATION IS -0.607108 -0.576242 0.547143 ANGLE IS 1.72 CENTER OF ROTATION 14.008004 6.801906-13.360852 SHIFT IS -0.027260 TOTAL SQUARE DIFF IS 0.8674 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.167279 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3554" RDCMND substituted energy or value "?RMS" to " 0.1673" Parameter: A <- "0.3554 0.1673" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *5400 0.3554 0.1673 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 262.48" Parameter: H <- "262.48" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 39.31128 262.47502 2.88854 ENER INTERN> 14.40877 85.59469 0.00000 42.90077 11.32855 ENER EXTERN> 0.46131 -115.38280 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 39.31" Parameter: B <- "39.31" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -115.38" Parameter: C <- "-115.38" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 0.46" Parameter: C <- " -114.92" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -114.92" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 14.41" Parameter: D <- "14.41" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 85.59" Parameter: D <- " 100.00" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 42.90" Parameter: D <- " 142.90" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 11.33" Parameter: D <- " 154.23" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 154.23" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 5400 ENER= 39.31 GRMS= 2.89 ELEC= -115.38 VDW= 0.46 RDTITL> *EXTERNAL= -114.92 INTERNAL= 154.23 USER= 0.00 HARM= 262.48 RDTITL> *BOND= 14.41 ANGL= 85.59 DIHE= 42.90 IMPR= 11.33 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21197 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21198 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 229.12455 -189.81327 1.17928 0.02000 MINI INTERN> 14.40877 85.59469 0.00000 42.90077 11.32855 MINI EXTERN> 0.46131 -115.38280 0.00000 0.00000 0.00000 MINI CONSTR> 189.81327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 219.82151 9.30304 1.40646 0.00360 MINI INTERN> 13.58049 81.94508 0.00000 45.59122 11.37009 MINI EXTERN> -21.57705 -112.49369 0.00000 0.00000 0.00000 MINI CONSTR> 201.40538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21190 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 217.46505 2.35646 1.69408 0.00156 MINI INTERN> 13.41243 83.54221 0.00000 45.98383 11.17041 MINI EXTERN> -27.78319 -111.70848 0.00000 0.00000 0.00000 MINI CONSTR> 202.84784 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 215.80562 1.65943 0.62326 0.00067 MINI INTERN> 12.78813 83.18195 0.00000 46.16253 11.17599 MINI EXTERN> -29.26146 -111.48532 0.00000 0.00000 0.00000 MINI CONSTR> 203.24380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21187 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 214.78403 1.02159 1.16487 0.00070 MINI INTERN> 12.66188 82.87719 0.00000 46.23626 11.09357 MINI EXTERN> -30.21710 -111.39830 0.00000 0.00000 0.00000 MINI CONSTR> 203.53052 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 213.82341 0.96061 0.78002 0.00072 MINI INTERN> 12.54503 82.52176 0.00000 46.28573 11.03328 MINI EXTERN> -30.88295 -111.35960 0.00000 0.00000 0.00000 MINI CONSTR> 203.68016 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21184 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 213.13630 0.68711 1.32452 0.00075 MINI INTERN> 12.49414 82.33505 0.00000 46.31077 10.98248 MINI EXTERN> -31.48980 -111.30073 0.00000 0.00000 0.00000 MINI CONSTR> 203.80438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 212.36594 0.77036 1.42616 0.00078 MINI INTERN> 12.41160 82.11152 0.00000 46.32271 10.93180 MINI EXTERN> -32.03504 -111.26293 0.00000 0.00000 0.00000 MINI CONSTR> 203.88628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21183 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 211.70209 0.66385 1.58488 0.00080 MINI INTERN> 12.35816 81.92001 0.00000 46.32207 10.88569 MINI EXTERN> -32.49011 -111.22818 0.00000 0.00000 0.00000 MINI CONSTR> 203.93445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 211.08599 0.61610 1.48691 0.00083 MINI INTERN> 12.33707 81.67776 0.00000 46.31750 10.84485 MINI EXTERN> -32.85644 -111.18541 0.00000 0.00000 0.00000 MINI CONSTR> 203.95065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21181 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 210.21556 0.87044 0.43812 0.00036 MINI INTERN> 12.41699 81.19399 0.00000 46.30995 10.79543 MINI EXTERN> -33.28802 -111.15236 0.00000 0.00000 0.00000 MINI CONSTR> 203.93958 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 209.94296 0.27259 1.61082 0.00090 MINI INTERN> 12.23820 81.34588 0.00000 46.27517 10.76956 MINI EXTERN> -33.50399 -111.13892 0.00000 0.00000 0.00000 MINI CONSTR> 203.95707 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21179 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 209.43419 0.50878 1.69150 0.00093 MINI INTERN> 12.18659 81.21254 0.00000 46.24483 10.73589 MINI EXTERN> -33.76971 -111.12212 0.00000 0.00000 0.00000 MINI CONSTR> 203.94616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 208.60587 0.82832 0.56250 0.00040 MINI INTERN> 12.44603 80.57635 0.00000 46.22759 10.68646 MINI EXTERN> -34.17457 -111.05515 0.00000 0.00000 0.00000 MINI CONSTR> 203.89915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21177 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 208.20320 0.40267 0.37572 0.00042 MINI INTERN> 12.29424 80.53387 0.00000 46.19567 10.66574 MINI EXTERN> -34.32248 -111.05012 0.00000 0.00000 0.00000 MINI CONSTR> 203.88628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 207.74207 0.46113 0.37469 0.00043 MINI INTERN> 12.28700 80.36755 0.00000 46.15667 10.63520 MINI EXTERN> -34.54237 -111.02312 0.00000 0.00000 0.00000 MINI CONSTR> 203.86113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21177 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 207.34889 0.39318 0.78854 0.00045 MINI INTERN> 12.54492 80.04811 0.00000 46.11843 10.59763 MINI EXTERN> -34.82005 -110.96428 0.00000 0.00000 0.00000 MINI CONSTR> 203.82414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 206.93995 0.40894 0.46708 0.00046 MINI INTERN> 12.34817 80.02412 0.00000 46.07610 10.57917 MINI EXTERN> -34.93225 -110.96347 0.00000 0.00000 0.00000 MINI CONSTR> 203.80811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 206.63519 0.30476 0.85918 0.00048 MINI INTERN> 12.61277 79.73017 0.00000 46.03796 10.54682 MINI EXTERN> -35.16669 -110.90061 0.00000 0.00000 0.00000 MINI CONSTR> 203.77478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 206.31245 0.32274 0.90746 0.00050 MINI INTERN> 12.66782 79.56645 0.00000 45.99689 10.52244 MINI EXTERN> -35.32895 -110.86357 0.00000 0.00000 0.00000 MINI CONSTR> 203.75137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 206.02315 0.28930 0.98552 0.00052 MINI INTERN> 12.74152 79.40415 0.00000 45.95602 10.49935 MINI EXTERN> -35.48135 -110.82638 0.00000 0.00000 0.00000 MINI CONSTR> 203.72984 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 205.75466 0.26849 0.93126 0.00054 MINI INTERN> 12.66290 79.36189 0.00000 45.91574 10.48518 MINI EXTERN> -35.56033 -110.82828 0.00000 0.00000 0.00000 MINI CONSTR> 203.71756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 205.47637 0.27830 0.93950 0.00056 MINI INTERN> 12.72780 79.19762 0.00000 45.87393 10.46336 MINI EXTERN> -35.70317 -110.78347 0.00000 0.00000 0.00000 MINI CONSTR> 203.70029 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 205.13085 0.34552 0.29559 0.00024 MINI INTERN> 11.99262 79.61886 0.00000 45.81337 10.47200 MINI EXTERN> -35.56298 -110.91918 0.00000 0.00000 0.00000 MINI CONSTR> 203.71616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 205.03078 0.10007 1.02826 0.00060 MINI INTERN> 12.82424 78.95366 0.00000 45.79509 10.42852 MINI EXTERN> -35.92169 -110.72593 0.00000 0.00000 0.00000 MINI CONSTR> 203.67690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 204.81201 0.21876 1.07348 0.00062 MINI INTERN> 12.95168 78.75899 0.00000 45.75623 10.40706 MINI EXTERN> -36.06650 -110.66098 0.00000 0.00000 0.00000 MINI CONSTR> 203.66554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 204.46028 0.35173 0.35642 0.00027 MINI INTERN> 11.85446 79.47697 0.00000 45.68037 10.43225 MINI EXTERN> -35.77070 -110.91419 0.00000 0.00000 0.00000 MINI CONSTR> 203.70112 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 204.28946 0.17083 0.23903 0.00028 MINI INTERN> 11.99520 79.28431 0.00000 45.65234 10.41487 MINI EXTERN> -35.89342 -110.85703 0.00000 0.00000 0.00000 MINI CONSTR> 203.69318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 204.09398 0.19548 0.23792 0.00029 MINI INTERN> 11.96942 79.22730 0.00000 45.60846 10.40250 MINI EXTERN> -35.95840 -110.84975 0.00000 0.00000 0.00000 MINI CONSTR> 203.69445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 203.92680 0.16718 0.50011 0.00030 MINI INTERN> 11.68623 79.41429 0.00000 45.55152 10.40230 MINI EXTERN> -35.90564 -110.93186 0.00000 0.00000 0.00000 MINI CONSTR> 203.70995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 203.75295 0.17385 0.29385 0.00031 MINI INTERN> 11.85754 79.18478 0.00000 45.52200 10.38358 MINI EXTERN> -36.04256 -110.85916 0.00000 0.00000 0.00000 MINI CONSTR> 203.70676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 203.62356 0.12939 0.54955 0.00032 MINI INTERN> 11.62651 79.34357 0.00000 45.47081 10.38378 MINI EXTERN> -35.99576 -110.93003 0.00000 0.00000 0.00000 MINI CONSTR> 203.72469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 203.48771 0.13585 0.58290 0.00033 MINI INTERN> 11.59122 79.31836 0.00000 45.43137 10.37559 MINI EXTERN> -36.03266 -110.93146 0.00000 0.00000 0.00000 MINI CONSTR> 203.73529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 203.36665 0.12106 0.63511 0.00034 MINI INTERN> 11.54422 79.31033 0.00000 45.39272 10.36875 MINI EXTERN> -36.05917 -110.93833 0.00000 0.00000 0.00000 MINI CONSTR> 203.74813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21176 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 203.25453 0.11212 0.59735 0.00036 MINI INTERN> 11.56612 79.23926 0.00000 45.36301 10.35990 MINI EXTERN> -36.11179 -110.91936 0.00000 0.00000 0.00000 MINI CONSTR> 203.75738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 203.13730 0.11723 0.60607 0.00037 MINI INTERN> 11.55042 79.20179 0.00000 45.32590 10.35223 MINI EXTERN> -36.14996 -110.91521 0.00000 0.00000 0.00000 MINI CONSTR> 203.77213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21174 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 202.99148 0.14582 0.19102 0.00016 MINI INTERN> 12.07354 78.66438 0.00000 45.31707 10.31975 MINI EXTERN> -36.42757 -110.71852 0.00000 0.00000 0.00000 MINI CONSTR> 203.76282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 202.95372 0.03776 0.66360 0.00040 MINI INTERN> 11.49732 79.16857 0.00000 45.26038 10.34086 MINI EXTERN> -36.19903 -110.91785 0.00000 0.00000 0.00000 MINI CONSTR> 203.80346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 202.79982 0.15390 0.19353 0.00017 MINI INTERN> 12.08430 78.56634 0.00000 45.25266 10.30509 MINI EXTERN> -36.50747 -110.69612 0.00000 0.00000 0.00000 MINI CONSTR> 203.79502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 202.72378 0.07605 0.15861 0.00018 MINI INTERN> 12.02505 78.58099 0.00000 45.22370 10.30213 MINI EXTERN> -36.51251 -110.70807 0.00000 0.00000 0.00000 MINI CONSTR> 203.81248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 202.64204 0.08174 0.15702 0.00019 MINI INTERN> 12.02926 78.53787 0.00000 45.19349 10.29575 MINI EXTERN> -36.54695 -110.69825 0.00000 0.00000 0.00000 MINI CONSTR> 203.83086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 202.56956 0.07248 0.31647 0.00019 MINI INTERN> 12.22446 78.33690 0.00000 45.16873 10.28092 MINI EXTERN> -36.65946 -110.62657 0.00000 0.00000 0.00000 MINI CONSTR> 203.84460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 202.49572 0.07385 0.19016 0.00020 MINI INTERN> 12.08646 78.41618 0.00000 45.13727 10.28186 MINI EXTERN> -36.63045 -110.66366 0.00000 0.00000 0.00000 MINI CONSTR> 203.86805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 202.42841 0.06731 0.22207 0.00021 MINI INTERN> 12.12414 78.34978 0.00000 45.10966 10.27483 MINI EXTERN> -36.67431 -110.64376 0.00000 0.00000 0.00000 MINI CONSTR> 203.88807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21174 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 202.38104 0.04737 0.35029 0.00021 MINI INTERN> 12.25631 78.21433 0.00000 45.08930 10.26469 MINI EXTERN> -36.75087 -110.59554 0.00000 0.00000 0.00000 MINI CONSTR> 203.90282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 202.32450 0.05654 0.38334 0.00022 MINI INTERN> 12.28680 78.15848 0.00000 45.06334 10.25858 MINI EXTERN> -36.78793 -110.57870 0.00000 0.00000 0.00000 MINI CONSTR> 203.92392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21174 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 202.27412 0.05037 0.37339 0.00023 MINI INTERN> 12.27596 78.14020 0.00000 45.03971 10.25507 MINI EXTERN> -36.80465 -110.57628 0.00000 0.00000 0.00000 MINI CONSTR> 203.94412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 202.22546 0.04867 0.38240 0.00024 MINI INTERN> 12.28300 78.10735 0.00000 45.01571 10.25075 MINI EXTERN> -36.82873 -110.56803 0.00000 0.00000 0.00000 MINI CONSTR> 203.96541 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21174 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 202.16480 0.06066 0.12363 0.00010 MINI INTERN> 11.90811 78.39365 0.00000 44.97960 10.26386 MINI EXTERN> -36.69285 -110.68701 0.00000 0.00000 0.00000 MINI CONSTR> 203.99945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 202.14681 0.01800 0.42645 0.00026 MINI INTERN> 12.32527 78.02751 0.00000 44.97393 10.24214 MINI EXTERN> -36.88155 -110.54493 0.00000 0.00000 0.00000 MINI CONSTR> 204.00444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21174 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 202.10751 0.03930 0.44857 0.00027 MINI INTERN> 12.34306 77.98911 0.00000 44.95183 10.23785 MINI EXTERN> -36.90709 -110.53363 0.00000 0.00000 0.00000 MINI CONSTR> 204.02639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 202.04451 0.06299 0.15218 0.00011 MINI INTERN> 11.85805 78.36728 0.00000 44.91119 10.25614 MINI EXTERN> -36.72458 -110.69029 0.00000 0.00000 0.00000 MINI CONSTR> 204.06673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21174 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 202.01428 0.03024 0.09973 0.00012 MINI INTERN> 11.92658 78.28824 0.00000 44.89770 10.25045 MINI EXTERN> -36.76789 -110.66193 0.00000 0.00000 0.00000 MINI CONSTR> 204.08112 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 201.97946 0.03482 0.10001 0.00012 MINI INTERN> 11.91734 78.27453 0.00000 44.87623 10.24790 MINI EXTERN> -36.77996 -110.66074 0.00000 0.00000 0.00000 MINI CONSTR> 204.10416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21173 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 201.95028 0.02918 0.21359 0.00013 MINI INTERN> 11.79713 78.36238 0.00000 44.84912 10.25075 MINI EXTERN> -36.74185 -110.70056 0.00000 0.00000 0.00000 MINI CONSTR> 204.13332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 201.91921 0.03107 0.12459 0.00013 MINI INTERN> 11.87682 78.27121 0.00000 44.83530 10.24452 MINI EXTERN> -36.79080 -110.66749 0.00000 0.00000 0.00000 MINI CONSTR> 204.14964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21172 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 201.89652 0.02268 0.23090 0.00014 MINI INTERN> 11.78567 78.33740 0.00000 44.81184 10.24655 MINI EXTERN> -36.76265 -110.69822 0.00000 0.00000 0.00000 MINI CONSTR> 204.17595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 201.87228 0.02424 0.24691 0.00014 MINI INTERN> 11.77719 78.32862 0.00000 44.79346 10.24475 MINI EXTERN> -36.77088 -110.69851 0.00000 0.00000 0.00000 MINI CONSTR> 204.19766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21172 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 201.85076 0.02152 0.26942 0.00015 MINI INTERN> 11.76338 78.32603 0.00000 44.77576 10.24338 MINI EXTERN> -36.77572 -110.70105 0.00000 0.00000 0.00000 MINI CONSTR> 204.21899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 201.83070 0.02006 0.25331 0.00015 MINI INTERN> 11.76963 78.30546 0.00000 44.76208 10.24132 MINI EXTERN> -36.78854 -110.69547 0.00000 0.00000 0.00000 MINI CONSTR> 204.23622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21172 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 201.80959 0.02111 0.25522 0.00016 MINI INTERN> 11.77704 78.28389 0.00000 44.74556 10.23906 MINI EXTERN> -36.80253 -110.69047 0.00000 0.00000 0.00000 MINI CONSTR> 204.25703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 201.78350 0.02609 0.08068 0.00007 MINI INTERN> 11.96407 78.09680 0.00000 44.74091 10.22822 MINI EXTERN> -36.89692 -110.61631 0.00000 0.00000 0.00000 MINI CONSTR> 204.26672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21172 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 201.77675 0.00675 0.28031 0.00017 MINI INTERN> 11.76104 78.27307 0.00000 44.71614 10.23670 MINI EXTERN> -36.81315 -110.69205 0.00000 0.00000 0.00000 MINI CONSTR> 204.29500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 201.74900 0.02775 0.08190 0.00007 MINI INTERN> 11.96372 78.06944 0.00000 44.71176 10.22501 MINI EXTERN> -36.91546 -110.61098 0.00000 0.00000 0.00000 MINI CONSTR> 204.30551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21172 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 201.73522 0.01378 0.06688 0.00008 MINI INTERN> 11.94805 78.07218 0.00000 44.69891 10.22448 MINI EXTERN> -36.91615 -110.61480 0.00000 0.00000 0.00000 MINI CONSTR> 204.32254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 201.72035 0.01486 0.06601 0.00008 MINI INTERN> 11.94792 78.05961 0.00000 44.68527 10.22308 MINI EXTERN> -36.92448 -110.61246 0.00000 0.00000 0.00000 MINI CONSTR> 204.34141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21172 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 201.70695 0.01341 0.13059 0.00008 MINI INTERN> 11.98653 78.01247 0.00000 44.67304 10.21984 MINI EXTERN> -36.94972 -110.59530 0.00000 0.00000 0.00000 MINI CONSTR> 204.36008 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 201.69360 0.01335 0.08037 0.00009 MINI INTERN> 11.95560 78.02858 0.00000 44.65965 10.22014 MINI EXTERN> -36.94356 -110.60493 0.00000 0.00000 0.00000 MINI CONSTR> 204.37813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21172 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 201.68128 0.01232 0.09139 0.00009 MINI INTERN> 11.95629 78.01618 0.00000 44.64697 10.21890 MINI EXTERN> -36.95139 -110.60238 0.00000 0.00000 0.00000 MINI CONSTR> 204.39671 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 201.67242 0.00886 0.14589 0.00009 MINI INTERN> 11.97492 77.99002 0.00000 44.63691 10.21704 MINI EXTERN> -36.96565 -110.59335 0.00000 0.00000 0.00000 MINI CONSTR> 204.41254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 201.66202 0.01041 0.15752 0.00010 MINI INTERN> 11.96578 77.98731 0.00000 44.62476 10.21645 MINI EXTERN> -36.96836 -110.59464 0.00000 0.00000 0.00000 MINI CONSTR> 204.43072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 201.65300 0.00901 0.17561 0.00010 MINI INTERN> 11.96247 77.98050 0.00000 44.61359 10.21570 MINI EXTERN> -36.97298 -110.59409 0.00000 0.00000 0.00000 MINI CONSTR> 204.44782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 201.64459 0.00841 0.16472 0.00010 MINI INTERN> 11.96144 77.97304 0.00000 44.60416 10.21497 MINI EXTERN> -36.97783 -110.59321 0.00000 0.00000 0.00000 MINI CONSTR> 204.46201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 201.63271 0.01188 0.04867 0.00004 MINI INTERN> 11.93421 77.98877 0.00000 44.59114 10.21539 MINI EXTERN> -36.97204 -110.60397 0.00000 0.00000 0.00000 MINI CONSTR> 204.47922 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 201.62884 0.00387 0.17853 0.00011 MINI INTERN> 11.94908 77.96621 0.00000 44.58364 10.21404 MINI EXTERN> -36.98329 -110.59486 0.00000 0.00000 0.00000 MINI CONSTR> 204.49403 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 201.62178 0.00705 0.18679 0.00011 MINI INTERN> 11.94477 77.96165 0.00000 44.57386 10.21357 MINI EXTERN> -36.98649 -110.59520 0.00000 0.00000 0.00000 MINI CONSTR> 204.50961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 201.61040 0.01139 0.06166 0.00005 MINI INTERN> 11.93437 77.96400 0.00000 44.56154 10.21327 MINI EXTERN> -36.98753 -110.60082 0.00000 0.00000 0.00000 MINI CONSTR> 204.52558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 201.60480 0.00560 0.04215 0.00005 MINI INTERN> 11.93422 77.95673 0.00000 44.55469 10.21278 MINI EXTERN> -36.99153 -110.59931 0.00000 0.00000 0.00000 MINI CONSTR> 204.53723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 201.59839 0.00641 0.04171 0.00005 MINI INTERN> 11.93427 77.94881 0.00000 44.54551 10.21220 MINI EXTERN> -36.99628 -110.59830 0.00000 0.00000 0.00000 MINI CONSTR> 204.55217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 201.59280 0.00559 0.08708 0.00005 MINI INTERN> 11.93659 77.94070 0.00000 44.53508 10.21154 MINI EXTERN> -37.00163 -110.59781 0.00000 0.00000 0.00000 MINI CONSTR> 204.56832 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 201.58714 0.00566 0.05182 0.00006 MINI INTERN> 11.93504 77.93394 0.00000 44.52812 10.21116 MINI EXTERN> -37.00522 -110.59661 0.00000 0.00000 0.00000 MINI CONSTR> 204.58071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 201.58205 0.00508 0.06259 0.00006 MINI INTERN> 11.93569 77.92665 0.00000 44.51960 10.21069 MINI EXTERN> -37.00958 -110.59584 0.00000 0.00000 0.00000 MINI CONSTR> 204.59485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 201.57848 0.00357 0.09543 0.00006 MINI INTERN> 11.93763 77.92028 0.00000 44.51200 10.21026 MINI EXTERN> -37.01352 -110.59533 0.00000 0.00000 0.00000 MINI CONSTR> 204.60716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 201.57417 0.00431 0.10516 0.00006 MINI INTERN> 11.93835 77.91341 0.00000 44.50408 10.20986 MINI EXTERN> -37.01755 -110.59457 0.00000 0.00000 0.00000 MINI CONSTR> 204.62059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 201.57033 0.00384 0.10224 0.00007 MINI INTERN> 11.93819 77.90776 0.00000 44.49760 10.20959 MINI EXTERN> -37.02072 -110.59402 0.00000 0.00000 0.00000 MINI CONSTR> 204.63193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 201.56656 0.00377 0.10420 0.00007 MINI INTERN> 11.93815 77.90191 0.00000 44.49069 10.20931 MINI EXTERN> -37.02404 -110.59350 0.00000 0.00000 0.00000 MINI CONSTR> 204.64404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 201.56187 0.00469 0.03364 0.00003 MINI INTERN> 11.93311 77.89743 0.00000 44.48636 10.20937 MINI EXTERN> -37.02568 -110.59285 0.00000 0.00000 0.00000 MINI CONSTR> 204.65413 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 201.56050 0.00137 0.11609 0.00007 MINI INTERN> 11.93888 77.89131 0.00000 44.47844 10.20886 MINI EXTERN> -37.02999 -110.59269 0.00000 0.00000 0.00000 MINI CONSTR> 204.66570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 201.55746 0.00304 0.12214 0.00008 MINI INTERN> 11.93886 77.88604 0.00000 44.47194 10.20867 MINI EXTERN> -37.03299 -110.59237 0.00000 0.00000 0.00000 MINI CONSTR> 204.67731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 201.55257 0.00489 0.04144 0.00003 MINI INTERN> 11.93305 77.88119 0.00000 44.46824 10.20889 MINI EXTERN> -37.03448 -110.59171 0.00000 0.00000 0.00000 MINI CONSTR> 204.68741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 201.55022 0.00235 0.02717 0.00003 MINI INTERN> 11.93350 77.87715 0.00000 44.46333 10.20874 MINI EXTERN> -37.03686 -110.59158 0.00000 0.00000 0.00000 MINI CONSTR> 204.69595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 201.54750 0.00272 0.02724 0.00004 MINI INTERN> 11.93355 77.87194 0.00000 44.45758 10.20865 MINI EXTERN> -37.03964 -110.59133 0.00000 0.00000 0.00000 MINI CONSTR> 204.70675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 201.54521 0.00230 0.05792 0.00004 MINI INTERN> 11.93347 77.86625 0.00000 44.45227 10.20866 MINI EXTERN> -37.04230 -110.59093 0.00000 0.00000 0.00000 MINI CONSTR> 204.71779 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 201.54277 0.00243 0.03388 0.00004 MINI INTERN> 11.93371 77.86208 0.00000 44.44713 10.20857 MINI EXTERN> -37.04473 -110.59093 0.00000 0.00000 0.00000 MINI CONSTR> 204.72694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 201.54097 0.00180 0.06308 0.00004 MINI INTERN> 11.93406 77.85677 0.00000 44.44242 10.20861 MINI EXTERN> -37.04713 -110.59061 0.00000 0.00000 0.00000 MINI CONSTR> 204.73685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 201.53905 0.00192 0.06690 0.00004 MINI INTERN> 11.93445 77.85207 0.00000 44.43770 10.20861 MINI EXTERN> -37.04946 -110.59049 0.00000 0.00000 0.00000 MINI CONSTR> 204.74616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 201.53732 0.00172 0.07293 0.00004 MINI INTERN> 11.93486 77.84754 0.00000 44.43324 10.20865 MINI EXTERN> -37.05167 -110.59040 0.00000 0.00000 0.00000 MINI CONSTR> 204.75512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 201.53572 0.00160 0.06866 0.00004 MINI INTERN> 11.93482 77.84416 0.00000 44.42938 10.20870 MINI EXTERN> -37.05356 -110.59047 0.00000 0.00000 0.00000 MINI CONSTR> 204.76270 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 201.53405 0.00167 0.06992 0.00005 MINI INTERN> 11.93528 77.83964 0.00000 44.42501 10.20875 MINI EXTERN> -37.05569 -110.59047 0.00000 0.00000 0.00000 MINI CONSTR> 204.77153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 201.53195 0.00210 0.02194 0.00002 MINI INTERN> 11.93415 77.83823 0.00000 44.42017 10.20875 MINI EXTERN> -37.05762 -110.59119 0.00000 0.00000 0.00000 MINI CONSTR> 204.77946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 201.53136 0.00059 0.07640 0.00005 MINI INTERN> 11.93586 77.83204 0.00000 44.41752 10.20894 MINI EXTERN> -37.05943 -110.59059 0.00000 0.00000 0.00000 MINI CONSTR> 204.78703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 201.53136 0.00059 0.07640 0.00002 STPD INTERN> 11.93586 77.83204 0.00000 44.41752 10.20894 STPD EXTERN> -37.05943 -110.59059 0.00000 0.00000 0.00000 STPD CONSTR> 204.78703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21171 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 201.53133 0.00003 0.06375 0.00000 MINI INTERN> 11.93414 77.83685 0.00000 44.41631 10.20879 MINI EXTERN> -37.05917 -110.59173 0.00000 0.00000 0.00000 MINI CONSTR> 204.78614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 3 201.50842 0.02291 0.00789 0.02000 CONJ INTERN> 11.93486 77.71386 0.00000 44.29931 10.21336 CONJ EXTERN> -37.12515 -110.59156 0.00000 0.00000 0.00000 CONJ CONSTR> 205.06376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "6000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 2.6925 ( PROT LYS 1 HT2 ) 2.6925 ( PROT LYS 1 N ) 3.3657 ( PROT LYS 1 HT3 ) 2.6925 ( PROT LYS 1 CA ) 3.3657 ( PROT LYS 1 CB ) 2.6925 ( PROT LYS 1 CG ) 2.6925 ( PROT LYS 1 CD ) 2.6925 ( PROT LYS 1 CE ) 2.6925 ( PROT LYS 1 NZ ) 2.6925 ( PROT LYS 1 HZ1 ) 2.6925 ( PROT LYS 1 HZ2 ) 2.6925 ( PROT LYS 1 HZ3 ) 2.6925 ( PROT LYS 1 C ) 3.3657 ( PROT LYS 1 O ) 3.3657 ( PROT MET 2 N ) 3.3657 ( PROT MET 2 H ) 2.6925 ( PROT MET 2 CA ) 3.3657 ( PROT MET 2 CB ) 2.6925 ( PROT MET 2 CG ) 2.6925 ( PROT MET 2 SD ) 2.6925 ( PROT MET 2 CE ) 2.6925 ( PROT MET 2 C ) 3.3657 ( PROT MET 2 O ) 3.3657 ( PROT LYS 3 N ) 3.3657 ( PROT LYS 3 H ) 2.6925 ( PROT LYS 3 CA ) 3.3657 ( PROT LYS 3 CB ) 2.6925 ( PROT LYS 3 CG ) 2.6925 ( PROT LYS 3 CD ) 2.6925 ( PROT LYS 3 CE ) 2.6925 ( PROT LYS 3 NZ ) 2.6925 ( PROT LYS 3 HZ1 ) 2.6925 ( PROT LYS 3 HZ2 ) 2.6925 ( PROT LYS 3 HZ3 ) 2.6925 ( PROT LYS 3 C ) 3.3657 ( PROT LYS 3 O ) 3.3657 ( PROT ALA 4 N ) 3.3657 ( PROT ALA 4 H ) 2.6925 ( PROT ALA 4 CA ) 3.3657 ( PROT ALA 4 CB ) 2.6925 ( PROT ALA 4 C ) 3.3657 ( PROT ALA 4 O ) 3.3657 ( PROT VAL 5 N ) 3.3657 ( PROT VAL 5 H ) 2.6925 ( PROT VAL 5 CA ) 3.3657 ( PROT VAL 5 CB ) 2.6925 ( PROT VAL 5 CG1 ) 2.6925 ( PROT VAL 5 CG2 ) 2.6925 ( PROT VAL 5 C ) 3.3657 ( PROT VAL 5 O ) 3.3657 ( PROT MET 6 N ) 3.3657 ( PROT MET 6 H ) 2.6925 ( PROT MET 6 CA ) 3.3657 ( PROT MET 6 CB ) 2.6925 ( PROT MET 6 CG ) 2.6925 ( PROT MET 6 SD ) 2.6925 ( PROT MET 6 CE ) 2.6925 ( PROT MET 6 C ) 3.3657 ( PROT MET 6 O ) 3.3657 ( PROT ILE 7 N ) 3.3657 ( PROT ILE 7 H ) 2.6925 ( PROT ILE 7 CA ) 3.3657 ( PROT ILE 7 CB ) 2.6925 ( PROT ILE 7 CG2 ) 2.6925 ( PROT ILE 7 CG1 ) 2.6925 ( PROT ILE 7 CD ) 2.6925 ( PROT ILE 7 C ) 3.3657 ( PROT ILE 7 O ) 3.3657 ( PROT GLY 8 N ) 3.3657 ( PROT GLY 8 H ) 2.6925 ( PROT GLY 8 CA ) 3.3657 ( PROT GLY 8 C ) 3.3657 ( PROT GLY 8 O ) 3.3657 ( PROT ALA 9 N ) 3.3657 ( PROT ALA 9 H ) 2.6925 ( PROT ALA 9 CA ) 3.3657 ( PROT ALA 9 CB ) 2.6925 ( PROT ALA 9 C ) 3.3657 ( PROT ALA 9 O ) 3.3657 ( PROT CYS 10 N ) 3.3657 ( PROT CYS 10 H ) 2.6925 ( PROT CYS 10 CA ) 3.3657 ( PROT CYS 10 CB ) 2.6925 ( PROT CYS 10 SG ) 2.6925 ( PROT CYS 10 C ) 3.3657 ( PROT CYS 10 O ) 3.3657 ( PROT PHE 11 N ) 3.3657 ( PROT PHE 11 H ) 2.6925 ( PROT PHE 11 CA ) 3.3657 ( PROT PHE 11 CB ) 2.6925 ( PROT PHE 11 CG ) 2.6925 ( PROT PHE 11 CD1 ) 2.6925 ( PROT PHE 11 CD2 ) 2.6925 ( PROT PHE 11 CE1 ) 2.6925 ( PROT PHE 11 CE2 ) 2.6925 ( PROT PHE 11 CZ ) 2.6925 ( PROT PHE 11 C ) 3.3657 ( PROT PHE 11 O ) 3.3657 ( PROT LEU 12 N ) 3.3657 ( PROT LEU 12 H ) 2.6925 ( PROT LEU 12 CA ) 3.3657 ( PROT LEU 12 CB ) 2.6925 ( PROT LEU 12 CG ) 2.6925 ( PROT LEU 12 CD1 ) 2.6925 ( PROT LEU 12 CD2 ) 2.6925 ( PROT LEU 12 C ) 3.3657 ( PROT LEU 12 O ) 3.3657 ( PROT ILE 13 N ) 3.3657 ( PROT ILE 13 H ) 2.6925 ( PROT ILE 13 CA ) 3.3657 ( PROT ILE 13 CB ) 2.6925 ( PROT ILE 13 CG2 ) 2.6925 ( PROT ILE 13 CG1 ) 2.6925 ( PROT ILE 13 CD ) 2.6925 ( PROT ILE 13 C ) 3.3657 ( PROT ILE 13 O ) 3.3657 ( PROT ASH 14 N ) 3.3657 ( PROT ASH 14 H ) 2.6925 ( PROT ASH 14 CA ) 3.3657 ( PROT ASH 14 CB ) 2.6925 ( PROT ASH 14 CG ) 2.6925 ( PROT ASH 14 OD1 ) 2.6925 ( PROT ASH 14 OD2 ) 2.6925 ( PROT ASH 14 HD2 ) 2.6925 ( PROT ASH 14 C ) 3.3657 ( PROT ASH 14 O ) 3.3657 ( PROT PHE 15 N ) 3.3657 ( PROT PHE 15 H ) 2.6925 ( PROT PHE 15 CA ) 3.3657 ( PROT PHE 15 CB ) 2.6925 ( PROT PHE 15 CG ) 2.6925 ( PROT PHE 15 CD1 ) 2.6925 ( PROT PHE 15 CD2 ) 2.6925 ( PROT PHE 15 CE1 ) 2.6925 ( PROT PHE 15 CE2 ) 2.6925 ( PROT PHE 15 CZ ) 2.6925 ( PROT PHE 15 C ) 3.3657 ( PROT PHE 15 O ) 3.3657 ( PROT MET 16 N ) 3.3657 ( PROT MET 16 H ) 2.6925 ( PROT MET 16 CA ) 3.3657 ( PROT MET 16 CB ) 2.6925 ( PROT MET 16 CG ) 2.6925 ( PROT MET 16 SD ) 2.6925 ( PROT MET 16 CE ) 2.6925 ( PROT MET 16 C ) 3.3657 ( PROT MET 16 O ) 3.3657 ( PROT PHE 17 N ) 3.3657 ( PROT PHE 17 H ) 2.6925 ( PROT PHE 17 CA ) 3.3657 ( PROT PHE 17 CB ) 2.6925 ( PROT PHE 17 CG ) 2.6925 ( PROT PHE 17 CD1 ) 2.6925 ( PROT PHE 17 CD2 ) 2.6925 ( PROT PHE 17 CE1 ) 2.6925 ( PROT PHE 17 CE2 ) 2.6925 ( PROT PHE 17 CZ ) 2.6925 ( PROT PHE 17 C ) 3.3657 ( PROT PHE 17 O ) 3.3657 ( PROT PHE 18 N ) 3.3657 ( PROT PHE 18 H ) 2.6925 ( PROT PHE 18 CA ) 3.3657 ( PROT PHE 18 CB ) 2.6925 ( PROT PHE 18 CG ) 2.6925 ( PROT PHE 18 CD1 ) 2.6925 ( PROT PHE 18 CD2 ) 2.6925 ( PROT PHE 18 CE1 ) 2.6925 ( PROT PHE 18 CE2 ) 2.6925 ( PROT PHE 18 CZ ) 2.6925 ( PROT PHE 18 C ) 3.3657 ( PROT PHE 18 O ) 3.3657 ( PROT GLU 19 N ) 3.3657 ( PROT GLU 19 H ) 2.6925 ( PROT GLU 19 CA ) 3.3657 ( PROT GLU 19 CB ) 2.6925 ( PROT GLU 19 CG ) 2.6925 ( PROT GLU 19 CD ) 2.6925 ( PROT GLU 19 OE1 ) 2.6925 ( PROT GLU 19 OE2 ) 2.6925 ( PROT GLU 19 C ) 3.3657 ( PROT GLU 19 O ) 3.3657 ( PROT SER 20 N ) 3.3657 ( PROT SER 20 H ) 2.6925 ( PROT SER 20 CA ) 3.3657 ( PROT SER 20 CB ) 2.6925 ( PROT SER 20 OG ) 2.6925 ( PROT SER 20 HG ) 2.6925 ( PROT SER 20 C ) 3.3657 ( PROT SER 20 O ) 3.3657 ( PROT THR 21 N ) 3.3657 ( PROT THR 21 H ) 2.6925 ( PROT THR 21 CA ) 3.3657 ( PROT THR 21 CB ) 2.6925 ( PROT THR 21 OG1 ) 2.6925 ( PROT THR 21 HG1 ) 2.6925 ( PROT THR 21 CG2 ) 2.6925 ( PROT THR 21 C ) 3.3657 ( PROT THR 21 O ) 3.3657 ( PROT GLY 22 N ) 3.3657 ( PROT GLY 22 H ) 2.6925 ( PROT GLY 22 CA ) 3.3657 ( PROT GLY 22 C ) 3.3657 ( PROT GLY 22 O ) 3.3657 ( PROT SER 23 N ) 3.3657 ( PROT SER 23 H ) 2.6925 ( PROT SER 23 CA ) 3.3657 ( PROT SER 23 CB ) 2.6925 ( PROT SER 23 OG ) 2.6925 ( PROT SER 23 HG ) 2.6925 ( PROT SER 23 C ) 3.3657 ( PROT SER 23 O ) 3.3657 ( PROT GLN 24 N ) 3.3657 ( PROT GLN 24 H ) 2.6925 ( PROT GLN 24 CA ) 3.3657 ( PROT GLN 24 CB ) 2.6925 ( PROT GLN 24 CG ) 2.6925 ( PROT GLN 24 CD ) 2.6925 ( PROT GLN 24 OE1 ) 2.6925 ( PROT GLN 24 NE2 ) 2.6925 ( PROT GLN 24 HE21 ) 2.6925 ( PROT GLN 24 HE22 ) 2.6925 ( PROT GLN 24 C ) 3.3657 ( PROT GLN 24 O ) 3.3657 ( PROT GLU 25 N ) 3.3657 ( PROT GLU 25 H ) 2.6925 ( PROT GLU 25 CA ) 3.3657 ( PROT GLU 25 CB ) 2.6925 ( PROT GLU 25 CG ) 2.6925 ( PROT GLU 25 CD ) 2.6925 ( PROT GLU 25 OE1 ) 2.6925 ( PROT GLU 25 OE2 ) 2.6925 ( PROT GLU 25 C ) 3.3657 ( PROT GLU 25 O ) 3.3657 ( PROT GLN 26 N ) 3.3657 ( PROT GLN 26 H ) 2.6925 ( PROT GLN 26 CA ) 3.3657 ( PROT GLN 26 CB ) 2.6925 ( PROT GLN 26 CG ) 2.6925 ( PROT GLN 26 CD ) 2.6925 ( PROT GLN 26 OE1 ) 2.6925 ( PROT GLN 26 NE2 ) 2.6925 ( PROT GLN 26 HE21 ) 2.6925 ( PROT GLN 26 HE22 ) 2.6925 ( PROT GLN 26 C ) 3.3657 ( PROT GLN 26 O ) 3.3657 ( PROT LYS 27 N ) 3.3657 ( PROT LYS 27 H ) 2.6925 ( PROT LYS 27 CA ) 3.3657 ( PROT LYS 27 CB ) 2.6925 ( PROT LYS 27 CG ) 2.6925 ( PROT LYS 27 CD ) 2.6925 ( PROT LYS 27 CE ) 2.6925 ( PROT LYS 27 NZ ) 2.6925 ( PROT LYS 27 HZ1 ) 2.6925 ( PROT LYS 27 HZ2 ) 2.6925 ( PROT LYS 27 HZ3 ) 2.6925 ( PROT LYS 27 C ) 3.3657 ( PROT LYS 27 O ) 3.3657 ( PROT SER 28 N ) 3.3657 ( PROT SER 28 H ) 2.6925 ( PROT SER 28 CA ) 3.3657 ( PROT SER 28 CB ) 2.6925 ( PROT SER 28 OG ) 2.6925 ( PROT SER 28 HG ) 2.6925 ( PROT SER 28 C ) 3.3657 ( PROT SER 28 O ) 3.3657 ( PROT GLY 29 N ) 3.3657 ( PROT GLY 29 H ) 2.6925 ( PROT GLY 29 CA ) 3.3657 ( PROT GLY 29 C ) 3.3657 ( PROT GLY 29 O ) 3.3657 ( PROT VAL 30 N ) 3.3657 ( PROT VAL 30 H ) 2.6925 ( PROT VAL 30 CA ) 3.3657 ( PROT VAL 30 CB ) 2.6925 ( PROT VAL 30 CG1 ) 2.6925 ( PROT VAL 30 CG2 ) 2.6925 ( PROT VAL 30 C ) 3.3657 ( PROT VAL 30 O ) 3.3657 ( PROT TRP 31 N ) 3.3657 ( PROT TRP 31 H ) 2.6925 ( PROT TRP 31 CA ) 3.3657 ( PROT TRP 31 CB ) 2.6925 ( PROT TRP 31 CG ) 2.6925 ( PROT TRP 31 CD2 ) 2.6925 ( PROT TRP 31 CE2 ) 2.6925 ( PROT TRP 31 CE3 ) 2.6925 ( PROT TRP 31 CD1 ) 2.6925 ( PROT TRP 31 NE1 ) 2.6925 ( PROT TRP 31 HE1 ) 2.6925 ( PROT TRP 31 CZ2 ) 2.6925 ( PROT TRP 31 CZ3 ) 2.6925 ( PROT TRP 31 CH2 ) 2.6925 ( PROT TRP 31 C ) 3.3657 ( PROT TRP 31 OT1 ) 2.6925 ( PROT TRP 31 OT2 ) 2.6925 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63032 7.22833 -13.22005 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00049 0.00109 0.00013 ROTATION MATRIX 1.000000 -0.000070 -0.000340 0.000070 1.000000 0.000297 0.000340 -0.000298 1.000000 AXIS OF ROTATION IS 0.651079 0.743278 -0.153732 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 45.1055 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.389706 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3897" Parameter: A <- "0.3897" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.52009 7.24953 -13.40819 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.00814 0.00602 -0.03217 ROTATION MATRIX 0.999668 0.017976 0.018459 -0.017605 0.999644 -0.020063 -0.018813 0.019731 0.999628 AXIS OF ROTATION IS -0.611230 -0.572481 0.546501 ANGLE IS 1.87 CENTER OF ROTATION 13.988636 6.785307-13.394218 SHIFT IS -0.026003 TOTAL SQUARE DIFF IS 1.2466 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.200532 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3897" RDCMND substituted energy or value "?RMS" to " 0.2005" Parameter: A <- "0.3897 0.2005" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *6000 0.3897 0.2005 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 205.06" Parameter: H <- "205.06" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -3.55534 205.06376 2.05814 ENER INTERN> 11.93486 77.71386 0.00000 44.29931 10.21336 ENER EXTERN> -37.12515 -110.59156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -3.56" Parameter: B <- "-3.56" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -110.59" Parameter: C <- "-110.59" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -37.13" Parameter: C <- " -147.72" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -147.72" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 11.93" Parameter: D <- "11.93" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 77.71" Parameter: D <- " 89.64" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 44.30" Parameter: D <- " 133.94" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 10.21" Parameter: D <- " 144.15" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 144.15" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 6000 ENER= -3.56 GRMS= 2.06 ELEC= -110.59 VDW= -37.13 RDTITL> *EXTERNAL= -147.72 INTERNAL= 144.15 USER= 0.00 HARM= 205.06 RDTITL> *BOND= 11.93 ANGL= 77.71 DIHE= 44.30 IMPR= 10.21 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "6000" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_6000.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_6000.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 6000 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 6000 ENER= -3.56 GRMS= 2.06 ELEC= -110.59 VDW= -37.13 RDTITL> *EXTERNAL= -147.72 INTERNAL= 144.15 USER= 0.00 HARM= 205.06 RDTITL> *BOND= 11.93 ANGL= 77.71 DIHE= 44.30 IMPR= 10.21 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "6000" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_6000.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_6000.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 6000 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 6000 ENER= -3.56 GRMS= 2.06 ELEC= -110.59 VDW= -37.13 RDTITL> *EXTERNAL= -147.72 INTERNAL= 144.15 USER= 0.00 HARM= 205.06 RDTITL> *BOND= 11.93 ANGL= 77.71 DIHE= 44.30 IMPR= 10.21 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 6000 0.3897 0.2005 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "6000" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21171 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21171 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 144.17776 -147.73309 0.83593 0.02000 MINI INTERN> 11.93486 77.71386 0.00000 44.29931 10.21336 MINI EXTERN> -37.12515 -110.59156 0.00000 0.00000 0.00000 MINI CONSTR> 147.73309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 172.72019 -28.54243 15.34130 0.00864 MINI INTERN> 47.87137 70.81851 0.00000 48.17398 9.00398 MINI EXTERN> -54.40411 -104.16061 0.00000 0.00000 0.00000 MINI CONSTR> 155.41706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21159 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 143.53499 29.18520 6.69405 0.00373 MINI INTERN> 14.19796 81.53416 0.00000 46.26034 10.86087 MINI EXTERN> -57.01214 -108.88220 0.00000 0.00000 0.00000 MINI CONSTR> 156.57601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 136.32257 7.21242 0.47561 0.00067 MINI INTERN> 11.34256 76.45568 0.00000 46.91710 10.21488 MINI EXTERN> -57.94602 -107.22836 0.00000 0.00000 0.00000 MINI CONSTR> 156.56672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21156 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 135.62264 0.69993 1.02673 0.00070 MINI INTERN> 11.70526 76.22785 0.00000 46.86052 10.24464 MINI EXTERN> -59.05162 -107.22514 0.00000 0.00000 0.00000 MINI CONSTR> 156.86113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 134.93843 0.68422 1.02577 0.00072 MINI INTERN> 11.97016 75.68645 0.00000 46.89385 10.18433 MINI EXTERN> -59.76367 -107.07826 0.00000 0.00000 0.00000 MINI CONSTR> 157.04557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21150 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 134.28871 0.64972 1.08013 0.00075 MINI INTERN> 11.62533 75.74348 0.00000 46.88991 10.16107 MINI EXTERN> -60.19278 -107.15826 0.00000 0.00000 0.00000 MINI CONSTR> 157.21996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 133.72267 0.56603 1.21508 0.00078 MINI INTERN> 12.00621 75.21384 0.00000 46.88835 10.11403 MINI EXTERN> -60.85154 -106.99002 0.00000 0.00000 0.00000 MINI CONSTR> 157.34181 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21146 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 133.19373 0.52894 1.15645 0.00080 MINI INTERN> 11.88843 75.08179 0.00000 46.86358 10.08552 MINI EXTERN> -61.13876 -107.02257 0.00000 0.00000 0.00000 MINI CONSTR> 157.43574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 132.51848 0.67525 0.38070 0.00035 MINI INTERN> 11.01478 74.94264 0.00000 47.00309 9.90397 MINI EXTERN> -60.82955 -107.00408 0.00000 0.00000 0.00000 MINI CONSTR> 157.48762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21144 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 132.27303 0.24545 1.31835 0.00087 MINI INTERN> 11.84987 74.76970 0.00000 46.80414 10.02889 MINI EXTERN> -61.73755 -107.02348 0.00000 0.00000 0.00000 MINI CONSTR> 157.58146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 131.89675 0.37628 1.51580 0.00090 MINI INTERN> 11.68471 74.62711 0.00000 46.80647 9.96739 MINI EXTERN> -61.91835 -106.90482 0.00000 0.00000 0.00000 MINI CONSTR> 157.63425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21145 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 131.19624 0.70052 0.41731 0.00039 MINI INTERN> 10.85829 74.48273 0.00000 46.92470 9.80453 MINI EXTERN> -61.57627 -106.94495 0.00000 0.00000 0.00000 MINI CONSTR> 157.64721 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 130.83358 0.36266 0.33793 0.00040 MINI INTERN> 10.89443 74.35713 0.00000 46.87286 9.79992 MINI EXTERN> -61.83800 -106.93499 0.00000 0.00000 0.00000 MINI CONSTR> 157.68223 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21142 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 130.46212 0.37145 0.34859 0.00042 MINI INTERN> 10.83404 74.23737 0.00000 46.84058 9.77133 MINI EXTERN> -62.01233 -106.92091 0.00000 0.00000 0.00000 MINI CONSTR> 157.71205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 130.10075 0.36137 0.57910 0.00043 MINI INTERN> 10.63708 74.14289 0.00000 46.83990 9.70849 MINI EXTERN> -62.05739 -106.90530 0.00000 0.00000 0.00000 MINI CONSTR> 157.73509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21138 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 129.75516 0.34559 0.44623 0.00045 MINI INTERN> 10.72683 73.99436 0.00000 46.77121 9.71179 MINI EXTERN> -62.30835 -106.89950 0.00000 0.00000 0.00000 MINI CONSTR> 157.75882 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 129.45267 0.30249 0.53666 0.00046 MINI INTERN> 10.59662 73.93198 0.00000 46.75166 9.67659 MINI EXTERN> -62.38632 -106.89331 0.00000 0.00000 0.00000 MINI CONSTR> 157.77544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21138 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 129.18778 0.26489 0.70770 0.00048 MINI INTERN> 10.44259 73.88968 0.00000 46.73939 9.63660 MINI EXTERN> -62.42852 -106.88133 0.00000 0.00000 0.00000 MINI CONSTR> 157.78937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 128.90959 0.27819 0.79578 0.00050 MINI INTERN> 10.49064 73.76106 0.00000 46.69058 9.62094 MINI EXTERN> -62.56527 -106.89159 0.00000 0.00000 0.00000 MINI CONSTR> 157.80324 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21134 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 128.65660 0.25300 0.81344 0.00052 MINI INTERN> 10.34019 73.73909 0.00000 46.67134 9.59335 MINI EXTERN> -62.61855 -106.88440 0.00000 0.00000 0.00000 MINI CONSTR> 157.81559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 128.40297 0.25363 0.77602 0.00054 MINI INTERN> 10.30615 73.66412 0.00000 46.62638 9.58404 MINI EXTERN> -62.74509 -106.86264 0.00000 0.00000 0.00000 MINI CONSTR> 157.83000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21132 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 128.16179 0.24118 0.84446 0.00056 MINI INTERN> 10.43735 73.51668 0.00000 46.56323 9.58219 MINI EXTERN> -62.90188 -106.87814 0.00000 0.00000 0.00000 MINI CONSTR> 157.84237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 127.85958 0.30221 0.25845 0.00024 MINI INTERN> 10.86749 73.23802 0.00000 46.41122 9.65248 MINI EXTERN> -63.36072 -106.81694 0.00000 0.00000 0.00000 MINI CONSTR> 157.86803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21132 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 127.74107 0.11851 0.88315 0.00060 MINI INTERN> 10.16147 73.48286 0.00000 46.52335 9.53394 MINI EXTERN> -62.97205 -106.85374 0.00000 0.00000 0.00000 MINI CONSTR> 157.86525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 127.54110 0.19998 0.98370 0.00062 MINI INTERN> 10.33620 73.32535 0.00000 46.45767 9.53593 MINI EXTERN> -63.12001 -106.87149 0.00000 0.00000 0.00000 MINI CONSTR> 157.87745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21130 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 127.21621 0.32489 0.29604 0.00027 MINI INTERN> 10.91481 72.96391 0.00000 46.26929 9.62848 MINI EXTERN> -63.67596 -106.79259 0.00000 0.00000 0.00000 MINI CONSTR> 157.90826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 127.04324 0.17297 0.22813 0.00028 MINI INTERN> 10.81121 72.93040 0.00000 46.25412 9.60581 MINI EXTERN> -63.68068 -106.79482 0.00000 0.00000 0.00000 MINI CONSTR> 157.91720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21128 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 126.85859 0.18465 0.23759 0.00029 MINI INTERN> 10.83636 72.84408 0.00000 46.20813 9.60067 MINI EXTERN> -63.77544 -106.78692 0.00000 0.00000 0.00000 MINI CONSTR> 157.93171 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 126.68151 0.17708 0.39718 0.00030 MINI INTERN> 11.02035 72.70106 0.00000 46.12992 9.61577 MINI EXTERN> -63.96582 -106.77136 0.00000 0.00000 0.00000 MINI CONSTR> 157.95158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21127 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 126.50931 0.17220 0.26990 0.00031 MINI INTERN> 10.87258 72.68689 0.00000 46.12091 9.59025 MINI EXTERN> -63.94633 -106.77760 0.00000 0.00000 0.00000 MINI CONSTR> 157.96261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 126.34314 0.16616 0.30099 0.00032 MINI INTERN> 10.86679 72.62245 0.00000 46.08087 9.58384 MINI EXTERN> -64.02153 -106.76914 0.00000 0.00000 0.00000 MINI CONSTR> 157.97987 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21127 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 126.21671 0.12643 0.48241 0.00033 MINI INTERN> 11.07264 72.48853 0.00000 46.00903 9.60199 MINI EXTERN> -64.19542 -106.75972 0.00000 0.00000 0.00000 MINI CONSTR> 157.99967 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 126.06580 0.15091 0.48218 0.00034 MINI INTERN> 11.04372 72.44137 0.00000 45.97764 9.59365 MINI EXTERN> -64.24459 -106.76297 0.00000 0.00000 0.00000 MINI CONSTR> 158.01698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21125 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 125.91438 0.15142 0.37392 0.00036 MINI INTERN> 10.91368 72.42383 0.00000 45.96627 9.57275 MINI EXTERN> -64.23393 -106.76055 0.00000 0.00000 0.00000 MINI CONSTR> 158.03233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 125.81793 0.09645 0.53174 0.00037 MINI INTERN> 11.07452 72.31426 0.00000 45.90898 9.58580 MINI EXTERN> -64.36787 -106.74969 0.00000 0.00000 0.00000 MINI CONSTR> 158.05192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21125 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 125.70160 0.11633 0.58444 0.00038 MINI INTERN> 11.05128 72.26589 0.00000 45.88930 9.57366 MINI EXTERN> -64.37570 -106.77016 0.00000 0.00000 0.00000 MINI CONSTR> 158.06733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 125.55490 0.14670 0.17955 0.00017 MINI INTERN> 10.65167 72.34337 0.00000 45.93396 9.52035 MINI EXTERN> -64.19824 -106.77223 0.00000 0.00000 0.00000 MINI CONSTR> 158.07602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21123 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 125.49469 0.06021 0.60923 0.00041 MINI INTERN> 11.14983 72.12533 0.00000 45.81258 9.57873 MINI EXTERN> -64.53843 -106.74066 0.00000 0.00000 0.00000 MINI CONSTR> 158.10730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 125.39862 0.09607 0.68952 0.00043 MINI INTERN> 11.10191 72.09412 0.00000 45.80306 9.56347 MINI EXTERN> -64.51788 -106.76934 0.00000 0.00000 0.00000 MINI CONSTR> 158.12327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21124 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 125.23962 0.15899 0.19832 0.00019 MINI INTERN> 10.60253 72.20782 0.00000 45.86339 9.50198 MINI EXTERN> -64.29715 -106.77260 0.00000 0.00000 0.00000 MINI CONSTR> 158.13365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 125.15371 0.08591 0.16142 0.00019 MINI INTERN> 10.64301 72.15094 0.00000 45.83356 9.50532 MINI EXTERN> -64.35947 -106.77213 0.00000 0.00000 0.00000 MINI CONSTR> 158.15249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21123 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 125.06430 0.08941 0.16681 0.00020 MINI INTERN> 10.62025 72.11387 0.00000 45.81505 9.49952 MINI EXTERN> -64.38354 -106.77333 0.00000 0.00000 0.00000 MINI CONSTR> 158.17248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 124.97601 0.08829 0.26792 0.00021 MINI INTERN> 10.52474 72.10067 0.00000 45.81100 9.48246 MINI EXTERN> -64.35902 -106.77736 0.00000 0.00000 0.00000 MINI CONSTR> 158.19352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21123 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 124.89345 0.08257 0.20750 0.00021 MINI INTERN> 10.58147 72.03426 0.00000 45.78014 9.48786 MINI EXTERN> -64.42620 -106.77887 0.00000 0.00000 0.00000 MINI CONSTR> 158.21478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 124.81905 0.07440 0.24398 0.00022 MINI INTERN> 10.52931 72.01447 0.00000 45.77093 9.47920 MINI EXTERN> -64.42872 -106.78145 0.00000 0.00000 0.00000 MINI CONSTR> 158.23530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21123 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 124.75346 0.06558 0.33782 0.00023 MINI INTERN> 10.45653 72.00454 0.00000 45.76764 9.46710 MINI EXTERN> -64.41416 -106.78400 0.00000 0.00000 0.00000 MINI CONSTR> 158.25583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 124.68366 0.06981 0.36663 0.00024 MINI INTERN> 10.48692 71.94633 0.00000 45.74730 9.46671 MINI EXTERN> -64.44887 -106.79259 0.00000 0.00000 0.00000 MINI CONSTR> 158.27786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21123 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 124.62124 0.06242 0.38007 0.00025 MINI INTERN> 10.41988 71.93945 0.00000 45.74308 9.45836 MINI EXTERN> -64.44635 -106.79212 0.00000 0.00000 0.00000 MINI CONSTR> 158.29894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 124.55738 0.06386 0.40294 0.00026 MINI INTERN> 10.40761 71.90289 0.00000 45.72975 9.45508 MINI EXTERN> -64.46881 -106.79145 0.00000 0.00000 0.00000 MINI CONSTR> 158.32232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21123 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 124.49760 0.05978 0.38148 0.00027 MINI INTERN> 10.41736 71.86148 0.00000 45.71521 9.45531 MINI EXTERN> -64.49795 -106.79716 0.00000 0.00000 0.00000 MINI CONSTR> 158.34336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 124.43907 0.05853 0.41441 0.00028 MINI INTERN> 10.43837 71.81383 0.00000 45.69515 9.45779 MINI EXTERN> -64.54885 -106.78621 0.00000 0.00000 0.00000 MINI CONSTR> 158.36898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21123 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 124.36618 0.07290 0.12631 0.00012 MINI INTERN> 10.66402 71.68236 0.00000 45.63802 9.48836 MINI EXTERN> -64.71561 -106.78484 0.00000 0.00000 0.00000 MINI CONSTR> 158.39387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 124.33864 0.02754 0.43429 0.00030 MINI INTERN> 10.37182 71.77057 0.00000 45.68793 9.44731 MINI EXTERN> -64.54995 -106.80042 0.00000 0.00000 0.00000 MINI CONSTR> 158.41136 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21123 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 124.29250 0.04613 0.49808 0.00031 MINI INTERN> 10.46879 71.68800 0.00000 45.66525 9.45419 MINI EXTERN> -64.60370 -106.81500 0.00000 0.00000 0.00000 MINI CONSTR> 158.43497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 124.21273 0.07978 0.14161 0.00013 MINI INTERN> 10.67862 71.56387 0.00000 45.60479 9.48826 MINI EXTERN> -64.79633 -106.79102 0.00000 0.00000 0.00000 MINI CONSTR> 158.46453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 124.17058 0.04215 0.11156 0.00014 MINI INTERN> 10.64352 71.54288 0.00000 45.60475 9.48299 MINI EXTERN> -64.79226 -106.79539 0.00000 0.00000 0.00000 MINI CONSTR> 158.48407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 124.12542 0.04516 0.11689 0.00014 MINI INTERN> 10.65255 71.50248 0.00000 45.59545 9.48393 MINI EXTERN> -64.82016 -106.79706 0.00000 0.00000 0.00000 MINI CONSTR> 158.50822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 124.08231 0.04310 0.19494 0.00015 MINI INTERN> 10.71504 71.44268 0.00000 45.57673 9.49183 MINI EXTERN> -64.88132 -106.79847 0.00000 0.00000 0.00000 MINI CONSTR> 158.53583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 124.04078 0.04154 0.14113 0.00015 MINI INTERN> 10.66312 71.42643 0.00000 45.58086 9.48554 MINI EXTERN> -64.87119 -106.80116 0.00000 0.00000 0.00000 MINI CONSTR> 158.55717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 124.00370 0.03708 0.17492 0.00016 MINI INTERN> 10.69648 71.37869 0.00000 45.57063 9.48934 MINI EXTERN> -64.90813 -106.80462 0.00000 0.00000 0.00000 MINI CONSTR> 158.58132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 123.97153 0.03217 0.23975 0.00016 MINI INTERN> 10.73547 71.33225 0.00000 45.55960 9.49452 MINI EXTERN> -64.95120 -106.80480 0.00000 0.00000 0.00000 MINI CONSTR> 158.60569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 123.93573 0.03580 0.25282 0.00017 MINI INTERN> 10.72802 71.30119 0.00000 45.55957 9.49329 MINI EXTERN> -64.96124 -106.81440 0.00000 0.00000 0.00000 MINI CONSTR> 158.62931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 123.90546 0.03027 0.27834 0.00018 MINI INTERN> 10.73676 71.26497 0.00000 45.55416 9.49571 MINI EXTERN> -64.99077 -106.80840 0.00000 0.00000 0.00000 MINI CONSTR> 158.65303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 123.87482 0.03064 0.26573 0.00018 MINI INTERN> 10.74335 71.22835 0.00000 45.55390 9.49530 MINI EXTERN> -65.00076 -106.81872 0.00000 0.00000 0.00000 MINI CONSTR> 158.67340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 123.84636 0.02846 0.29170 0.00019 MINI INTERN> 10.69968 71.21219 0.00000 45.55886 9.49203 MINI EXTERN> -65.00195 -106.81068 0.00000 0.00000 0.00000 MINI CONSTR> 158.69623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 123.81005 0.03631 0.09081 0.00008 MINI INTERN> 10.58564 71.21605 0.00000 45.58249 9.47647 MINI EXTERN> -64.93575 -106.82626 0.00000 0.00000 0.00000 MINI CONSTR> 158.71141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 123.79517 0.01488 0.31203 0.00020 MINI INTERN> 10.76877 71.12068 0.00000 45.55130 9.49836 MINI EXTERN> -65.05302 -106.82935 0.00000 0.00000 0.00000 MINI CONSTR> 158.73843 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 123.77258 0.02259 0.35553 0.00021 MINI INTERN> 10.70927 71.11263 0.00000 45.55988 9.49421 MINI EXTERN> -65.04888 -106.81544 0.00000 0.00000 0.00000 MINI CONSTR> 158.76090 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 123.74785 0.02473 0.33953 0.00022 MINI INTERN> 10.77706 71.05260 0.00000 45.55036 9.50212 MINI EXTERN> -65.09661 -106.82086 0.00000 0.00000 0.00000 MINI CONSTR> 158.78318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 123.70815 0.03970 0.10597 0.00010 MINI INTERN> 10.55671 71.09821 0.00000 45.59546 9.47549 MINI EXTERN> -64.97465 -106.84115 0.00000 0.00000 0.00000 MINI CONSTR> 158.79808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 123.68711 0.02105 0.07996 0.00010 MINI INTERN> 10.57833 71.06220 0.00000 45.59367 9.47933 MINI EXTERN> -65.00176 -106.84239 0.00000 0.00000 0.00000 MINI CONSTR> 158.81771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 123.66482 0.02229 0.08439 0.00010 MINI INTERN> 10.56757 71.03433 0.00000 45.59966 9.47887 MINI EXTERN> -65.00838 -106.84641 0.00000 0.00000 0.00000 MINI CONSTR> 158.83918 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 123.64357 0.02125 0.14319 0.00011 MINI INTERN> 10.52551 71.01568 0.00000 45.61361 9.47400 MINI EXTERN> -64.99329 -106.85349 0.00000 0.00000 0.00000 MINI CONSTR> 158.86155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 123.62291 0.02067 0.11098 0.00011 MINI INTERN> 10.54376 70.97849 0.00000 45.61368 9.47793 MINI EXTERN> -65.02038 -106.85309 0.00000 0.00000 0.00000 MINI CONSTR> 158.88252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 123.60480 0.01811 0.13263 0.00011 MINI INTERN> 10.52230 70.95732 0.00000 45.62333 9.47626 MINI EXTERN> -65.01909 -106.85787 0.00000 0.00000 0.00000 MINI CONSTR> 158.90256 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 123.58869 0.01611 0.17213 0.00012 MINI INTERN> 10.49852 70.93770 0.00000 45.63489 9.47368 MINI EXTERN> -65.01211 -106.86587 0.00000 0.00000 0.00000 MINI CONSTR> 158.92188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 123.57176 0.01693 0.19577 0.00012 MINI INTERN> 10.49254 70.90860 0.00000 45.64102 9.47486 MINI EXTERN> -65.02556 -106.86307 0.00000 0.00000 0.00000 MINI CONSTR> 158.94336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 123.55612 0.01564 0.20037 0.00013 MINI INTERN> 10.47319 70.88904 0.00000 45.65158 9.47351 MINI EXTERN> -65.02401 -106.86931 0.00000 0.00000 0.00000 MINI CONSTR> 158.96213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 123.54031 0.01581 0.19065 0.00013 MINI INTERN> 10.48203 70.85789 0.00000 45.65787 9.47492 MINI EXTERN> -65.03450 -106.87838 0.00000 0.00000 0.00000 MINI CONSTR> 158.98049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 123.52555 0.01477 0.20913 0.00014 MINI INTERN> 10.48459 70.82677 0.00000 45.66246 9.47772 MINI EXTERN> -65.05512 -106.87225 0.00000 0.00000 0.00000 MINI CONSTR> 159.00138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 123.50674 0.01881 0.06510 0.00006 MINI INTERN> 10.58573 70.75871 0.00000 45.64990 9.49082 MINI EXTERN> -65.12191 -106.87655 0.00000 0.00000 0.00000 MINI CONSTR> 159.02004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 123.49890 0.00784 0.22293 0.00015 MINI INTERN> 10.46509 70.78126 0.00000 45.68437 9.47610 MINI EXTERN> -65.05306 -106.89191 0.00000 0.00000 0.00000 MINI CONSTR> 159.03705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 123.48708 0.01182 0.25400 0.00015 MINI INTERN> 10.46908 70.75073 0.00000 45.68843 9.47969 MINI EXTERN> -65.07747 -106.88088 0.00000 0.00000 0.00000 MINI CONSTR> 159.05750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 123.47417 0.01291 0.24156 0.00016 MINI INTERN> 10.42642 70.74198 0.00000 45.70624 9.47534 MINI EXTERN> -65.05869 -106.89173 0.00000 0.00000 0.00000 MINI CONSTR> 159.07463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 123.45365 0.02052 0.07633 0.00007 MINI INTERN> 10.59681 70.63944 0.00000 45.68131 9.49694 MINI EXTERN> -65.16655 -106.89029 0.00000 0.00000 0.00000 MINI CONSTR> 159.09598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 123.44270 0.01095 0.05726 0.00007 MINI INTERN> 10.57328 70.62411 0.00000 45.69361 9.49529 MINI EXTERN> -65.16117 -106.89404 0.00000 0.00000 0.00000 MINI CONSTR> 159.11162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 123.43090 0.01181 0.06018 0.00007 MINI INTERN> 10.57874 70.59330 0.00000 45.70207 9.49720 MINI EXTERN> -65.17326 -106.89759 0.00000 0.00000 0.00000 MINI CONSTR> 159.13044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21122 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 123.41952 0.01138 0.10021 0.00008 MINI INTERN> 10.61111 70.54990 0.00000 45.70662 9.50242 MINI EXTERN> -65.20153 -106.90045 0.00000 0.00000 0.00000 MINI CONSTR> 159.15145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 123.40849 0.01103 0.07153 0.00008 MINI INTERN> 10.58352 70.53449 0.00000 45.72086 9.50059 MINI EXTERN> -65.19499 -106.90409 0.00000 0.00000 0.00000 MINI CONSTR> 159.16812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21121 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 123.39853 0.00996 0.08897 0.00008 MINI INTERN> 10.59921 70.50068 0.00000 45.72830 9.50353 MINI EXTERN> -65.21117 -106.90842 0.00000 0.00000 0.00000 MINI CONSTR> 159.18640 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 123.39007 0.00845 0.12378 0.00008 MINI INTERN> 10.61800 70.46705 0.00000 45.73426 9.50723 MINI EXTERN> -65.23143 -106.90934 0.00000 0.00000 0.00000 MINI CONSTR> 159.20431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21121 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 123.38120 0.00887 0.13927 0.00009 MINI INTERN> 10.62002 70.44059 0.00000 45.74523 9.50809 MINI EXTERN> -65.23636 -106.91751 0.00000 0.00000 0.00000 MINI CONSTR> 159.22114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 123.37302 0.00818 0.14237 0.00009 MINI INTERN> 10.63117 70.41073 0.00000 45.75236 9.51070 MINI EXTERN> -65.25074 -106.91867 0.00000 0.00000 0.00000 MINI CONSTR> 159.23747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21121 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 123.36479 0.00824 0.13673 0.00009 MINI INTERN> 10.62014 70.39056 0.00000 45.76293 9.51113 MINI EXTERN> -65.25490 -106.91822 0.00000 0.00000 0.00000 MINI CONSTR> 159.25314 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 123.35712 0.00767 0.14947 0.00010 MINI INTERN> 10.61845 70.36738 0.00000 45.77507 9.51115 MINI EXTERN> -65.25474 -106.92858 0.00000 0.00000 0.00000 MINI CONSTR> 159.26840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21121 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 123.34955 0.00757 0.14266 0.00010 MINI INTERN> 10.63064 70.33769 0.00000 45.78188 9.51403 MINI EXTERN> -65.27017 -106.92875 0.00000 0.00000 0.00000 MINI CONSTR> 159.28422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 123.33992 0.00963 0.04730 0.00004 MINI INTERN> 10.53578 70.35333 0.00000 45.80849 9.50439 MINI EXTERN> -65.22454 -106.93392 0.00000 0.00000 0.00000 MINI CONSTR> 159.29639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21121 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 123.33631 0.00360 0.16076 0.00011 MINI INTERN> 10.64353 70.28550 0.00000 45.79929 9.51773 MINI EXTERN> -65.28972 -106.93468 0.00000 0.00000 0.00000 MINI CONSTR> 159.31466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 123.33043 0.00589 0.19033 0.00011 MINI INTERN> 10.60183 70.27881 0.00000 45.81560 9.51532 MINI EXTERN> -65.28057 -106.93088 0.00000 0.00000 0.00000 MINI CONSTR> 159.33033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21121 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 123.31944 0.01099 0.05300 0.00005 MINI INTERN> 10.52370 70.28767 0.00000 45.84133 9.50655 MINI EXTERN> -65.23714 -106.94446 0.00000 0.00000 0.00000 MINI CONSTR> 159.34179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 123.31944 0.01099 0.05300 0.00006 STPD INTERN> 10.52370 70.28767 0.00000 45.84133 9.50655 STPD EXTERN> -65.23714 -106.94446 0.00000 0.00000 0.00000 STPD CONSTR> 159.34179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21121 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21121 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 123.31944 0.01099 0.05300 0.00000 MINI INTERN> 10.52370 70.28767 0.00000 45.84133 9.50655 MINI EXTERN> -65.23714 -106.94446 0.00000 0.00000 0.00000 MINI CONSTR> 159.34179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 123.17711 0.14233 0.02767 0.00140 MINI INTERN> 10.47844 69.22311 0.00000 46.40405 9.55585 MINI EXTERN> -65.54767 -107.07790 0.00000 0.00000 0.00000 MINI CONSTR> 160.14124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 123.17213 0.00499 0.06883 0.00519 MINI INTERN> 10.50372 69.29778 0.00000 46.30546 9.52553 MINI EXTERN> -65.37262 -107.14981 0.00000 0.00000 0.00000 MINI CONSTR> 160.06206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 123.16169 0.01043 0.06810 0.01198 MINI INTERN> 10.50579 69.44562 0.00000 46.17568 9.52573 MINI EXTERN> -65.26268 -107.22089 0.00000 0.00000 0.00000 MINI CONSTR> 159.99244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 123.15468 0.00702 0.04561 0.00746 MINI INTERN> 10.53207 69.51728 0.00000 46.17334 9.56901 MINI EXTERN> -65.44501 -107.24326 0.00000 0.00000 0.00000 MINI CONSTR> 160.05125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 123.14985 0.00483 0.05357 0.00621 MINI INTERN> 10.54279 69.45500 0.00000 46.24098 9.57975 MINI EXTERN> -65.51328 -107.28149 0.00000 0.00000 0.00000 MINI CONSTR> 160.12611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 123.14383 0.00602 0.04081 0.00839 MINI INTERN> 10.51094 69.27095 0.00000 46.40477 9.60636 MINI EXTERN> -65.55693 -107.31218 0.00000 0.00000 0.00000 MINI CONSTR> 160.21992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 123.13942 0.00441 0.04019 0.00831 MINI INTERN> 10.49982 69.16472 0.00000 46.52459 9.60359 MINI EXTERN> -65.53917 -107.40490 0.00000 0.00000 0.00000 MINI CONSTR> 160.29077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 123.13607 0.00335 0.03167 0.00495 MINI INTERN> 10.51310 69.01553 0.00000 46.67027 9.62682 MINI EXTERN> -65.60352 -107.46809 0.00000 0.00000 0.00000 MINI CONSTR> 160.38195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 123.13373 0.00234 0.02972 0.00490 MINI INTERN> 10.49324 68.96850 0.00000 46.75051 9.62056 MINI EXTERN> -65.67045 -107.47700 0.00000 0.00000 0.00000 MINI CONSTR> 160.44837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 123.13057 0.00316 0.03554 0.01014 MINI INTERN> 10.48423 68.88843 0.00000 46.81743 9.62341 MINI EXTERN> -65.68506 -107.48055 0.00000 0.00000 0.00000 MINI CONSTR> 160.48268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 123.12727 0.00330 0.03771 0.00803 MINI INTERN> 10.50542 68.87045 0.00000 46.88092 9.61724 MINI EXTERN> -65.79322 -107.45189 0.00000 0.00000 0.00000 MINI CONSTR> 160.49836 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 123.12403 0.00324 0.03457 0.00828 MINI INTERN> 10.49403 68.86202 0.00000 46.90118 9.62744 MINI EXTERN> -65.78684 -107.45386 0.00000 0.00000 0.00000 MINI CONSTR> 160.48007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 123.12010 0.00394 0.03728 0.01303 MINI INTERN> 10.49350 68.87961 0.00000 46.93537 9.62740 MINI EXTERN> -65.82765 -107.45875 0.00000 0.00000 0.00000 MINI CONSTR> 160.47060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 123.11668 0.00342 0.03805 0.01115 MINI INTERN> 10.49928 68.91091 0.00000 46.95919 9.62570 MINI EXTERN> -65.91554 -107.43597 0.00000 0.00000 0.00000 MINI CONSTR> 160.47310 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 123.11411 0.00256 0.02332 0.00595 MINI INTERN> 10.51077 68.92242 0.00000 46.96002 9.61986 MINI EXTERN> -65.95547 -107.39383 0.00000 0.00000 0.00000 MINI CONSTR> 160.45034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 123.11276 0.00135 0.01937 0.00502 MINI INTERN> 10.50347 68.91705 0.00000 46.96927 9.60667 MINI EXTERN> -65.92459 -107.37963 0.00000 0.00000 0.00000 MINI CONSTR> 160.42052 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 123.11182 0.00095 0.01720 0.00293 MINI INTERN> 10.49994 68.89979 0.00000 46.96991 9.60617 MINI EXTERN> -65.92666 -107.35348 0.00000 0.00000 0.00000 MINI CONSTR> 160.41615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 123.11124 0.00058 0.01516 0.00208 MINI INTERN> 10.50094 68.91112 0.00000 46.97375 9.60563 MINI EXTERN> -65.96562 -107.33960 0.00000 0.00000 0.00000 MINI CONSTR> 160.42502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 123.11075 0.00049 0.01322 0.00209 MINI INTERN> 10.49979 68.90405 0.00000 46.97707 9.60374 MINI EXTERN> -65.97976 -107.31972 0.00000 0.00000 0.00000 MINI CONSTR> 160.42558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 99 123.11049 0.00026 0.00956 0.02000 CONJ INTERN> 10.50018 68.90207 0.00000 46.97816 9.60205 CONJ EXTERN> -65.97789 -107.31714 0.00000 0.00000 0.00000 CONJ CONSTR> 160.42307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "6600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 1.7502 ( PROT LYS 1 HT2 ) 1.7502 ( PROT LYS 1 N ) 2.1877 ( PROT LYS 1 HT3 ) 1.7502 ( PROT LYS 1 CA ) 2.1877 ( PROT LYS 1 CB ) 1.7502 ( PROT LYS 1 CG ) 1.7502 ( PROT LYS 1 CD ) 1.7502 ( PROT LYS 1 CE ) 1.7502 ( PROT LYS 1 NZ ) 1.7502 ( PROT LYS 1 HZ1 ) 1.7502 ( PROT LYS 1 HZ2 ) 1.7502 ( PROT LYS 1 HZ3 ) 1.7502 ( PROT LYS 1 C ) 2.1877 ( PROT LYS 1 O ) 2.1877 ( PROT MET 2 N ) 2.1877 ( PROT MET 2 H ) 1.7502 ( PROT MET 2 CA ) 2.1877 ( PROT MET 2 CB ) 1.7502 ( PROT MET 2 CG ) 1.7502 ( PROT MET 2 SD ) 1.7502 ( PROT MET 2 CE ) 1.7502 ( PROT MET 2 C ) 2.1877 ( PROT MET 2 O ) 2.1877 ( PROT LYS 3 N ) 2.1877 ( PROT LYS 3 H ) 1.7502 ( PROT LYS 3 CA ) 2.1877 ( PROT LYS 3 CB ) 1.7502 ( PROT LYS 3 CG ) 1.7502 ( PROT LYS 3 CD ) 1.7502 ( PROT LYS 3 CE ) 1.7502 ( PROT LYS 3 NZ ) 1.7502 ( PROT LYS 3 HZ1 ) 1.7502 ( PROT LYS 3 HZ2 ) 1.7502 ( PROT LYS 3 HZ3 ) 1.7502 ( PROT LYS 3 C ) 2.1877 ( PROT LYS 3 O ) 2.1877 ( PROT ALA 4 N ) 2.1877 ( PROT ALA 4 H ) 1.7502 ( PROT ALA 4 CA ) 2.1877 ( PROT ALA 4 CB ) 1.7502 ( PROT ALA 4 C ) 2.1877 ( PROT ALA 4 O ) 2.1877 ( PROT VAL 5 N ) 2.1877 ( PROT VAL 5 H ) 1.7502 ( PROT VAL 5 CA ) 2.1877 ( PROT VAL 5 CB ) 1.7502 ( PROT VAL 5 CG1 ) 1.7502 ( PROT VAL 5 CG2 ) 1.7502 ( PROT VAL 5 C ) 2.1877 ( PROT VAL 5 O ) 2.1877 ( PROT MET 6 N ) 2.1877 ( PROT MET 6 H ) 1.7502 ( PROT MET 6 CA ) 2.1877 ( PROT MET 6 CB ) 1.7502 ( PROT MET 6 CG ) 1.7502 ( PROT MET 6 SD ) 1.7502 ( PROT MET 6 CE ) 1.7502 ( PROT MET 6 C ) 2.1877 ( PROT MET 6 O ) 2.1877 ( PROT ILE 7 N ) 2.1877 ( PROT ILE 7 H ) 1.7502 ( PROT ILE 7 CA ) 2.1877 ( PROT ILE 7 CB ) 1.7502 ( PROT ILE 7 CG2 ) 1.7502 ( PROT ILE 7 CG1 ) 1.7502 ( PROT ILE 7 CD ) 1.7502 ( PROT ILE 7 C ) 2.1877 ( PROT ILE 7 O ) 2.1877 ( PROT GLY 8 N ) 2.1877 ( PROT GLY 8 H ) 1.7502 ( PROT GLY 8 CA ) 2.1877 ( PROT GLY 8 C ) 2.1877 ( PROT GLY 8 O ) 2.1877 ( PROT ALA 9 N ) 2.1877 ( PROT ALA 9 H ) 1.7502 ( PROT ALA 9 CA ) 2.1877 ( PROT ALA 9 CB ) 1.7502 ( PROT ALA 9 C ) 2.1877 ( PROT ALA 9 O ) 2.1877 ( PROT CYS 10 N ) 2.1877 ( PROT CYS 10 H ) 1.7502 ( PROT CYS 10 CA ) 2.1877 ( PROT CYS 10 CB ) 1.7502 ( PROT CYS 10 SG ) 1.7502 ( PROT CYS 10 C ) 2.1877 ( PROT CYS 10 O ) 2.1877 ( PROT PHE 11 N ) 2.1877 ( PROT PHE 11 H ) 1.7502 ( PROT PHE 11 CA ) 2.1877 ( PROT PHE 11 CB ) 1.7502 ( PROT PHE 11 CG ) 1.7502 ( PROT PHE 11 CD1 ) 1.7502 ( PROT PHE 11 CD2 ) 1.7502 ( PROT PHE 11 CE1 ) 1.7502 ( PROT PHE 11 CE2 ) 1.7502 ( PROT PHE 11 CZ ) 1.7502 ( PROT PHE 11 C ) 2.1877 ( PROT PHE 11 O ) 2.1877 ( PROT LEU 12 N ) 2.1877 ( PROT LEU 12 H ) 1.7502 ( PROT LEU 12 CA ) 2.1877 ( PROT LEU 12 CB ) 1.7502 ( PROT LEU 12 CG ) 1.7502 ( PROT LEU 12 CD1 ) 1.7502 ( PROT LEU 12 CD2 ) 1.7502 ( PROT LEU 12 C ) 2.1877 ( PROT LEU 12 O ) 2.1877 ( PROT ILE 13 N ) 2.1877 ( PROT ILE 13 H ) 1.7502 ( PROT ILE 13 CA ) 2.1877 ( PROT ILE 13 CB ) 1.7502 ( PROT ILE 13 CG2 ) 1.7502 ( PROT ILE 13 CG1 ) 1.7502 ( PROT ILE 13 CD ) 1.7502 ( PROT ILE 13 C ) 2.1877 ( PROT ILE 13 O ) 2.1877 ( PROT ASH 14 N ) 2.1877 ( PROT ASH 14 H ) 1.7502 ( PROT ASH 14 CA ) 2.1877 ( PROT ASH 14 CB ) 1.7502 ( PROT ASH 14 CG ) 1.7502 ( PROT ASH 14 OD1 ) 1.7502 ( PROT ASH 14 OD2 ) 1.7502 ( PROT ASH 14 HD2 ) 1.7502 ( PROT ASH 14 C ) 2.1877 ( PROT ASH 14 O ) 2.1877 ( PROT PHE 15 N ) 2.1877 ( PROT PHE 15 H ) 1.7502 ( PROT PHE 15 CA ) 2.1877 ( PROT PHE 15 CB ) 1.7502 ( PROT PHE 15 CG ) 1.7502 ( PROT PHE 15 CD1 ) 1.7502 ( PROT PHE 15 CD2 ) 1.7502 ( PROT PHE 15 CE1 ) 1.7502 ( PROT PHE 15 CE2 ) 1.7502 ( PROT PHE 15 CZ ) 1.7502 ( PROT PHE 15 C ) 2.1877 ( PROT PHE 15 O ) 2.1877 ( PROT MET 16 N ) 2.1877 ( PROT MET 16 H ) 1.7502 ( PROT MET 16 CA ) 2.1877 ( PROT MET 16 CB ) 1.7502 ( PROT MET 16 CG ) 1.7502 ( PROT MET 16 SD ) 1.7502 ( PROT MET 16 CE ) 1.7502 ( PROT MET 16 C ) 2.1877 ( PROT MET 16 O ) 2.1877 ( PROT PHE 17 N ) 2.1877 ( PROT PHE 17 H ) 1.7502 ( PROT PHE 17 CA ) 2.1877 ( PROT PHE 17 CB ) 1.7502 ( PROT PHE 17 CG ) 1.7502 ( PROT PHE 17 CD1 ) 1.7502 ( PROT PHE 17 CD2 ) 1.7502 ( PROT PHE 17 CE1 ) 1.7502 ( PROT PHE 17 CE2 ) 1.7502 ( PROT PHE 17 CZ ) 1.7502 ( PROT PHE 17 C ) 2.1877 ( PROT PHE 17 O ) 2.1877 ( PROT PHE 18 N ) 2.1877 ( PROT PHE 18 H ) 1.7502 ( PROT PHE 18 CA ) 2.1877 ( PROT PHE 18 CB ) 1.7502 ( PROT PHE 18 CG ) 1.7502 ( PROT PHE 18 CD1 ) 1.7502 ( PROT PHE 18 CD2 ) 1.7502 ( PROT PHE 18 CE1 ) 1.7502 ( PROT PHE 18 CE2 ) 1.7502 ( PROT PHE 18 CZ ) 1.7502 ( PROT PHE 18 C ) 2.1877 ( PROT PHE 18 O ) 2.1877 ( PROT GLU 19 N ) 2.1877 ( PROT GLU 19 H ) 1.7502 ( PROT GLU 19 CA ) 2.1877 ( PROT GLU 19 CB ) 1.7502 ( PROT GLU 19 CG ) 1.7502 ( PROT GLU 19 CD ) 1.7502 ( PROT GLU 19 OE1 ) 1.7502 ( PROT GLU 19 OE2 ) 1.7502 ( PROT GLU 19 C ) 2.1877 ( PROT GLU 19 O ) 2.1877 ( PROT SER 20 N ) 2.1877 ( PROT SER 20 H ) 1.7502 ( PROT SER 20 CA ) 2.1877 ( PROT SER 20 CB ) 1.7502 ( PROT SER 20 OG ) 1.7502 ( PROT SER 20 HG ) 1.7502 ( PROT SER 20 C ) 2.1877 ( PROT SER 20 O ) 2.1877 ( PROT THR 21 N ) 2.1877 ( PROT THR 21 H ) 1.7502 ( PROT THR 21 CA ) 2.1877 ( PROT THR 21 CB ) 1.7502 ( PROT THR 21 OG1 ) 1.7502 ( PROT THR 21 HG1 ) 1.7502 ( PROT THR 21 CG2 ) 1.7502 ( PROT THR 21 C ) 2.1877 ( PROT THR 21 O ) 2.1877 ( PROT GLY 22 N ) 2.1877 ( PROT GLY 22 H ) 1.7502 ( PROT GLY 22 CA ) 2.1877 ( PROT GLY 22 C ) 2.1877 ( PROT GLY 22 O ) 2.1877 ( PROT SER 23 N ) 2.1877 ( PROT SER 23 H ) 1.7502 ( PROT SER 23 CA ) 2.1877 ( PROT SER 23 CB ) 1.7502 ( PROT SER 23 OG ) 1.7502 ( PROT SER 23 HG ) 1.7502 ( PROT SER 23 C ) 2.1877 ( PROT SER 23 O ) 2.1877 ( PROT GLN 24 N ) 2.1877 ( PROT GLN 24 H ) 1.7502 ( PROT GLN 24 CA ) 2.1877 ( PROT GLN 24 CB ) 1.7502 ( PROT GLN 24 CG ) 1.7502 ( PROT GLN 24 CD ) 1.7502 ( PROT GLN 24 OE1 ) 1.7502 ( PROT GLN 24 NE2 ) 1.7502 ( PROT GLN 24 HE21 ) 1.7502 ( PROT GLN 24 HE22 ) 1.7502 ( PROT GLN 24 C ) 2.1877 ( PROT GLN 24 O ) 2.1877 ( PROT GLU 25 N ) 2.1877 ( PROT GLU 25 H ) 1.7502 ( PROT GLU 25 CA ) 2.1877 ( PROT GLU 25 CB ) 1.7502 ( PROT GLU 25 CG ) 1.7502 ( PROT GLU 25 CD ) 1.7502 ( PROT GLU 25 OE1 ) 1.7502 ( PROT GLU 25 OE2 ) 1.7502 ( PROT GLU 25 C ) 2.1877 ( PROT GLU 25 O ) 2.1877 ( PROT GLN 26 N ) 2.1877 ( PROT GLN 26 H ) 1.7502 ( PROT GLN 26 CA ) 2.1877 ( PROT GLN 26 CB ) 1.7502 ( PROT GLN 26 CG ) 1.7502 ( PROT GLN 26 CD ) 1.7502 ( PROT GLN 26 OE1 ) 1.7502 ( PROT GLN 26 NE2 ) 1.7502 ( PROT GLN 26 HE21 ) 1.7502 ( PROT GLN 26 HE22 ) 1.7502 ( PROT GLN 26 C ) 2.1877 ( PROT GLN 26 O ) 2.1877 ( PROT LYS 27 N ) 2.1877 ( PROT LYS 27 H ) 1.7502 ( PROT LYS 27 CA ) 2.1877 ( PROT LYS 27 CB ) 1.7502 ( PROT LYS 27 CG ) 1.7502 ( PROT LYS 27 CD ) 1.7502 ( PROT LYS 27 CE ) 1.7502 ( PROT LYS 27 NZ ) 1.7502 ( PROT LYS 27 HZ1 ) 1.7502 ( PROT LYS 27 HZ2 ) 1.7502 ( PROT LYS 27 HZ3 ) 1.7502 ( PROT LYS 27 C ) 2.1877 ( PROT LYS 27 O ) 2.1877 ( PROT SER 28 N ) 2.1877 ( PROT SER 28 H ) 1.7502 ( PROT SER 28 CA ) 2.1877 ( PROT SER 28 CB ) 1.7502 ( PROT SER 28 OG ) 1.7502 ( PROT SER 28 HG ) 1.7502 ( PROT SER 28 C ) 2.1877 ( PROT SER 28 O ) 2.1877 ( PROT GLY 29 N ) 2.1877 ( PROT GLY 29 H ) 1.7502 ( PROT GLY 29 CA ) 2.1877 ( PROT GLY 29 C ) 2.1877 ( PROT GLY 29 O ) 2.1877 ( PROT VAL 30 N ) 2.1877 ( PROT VAL 30 H ) 1.7502 ( PROT VAL 30 CA ) 2.1877 ( PROT VAL 30 CB ) 1.7502 ( PROT VAL 30 CG1 ) 1.7502 ( PROT VAL 30 CG2 ) 1.7502 ( PROT VAL 30 C ) 2.1877 ( PROT VAL 30 O ) 2.1877 ( PROT TRP 31 N ) 2.1877 ( PROT TRP 31 H ) 1.7502 ( PROT TRP 31 CA ) 2.1877 ( PROT TRP 31 CB ) 1.7502 ( PROT TRP 31 CG ) 1.7502 ( PROT TRP 31 CD2 ) 1.7502 ( PROT TRP 31 CE2 ) 1.7502 ( PROT TRP 31 CE3 ) 1.7502 ( PROT TRP 31 CD1 ) 1.7502 ( PROT TRP 31 NE1 ) 1.7502 ( PROT TRP 31 HE1 ) 1.7502 ( PROT TRP 31 CZ2 ) 1.7502 ( PROT TRP 31 CZ3 ) 1.7502 ( PROT TRP 31 CH2 ) 1.7502 ( PROT TRP 31 C ) 2.1877 ( PROT TRP 31 OT1 ) 1.7502 ( PROT TRP 31 OT2 ) 1.7502 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.63018 7.22789 -13.21994 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00063 0.00154 0.00002 ROTATION MATRIX 1.000000 -0.000151 -0.000431 0.000151 1.000000 0.000407 0.000431 -0.000407 1.000000 AXIS OF ROTATION IS 0.665313 0.704380 -0.247404 ANGLE IS 0.04 TOTAL SQUARE DIFF IS 54.3045 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.427602 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4276" Parameter: A <- "0.4276" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.52181 7.25078 -13.40991 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.00641 0.00476 -0.03045 ROTATION MATRIX 0.999645 0.018647 0.019020 -0.018246 0.999611 -0.021080 -0.019405 0.020725 0.999597 AXIS OF ROTATION IS -0.617370 -0.567457 0.544837 ANGLE IS 1.94 CENTER OF ROTATION 13.958531 6.801331-13.404501 SHIFT IS -0.023252 TOTAL SQUARE DIFF IS 1.8222 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.242446 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4276" RDCMND substituted energy or value "?RMS" to " 0.2424" Parameter: A <- "0.4276 0.2424" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *6600 0.4276 0.2424 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 160.42" Parameter: H <- "160.42" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -37.31257 160.42307 1.46776 ENER INTERN> 10.50018 68.90207 0.00000 46.97816 9.60205 ENER EXTERN> -65.97789 -107.31714 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -37.31" Parameter: B <- "-37.31" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -107.32" Parameter: C <- "-107.32" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -65.98" Parameter: C <- " -173.30" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -173.30" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 10.50" Parameter: D <- "10.50" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 68.90" Parameter: D <- " 79.40" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 46.98" Parameter: D <- " 126.38" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 9.60" Parameter: D <- " 135.98" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 135.98" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 6600 ENER= -37.31 GRMS= 1.47 ELEC= -107.32 VDW= -65.98 RDTITL> *EXTERNAL= -173.30 INTERNAL= 135.98 USER= 0.00 HARM= 160.42 RDTITL> *BOND= 10.50 ANGL= 68.90 DIHE= 46.98 IMPR= 9.60 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21121 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21125 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 76.98587 -114.29844 0.58766 0.02000 MINI INTERN> 10.50018 68.90207 0.00000 46.97816 9.60205 MINI EXTERN> -65.97789 -107.31714 0.00000 0.00000 0.00000 MINI CONSTR> 114.29844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 110.21560 -33.22973 15.88003 0.00864 MINI INTERN> 48.97732 62.65863 0.00000 50.53193 8.55858 MINI EXTERN> -79.43519 -100.95239 0.00000 0.00000 0.00000 MINI CONSTR> 119.87672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21114 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 72.46522 37.75038 0.42206 0.00156 MINI INTERN> 10.16627 68.01800 0.00000 49.38077 9.65936 MINI EXTERN> -80.78248 -104.38880 0.00000 0.00000 0.00000 MINI CONSTR> 120.41210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 71.81385 0.65136 0.90948 0.00067 MINI INTERN> 10.39587 67.97711 0.00000 49.31759 9.63887 MINI EXTERN> -81.87796 -104.40282 0.00000 0.00000 0.00000 MINI CONSTR> 120.76519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21106 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 71.41270 0.40115 0.97075 0.00070 MINI INTERN> 10.19603 67.90873 0.00000 49.35130 9.57562 MINI EXTERN> -82.13459 -104.42950 0.00000 0.00000 0.00000 MINI CONSTR> 120.94511 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 71.02912 0.38358 0.95473 0.00072 MINI INTERN> 9.96143 67.87276 0.00000 49.36422 9.53167 MINI EXTERN> -82.30939 -104.49440 0.00000 0.00000 0.00000 MINI CONSTR> 121.10283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 70.58674 0.44238 0.33071 0.00031 MINI INTERN> 10.22122 67.08208 0.00000 49.35229 9.46315 MINI EXTERN> -82.37802 -104.36635 0.00000 0.00000 0.00000 MINI CONSTR> 121.21237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 70.28192 0.30482 0.30633 0.00032 MINI INTERN> 10.19369 66.94298 0.00000 49.34053 9.43435 MINI EXTERN> -82.61828 -104.34711 0.00000 0.00000 0.00000 MINI CONSTR> 121.33575 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21101 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 69.98269 0.29923 0.30155 0.00034 MINI INTERN> 10.18460 66.78941 0.00000 49.32387 9.40616 MINI EXTERN> -82.84485 -104.33060 0.00000 0.00000 0.00000 MINI CONSTR> 121.45411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 69.68516 0.29753 0.29694 0.00035 MINI INTERN> 10.16244 66.64809 0.00000 49.30335 9.38055 MINI EXTERN> -83.06970 -104.30830 0.00000 0.00000 0.00000 MINI CONSTR> 121.56873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21101 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 69.40064 0.28451 0.43073 0.00036 MINI INTERN> 10.28870 66.33827 0.00000 49.27336 9.33984 MINI EXTERN> -83.26274 -104.25554 0.00000 0.00000 0.00000 MINI CONSTR> 121.67876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 69.15496 0.24569 0.29601 0.00037 MINI INTERN> 10.14964 66.37455 0.00000 49.25535 9.33283 MINI EXTERN> -83.44414 -104.27691 0.00000 0.00000 0.00000 MINI CONSTR> 121.76364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 68.89642 0.25854 0.51795 0.00039 MINI INTERN> 10.28883 66.05167 0.00000 49.21820 9.28900 MINI EXTERN> -83.60577 -104.20873 0.00000 0.00000 0.00000 MINI CONSTR> 121.86322 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 68.65266 0.24376 0.42151 0.00040 MINI INTERN> 10.21460 66.00487 0.00000 49.19409 9.27417 MINI EXTERN> -83.76355 -104.21351 0.00000 0.00000 0.00000 MINI CONSTR> 121.94199 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21102 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 68.41244 0.24022 0.46098 0.00042 MINI INTERN> 10.23099 65.88229 0.00000 49.15900 9.25575 MINI EXTERN> -83.92999 -104.20890 0.00000 0.00000 0.00000 MINI CONSTR> 122.02329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 68.21414 0.19830 0.58740 0.00043 MINI INTERN> 10.30333 65.66272 0.00000 49.12617 9.22117 MINI EXTERN> -84.03653 -104.15690 0.00000 0.00000 0.00000 MINI CONSTR> 122.09418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21102 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 67.99712 0.21702 0.70632 0.00045 MINI INTERN> 10.37618 65.54851 0.00000 49.07795 9.21311 MINI EXTERN> -84.21827 -104.16943 0.00000 0.00000 0.00000 MINI CONSTR> 122.16906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 67.81652 0.18059 0.79170 0.00046 MINI INTERN> 10.36603 65.47196 0.00000 49.04731 9.19641 MINI EXTERN> -84.32934 -104.16616 0.00000 0.00000 0.00000 MINI CONSTR> 122.23031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21098 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 67.62101 0.19551 0.73082 0.00048 MINI INTERN> 10.31825 65.39571 0.00000 49.01804 9.17964 MINI EXTERN> -84.42406 -104.15297 0.00000 0.00000 0.00000 MINI CONSTR> 122.28641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 67.42251 0.19850 0.66454 0.00050 MINI INTERN> 10.29096 65.25808 0.00000 48.98525 9.15376 MINI EXTERN> -84.50301 -104.10651 0.00000 0.00000 0.00000 MINI CONSTR> 122.34398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21097 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 67.23016 0.19236 0.72812 0.00052 MINI INTERN> 10.37948 65.12066 0.00000 48.93499 9.14430 MINI EXTERN> -84.65392 -104.09870 0.00000 0.00000 0.00000 MINI CONSTR> 122.40334 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 66.99312 0.23703 0.22994 0.00022 MINI INTERN> 9.86279 65.54886 0.00000 48.92427 9.18325 MINI EXTERN> -84.79431 -104.19014 0.00000 0.00000 0.00000 MINI CONSTR> 122.45841 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21095 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 66.93177 0.06135 0.94141 0.00056 MINI INTERN> 10.28794 65.12439 0.00000 48.86865 9.13504 MINI EXTERN> -84.84634 -104.14163 0.00000 0.00000 0.00000 MINI CONSTR> 122.50372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 66.77515 0.15662 0.95064 0.00058 MINI INTERN> 10.32673 64.97352 0.00000 48.83212 9.11024 MINI EXTERN> -84.90466 -104.11277 0.00000 0.00000 0.00000 MINI CONSTR> 122.54997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21094 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 66.60545 0.16970 0.85626 0.00060 MINI INTERN> 10.32681 64.80319 0.00000 48.79860 9.07864 MINI EXTERN> -84.93908 -104.05760 0.00000 0.00000 0.00000 MINI CONSTR> 122.59489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 66.33296 0.27249 0.28803 0.00026 MINI INTERN> 9.76500 65.32968 0.00000 48.77457 9.14413 MINI EXTERN> -85.15423 -104.17806 0.00000 0.00000 0.00000 MINI CONSTR> 122.65186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21093 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 66.19618 0.13678 0.21803 0.00027 MINI INTERN> 9.82627 65.18861 0.00000 48.73694 9.12712 MINI EXTERN> -85.21214 -104.15854 0.00000 0.00000 0.00000 MINI CONSTR> 122.68791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 66.05039 0.14579 0.35977 0.00028 MINI INTERN> 9.71629 65.25505 0.00000 48.70135 9.13051 MINI EXTERN> -85.31067 -104.17832 0.00000 0.00000 0.00000 MINI CONSTR> 122.73617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21091 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 65.90908 0.14131 0.30703 0.00029 MINI INTERN> 9.77127 65.12255 0.00000 48.66176 9.11388 MINI EXTERN> -85.36710 -104.16651 0.00000 0.00000 0.00000 MINI CONSTR> 122.77322 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 65.78832 0.12076 0.40935 0.00030 MINI INTERN> 9.69104 65.16730 0.00000 48.62838 9.11623 MINI EXTERN> -85.44992 -104.17878 0.00000 0.00000 0.00000 MINI CONSTR> 122.81408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21091 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 65.63888 0.14945 0.26221 0.00031 MINI INTERN> 9.73904 65.00399 0.00000 48.58839 9.09320 MINI EXTERN> -85.48743 -104.14912 0.00000 0.00000 0.00000 MINI CONSTR> 122.85080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 65.52999 0.10889 0.48742 0.00032 MINI INTERN> 9.67839 65.05775 0.00000 48.55470 9.09593 MINI EXTERN> -85.56490 -104.18296 0.00000 0.00000 0.00000 MINI CONSTR> 122.89108 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21091 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 65.41850 0.11149 0.51661 0.00033 MINI INTERN> 9.65801 65.03536 0.00000 48.51975 9.09177 MINI EXTERN> -85.62849 -104.18443 0.00000 0.00000 0.00000 MINI CONSTR> 122.92652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 65.30824 0.11026 0.51805 0.00034 MINI INTERN> 9.64844 64.99792 0.00000 48.48410 9.08659 MINI EXTERN> -85.68904 -104.18048 0.00000 0.00000 0.00000 MINI CONSTR> 122.96072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21090 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 65.20181 0.10643 0.55042 0.00036 MINI INTERN> 9.66273 64.89732 0.00000 48.44814 9.07132 MINI EXTERN> -85.72575 -104.14588 0.00000 0.00000 0.00000 MINI CONSTR> 122.99394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 65.09245 0.10936 0.51207 0.00037 MINI INTERN> 9.65025 64.88007 0.00000 48.41269 9.06981 MINI EXTERN> -85.78854 -104.15876 0.00000 0.00000 0.00000 MINI CONSTR> 123.02693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21090 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 64.95926 0.13318 0.17856 0.00016 MINI INTERN> 9.85709 64.53475 0.00000 48.36655 9.03142 MINI EXTERN> -85.78077 -104.10071 0.00000 0.00000 0.00000 MINI CONSTR> 123.05092 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 64.90216 0.05710 0.58619 0.00040 MINI INTERN> 9.65307 64.79567 0.00000 48.34319 9.05735 MINI EXTERN> -85.88673 -104.15143 0.00000 0.00000 0.00000 MINI CONSTR> 123.09105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21088 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 64.82486 0.07730 0.72353 0.00041 MINI INTERN> 9.80848 64.62506 0.00000 48.30328 9.03904 MINI EXTERN> -85.90796 -104.16016 0.00000 0.00000 0.00000 MINI CONSTR> 123.11712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 64.67135 0.15351 0.20237 0.00018 MINI INTERN> 9.85307 64.39424 0.00000 48.26581 9.00967 MINI EXTERN> -85.90254 -104.09241 0.00000 0.00000 0.00000 MINI CONSTR> 123.14350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21088 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 64.58962 0.08174 0.16622 0.00019 MINI INTERN> 9.82273 64.39271 0.00000 48.23881 9.00784 MINI EXTERN> -85.94243 -104.10031 0.00000 0.00000 0.00000 MINI CONSTR> 123.17027 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 64.49880 0.09081 0.15740 0.00019 MINI INTERN> 9.81198 64.36234 0.00000 48.20558 9.00295 MINI EXTERN> -85.98427 -104.10081 0.00000 0.00000 0.00000 MINI CONSTR> 123.20104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21087 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 64.41104 0.08776 0.16518 0.00020 MINI INTERN> 9.81440 64.31537 0.00000 48.17220 8.99581 MINI EXTERN> -86.01911 -104.09886 0.00000 0.00000 0.00000 MINI CONSTR> 123.23123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 64.32379 0.08725 0.26476 0.00021 MINI INTERN> 9.86479 64.21603 0.00000 48.13323 8.98304 MINI EXTERN> -86.04645 -104.09004 0.00000 0.00000 0.00000 MINI CONSTR> 123.26319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21086 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 64.24519 0.07860 0.22604 0.00021 MINI INTERN> 9.83195 64.20861 0.00000 48.10543 8.97989 MINI EXTERN> -86.08066 -104.09101 0.00000 0.00000 0.00000 MINI CONSTR> 123.29098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 64.16647 0.07872 0.23690 0.00022 MINI INTERN> 9.83570 64.17465 0.00000 48.07339 8.97516 MINI EXTERN> -86.11587 -104.09645 0.00000 0.00000 0.00000 MINI CONSTR> 123.31988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21085 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 64.09946 0.06701 0.32605 0.00023 MINI INTERN> 9.85095 64.10951 0.00000 48.04247 8.96455 MINI EXTERN> -86.13267 -104.08323 0.00000 0.00000 0.00000 MINI CONSTR> 123.34787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 64.02192 0.07753 0.26949 0.00024 MINI INTERN> 9.83224 64.10848 0.00000 48.01342 8.96436 MINI EXTERN> -86.17390 -104.09822 0.00000 0.00000 0.00000 MINI CONSTR> 123.37554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21085 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 63.96222 0.05970 0.34852 0.00025 MINI INTERN> 9.84344 64.05593 0.00000 47.98557 8.95506 MINI EXTERN> -86.18736 -104.09208 0.00000 0.00000 0.00000 MINI CONSTR> 123.40166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 63.90016 0.06206 0.42924 0.00026 MINI INTERN> 9.82281 64.03717 0.00000 47.95572 8.95050 MINI EXTERN> -86.21710 -104.08008 0.00000 0.00000 0.00000 MINI CONSTR> 123.43114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21085 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 63.83422 0.06595 0.37968 0.00027 MINI INTERN> 9.81661 64.01009 0.00000 47.93048 8.94543 MINI EXTERN> -86.23694 -104.08715 0.00000 0.00000 0.00000 MINI CONSTR> 123.45569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 63.77448 0.05974 0.43273 0.00028 MINI INTERN> 9.83894 63.99666 0.00000 47.90046 8.94584 MINI EXTERN> -86.27872 -104.11070 0.00000 0.00000 0.00000 MINI CONSTR> 123.48200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21084 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 63.69654 0.07794 0.13647 0.00012 MINI INTERN> 9.74996 64.05910 0.00000 47.87730 8.95376 MINI EXTERN> -86.33544 -104.11619 0.00000 0.00000 0.00000 MINI CONSTR> 123.50804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 63.65931 0.03723 0.41997 0.00030 MINI INTERN> 9.79771 63.94136 0.00000 47.85248 8.93111 MINI EXTERN> -86.30019 -104.09617 0.00000 0.00000 0.00000 MINI CONSTR> 123.53301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21083 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 63.57125 0.08806 0.12727 0.00013 MINI INTERN> 9.74456 64.00229 0.00000 47.81988 8.94430 MINI EXTERN> -86.38483 -104.11871 0.00000 0.00000 0.00000 MINI CONSTR> 123.56376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 63.54661 0.02464 0.51297 0.00032 MINI INTERN> 9.79924 63.89449 0.00000 47.78969 8.92627 MINI EXTERN> -86.36824 -104.08592 0.00000 0.00000 0.00000 MINI CONSTR> 123.59107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21083 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 63.49236 0.05425 0.49331 0.00033 MINI INTERN> 9.83873 63.83856 0.00000 47.76361 8.91941 MINI EXTERN> -86.37826 -104.10447 0.00000 0.00000 0.00000 MINI CONSTR> 123.61478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 63.40498 0.08738 0.16004 0.00014 MINI INTERN> 9.72859 63.94623 0.00000 47.73904 8.93450 MINI EXTERN> -86.46168 -104.12600 0.00000 0.00000 0.00000 MINI CONSTR> 123.64431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21082 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 63.35757 0.04741 0.12016 0.00015 MINI INTERN> 9.73954 63.90460 0.00000 47.71573 8.92866 MINI EXTERN> -86.47295 -104.12450 0.00000 0.00000 0.00000 MINI CONSTR> 123.66649 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 63.30452 0.05305 0.19274 0.00015 MINI INTERN> 9.71906 63.91229 0.00000 47.68792 8.92823 MINI EXTERN> -86.50807 -104.13157 0.00000 0.00000 0.00000 MINI CONSTR> 123.69664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21082 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 63.25942 0.04509 0.11671 0.00016 MINI INTERN> 9.73574 63.86045 0.00000 47.66565 8.92134 MINI EXTERN> -86.51336 -104.12775 0.00000 0.00000 0.00000 MINI CONSTR> 123.71736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 63.21184 0.04758 0.23150 0.00016 MINI INTERN> 9.71683 63.87707 0.00000 47.63856 8.92208 MINI EXTERN> -86.55121 -104.13911 0.00000 0.00000 0.00000 MINI CONSTR> 123.74762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21082 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 63.16618 0.04566 0.18426 0.00017 MINI INTERN> 9.71701 63.84302 0.00000 47.61530 8.91697 MINI EXTERN> -86.56360 -104.13358 0.00000 0.00000 0.00000 MINI CONSTR> 123.77107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 63.12750 0.03868 0.25912 0.00018 MINI INTERN> 9.72189 63.83580 0.00000 47.59145 8.91582 MINI EXTERN> -86.58986 -104.14381 0.00000 0.00000 0.00000 MINI CONSTR> 123.79621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 63.08742 0.04008 0.27580 0.00018 MINI INTERN> 9.70951 63.82202 0.00000 47.56863 8.91262 MINI EXTERN> -86.60823 -104.13821 0.00000 0.00000 0.00000 MINI CONSTR> 123.82109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 63.04849 0.03894 0.28652 0.00019 MINI INTERN> 9.72410 63.79984 0.00000 47.54533 8.91027 MINI EXTERN> -86.62878 -104.14698 0.00000 0.00000 0.00000 MINI CONSTR> 123.84470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 63.01092 0.03757 0.31196 0.00020 MINI INTERN> 9.71143 63.78528 0.00000 47.52303 8.90673 MINI EXTERN> -86.64468 -104.14049 0.00000 0.00000 0.00000 MINI CONSTR> 123.86961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 62.97317 0.03775 0.29519 0.00020 MINI INTERN> 9.73181 63.75649 0.00000 47.50117 8.90390 MINI EXTERN> -86.66064 -104.15109 0.00000 0.00000 0.00000 MINI CONSTR> 123.89152 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 62.93825 0.03491 0.32550 0.00021 MINI INTERN> 9.71177 63.73854 0.00000 47.48037 8.89902 MINI EXTERN> -86.66933 -104.13792 0.00000 0.00000 0.00000 MINI CONSTR> 123.91580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 62.89285 0.04540 0.10263 0.00009 MINI INTERN> 9.73192 63.67243 0.00000 47.46173 8.89045 MINI EXTERN> -86.65764 -104.14003 0.00000 0.00000 0.00000 MINI CONSTR> 123.93399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 62.87364 0.01922 0.35398 0.00023 MINI INTERN> 9.75093 63.69633 0.00000 47.43730 8.89549 MINI EXTERN> -86.70745 -104.15913 0.00000 0.00000 0.00000 MINI CONSTR> 123.96018 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 62.84344 0.03020 0.38731 0.00024 MINI INTERN> 9.71932 63.68787 0.00000 47.41797 8.89125 MINI EXTERN> -86.71647 -104.14088 0.00000 0.00000 0.00000 MINI CONSTR> 123.98437 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 62.80945 0.03398 0.35454 0.00025 MINI INTERN> 9.74201 63.67435 0.00000 47.39522 8.89182 MINI EXTERN> -86.74534 -104.15603 0.00000 0.00000 0.00000 MINI CONSTR> 124.00742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 62.77635 0.03310 0.36708 0.00025 MINI INTERN> 9.73232 63.66493 0.00000 47.37492 8.88850 MINI EXTERN> -86.75840 -104.15853 0.00000 0.00000 0.00000 MINI CONSTR> 124.03263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 62.72313 0.05323 0.11477 0.00011 MINI INTERN> 9.73110 63.58262 0.00000 47.35602 8.87530 MINI EXTERN> -86.72625 -104.14980 0.00000 0.00000 0.00000 MINI CONSTR> 124.05412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 62.69512 0.02801 0.09182 0.00011 MINI INTERN> 9.72421 63.57749 0.00000 47.33861 8.87385 MINI EXTERN> -86.74180 -104.15241 0.00000 0.00000 0.00000 MINI CONSTR> 124.07516 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 62.66411 0.03101 0.14997 0.00012 MINI INTERN> 9.73622 63.54306 0.00000 47.31599 8.86897 MINI EXTERN> -86.74781 -104.15299 0.00000 0.00000 0.00000 MINI CONSTR> 124.10067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 62.63818 0.02592 0.09335 0.00012 MINI INTERN> 9.72240 63.54756 0.00000 47.30087 8.86852 MINI EXTERN> -86.76518 -104.15610 0.00000 0.00000 0.00000 MINI CONSTR> 124.12012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 62.61162 0.02656 0.17842 0.00013 MINI INTERN> 9.73158 63.51400 0.00000 47.27989 8.86337 MINI EXTERN> -86.76750 -104.15422 0.00000 0.00000 0.00000 MINI CONSTR> 124.14451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 62.58469 0.02693 0.14296 0.00013 MINI INTERN> 9.73090 63.50700 0.00000 47.26282 8.86207 MINI EXTERN> -86.78258 -104.16098 0.00000 0.00000 0.00000 MINI CONSTR> 124.16548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21081 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 62.56219 0.02250 0.19517 0.00014 MINI INTERN> 9.72915 63.48715 0.00000 47.24522 8.85823 MINI EXTERN> -86.78685 -104.15802 0.00000 0.00000 0.00000 MINI CONSTR> 124.18732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 62.53874 0.02346 0.22580 0.00014 MINI INTERN> 9.74242 63.47118 0.00000 47.22698 8.85639 MINI EXTERN> -86.79990 -104.16728 0.00000 0.00000 0.00000 MINI CONSTR> 124.20895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21080 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 62.51677 0.02196 0.23629 0.00015 MINI INTERN> 9.73990 63.45885 0.00000 47.21107 8.85371 MINI EXTERN> -86.80725 -104.16893 0.00000 0.00000 0.00000 MINI CONSTR> 124.22943 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 62.49367 0.02310 0.21405 0.00015 MINI INTERN> 9.72385 63.45096 0.00000 47.19581 8.85095 MINI EXTERN> -86.81402 -104.16394 0.00000 0.00000 0.00000 MINI CONSTR> 124.25006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21079 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 62.47384 0.01983 0.27110 0.00016 MINI INTERN> 9.74325 63.43314 0.00000 47.17768 8.84912 MINI EXTERN> -86.82637 -104.17461 0.00000 0.00000 0.00000 MINI CONSTR> 124.27163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 62.45261 0.02123 0.24949 0.00016 MINI INTERN> 9.73587 63.42552 0.00000 47.16354 8.84700 MINI EXTERN> -86.83430 -104.17568 0.00000 0.00000 0.00000 MINI CONSTR> 124.29067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21080 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 62.43089 0.02172 0.23497 0.00017 MINI INTERN> 9.71688 63.41826 0.00000 47.14843 8.84398 MINI EXTERN> -86.83975 -104.16885 0.00000 0.00000 0.00000 MINI CONSTR> 124.31195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 62.40418 0.02671 0.07926 0.00007 MINI INTERN> 9.71118 63.43303 0.00000 47.13279 8.84685 MINI EXTERN> -86.87271 -104.17876 0.00000 0.00000 0.00000 MINI CONSTR> 124.33182 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21079 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 62.39392 0.01026 0.27214 0.00018 MINI INTERN> 9.71254 63.39696 0.00000 47.11807 8.83926 MINI EXTERN> -86.85469 -104.17077 0.00000 0.00000 0.00000 MINI CONSTR> 124.35256 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 62.36484 0.02908 0.08668 0.00008 MINI INTERN> 9.70968 63.41245 0.00000 47.10161 8.84286 MINI EXTERN> -86.89185 -104.18302 0.00000 0.00000 0.00000 MINI CONSTR> 124.37310 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21078 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 62.35747 0.00737 0.27915 0.00020 MINI INTERN> 9.71603 63.37083 0.00000 47.08843 8.83449 MINI EXTERN> -86.86751 -104.17701 0.00000 0.00000 0.00000 MINI CONSTR> 124.39222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 62.32672 0.03075 0.09561 0.00008 MINI INTERN> 9.70730 63.39242 0.00000 47.07065 8.83874 MINI EXTERN> -86.91008 -104.18737 0.00000 0.00000 0.00000 MINI CONSTR> 124.41506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21079 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 62.31020 0.01652 0.06859 0.00009 MINI INTERN> 9.70816 63.37649 0.00000 47.05760 8.83609 MINI EXTERN> -86.91261 -104.18809 0.00000 0.00000 0.00000 MINI CONSTR> 124.43255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 62.30481 0.00539 0.31285 0.00022 MINI INTERN> 9.73198 63.32541 0.00000 47.03959 8.82842 MINI EXTERN> -86.89313 -104.18293 0.00000 0.00000 0.00000 MINI CONSTR> 124.45546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21078 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 62.27240 0.03240 0.11878 0.00009 MINI INTERN> 9.70222 63.36502 0.00000 47.02481 8.83257 MINI EXTERN> -86.93680 -104.19443 0.00000 0.00000 0.00000 MINI CONSTR> 124.47902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 62.25517 0.01723 0.08277 0.00010 MINI INTERN> 9.70343 63.34847 0.00000 47.01073 8.82995 MINI EXTERN> -86.94020 -104.19538 0.00000 0.00000 0.00000 MINI CONSTR> 124.49816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21077 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 62.23973 0.01544 0.06669 0.00010 MINI INTERN> 9.70479 63.33445 0.00000 46.99732 8.82767 MINI EXTERN> -86.94474 -104.19641 0.00000 0.00000 0.00000 MINI CONSTR> 124.51664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 62.22418 0.01556 0.15011 0.00011 MINI INTERN> 9.69735 63.34068 0.00000 46.98182 8.82672 MINI EXTERN> -86.96152 -104.20173 0.00000 0.00000 0.00000 MINI CONSTR> 124.54085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21076 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 62.20677 0.01740 0.09080 0.00011 MINI INTERN> 9.69817 63.32088 0.00000 46.96755 8.82396 MINI EXTERN> -86.96289 -104.20090 0.00000 0.00000 0.00000 MINI CONSTR> 124.56001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 62.19447 0.01230 0.16088 0.00011 MINI INTERN> 9.69754 63.32232 0.00000 46.95433 8.82293 MINI EXTERN> -86.97584 -104.20730 0.00000 0.00000 0.00000 MINI CONSTR> 124.58049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21075 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 62.18222 0.01226 0.19319 0.00012 MINI INTERN> 9.68775 63.31663 0.00000 46.94181 8.82079 MINI EXTERN> -86.98128 -104.20329 0.00000 0.00000 0.00000 MINI CONSTR> 124.59981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 62.18222 0.01226 0.19319 0.00006 STPD INTERN> 9.68775 63.31663 0.00000 46.94181 8.82079 STPD EXTERN> -86.98128 -104.20329 0.00000 0.00000 0.00000 STPD CONSTR> 124.59981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21075 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21075 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 62.18145 0.00077 0.10726 0.00000 MINI INTERN> 9.71779 63.27789 0.00000 46.94167 8.81892 MINI EXTERN> -86.96524 -104.20339 0.00000 0.00000 0.00000 MINI CONSTR> 124.59380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 61.73520 0.44625 0.02158 0.00160 MINI INTERN> 9.68854 62.70379 0.00000 46.13701 8.70765 MINI EXTERN> -87.48328 -104.29468 0.00000 0.00000 0.00000 MINI CONSTR> 126.27617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 61.72753 0.00766 0.07102 0.01034 MINI INTERN> 9.67194 62.67229 0.00000 46.06268 8.64747 MINI EXTERN> -86.94051 -104.44585 0.00000 0.00000 0.00000 MINI CONSTR> 126.05951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 61.71067 0.01687 0.07337 0.02084 MINI INTERN> 9.67899 62.67875 0.00000 46.02555 8.66862 MINI EXTERN> -86.68975 -104.42257 0.00000 0.00000 0.00000 MINI CONSTR> 125.77107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 61.69975 0.01092 0.05534 0.00849 MINI INTERN> 9.75145 62.73995 0.00000 46.05419 8.66160 MINI EXTERN> -86.93098 -104.39558 0.00000 0.00000 0.00000 MINI CONSTR> 125.81911 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 61.69331 0.00644 0.04776 0.00739 MINI INTERN> 9.75225 62.65342 0.00000 46.10449 8.67127 MINI EXTERN> -87.12059 -104.37699 0.00000 0.00000 0.00000 MINI CONSTR> 126.00946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 61.68653 0.00678 0.05477 0.01272 MINI INTERN> 9.72985 62.60974 0.00000 46.09174 8.64788 MINI EXTERN> -87.22039 -104.45248 0.00000 0.00000 0.00000 MINI CONSTR> 126.28019 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 61.67799 0.00854 0.05686 0.01121 MINI INTERN> 9.72632 62.47797 0.00000 45.99010 8.62644 MINI EXTERN> -87.27601 -104.49226 0.00000 0.00000 0.00000 MINI CONSTR> 126.62542 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 61.67055 0.00744 0.04889 0.01164 MINI INTERN> 9.72857 62.37527 0.00000 45.93507 8.60616 MINI EXTERN> -87.38274 -104.52526 0.00000 0.00000 0.00000 MINI CONSTR> 126.93348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 61.66434 0.00621 0.05049 0.01230 MINI INTERN> 9.71169 62.20329 0.00000 45.83654 8.60227 MINI EXTERN> -87.37169 -104.46034 0.00000 0.00000 0.00000 MINI CONSTR> 127.14258 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 61.65371 0.01063 0.08429 0.02225 MINI INTERN> 9.69689 62.05330 0.00000 45.69309 8.59661 MINI EXTERN> -87.33229 -104.44069 0.00000 0.00000 0.00000 MINI CONSTR> 127.38680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 61.60657 0.04715 0.19290 0.11044 MINI INTERN> 9.67822 61.45371 0.00000 45.32665 8.43204 MINI EXTERN> -87.70645 -104.19427 0.00000 0.00000 0.00000 MINI CONSTR> 128.61667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 61.57878 0.02779 0.23721 0.04679 MINI INTERN> 9.55398 60.98435 0.00000 45.17886 8.43750 MINI EXTERN> -88.78129 -103.41930 0.00000 0.00000 0.00000 MINI CONSTR> 129.62468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 61.56017 0.01861 0.27382 0.03379 MINI INTERN> 9.46864 60.61683 0.00000 45.08722 8.41593 MINI EXTERN> -89.69595 -102.69914 0.00000 0.00000 0.00000 MINI CONSTR> 130.36665 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 61.54501 0.01516 0.30020 0.02758 MINI INTERN> 9.39338 60.39192 0.00000 44.97199 8.38251 MINI EXTERN> -90.49786 -102.07493 0.00000 0.00000 0.00000 MINI CONSTR> 130.97801 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 61.53210 0.01291 0.31263 0.02385 MINI INTERN> 9.36161 60.23758 0.00000 44.85811 8.34824 MINI EXTERN> -91.21699 -101.54225 0.00000 0.00000 0.00000 MINI CONSTR> 131.48580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 61.52055 0.01155 0.32558 0.02176 MINI INTERN> 9.35116 60.13500 0.00000 44.74730 8.30979 MINI EXTERN> -91.82169 -101.11608 0.00000 0.00000 0.00000 MINI CONSTR> 131.91508 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 61.51002 0.01053 0.33267 0.01978 MINI INTERN> 9.33429 60.05621 0.00000 44.63901 8.27297 MINI EXTERN> -92.28398 -100.78407 0.00000 0.00000 0.00000 MINI CONSTR> 132.27560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 61.50010 0.00991 0.34073 0.01892 MINI INTERN> 9.30290 59.97461 0.00000 44.53086 8.24697 MINI EXTERN> -92.60862 -100.52662 0.00000 0.00000 0.00000 MINI CONSTR> 132.58000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 61.49069 0.00941 0.34243 0.01791 MINI INTERN> 9.27816 59.88238 0.00000 44.41576 8.23454 MINI EXTERN> -92.81169 -100.34309 0.00000 0.00000 0.00000 MINI CONSTR> 132.83463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 61.48157 0.00912 0.34815 0.01754 MINI INTERN> 9.28817 59.77373 0.00000 44.28443 8.22957 MINI EXTERN> -92.92465 -100.21630 0.00000 0.00000 0.00000 MINI CONSTR> 133.04661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 61.48157 0.00912 0.34815 0.02000 CONJ INTERN> 9.28817 59.77373 0.00000 44.28443 8.22957 CONJ EXTERN> -92.92465 -100.21630 0.00000 0.00000 0.00000 CONJ CONSTR> 133.04661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "7200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 1.1376 ( PROT LYS 1 HT2 ) 1.1376 ( PROT LYS 1 N ) 1.4220 ( PROT LYS 1 HT3 ) 1.1376 ( PROT LYS 1 CA ) 1.4220 ( PROT LYS 1 CB ) 1.1376 ( PROT LYS 1 CG ) 1.1376 ( PROT LYS 1 CD ) 1.1376 ( PROT LYS 1 CE ) 1.1376 ( PROT LYS 1 NZ ) 1.1376 ( PROT LYS 1 HZ1 ) 1.1376 ( PROT LYS 1 HZ2 ) 1.1376 ( PROT LYS 1 HZ3 ) 1.1376 ( PROT LYS 1 C ) 1.4220 ( PROT LYS 1 O ) 1.4220 ( PROT MET 2 N ) 1.4220 ( PROT MET 2 H ) 1.1376 ( PROT MET 2 CA ) 1.4220 ( PROT MET 2 CB ) 1.1376 ( PROT MET 2 CG ) 1.1376 ( PROT MET 2 SD ) 1.1376 ( PROT MET 2 CE ) 1.1376 ( PROT MET 2 C ) 1.4220 ( PROT MET 2 O ) 1.4220 ( PROT LYS 3 N ) 1.4220 ( PROT LYS 3 H ) 1.1376 ( PROT LYS 3 CA ) 1.4220 ( PROT LYS 3 CB ) 1.1376 ( PROT LYS 3 CG ) 1.1376 ( PROT LYS 3 CD ) 1.1376 ( PROT LYS 3 CE ) 1.1376 ( PROT LYS 3 NZ ) 1.1376 ( PROT LYS 3 HZ1 ) 1.1376 ( PROT LYS 3 HZ2 ) 1.1376 ( PROT LYS 3 HZ3 ) 1.1376 ( PROT LYS 3 C ) 1.4220 ( PROT LYS 3 O ) 1.4220 ( PROT ALA 4 N ) 1.4220 ( PROT ALA 4 H ) 1.1376 ( PROT ALA 4 CA ) 1.4220 ( PROT ALA 4 CB ) 1.1376 ( PROT ALA 4 C ) 1.4220 ( PROT ALA 4 O ) 1.4220 ( PROT VAL 5 N ) 1.4220 ( PROT VAL 5 H ) 1.1376 ( PROT VAL 5 CA ) 1.4220 ( PROT VAL 5 CB ) 1.1376 ( PROT VAL 5 CG1 ) 1.1376 ( PROT VAL 5 CG2 ) 1.1376 ( PROT VAL 5 C ) 1.4220 ( PROT VAL 5 O ) 1.4220 ( PROT MET 6 N ) 1.4220 ( PROT MET 6 H ) 1.1376 ( PROT MET 6 CA ) 1.4220 ( PROT MET 6 CB ) 1.1376 ( PROT MET 6 CG ) 1.1376 ( PROT MET 6 SD ) 1.1376 ( PROT MET 6 CE ) 1.1376 ( PROT MET 6 C ) 1.4220 ( PROT MET 6 O ) 1.4220 ( PROT ILE 7 N ) 1.4220 ( PROT ILE 7 H ) 1.1376 ( PROT ILE 7 CA ) 1.4220 ( PROT ILE 7 CB ) 1.1376 ( PROT ILE 7 CG2 ) 1.1376 ( PROT ILE 7 CG1 ) 1.1376 ( PROT ILE 7 CD ) 1.1376 ( PROT ILE 7 C ) 1.4220 ( PROT ILE 7 O ) 1.4220 ( PROT GLY 8 N ) 1.4220 ( PROT GLY 8 H ) 1.1376 ( PROT GLY 8 CA ) 1.4220 ( PROT GLY 8 C ) 1.4220 ( PROT GLY 8 O ) 1.4220 ( PROT ALA 9 N ) 1.4220 ( PROT ALA 9 H ) 1.1376 ( PROT ALA 9 CA ) 1.4220 ( PROT ALA 9 CB ) 1.1376 ( PROT ALA 9 C ) 1.4220 ( PROT ALA 9 O ) 1.4220 ( PROT CYS 10 N ) 1.4220 ( PROT CYS 10 H ) 1.1376 ( PROT CYS 10 CA ) 1.4220 ( PROT CYS 10 CB ) 1.1376 ( PROT CYS 10 SG ) 1.1376 ( PROT CYS 10 C ) 1.4220 ( PROT CYS 10 O ) 1.4220 ( PROT PHE 11 N ) 1.4220 ( PROT PHE 11 H ) 1.1376 ( PROT PHE 11 CA ) 1.4220 ( PROT PHE 11 CB ) 1.1376 ( PROT PHE 11 CG ) 1.1376 ( PROT PHE 11 CD1 ) 1.1376 ( PROT PHE 11 CD2 ) 1.1376 ( PROT PHE 11 CE1 ) 1.1376 ( PROT PHE 11 CE2 ) 1.1376 ( PROT PHE 11 CZ ) 1.1376 ( PROT PHE 11 C ) 1.4220 ( PROT PHE 11 O ) 1.4220 ( PROT LEU 12 N ) 1.4220 ( PROT LEU 12 H ) 1.1376 ( PROT LEU 12 CA ) 1.4220 ( PROT LEU 12 CB ) 1.1376 ( PROT LEU 12 CG ) 1.1376 ( PROT LEU 12 CD1 ) 1.1376 ( PROT LEU 12 CD2 ) 1.1376 ( PROT LEU 12 C ) 1.4220 ( PROT LEU 12 O ) 1.4220 ( PROT ILE 13 N ) 1.4220 ( PROT ILE 13 H ) 1.1376 ( PROT ILE 13 CA ) 1.4220 ( PROT ILE 13 CB ) 1.1376 ( PROT ILE 13 CG2 ) 1.1376 ( PROT ILE 13 CG1 ) 1.1376 ( PROT ILE 13 CD ) 1.1376 ( PROT ILE 13 C ) 1.4220 ( PROT ILE 13 O ) 1.4220 ( PROT ASH 14 N ) 1.4220 ( PROT ASH 14 H ) 1.1376 ( PROT ASH 14 CA ) 1.4220 ( PROT ASH 14 CB ) 1.1376 ( PROT ASH 14 CG ) 1.1376 ( PROT ASH 14 OD1 ) 1.1376 ( PROT ASH 14 OD2 ) 1.1376 ( PROT ASH 14 HD2 ) 1.1376 ( PROT ASH 14 C ) 1.4220 ( PROT ASH 14 O ) 1.4220 ( PROT PHE 15 N ) 1.4220 ( PROT PHE 15 H ) 1.1376 ( PROT PHE 15 CA ) 1.4220 ( PROT PHE 15 CB ) 1.1376 ( PROT PHE 15 CG ) 1.1376 ( PROT PHE 15 CD1 ) 1.1376 ( PROT PHE 15 CD2 ) 1.1376 ( PROT PHE 15 CE1 ) 1.1376 ( PROT PHE 15 CE2 ) 1.1376 ( PROT PHE 15 CZ ) 1.1376 ( PROT PHE 15 C ) 1.4220 ( PROT PHE 15 O ) 1.4220 ( PROT MET 16 N ) 1.4220 ( PROT MET 16 H ) 1.1376 ( PROT MET 16 CA ) 1.4220 ( PROT MET 16 CB ) 1.1376 ( PROT MET 16 CG ) 1.1376 ( PROT MET 16 SD ) 1.1376 ( PROT MET 16 CE ) 1.1376 ( PROT MET 16 C ) 1.4220 ( PROT MET 16 O ) 1.4220 ( PROT PHE 17 N ) 1.4220 ( PROT PHE 17 H ) 1.1376 ( PROT PHE 17 CA ) 1.4220 ( PROT PHE 17 CB ) 1.1376 ( PROT PHE 17 CG ) 1.1376 ( PROT PHE 17 CD1 ) 1.1376 ( PROT PHE 17 CD2 ) 1.1376 ( PROT PHE 17 CE1 ) 1.1376 ( PROT PHE 17 CE2 ) 1.1376 ( PROT PHE 17 CZ ) 1.1376 ( PROT PHE 17 C ) 1.4220 ( PROT PHE 17 O ) 1.4220 ( PROT PHE 18 N ) 1.4220 ( PROT PHE 18 H ) 1.1376 ( PROT PHE 18 CA ) 1.4220 ( PROT PHE 18 CB ) 1.1376 ( PROT PHE 18 CG ) 1.1376 ( PROT PHE 18 CD1 ) 1.1376 ( PROT PHE 18 CD2 ) 1.1376 ( PROT PHE 18 CE1 ) 1.1376 ( PROT PHE 18 CE2 ) 1.1376 ( PROT PHE 18 CZ ) 1.1376 ( PROT PHE 18 C ) 1.4220 ( PROT PHE 18 O ) 1.4220 ( PROT GLU 19 N ) 1.4220 ( PROT GLU 19 H ) 1.1376 ( PROT GLU 19 CA ) 1.4220 ( PROT GLU 19 CB ) 1.1376 ( PROT GLU 19 CG ) 1.1376 ( PROT GLU 19 CD ) 1.1376 ( PROT GLU 19 OE1 ) 1.1376 ( PROT GLU 19 OE2 ) 1.1376 ( PROT GLU 19 C ) 1.4220 ( PROT GLU 19 O ) 1.4220 ( PROT SER 20 N ) 1.4220 ( PROT SER 20 H ) 1.1376 ( PROT SER 20 CA ) 1.4220 ( PROT SER 20 CB ) 1.1376 ( PROT SER 20 OG ) 1.1376 ( PROT SER 20 HG ) 1.1376 ( PROT SER 20 C ) 1.4220 ( PROT SER 20 O ) 1.4220 ( PROT THR 21 N ) 1.4220 ( PROT THR 21 H ) 1.1376 ( PROT THR 21 CA ) 1.4220 ( PROT THR 21 CB ) 1.1376 ( PROT THR 21 OG1 ) 1.1376 ( PROT THR 21 HG1 ) 1.1376 ( PROT THR 21 CG2 ) 1.1376 ( PROT THR 21 C ) 1.4220 ( PROT THR 21 O ) 1.4220 ( PROT GLY 22 N ) 1.4220 ( PROT GLY 22 H ) 1.1376 ( PROT GLY 22 CA ) 1.4220 ( PROT GLY 22 C ) 1.4220 ( PROT GLY 22 O ) 1.4220 ( PROT SER 23 N ) 1.4220 ( PROT SER 23 H ) 1.1376 ( PROT SER 23 CA ) 1.4220 ( PROT SER 23 CB ) 1.1376 ( PROT SER 23 OG ) 1.1376 ( PROT SER 23 HG ) 1.1376 ( PROT SER 23 C ) 1.4220 ( PROT SER 23 O ) 1.4220 ( PROT GLN 24 N ) 1.4220 ( PROT GLN 24 H ) 1.1376 ( PROT GLN 24 CA ) 1.4220 ( PROT GLN 24 CB ) 1.1376 ( PROT GLN 24 CG ) 1.1376 ( PROT GLN 24 CD ) 1.1376 ( PROT GLN 24 OE1 ) 1.1376 ( PROT GLN 24 NE2 ) 1.1376 ( PROT GLN 24 HE21 ) 1.1376 ( PROT GLN 24 HE22 ) 1.1376 ( PROT GLN 24 C ) 1.4220 ( PROT GLN 24 O ) 1.4220 ( PROT GLU 25 N ) 1.4220 ( PROT GLU 25 H ) 1.1376 ( PROT GLU 25 CA ) 1.4220 ( PROT GLU 25 CB ) 1.1376 ( PROT GLU 25 CG ) 1.1376 ( PROT GLU 25 CD ) 1.1376 ( PROT GLU 25 OE1 ) 1.1376 ( PROT GLU 25 OE2 ) 1.1376 ( PROT GLU 25 C ) 1.4220 ( PROT GLU 25 O ) 1.4220 ( PROT GLN 26 N ) 1.4220 ( PROT GLN 26 H ) 1.1376 ( PROT GLN 26 CA ) 1.4220 ( PROT GLN 26 CB ) 1.1376 ( PROT GLN 26 CG ) 1.1376 ( PROT GLN 26 CD ) 1.1376 ( PROT GLN 26 OE1 ) 1.1376 ( PROT GLN 26 NE2 ) 1.1376 ( PROT GLN 26 HE21 ) 1.1376 ( PROT GLN 26 HE22 ) 1.1376 ( PROT GLN 26 C ) 1.4220 ( PROT GLN 26 O ) 1.4220 ( PROT LYS 27 N ) 1.4220 ( PROT LYS 27 H ) 1.1376 ( PROT LYS 27 CA ) 1.4220 ( PROT LYS 27 CB ) 1.1376 ( PROT LYS 27 CG ) 1.1376 ( PROT LYS 27 CD ) 1.1376 ( PROT LYS 27 CE ) 1.1376 ( PROT LYS 27 NZ ) 1.1376 ( PROT LYS 27 HZ1 ) 1.1376 ( PROT LYS 27 HZ2 ) 1.1376 ( PROT LYS 27 HZ3 ) 1.1376 ( PROT LYS 27 C ) 1.4220 ( PROT LYS 27 O ) 1.4220 ( PROT SER 28 N ) 1.4220 ( PROT SER 28 H ) 1.1376 ( PROT SER 28 CA ) 1.4220 ( PROT SER 28 CB ) 1.1376 ( PROT SER 28 OG ) 1.1376 ( PROT SER 28 HG ) 1.1376 ( PROT SER 28 C ) 1.4220 ( PROT SER 28 O ) 1.4220 ( PROT GLY 29 N ) 1.4220 ( PROT GLY 29 H ) 1.1376 ( PROT GLY 29 CA ) 1.4220 ( PROT GLY 29 C ) 1.4220 ( PROT GLY 29 O ) 1.4220 ( PROT VAL 30 N ) 1.4220 ( PROT VAL 30 H ) 1.1376 ( PROT VAL 30 CA ) 1.4220 ( PROT VAL 30 CB ) 1.1376 ( PROT VAL 30 CG1 ) 1.1376 ( PROT VAL 30 CG2 ) 1.1376 ( PROT VAL 30 C ) 1.4220 ( PROT VAL 30 O ) 1.4220 ( PROT TRP 31 N ) 1.4220 ( PROT TRP 31 H ) 1.1376 ( PROT TRP 31 CA ) 1.4220 ( PROT TRP 31 CB ) 1.1376 ( PROT TRP 31 CG ) 1.1376 ( PROT TRP 31 CD2 ) 1.1376 ( PROT TRP 31 CE2 ) 1.1376 ( PROT TRP 31 CE3 ) 1.1376 ( PROT TRP 31 CD1 ) 1.1376 ( PROT TRP 31 NE1 ) 1.1376 ( PROT TRP 31 HE1 ) 1.1376 ( PROT TRP 31 CZ2 ) 1.1376 ( PROT TRP 31 CZ3 ) 1.1376 ( PROT TRP 31 CH2 ) 1.1376 ( PROT TRP 31 C ) 1.4220 ( PROT TRP 31 OT1 ) 1.1376 ( PROT TRP 31 OT2 ) 1.1376 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.62908 7.22782 -13.21859 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00173 0.00160 -0.00133 ROTATION MATRIX 0.999999 -0.001078 -0.001289 0.001080 0.999998 0.001359 0.001287 -0.001361 0.999998 AXIS OF ROTATION IS 0.629164 0.595923 -0.499028 ANGLE IS 0.12 TOTAL SQUARE DIFF IS 69.5493 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.483914 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4839" Parameter: A <- "0.4839" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.52507 7.25031 -13.41076 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.00315 0.00524 -0.02959 ROTATION MATRIX 0.999646 0.018711 0.018895 -0.018310 0.999608 -0.021181 -0.019284 0.020827 0.999597 AXIS OF ROTATION IS -0.619849 -0.563361 0.546271 ANGLE IS 1.94 CENTER OF ROTATION 13.934074 6.762606-13.468923 SHIFT IS -0.021068 TOTAL SQUARE DIFF IS 2.8098 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.301061 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4839" RDCMND substituted energy or value "?RMS" to " 0.3011" Parameter: A <- "0.4839 0.3011" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *7200 0.4839 0.3011 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 133.05" Parameter: H <- "133.05" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -71.56503 133.04661 1.05214 ENER INTERN> 9.28817 59.77373 0.00000 44.28443 8.22957 ENER EXTERN> -92.92465 -100.21630 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -71.57" Parameter: B <- "-71.57" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -100.22" Parameter: C <- "-100.22" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -92.92" Parameter: C <- " -193.14" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -193.14" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 9.29" Parameter: D <- "9.29" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 59.77" Parameter: D <- " 69.06" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 44.28" Parameter: D <- " 113.34" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.23" Parameter: D <- " 121.57" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 121.57" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 7200 ENER= -71.57 GRMS= 1.05 ELEC= -100.22 VDW= -92.92 RDTITL> *EXTERNAL= -193.14 INTERNAL= 121.57 USER= 0.00 HARM= 133.05 RDTITL> *BOND= 9.29 ANGL= 59.77 DIHE= 44.28 IMPR= 8.23 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "7200" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_7200.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_7200.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 7200 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 7200 ENER= -71.57 GRMS= 1.05 ELEC= -100.22 VDW= -92.92 RDTITL> *EXTERNAL= -193.14 INTERNAL= 121.57 USER= 0.00 HARM= 133.05 RDTITL> *BOND= 9.29 ANGL= 59.77 DIHE= 44.28 IMPR= 8.23 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "7200" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_7200.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_7200.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 7200 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 7200 ENER= -71.57 GRMS= 1.05 ELEC= -100.22 VDW= -92.92 RDTITL> *EXTERNAL= -193.14 INTERNAL= 121.57 USER= 0.00 HARM= 133.05 RDTITL> *BOND= 9.29 ANGL= 59.77 DIHE= 44.28 IMPR= 8.23 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 7200 0.4839 0.3011 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "7200" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21075 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21059 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 21.40384 -92.96888 0.48786 0.02000 MINI INTERN> 9.28817 59.77373 0.00000 44.28443 8.22957 MINI EXTERN> -92.92465 -100.21630 0.00000 0.00000 0.00000 MINI CONSTR> 92.96888 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 18.96556 2.43828 1.55686 0.00150 MINI INTERN> 10.03665 60.46005 0.00000 45.55081 8.26049 MINI EXTERN> -102.78939 -98.67899 0.00000 0.00000 0.00000 MINI CONSTR> 96.12592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21042 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 18.20548 0.76008 0.73625 0.00065 MINI INTERN> 9.59906 59.45750 0.00000 45.64543 8.12927 MINI EXTERN> -101.79477 -99.04285 0.00000 0.00000 0.00000 MINI CONSTR> 96.21185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 17.99217 0.21331 1.20299 0.00067 MINI INTERN> 9.63066 59.30188 0.00000 45.60761 8.09925 MINI EXTERN> -101.83311 -99.16738 0.00000 0.00000 0.00000 MINI CONSTR> 96.35326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21043 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 17.57650 0.41568 0.29381 0.00029 MINI INTERN> 9.37207 59.18924 0.00000 45.61904 8.05021 MINI EXTERN> -101.93650 -99.18515 0.00000 0.00000 0.00000 MINI CONSTR> 96.46759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 17.35069 0.22581 0.26038 0.00030 MINI INTERN> 9.35343 59.05549 0.00000 45.62252 8.02440 MINI EXTERN> -102.08413 -99.20945 0.00000 0.00000 0.00000 MINI CONSTR> 96.58843 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21044 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 17.12955 0.22114 0.25689 0.00031 MINI INTERN> 9.33967 58.93333 0.00000 45.62471 7.99974 MINI EXTERN> -102.25995 -99.21979 0.00000 0.00000 0.00000 MINI CONSTR> 96.71184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 16.93102 0.19853 0.52822 0.00032 MINI INTERN> 9.37035 58.77690 0.00000 45.63674 7.96564 MINI EXTERN> -102.45952 -99.19935 0.00000 0.00000 0.00000 MINI CONSTR> 96.84026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21043 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 16.73000 0.20102 0.34006 0.00034 MINI INTERN> 9.34304 58.69879 0.00000 45.62342 7.95457 MINI EXTERN> -102.62464 -99.20663 0.00000 0.00000 0.00000 MINI CONSTR> 96.94145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 16.57489 0.15511 0.59196 0.00035 MINI INTERN> 9.40767 58.55285 0.00000 45.62478 7.92894 MINI EXTERN> -102.81166 -99.17416 0.00000 0.00000 0.00000 MINI CONSTR> 97.04648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21045 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 16.39967 0.17522 0.61039 0.00036 MINI INTERN> 9.41804 58.44945 0.00000 45.61529 7.91161 MINI EXTERN> -102.98289 -99.15779 0.00000 0.00000 0.00000 MINI CONSTR> 97.14597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 16.23270 0.16697 0.65427 0.00037 MINI INTERN> 9.43469 58.34519 0.00000 45.60421 7.89437 MINI EXTERN> -103.15043 -99.13757 0.00000 0.00000 0.00000 MINI CONSTR> 97.24225 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21044 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 16.07778 0.15492 0.70882 0.00039 MINI INTERN> 9.45554 58.24650 0.00000 45.59058 7.87865 MINI EXTERN> -103.30965 -99.11589 0.00000 0.00000 0.00000 MINI CONSTR> 97.33205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 15.92930 0.14848 0.66851 0.00040 MINI INTERN> 9.43962 58.18655 0.00000 45.57273 7.86906 MINI EXTERN> -103.44021 -99.10603 0.00000 0.00000 0.00000 MINI CONSTR> 97.40758 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21044 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 15.77264 0.15666 0.69087 0.00042 MINI INTERN> 9.44767 58.09544 0.00000 45.55531 7.85457 MINI EXTERN> -103.58734 -99.08542 0.00000 0.00000 0.00000 MINI CONSTR> 97.49241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 15.56815 0.20449 0.21222 0.00018 MINI INTERN> 9.21133 58.20861 0.00000 45.51903 7.86261 MINI EXTERN> -103.65306 -99.15097 0.00000 0.00000 0.00000 MINI CONSTR> 97.57060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21043 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 15.49301 0.07514 0.75502 0.00045 MINI INTERN> 9.47081 57.92997 0.00000 45.51681 7.82905 MINI EXTERN> -103.85261 -99.04365 0.00000 0.00000 0.00000 MINI CONSTR> 97.64264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 15.35425 0.13876 0.77686 0.00046 MINI INTERN> 9.47796 57.85073 0.00000 45.49526 7.81684 MINI EXTERN> -103.97762 -99.02330 0.00000 0.00000 0.00000 MINI CONSTR> 97.71437 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21039 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 15.21953 0.13472 0.81211 0.00048 MINI INTERN> 9.49252 57.76726 0.00000 45.47244 7.80437 MINI EXTERN> -104.10052 -99.00089 0.00000 0.00000 0.00000 MINI CONSTR> 97.78435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 15.00083 0.21870 0.25662 0.00021 MINI INTERN> 9.14445 57.97449 0.00000 45.42719 7.82002 MINI EXTERN> -104.12052 -99.09935 0.00000 0.00000 0.00000 MINI CONSTR> 97.85454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21039 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 14.88740 0.11343 0.19486 0.00022 MINI INTERN> 9.16443 57.88846 0.00000 45.40999 7.80802 MINI EXTERN> -104.21600 -99.07307 0.00000 0.00000 0.00000 MINI CONSTR> 97.90559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 14.75567 0.13174 0.19226 0.00022 MINI INTERN> 9.15545 57.82754 0.00000 45.38402 7.79795 MINI EXTERN> -104.31970 -99.05660 0.00000 0.00000 0.00000 MINI CONSTR> 97.96701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21037 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 14.62510 0.13056 0.19343 0.00023 MINI INTERN> 9.14343 57.77087 0.00000 45.35653 7.78839 MINI EXTERN> -104.41986 -99.04122 0.00000 0.00000 0.00000 MINI CONSTR> 98.02697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 14.49926 0.12584 0.37138 0.00024 MINI INTERN> 9.06937 57.79072 0.00000 45.32049 7.78497 MINI EXTERN> -104.50612 -99.05207 0.00000 0.00000 0.00000 MINI CONSTR> 98.09190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21037 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 14.37825 0.12101 0.24310 0.00025 MINI INTERN> 9.09957 57.68831 0.00000 45.29861 7.77241 MINI EXTERN> -104.60028 -99.01955 0.00000 0.00000 0.00000 MINI CONSTR> 98.13918 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 14.25742 0.12084 0.24856 0.00026 MINI INTERN> 9.09077 57.63485 0.00000 45.26955 7.76362 MINI EXTERN> -104.69033 -99.00295 0.00000 0.00000 0.00000 MINI CONSTR> 98.19191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 14.13997 0.11745 0.27728 0.00027 MINI INTERN> 9.07566 57.59100 0.00000 45.23938 7.75567 MINI EXTERN> -104.77599 -98.98901 0.00000 0.00000 0.00000 MINI CONSTR> 98.24327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 14.04669 0.09328 0.44633 0.00028 MINI INTERN> 9.02791 57.60159 0.00000 45.20865 7.75195 MINI EXTERN> -104.84262 -98.99200 0.00000 0.00000 0.00000 MINI CONSTR> 98.29122 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21032 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 13.93538 0.11131 0.45139 0.00029 MINI INTERN> 9.03058 57.54315 0.00000 45.17962 7.74309 MINI EXTERN> -104.92849 -98.97002 0.00000 0.00000 0.00000 MINI CONSTR> 98.33745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 13.82546 0.10992 0.47044 0.00030 MINI INTERN> 9.04061 57.48085 0.00000 45.14938 7.73402 MINI EXTERN> -105.01825 -98.94432 0.00000 0.00000 0.00000 MINI CONSTR> 98.38317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 13.72018 0.10528 0.50684 0.00031 MINI INTERN> 9.05126 57.42277 0.00000 45.11809 7.72550 MINI EXTERN> -105.10563 -98.91935 0.00000 0.00000 0.00000 MINI CONSTR> 98.42753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 13.62001 0.10017 0.48846 0.00032 MINI INTERN> 9.05068 57.37018 0.00000 45.09006 7.71794 MINI EXTERN> -105.17218 -98.90270 0.00000 0.00000 0.00000 MINI CONSTR> 98.46603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 13.51973 0.10028 0.51646 0.00033 MINI INTERN> 9.05577 57.31988 0.00000 45.05800 7.71037 MINI EXTERN> -105.25015 -98.88114 0.00000 0.00000 0.00000 MINI CONSTR> 98.50700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 13.41678 0.10295 0.53625 0.00034 MINI INTERN> 9.06039 57.27062 0.00000 45.02280 7.70321 MINI EXTERN> -105.32949 -98.85898 0.00000 0.00000 0.00000 MINI CONSTR> 98.54823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21027 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 13.31238 0.10441 0.54545 0.00036 MINI INTERN> 9.05997 57.22650 0.00000 44.98487 7.69695 MINI EXTERN> -105.40585 -98.83922 0.00000 0.00000 0.00000 MINI CONSTR> 98.58916 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 13.17578 0.13660 0.16479 0.00015 MINI INTERN> 9.07148 57.09207 0.00000 44.96274 7.68396 MINI EXTERN> -105.41861 -98.83999 0.00000 0.00000 0.00000 MINI CONSTR> 98.62414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21026 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 13.12611 0.04967 0.58600 0.00038 MINI INTERN> 9.05491 57.15148 0.00000 44.91531 7.68567 MINI EXTERN> -105.53759 -98.80629 0.00000 0.00000 0.00000 MINI CONSTR> 98.66262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 13.03262 0.09349 0.60019 0.00040 MINI INTERN> 9.05846 57.10946 0.00000 44.87831 7.68069 MINI EXTERN> -105.60406 -98.78891 0.00000 0.00000 0.00000 MINI CONSTR> 98.69867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21023 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 12.94059 0.09203 0.62341 0.00041 MINI INTERN> 9.06857 57.06589 0.00000 44.83921 7.67646 MINI EXTERN> -105.67314 -98.77101 0.00000 0.00000 0.00000 MINI CONSTR> 98.73461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 12.79246 0.14813 0.19154 0.00018 MINI INTERN> 9.04337 56.92128 0.00000 44.83463 7.65693 MINI EXTERN> -105.64171 -98.78867 0.00000 0.00000 0.00000 MINI CONSTR> 98.76663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21022 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 12.71413 0.07834 0.15324 0.00019 MINI INTERN> 9.03819 56.89613 0.00000 44.80321 7.65394 MINI EXTERN> -105.69773 -98.77407 0.00000 0.00000 0.00000 MINI CONSTR> 98.79446 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 12.62408 0.09005 0.15053 0.00019 MINI INTERN> 9.03138 56.85855 0.00000 44.77024 7.64822 MINI EXTERN> -105.75047 -98.76081 0.00000 0.00000 0.00000 MINI CONSTR> 98.82696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21021 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 12.53339 0.09068 0.15015 0.00020 MINI INTERN> 9.02406 56.82073 0.00000 44.73685 7.64231 MINI EXTERN> -105.80214 -98.74794 0.00000 0.00000 0.00000 MINI CONSTR> 98.85953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 12.44183 0.09156 0.27587 0.00021 MINI INTERN> 9.00098 56.76971 0.00000 44.71253 7.62929 MINI EXTERN> -105.82366 -98.74188 0.00000 0.00000 0.00000 MINI CONSTR> 98.89486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21021 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 12.36132 0.08051 0.20826 0.00021 MINI INTERN> 9.00037 56.74549 0.00000 44.67732 7.62780 MINI EXTERN> -105.88350 -98.72797 0.00000 0.00000 0.00000 MINI CONSTR> 98.92181 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 12.28508 0.07624 0.24043 0.00022 MINI INTERN> 8.99264 56.70684 0.00000 44.65008 7.62108 MINI EXTERN> -105.91758 -98.71752 0.00000 0.00000 0.00000 MINI CONSTR> 98.94954 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21023 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 12.21882 0.06626 0.34304 0.00023 MINI INTERN> 8.97943 56.67420 0.00000 44.62840 7.61243 MINI EXTERN> -105.93878 -98.71297 0.00000 0.00000 0.00000 MINI CONSTR> 98.97611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 12.13340 0.08542 0.21135 0.00024 MINI INTERN> 8.98234 56.64650 0.00000 44.58832 7.61287 MINI EXTERN> -106.00608 -98.69295 0.00000 0.00000 0.00000 MINI CONSTR> 99.00240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21023 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 12.07171 0.06168 0.36149 0.00025 MINI INTERN> 8.96010 56.61487 0.00000 44.57115 7.60176 MINI EXTERN> -106.01349 -98.69129 0.00000 0.00000 0.00000 MINI CONSTR> 99.02861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 11.99550 0.07621 0.37667 0.00026 MINI INTERN> 8.94122 56.58941 0.00000 44.54246 7.59535 MINI EXTERN> -106.04872 -98.68019 0.00000 0.00000 0.00000 MINI CONSTR> 99.05598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21025 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 11.92288 0.07262 0.40969 0.00027 MINI INTERN> 8.91808 56.56598 0.00000 44.51516 7.58827 MINI EXTERN> -106.07856 -98.66892 0.00000 0.00000 0.00000 MINI CONSTR> 99.08287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 11.85470 0.06818 0.39737 0.00028 MINI INTERN> 8.91638 56.53827 0.00000 44.48643 7.58477 MINI EXTERN> -106.11774 -98.65968 0.00000 0.00000 0.00000 MINI CONSTR> 99.10628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21024 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 11.78718 0.06753 0.42261 0.00029 MINI INTERN> 8.89678 56.51633 0.00000 44.45750 7.57955 MINI EXTERN> -106.14879 -98.64520 0.00000 0.00000 0.00000 MINI CONSTR> 99.13100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 11.70113 0.08604 0.13875 0.00012 MINI INTERN> 8.99866 56.46389 0.00000 44.38968 7.59642 MINI EXTERN> -106.28306 -98.61812 0.00000 0.00000 0.00000 MINI CONSTR> 99.15365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21024 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 11.66442 0.03671 0.45515 0.00031 MINI INTERN> 8.87888 56.46679 0.00000 44.40774 7.56942 MINI EXTERN> -106.20428 -98.63000 0.00000 0.00000 0.00000 MINI CONSTR> 99.17587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 11.57008 0.09434 0.13861 0.00013 MINI INTERN> 8.99497 56.40639 0.00000 44.33091 7.58928 MINI EXTERN> -106.35399 -98.59739 0.00000 0.00000 0.00000 MINI CONSTR> 99.19991 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21024 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 11.54072 0.02936 0.48766 0.00033 MINI INTERN> 8.84834 56.42579 0.00000 44.35610 7.55920 MINI EXTERN> -106.25926 -98.61066 0.00000 0.00000 0.00000 MINI CONSTR> 99.22121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 11.47994 0.06079 0.52524 0.00034 MINI INTERN> 8.84536 56.40397 0.00000 44.32912 7.55467 MINI EXTERN> -106.29511 -98.60269 0.00000 0.00000 0.00000 MINI CONSTR> 99.24461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21022 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 11.38249 0.09745 0.17016 0.00015 MINI INTERN> 9.01120 56.31740 0.00000 44.23785 7.58204 MINI EXTERN> -106.46857 -98.56472 0.00000 0.00000 0.00000 MINI CONSTR> 99.26728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 11.32962 0.05287 0.12556 0.00015 MINI INTERN> 8.97320 56.30550 0.00000 44.22397 7.57450 MINI EXTERN> -106.47264 -98.55998 0.00000 0.00000 0.00000 MINI CONSTR> 99.28507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21022 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 11.31314 0.01648 0.58304 0.00038 MINI INTERN> 8.80541 56.34756 0.00000 44.25633 7.54032 MINI EXTERN> -106.36678 -98.57733 0.00000 0.00000 0.00000 MINI CONSTR> 99.30763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 11.20881 0.10433 0.20857 0.00016 MINI INTERN> 9.02941 56.23246 0.00000 44.14872 7.57554 MINI EXTERN> -106.57385 -98.53409 0.00000 0.00000 0.00000 MINI CONSTR> 99.33062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21022 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 11.15275 0.05605 0.15881 0.00017 MINI INTERN> 8.99425 56.21854 0.00000 44.13112 7.56876 MINI EXTERN> -106.58207 -98.52736 0.00000 0.00000 0.00000 MINI CONSTR> 99.34951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 11.09774 0.05501 0.17840 0.00018 MINI INTERN> 9.00590 56.18967 0.00000 44.10142 7.56718 MINI EXTERN> -106.61819 -98.51822 0.00000 0.00000 0.00000 MINI CONSTR> 99.36998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21022 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 11.04594 0.05180 0.20212 0.00018 MINI INTERN> 9.01891 56.16204 0.00000 44.07052 7.56658 MINI EXTERN> -106.65498 -98.50670 0.00000 0.00000 0.00000 MINI CONSTR> 99.38957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 10.99192 0.05401 0.19288 0.00019 MINI INTERN> 9.01257 56.13916 0.00000 44.04548 7.56317 MINI EXTERN> -106.67934 -98.49825 0.00000 0.00000 0.00000 MINI CONSTR> 99.40912 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21020 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 10.94730 0.04462 0.29030 0.00020 MINI INTERN> 9.06638 56.10004 0.00000 44.00553 7.56715 MINI EXTERN> -106.73615 -98.48449 0.00000 0.00000 0.00000 MINI CONSTR> 99.42883 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 10.89316 0.05414 0.29048 0.00020 MINI INTERN> 9.07109 56.07063 0.00000 43.97804 7.56463 MINI EXTERN> -106.76435 -98.47582 0.00000 0.00000 0.00000 MINI CONSTR> 99.44894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21018 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 10.83855 0.05461 0.23385 0.00021 MINI INTERN> 9.02871 56.06207 0.00000 43.96106 7.55789 MINI EXTERN> -106.76870 -98.46957 0.00000 0.00000 0.00000 MINI CONSTR> 99.46709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 10.79979 0.03877 0.31751 0.00022 MINI INTERN> 9.07703 56.02700 0.00000 43.92538 7.56134 MINI EXTERN> -106.81858 -98.45722 0.00000 0.00000 0.00000 MINI CONSTR> 99.48485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21018 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 10.75563 0.04416 0.38759 0.00023 MINI INTERN> 9.10096 55.99336 0.00000 43.89727 7.56004 MINI EXTERN> -106.85224 -98.44821 0.00000 0.00000 0.00000 MINI CONSTR> 99.50445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 10.71019 0.04544 0.35458 0.00024 MINI INTERN> 9.08985 55.97846 0.00000 43.87574 7.55761 MINI EXTERN> -106.87145 -98.44033 0.00000 0.00000 0.00000 MINI CONSTR> 99.52031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21018 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 10.65010 0.06009 0.11617 0.00010 MINI INTERN> 8.89384 56.02586 0.00000 43.89864 7.53339 MINI EXTERN> -106.79059 -98.44593 0.00000 0.00000 0.00000 MINI CONSTR> 99.53489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 10.62329 0.02681 0.37487 0.00025 MINI INTERN> 9.10737 55.93201 0.00000 43.82198 7.55613 MINI EXTERN> -106.92785 -98.42114 0.00000 0.00000 0.00000 MINI CONSTR> 99.55479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21018 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 10.55773 0.06556 0.11566 0.00011 MINI INTERN> 8.88556 55.98628 0.00000 43.85026 7.52855 MINI EXTERN> -106.83455 -98.42877 0.00000 0.00000 0.00000 MINI CONSTR> 99.57040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 10.53606 0.02167 0.40548 0.00027 MINI INTERN> 9.12542 55.88042 0.00000 43.76945 7.55366 MINI EXTERN> -106.98028 -98.40283 0.00000 0.00000 0.00000 MINI CONSTR> 99.59021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21017 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 10.49596 0.04010 0.45756 0.00028 MINI INTERN> 9.10793 55.87305 0.00000 43.74878 7.54940 MINI EXTERN> -106.98819 -98.40220 0.00000 0.00000 0.00000 MINI CONSTR> 99.60720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 10.42666 0.06930 0.13290 0.00012 MINI INTERN> 8.85641 55.93656 0.00000 43.78413 7.51968 MINI EXTERN> -106.88726 -98.40465 0.00000 0.00000 0.00000 MINI CONSTR> 99.62178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21016 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 10.38853 0.03814 0.10632 0.00013 MINI INTERN> 8.88373 55.90719 0.00000 43.75622 7.52158 MINI EXTERN> -106.92115 -98.39571 0.00000 0.00000 0.00000 MINI CONSTR> 99.63667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 10.37723 0.01130 0.49714 0.00032 MINI INTERN> 9.13642 55.79257 0.00000 43.67393 7.54668 MINI EXTERN> -107.06573 -98.36456 0.00000 0.00000 0.00000 MINI CONSTR> 99.65791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21013 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 10.30325 0.07398 0.16277 0.00014 MINI INTERN> 8.82318 55.89190 0.00000 43.72109 7.51082 MINI EXTERN> -106.93374 -98.38140 0.00000 0.00000 0.00000 MINI CONSTR> 99.67142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 10.26692 0.03633 0.10335 0.00014 MINI INTERN> 8.87619 55.85188 0.00000 43.68812 7.51606 MINI EXTERN> -106.97956 -98.37122 0.00000 0.00000 0.00000 MINI CONSTR> 99.68545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21012 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 10.22292 0.04400 0.10602 0.00015 MINI INTERN> 8.86674 55.83464 0.00000 43.66464 7.51331 MINI EXTERN> -106.99724 -98.36252 0.00000 0.00000 0.00000 MINI CONSTR> 99.70336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 10.18321 0.03971 0.21953 0.00015 MINI INTERN> 8.77198 55.85730 0.00000 43.66098 7.50021 MINI EXTERN> -106.97107 -98.35770 0.00000 0.00000 0.00000 MINI CONSTR> 99.72150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21011 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 10.14134 0.04187 0.13204 0.00016 MINI INTERN> 8.82987 55.81131 0.00000 43.62441 7.50606 MINI EXTERN> -107.02081 -98.34664 0.00000 0.00000 0.00000 MINI CONSTR> 99.73715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 10.10051 0.04083 0.14592 0.00016 MINI INTERN> 8.81453 55.79938 0.00000 43.60248 7.50312 MINI EXTERN> -107.03518 -98.33815 0.00000 0.00000 0.00000 MINI CONSTR> 99.75433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 10.06865 0.03186 0.24910 0.00017 MINI INTERN> 8.74242 55.81484 0.00000 43.59797 7.49263 MINI EXTERN> -107.01639 -98.33282 0.00000 0.00000 0.00000 MINI CONSTR> 99.76999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 10.03325 0.03539 0.27535 0.00018 MINI INTERN> 8.73419 55.80621 0.00000 43.57476 7.49147 MINI EXTERN> -107.03406 -98.32504 0.00000 0.00000 0.00000 MINI CONSTR> 99.78572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21009 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 10.00022 0.03304 0.28360 0.00018 MINI INTERN> 8.71076 55.79679 0.00000 43.56102 7.48685 MINI EXTERN> -107.03708 -98.31824 0.00000 0.00000 0.00000 MINI CONSTR> 99.80012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 9.96606 0.03416 0.26997 0.00019 MINI INTERN> 8.71787 55.77567 0.00000 43.53922 7.48651 MINI EXTERN> -107.05676 -98.31072 0.00000 0.00000 0.00000 MINI CONSTR> 99.81427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21009 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 9.93109 0.03497 0.30985 0.00020 MINI INTERN> 8.69172 55.77345 0.00000 43.51957 7.48292 MINI EXTERN> -107.06542 -98.30193 0.00000 0.00000 0.00000 MINI CONSTR> 99.83078 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 9.89817 0.03291 0.29577 0.00020 MINI INTERN> 8.69944 55.74953 0.00000 43.50006 7.48193 MINI EXTERN> -107.08239 -98.29492 0.00000 0.00000 0.00000 MINI CONSTR> 99.84453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21008 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 9.86473 0.03345 0.31554 0.00021 MINI INTERN> 8.71124 55.73369 0.00000 43.47151 7.48388 MINI EXTERN> -107.10952 -98.28588 0.00000 0.00000 0.00000 MINI CONSTR> 99.85980 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 9.82250 0.04223 0.09742 0.00009 MINI INTERN> 8.89018 55.62273 0.00000 43.41376 7.50268 MINI EXTERN> -107.20699 -98.27333 0.00000 0.00000 0.00000 MINI CONSTR> 99.87347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21006 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 9.80527 0.01723 0.33287 0.00023 MINI INTERN> 8.66665 55.71781 0.00000 43.44585 7.47534 MINI EXTERN> -107.11388 -98.27342 0.00000 0.00000 0.00000 MINI CONSTR> 99.88693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 9.77401 0.03126 0.35963 0.00023 MINI INTERN> 8.67185 55.70545 0.00000 43.41924 7.47653 MINI EXTERN> -107.13679 -98.26417 0.00000 0.00000 0.00000 MINI CONSTR> 99.90191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21006 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 9.72605 0.04797 0.11297 0.00010 MINI INTERN> 8.90698 55.56415 0.00000 43.34720 7.50173 MINI EXTERN> -107.26101 -98.24986 0.00000 0.00000 0.00000 MINI CONSTR> 99.91685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 9.71592 0.01012 0.36661 0.00025 MINI INTERN> 8.63234 55.69018 0.00000 43.39156 7.46940 MINI EXTERN> -107.14435 -98.25182 0.00000 0.00000 0.00000 MINI CONSTR> 99.92863 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21006 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 9.66306 0.05287 0.11432 0.00011 MINI INTERN> 8.90540 55.53101 0.00000 43.30594 7.49984 MINI EXTERN> -107.29004 -98.23455 0.00000 0.00000 0.00000 MINI CONSTR> 99.94545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 9.63611 0.02695 0.09221 0.00011 MINI INTERN> 8.87359 55.53251 0.00000 43.29497 7.49592 MINI EXTERN> -107.28911 -98.22903 0.00000 0.00000 0.00000 MINI CONSTR> 99.95725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21006 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 9.60534 0.03076 0.15242 0.00012 MINI INTERN> 8.93814 55.48412 0.00000 43.25915 7.50175 MINI EXTERN> -107.33183 -98.21896 0.00000 0.00000 0.00000 MINI CONSTR> 99.97297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 9.60534 0.03076 0.15242 0.00014 STPD INTERN> 8.93814 55.48412 0.00000 43.25915 7.50175 STPD EXTERN> -107.33183 -98.21896 0.00000 0.00000 0.00000 STPD CONSTR> 99.97297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21006 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21006 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 9.60534 0.03076 0.15242 0.00000 MINI INTERN> 8.93814 55.48412 0.00000 43.25915 7.50175 MINI EXTERN> -107.33183 -98.21896 0.00000 0.00000 0.00000 MINI CONSTR> 99.97297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 8.38888 1.21647 0.50997 0.06299 MINI INTERN> 8.83456 54.25253 0.00000 41.88551 7.48229 MINI EXTERN> -109.03568 -96.99379 0.00000 0.00000 0.00000 MINI CONSTR> 101.96346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 8.21457 0.17431 0.35330 0.02946 MINI INTERN> 8.68788 54.24117 0.00000 41.63816 7.47279 MINI EXTERN> -109.13947 -96.98136 0.00000 0.00000 0.00000 MINI CONSTR> 102.29539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 8.05718 0.15739 0.31350 0.02835 MINI INTERN> 8.69153 53.98041 0.00000 41.33679 7.36879 MINI EXTERN> -108.01325 -97.72746 0.00000 0.00000 0.00000 MINI CONSTR> 102.42037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 7.97670 0.08048 0.27181 0.01684 MINI INTERN> 8.68598 54.12401 0.00000 41.11218 7.39372 MINI EXTERN> -107.96615 -97.84392 0.00000 0.00000 0.00000 MINI CONSTR> 102.47089 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 7.91189 0.06481 0.23100 0.01543 MINI INTERN> 8.66354 54.05052 0.00000 40.95674 7.38518 MINI EXTERN> -107.89470 -97.76314 0.00000 0.00000 0.00000 MINI CONSTR> 102.51375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 7.83190 0.07999 0.30184 0.02085 MINI INTERN> 8.68991 53.93210 0.00000 41.09101 7.28945 MINI EXTERN> -108.01071 -97.73688 0.00000 0.00000 0.00000 MINI CONSTR> 102.57701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 7.74019 0.09171 0.27700 0.02602 MINI INTERN> 8.67391 53.96551 0.00000 41.00947 7.29832 MINI EXTERN> -108.25497 -97.57867 0.00000 0.00000 0.00000 MINI CONSTR> 102.62663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 7.63418 0.10601 0.30457 0.03084 MINI INTERN> 8.62403 53.70005 0.00000 41.05287 7.33112 MINI EXTERN> -107.94021 -97.74175 0.00000 0.00000 0.00000 MINI CONSTR> 102.60806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 7.51523 0.11895 0.30226 0.03958 MINI INTERN> 8.66300 53.45414 0.00000 40.93019 7.30841 MINI EXTERN> -107.81352 -97.58596 0.00000 0.00000 0.00000 MINI CONSTR> 102.55897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 7.40025 0.11498 0.29614 0.04226 MINI INTERN> 8.62510 53.30299 0.00000 40.96281 7.22485 MINI EXTERN> -107.70863 -97.54831 0.00000 0.00000 0.00000 MINI CONSTR> 102.54146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 7.32511 0.07515 0.27962 0.02123 MINI INTERN> 8.64912 53.18464 0.00000 40.89578 7.20818 MINI EXTERN> -107.77405 -97.41286 0.00000 0.00000 0.00000 MINI CONSTR> 102.57429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 7.26292 0.06219 0.23688 0.02411 MINI INTERN> 8.66741 53.05230 0.00000 40.84018 7.26855 MINI EXTERN> -107.94080 -97.25818 0.00000 0.00000 0.00000 MINI CONSTR> 102.63346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 7.20883 0.05409 0.23455 0.01554 MINI INTERN> 8.67770 52.89433 0.00000 40.76504 7.23043 MINI EXTERN> -107.93464 -97.11052 0.00000 0.00000 0.00000 MINI CONSTR> 102.68648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 7.16446 0.04437 0.18597 0.01538 MINI INTERN> 8.58361 52.83780 0.00000 40.76972 7.24445 MINI EXTERN> -108.09388 -96.90015 0.00000 0.00000 0.00000 MINI CONSTR> 102.72292 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 7.12889 0.03557 0.17794 0.01579 MINI INTERN> 8.57912 52.63606 0.00000 40.73154 7.21834 MINI EXTERN> -107.94840 -96.81166 0.00000 0.00000 0.00000 MINI CONSTR> 102.72389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 7.08828 0.04060 0.18080 0.02084 MINI INTERN> 8.55031 52.49635 0.00000 40.76749 7.24498 MINI EXTERN> -107.78702 -96.89878 0.00000 0.00000 0.00000 MINI CONSTR> 102.71496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 7.05261 0.03567 0.17806 0.02132 MINI INTERN> 8.57030 52.47705 0.00000 40.74318 7.22494 MINI EXTERN> -107.72900 -96.93546 0.00000 0.00000 0.00000 MINI CONSTR> 102.70160 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 7.01166 0.04095 0.21418 0.02098 MINI INTERN> 8.57858 52.47124 0.00000 40.70338 7.34969 MINI EXTERN> -107.83251 -96.95454 0.00000 0.00000 0.00000 MINI CONSTR> 102.69581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 6.96543 0.04623 0.20304 0.02343 MINI INTERN> 8.59601 52.52665 0.00000 40.69248 7.35101 MINI EXTERN> -108.09898 -96.80765 0.00000 0.00000 0.00000 MINI CONSTR> 102.70591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 6.92669 0.03874 0.18438 0.01968 MINI INTERN> 8.61416 52.66844 0.00000 40.70884 7.35005 MINI EXTERN> -108.24310 -96.88386 0.00000 0.00000 0.00000 MINI CONSTR> 102.71216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 6.92669 0.03874 0.18438 0.02000 CONJ INTERN> 8.61416 52.66844 0.00000 40.70884 7.35005 CONJ EXTERN> -108.24310 -96.88386 0.00000 0.00000 0.00000 CONJ CONSTR> 102.71216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "7800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.73944 ( PROT LYS 1 HT2 ) 0.73944 ( PROT LYS 1 N ) 0.92430 ( PROT LYS 1 HT3 ) 0.73944 ( PROT LYS 1 CA ) 0.92430 ( PROT LYS 1 CB ) 0.73944 ( PROT LYS 1 CG ) 0.73944 ( PROT LYS 1 CD ) 0.73944 ( PROT LYS 1 CE ) 0.73944 ( PROT LYS 1 NZ ) 0.73944 ( PROT LYS 1 HZ1 ) 0.73944 ( PROT LYS 1 HZ2 ) 0.73944 ( PROT LYS 1 HZ3 ) 0.73944 ( PROT LYS 1 C ) 0.92430 ( PROT LYS 1 O ) 0.92430 ( PROT MET 2 N ) 0.92430 ( PROT MET 2 H ) 0.73944 ( PROT MET 2 CA ) 0.92430 ( PROT MET 2 CB ) 0.73944 ( PROT MET 2 CG ) 0.73944 ( PROT MET 2 SD ) 0.73944 ( PROT MET 2 CE ) 0.73944 ( PROT MET 2 C ) 0.92430 ( PROT MET 2 O ) 0.92430 ( PROT LYS 3 N ) 0.92430 ( PROT LYS 3 H ) 0.73944 ( PROT LYS 3 CA ) 0.92430 ( PROT LYS 3 CB ) 0.73944 ( PROT LYS 3 CG ) 0.73944 ( PROT LYS 3 CD ) 0.73944 ( PROT LYS 3 CE ) 0.73944 ( PROT LYS 3 NZ ) 0.73944 ( PROT LYS 3 HZ1 ) 0.73944 ( PROT LYS 3 HZ2 ) 0.73944 ( PROT LYS 3 HZ3 ) 0.73944 ( PROT LYS 3 C ) 0.92430 ( PROT LYS 3 O ) 0.92430 ( PROT ALA 4 N ) 0.92430 ( PROT ALA 4 H ) 0.73944 ( PROT ALA 4 CA ) 0.92430 ( PROT ALA 4 CB ) 0.73944 ( PROT ALA 4 C ) 0.92430 ( PROT ALA 4 O ) 0.92430 ( PROT VAL 5 N ) 0.92430 ( PROT VAL 5 H ) 0.73944 ( PROT VAL 5 CA ) 0.92430 ( PROT VAL 5 CB ) 0.73944 ( PROT VAL 5 CG1 ) 0.73944 ( PROT VAL 5 CG2 ) 0.73944 ( PROT VAL 5 C ) 0.92430 ( PROT VAL 5 O ) 0.92430 ( PROT MET 6 N ) 0.92430 ( PROT MET 6 H ) 0.73944 ( PROT MET 6 CA ) 0.92430 ( PROT MET 6 CB ) 0.73944 ( PROT MET 6 CG ) 0.73944 ( PROT MET 6 SD ) 0.73944 ( PROT MET 6 CE ) 0.73944 ( PROT MET 6 C ) 0.92430 ( PROT MET 6 O ) 0.92430 ( PROT ILE 7 N ) 0.92430 ( PROT ILE 7 H ) 0.73944 ( PROT ILE 7 CA ) 0.92430 ( PROT ILE 7 CB ) 0.73944 ( PROT ILE 7 CG2 ) 0.73944 ( PROT ILE 7 CG1 ) 0.73944 ( PROT ILE 7 CD ) 0.73944 ( PROT ILE 7 C ) 0.92430 ( PROT ILE 7 O ) 0.92430 ( PROT GLY 8 N ) 0.92430 ( PROT GLY 8 H ) 0.73944 ( PROT GLY 8 CA ) 0.92430 ( PROT GLY 8 C ) 0.92430 ( PROT GLY 8 O ) 0.92430 ( PROT ALA 9 N ) 0.92430 ( PROT ALA 9 H ) 0.73944 ( PROT ALA 9 CA ) 0.92430 ( PROT ALA 9 CB ) 0.73944 ( PROT ALA 9 C ) 0.92430 ( PROT ALA 9 O ) 0.92430 ( PROT CYS 10 N ) 0.92430 ( PROT CYS 10 H ) 0.73944 ( PROT CYS 10 CA ) 0.92430 ( PROT CYS 10 CB ) 0.73944 ( PROT CYS 10 SG ) 0.73944 ( PROT CYS 10 C ) 0.92430 ( PROT CYS 10 O ) 0.92430 ( PROT PHE 11 N ) 0.92430 ( PROT PHE 11 H ) 0.73944 ( PROT PHE 11 CA ) 0.92430 ( PROT PHE 11 CB ) 0.73944 ( PROT PHE 11 CG ) 0.73944 ( PROT PHE 11 CD1 ) 0.73944 ( PROT PHE 11 CD2 ) 0.73944 ( PROT PHE 11 CE1 ) 0.73944 ( PROT PHE 11 CE2 ) 0.73944 ( PROT PHE 11 CZ ) 0.73944 ( PROT PHE 11 C ) 0.92430 ( PROT PHE 11 O ) 0.92430 ( PROT LEU 12 N ) 0.92430 ( PROT LEU 12 H ) 0.73944 ( PROT LEU 12 CA ) 0.92430 ( PROT LEU 12 CB ) 0.73944 ( PROT LEU 12 CG ) 0.73944 ( PROT LEU 12 CD1 ) 0.73944 ( PROT LEU 12 CD2 ) 0.73944 ( PROT LEU 12 C ) 0.92430 ( PROT LEU 12 O ) 0.92430 ( PROT ILE 13 N ) 0.92430 ( PROT ILE 13 H ) 0.73944 ( PROT ILE 13 CA ) 0.92430 ( PROT ILE 13 CB ) 0.73944 ( PROT ILE 13 CG2 ) 0.73944 ( PROT ILE 13 CG1 ) 0.73944 ( PROT ILE 13 CD ) 0.73944 ( PROT ILE 13 C ) 0.92430 ( PROT ILE 13 O ) 0.92430 ( PROT ASH 14 N ) 0.92430 ( PROT ASH 14 H ) 0.73944 ( PROT ASH 14 CA ) 0.92430 ( PROT ASH 14 CB ) 0.73944 ( PROT ASH 14 CG ) 0.73944 ( PROT ASH 14 OD1 ) 0.73944 ( PROT ASH 14 OD2 ) 0.73944 ( PROT ASH 14 HD2 ) 0.73944 ( PROT ASH 14 C ) 0.92430 ( PROT ASH 14 O ) 0.92430 ( PROT PHE 15 N ) 0.92430 ( PROT PHE 15 H ) 0.73944 ( PROT PHE 15 CA ) 0.92430 ( PROT PHE 15 CB ) 0.73944 ( PROT PHE 15 CG ) 0.73944 ( PROT PHE 15 CD1 ) 0.73944 ( PROT PHE 15 CD2 ) 0.73944 ( PROT PHE 15 CE1 ) 0.73944 ( PROT PHE 15 CE2 ) 0.73944 ( PROT PHE 15 CZ ) 0.73944 ( PROT PHE 15 C ) 0.92430 ( PROT PHE 15 O ) 0.92430 ( PROT MET 16 N ) 0.92430 ( PROT MET 16 H ) 0.73944 ( PROT MET 16 CA ) 0.92430 ( PROT MET 16 CB ) 0.73944 ( PROT MET 16 CG ) 0.73944 ( PROT MET 16 SD ) 0.73944 ( PROT MET 16 CE ) 0.73944 ( PROT MET 16 C ) 0.92430 ( PROT MET 16 O ) 0.92430 ( PROT PHE 17 N ) 0.92430 ( PROT PHE 17 H ) 0.73944 ( PROT PHE 17 CA ) 0.92430 ( PROT PHE 17 CB ) 0.73944 ( PROT PHE 17 CG ) 0.73944 ( PROT PHE 17 CD1 ) 0.73944 ( PROT PHE 17 CD2 ) 0.73944 ( PROT PHE 17 CE1 ) 0.73944 ( PROT PHE 17 CE2 ) 0.73944 ( PROT PHE 17 CZ ) 0.73944 ( PROT PHE 17 C ) 0.92430 ( PROT PHE 17 O ) 0.92430 ( PROT PHE 18 N ) 0.92430 ( PROT PHE 18 H ) 0.73944 ( PROT PHE 18 CA ) 0.92430 ( PROT PHE 18 CB ) 0.73944 ( PROT PHE 18 CG ) 0.73944 ( PROT PHE 18 CD1 ) 0.73944 ( PROT PHE 18 CD2 ) 0.73944 ( PROT PHE 18 CE1 ) 0.73944 ( PROT PHE 18 CE2 ) 0.73944 ( PROT PHE 18 CZ ) 0.73944 ( PROT PHE 18 C ) 0.92430 ( PROT PHE 18 O ) 0.92430 ( PROT GLU 19 N ) 0.92430 ( PROT GLU 19 H ) 0.73944 ( PROT GLU 19 CA ) 0.92430 ( PROT GLU 19 CB ) 0.73944 ( PROT GLU 19 CG ) 0.73944 ( PROT GLU 19 CD ) 0.73944 ( PROT GLU 19 OE1 ) 0.73944 ( PROT GLU 19 OE2 ) 0.73944 ( PROT GLU 19 C ) 0.92430 ( PROT GLU 19 O ) 0.92430 ( PROT SER 20 N ) 0.92430 ( PROT SER 20 H ) 0.73944 ( PROT SER 20 CA ) 0.92430 ( PROT SER 20 CB ) 0.73944 ( PROT SER 20 OG ) 0.73944 ( PROT SER 20 HG ) 0.73944 ( PROT SER 20 C ) 0.92430 ( PROT SER 20 O ) 0.92430 ( PROT THR 21 N ) 0.92430 ( PROT THR 21 H ) 0.73944 ( PROT THR 21 CA ) 0.92430 ( PROT THR 21 CB ) 0.73944 ( PROT THR 21 OG1 ) 0.73944 ( PROT THR 21 HG1 ) 0.73944 ( PROT THR 21 CG2 ) 0.73944 ( PROT THR 21 C ) 0.92430 ( PROT THR 21 O ) 0.92430 ( PROT GLY 22 N ) 0.92430 ( PROT GLY 22 H ) 0.73944 ( PROT GLY 22 CA ) 0.92430 ( PROT GLY 22 C ) 0.92430 ( PROT GLY 22 O ) 0.92430 ( PROT SER 23 N ) 0.92430 ( PROT SER 23 H ) 0.73944 ( PROT SER 23 CA ) 0.92430 ( PROT SER 23 CB ) 0.73944 ( PROT SER 23 OG ) 0.73944 ( PROT SER 23 HG ) 0.73944 ( PROT SER 23 C ) 0.92430 ( PROT SER 23 O ) 0.92430 ( PROT GLN 24 N ) 0.92430 ( PROT GLN 24 H ) 0.73944 ( PROT GLN 24 CA ) 0.92430 ( PROT GLN 24 CB ) 0.73944 ( PROT GLN 24 CG ) 0.73944 ( PROT GLN 24 CD ) 0.73944 ( PROT GLN 24 OE1 ) 0.73944 ( PROT GLN 24 NE2 ) 0.73944 ( PROT GLN 24 HE21 ) 0.73944 ( PROT GLN 24 HE22 ) 0.73944 ( PROT GLN 24 C ) 0.92430 ( PROT GLN 24 O ) 0.92430 ( PROT GLU 25 N ) 0.92430 ( PROT GLU 25 H ) 0.73944 ( PROT GLU 25 CA ) 0.92430 ( PROT GLU 25 CB ) 0.73944 ( PROT GLU 25 CG ) 0.73944 ( PROT GLU 25 CD ) 0.73944 ( PROT GLU 25 OE1 ) 0.73944 ( PROT GLU 25 OE2 ) 0.73944 ( PROT GLU 25 C ) 0.92430 ( PROT GLU 25 O ) 0.92430 ( PROT GLN 26 N ) 0.92430 ( PROT GLN 26 H ) 0.73944 ( PROT GLN 26 CA ) 0.92430 ( PROT GLN 26 CB ) 0.73944 ( PROT GLN 26 CG ) 0.73944 ( PROT GLN 26 CD ) 0.73944 ( PROT GLN 26 OE1 ) 0.73944 ( PROT GLN 26 NE2 ) 0.73944 ( PROT GLN 26 HE21 ) 0.73944 ( PROT GLN 26 HE22 ) 0.73944 ( PROT GLN 26 C ) 0.92430 ( PROT GLN 26 O ) 0.92430 ( PROT LYS 27 N ) 0.92430 ( PROT LYS 27 H ) 0.73944 ( PROT LYS 27 CA ) 0.92430 ( PROT LYS 27 CB ) 0.73944 ( PROT LYS 27 CG ) 0.73944 ( PROT LYS 27 CD ) 0.73944 ( PROT LYS 27 CE ) 0.73944 ( PROT LYS 27 NZ ) 0.73944 ( PROT LYS 27 HZ1 ) 0.73944 ( PROT LYS 27 HZ2 ) 0.73944 ( PROT LYS 27 HZ3 ) 0.73944 ( PROT LYS 27 C ) 0.92430 ( PROT LYS 27 O ) 0.92430 ( PROT SER 28 N ) 0.92430 ( PROT SER 28 H ) 0.73944 ( PROT SER 28 CA ) 0.92430 ( PROT SER 28 CB ) 0.73944 ( PROT SER 28 OG ) 0.73944 ( PROT SER 28 HG ) 0.73944 ( PROT SER 28 C ) 0.92430 ( PROT SER 28 O ) 0.92430 ( PROT GLY 29 N ) 0.92430 ( PROT GLY 29 H ) 0.73944 ( PROT GLY 29 CA ) 0.92430 ( PROT GLY 29 C ) 0.92430 ( PROT GLY 29 O ) 0.92430 ( PROT VAL 30 N ) 0.92430 ( PROT VAL 30 H ) 0.73944 ( PROT VAL 30 CA ) 0.92430 ( PROT VAL 30 CB ) 0.73944 ( PROT VAL 30 CG1 ) 0.73944 ( PROT VAL 30 CG2 ) 0.73944 ( PROT VAL 30 C ) 0.92430 ( PROT VAL 30 O ) 0.92430 ( PROT TRP 31 N ) 0.92430 ( PROT TRP 31 H ) 0.73944 ( PROT TRP 31 CA ) 0.92430 ( PROT TRP 31 CB ) 0.73944 ( PROT TRP 31 CG ) 0.73944 ( PROT TRP 31 CD2 ) 0.73944 ( PROT TRP 31 CE2 ) 0.73944 ( PROT TRP 31 CE3 ) 0.73944 ( PROT TRP 31 CD1 ) 0.73944 ( PROT TRP 31 NE1 ) 0.73944 ( PROT TRP 31 HE1 ) 0.73944 ( PROT TRP 31 CZ2 ) 0.73944 ( PROT TRP 31 CZ3 ) 0.73944 ( PROT TRP 31 CH2 ) 0.73944 ( PROT TRP 31 C ) 0.92430 ( PROT TRP 31 OT1 ) 0.73944 ( PROT TRP 31 OT2 ) 0.73944 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.62906 7.22567 -13.21994 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00174 0.00375 0.00003 ROTATION MATRIX 1.000000 0.000376 0.000020 -0.000376 1.000000 -0.000041 -0.000020 0.000041 1.000000 AXIS OF ROTATION IS -0.107537 -0.054081 0.992729 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 82.7189 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.527745 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.5277" Parameter: A <- "0.5277" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.52967 7.25645 -13.41534 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.00144 -0.00090 -0.02501 ROTATION MATRIX 0.999604 0.019691 0.020098 -0.019238 0.999562 -0.022510 -0.020532 0.022115 0.999545 AXIS OF ROTATION IS -0.621379 -0.565745 0.542053 ANGLE IS 2.06 CENTER OF ROTATION 13.936574 6.801550-13.434879 SHIFT IS -0.012152 TOTAL SQUARE DIFF IS 3.5633 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.339037 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.5277" RDCMND substituted energy or value "?RMS" to " 0.3390" Parameter: A <- "0.5277 0.3390" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *7800 0.5277 0.3390 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 102.71" Parameter: H <- "102.71" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -95.78547 102.71216 0.77600 ENER INTERN> 8.61416 52.66844 0.00000 40.70884 7.35005 ENER EXTERN> -108.24310 -96.88386 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -95.79" Parameter: B <- "-95.79" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -96.88" Parameter: C <- "-96.88" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -108.24" Parameter: C <- " -205.12" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -205.12" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 8.61" Parameter: D <- "8.61" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 52.67" Parameter: D <- " 61.28" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 40.71" Parameter: D <- " 101.99" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.35" Parameter: D <- " 109.34" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 109.34" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 7800 ENER= -95.79 GRMS= 0.78 ELEC= -96.88 VDW= -108.24 RDTITL> *EXTERNAL= -205.12 INTERNAL= 109.34 USER= 0.00 HARM= 102.71 RDTITL> *BOND= 8.61 ANGL= 52.67 DIHE= 40.71 IMPR= 7.35 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 21006 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20967 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -24.41003 -71.37544 0.34202 0.02000 MINI INTERN> 8.61416 52.66844 0.00000 40.70884 7.35005 MINI EXTERN> -108.24310 -96.88386 0.00000 0.00000 0.00000 MINI CONSTR> 71.37544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -18.96693 -5.44310 7.08776 0.00360 MINI INTERN> 14.98698 53.31513 0.00000 42.31776 7.49853 MINI EXTERN> -118.09530 -93.25902 0.00000 0.00000 0.00000 MINI CONSTR> 74.26901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20950 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -26.10110 7.13417 0.25199 0.00065 MINI INTERN> 8.78857 52.41627 0.00000 42.14282 7.42847 MINI EXTERN> -117.07804 -94.07969 0.00000 0.00000 0.00000 MINI CONSTR> 74.28049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -26.33869 0.23759 0.35746 0.00028 MINI INTERN> 8.75995 52.04965 0.00000 42.04168 7.36816 MINI EXTERN> -116.40582 -94.51980 0.00000 0.00000 0.00000 MINI CONSTR> 74.36750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20947 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -26.45005 0.11136 0.47294 0.00029 MINI INTERN> 8.76959 51.93143 0.00000 42.00883 7.34368 MINI EXTERN> -116.30945 -94.63922 0.00000 0.00000 0.00000 MINI CONSTR> 74.44509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -26.57447 0.12442 0.47549 0.00030 MINI INTERN> 8.74147 51.86511 0.00000 41.97700 7.32397 MINI EXTERN> -116.27398 -94.74268 0.00000 0.00000 0.00000 MINI CONSTR> 74.53464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20947 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -26.69703 0.12256 0.49305 0.00031 MINI INTERN> 8.70728 51.81850 0.00000 41.94748 7.30749 MINI EXTERN> -116.28357 -94.82747 0.00000 0.00000 0.00000 MINI CONSTR> 74.63326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -26.81339 0.11636 0.53088 0.00032 MINI INTERN> 8.68412 51.76943 0.00000 41.92129 7.29293 MINI EXTERN> -116.32619 -94.89067 0.00000 0.00000 0.00000 MINI CONSTR> 74.73571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20947 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -26.92142 0.10803 0.57519 0.00034 MINI INTERN> 8.67165 51.71493 0.00000 41.89821 7.27997 MINI EXTERN> -116.38876 -94.93379 0.00000 0.00000 0.00000 MINI CONSTR> 74.83636 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -27.02568 0.10426 0.54195 0.00035 MINI INTERN> 8.65825 51.65855 0.00000 41.87968 7.26834 MINI EXTERN> -116.45220 -94.96254 0.00000 0.00000 0.00000 MINI CONSTR> 74.92425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20947 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -27.13628 0.11060 0.55815 0.00036 MINI INTERN> 8.63742 51.61670 0.00000 41.85744 7.25700 MINI EXTERN> -116.53460 -94.99791 0.00000 0.00000 0.00000 MINI CONSTR> 75.02768 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -27.24678 0.11051 0.56040 0.00037 MINI INTERN> 8.62150 51.56936 0.00000 41.83605 7.24573 MINI EXTERN> -116.62409 -95.02555 0.00000 0.00000 0.00000 MINI CONSTR> 75.13021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20945 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -27.38619 0.13941 0.18111 0.00016 MINI INTERN> 8.58528 51.51772 0.00000 41.81641 7.22977 MINI EXTERN> -116.69482 -95.06016 0.00000 0.00000 0.00000 MINI CONSTR> 75.21961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -27.43222 0.04603 0.62234 0.00040 MINI INTERN> 8.61405 51.46345 0.00000 41.79960 7.22636 MINI EXTERN> -116.79406 -95.05557 0.00000 0.00000 0.00000 MINI CONSTR> 75.31395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20941 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -27.53227 0.10005 0.64252 0.00042 MINI INTERN> 8.60704 51.41747 0.00000 41.77844 7.21640 MINI EXTERN> -116.89031 -95.07331 0.00000 0.00000 0.00000 MINI CONSTR> 75.41199 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -27.62839 0.09612 0.67474 0.00043 MINI INTERN> 8.60230 51.37324 0.00000 41.75704 7.20666 MINI EXTERN> -116.98741 -95.08930 0.00000 0.00000 0.00000 MINI CONSTR> 75.50907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20938 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -27.78703 0.15864 0.21933 0.00019 MINI INTERN> 8.56029 51.28777 0.00000 41.73959 7.18941 MINI EXTERN> -117.05496 -95.10796 0.00000 0.00000 0.00000 MINI CONSTR> 75.59882 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -27.86877 0.08174 0.15898 0.00019 MINI INTERN> 8.54826 51.25039 0.00000 41.72305 7.18301 MINI EXTERN> -117.13030 -95.11553 0.00000 0.00000 0.00000 MINI CONSTR> 75.67236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20938 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -27.96541 0.09664 0.15758 0.00020 MINI INTERN> 8.54202 51.19652 0.00000 41.70257 7.17394 MINI EXTERN> -117.21876 -95.12504 0.00000 0.00000 0.00000 MINI CONSTR> 75.76336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -28.06123 0.09582 0.15930 0.00021 MINI INTERN> 8.53652 51.14250 0.00000 41.68155 7.16495 MINI EXTERN> -117.30602 -95.13436 0.00000 0.00000 0.00000 MINI CONSTR> 75.85364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20936 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -28.15309 0.09186 0.30876 0.00022 MINI INTERN> 8.55280 51.06398 0.00000 41.65923 7.15397 MINI EXTERN> -117.39101 -95.14272 0.00000 0.00000 0.00000 MINI CONSTR> 75.95066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -28.24303 0.08994 0.19877 0.00022 MINI INTERN> 8.53218 51.03235 0.00000 41.63951 7.14758 MINI EXTERN> -117.46938 -95.15178 0.00000 0.00000 0.00000 MINI CONSTR> 76.02650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20935 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -28.33346 0.09042 0.20092 0.00023 MINI INTERN> 8.52793 50.98078 0.00000 41.61764 7.13946 MINI EXTERN> -117.54986 -95.16069 0.00000 0.00000 0.00000 MINI CONSTR> 76.11128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -28.42245 0.08899 0.21945 0.00024 MINI INTERN> 8.52610 50.92720 0.00000 41.59529 7.13132 MINI EXTERN> -117.62837 -95.16958 0.00000 0.00000 0.00000 MINI CONSTR> 76.19560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20937 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -28.49340 0.07096 0.37159 0.00025 MINI INTERN> 8.54819 50.85628 0.00000 41.57445 7.12303 MINI EXTERN> -117.69442 -95.17637 0.00000 0.00000 0.00000 MINI CONSTR> 76.27543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -28.57718 0.08377 0.37448 0.00026 MINI INTERN> 8.54530 50.80821 0.00000 41.55213 7.11577 MINI EXTERN> -117.76708 -95.18520 0.00000 0.00000 0.00000 MINI CONSTR> 76.35369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20935 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -28.66068 0.08351 0.38871 0.00027 MINI INTERN> 8.54350 50.75826 0.00000 41.52889 7.10830 MINI EXTERN> -117.83885 -95.19366 0.00000 0.00000 0.00000 MINI CONSTR> 76.43287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -28.74076 0.08008 0.42147 0.00028 MINI INTERN> 8.54437 50.71113 0.00000 41.50545 7.10107 MINI EXTERN> -117.90965 -95.20415 0.00000 0.00000 0.00000 MINI CONSTR> 76.51102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20934 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -28.81283 0.07206 0.47000 0.00029 MINI INTERN> 8.54837 50.65755 0.00000 41.48307 7.09325 MINI EXTERN> -117.97159 -95.20731 0.00000 0.00000 0.00000 MINI CONSTR> 76.58384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -28.88496 0.07213 0.43487 0.00030 MINI INTERN> 8.53906 50.62959 0.00000 41.46346 7.08813 MINI EXTERN> -118.03209 -95.21913 0.00000 0.00000 0.00000 MINI CONSTR> 76.64602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20932 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -28.96209 0.07713 0.45140 0.00031 MINI INTERN> 8.53558 50.58790 0.00000 41.44015 7.08092 MINI EXTERN> -118.09726 -95.22872 0.00000 0.00000 0.00000 MINI CONSTR> 76.71934 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -29.03941 0.07732 0.46216 0.00032 MINI INTERN> 8.52426 50.55037 0.00000 41.41521 7.07363 MINI EXTERN> -118.16000 -95.23439 0.00000 0.00000 0.00000 MINI CONSTR> 76.79151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20932 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -29.13546 0.09605 0.15017 0.00014 MINI INTERN> 8.46000 50.59214 0.00000 41.39354 7.06962 MINI EXTERN> -118.24872 -95.25349 0.00000 0.00000 0.00000 MINI CONSTR> 76.85144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -29.16876 0.03330 0.50104 0.00034 MINI INTERN> 8.52949 50.47351 0.00000 41.37476 7.06180 MINI EXTERN> -118.27050 -95.25420 0.00000 0.00000 0.00000 MINI CONSTR> 76.91638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20929 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -29.23932 0.07056 0.52739 0.00036 MINI INTERN> 8.51787 50.43943 0.00000 41.34946 7.05470 MINI EXTERN> -118.32747 -95.25762 0.00000 0.00000 0.00000 MINI CONSTR> 76.98432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -29.34608 0.10677 0.17430 0.00015 MINI INTERN> 8.44679 50.48978 0.00000 41.32606 7.05158 MINI EXTERN> -118.42485 -95.28118 0.00000 0.00000 0.00000 MINI CONSTR> 77.04573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20927 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -29.36357 0.01748 0.56468 0.00038 MINI INTERN> 8.52822 50.36991 0.00000 41.30951 7.04327 MINI EXTERN> -118.43554 -95.28322 0.00000 0.00000 0.00000 MINI CONSTR> 77.10428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -29.47518 0.11162 0.20243 0.00017 MINI INTERN> 8.44011 50.42900 0.00000 41.28304 7.04053 MINI EXTERN> -118.53317 -95.30008 0.00000 0.00000 0.00000 MINI CONSTR> 77.16539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20926 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -29.53234 0.05715 0.13767 0.00017 MINI INTERN> 8.43834 50.38723 0.00000 41.26522 7.03526 MINI EXTERN> -118.56816 -95.30426 0.00000 0.00000 0.00000 MINI CONSTR> 77.21404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -29.59674 0.06440 0.23844 0.00018 MINI INTERN> 8.43238 50.37332 0.00000 41.24066 7.03003 MINI EXTERN> -118.63489 -95.31705 0.00000 0.00000 0.00000 MINI CONSTR> 77.27881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20927 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -29.65492 0.05818 0.13019 0.00019 MINI INTERN> 8.43303 50.32391 0.00000 41.22389 7.02466 MINI EXTERN> -118.66453 -95.32139 0.00000 0.00000 0.00000 MINI CONSTR> 77.32552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -29.72296 0.06804 0.26542 0.00019 MINI INTERN> 8.42687 50.31092 0.00000 41.19630 7.01938 MINI EXTERN> -118.73787 -95.33457 0.00000 0.00000 0.00000 MINI CONSTR> 77.39601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20925 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -29.78695 0.06399 0.19431 0.00020 MINI INTERN> 8.42696 50.26799 0.00000 41.17706 7.01372 MINI EXTERN> -118.77799 -95.34369 0.00000 0.00000 0.00000 MINI CONSTR> 77.44900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -29.83884 0.05189 0.29411 0.00021 MINI INTERN> 8.42260 50.25608 0.00000 41.15476 7.00948 MINI EXTERN> -118.83327 -95.35255 0.00000 0.00000 0.00000 MINI CONSTR> 77.50407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20923 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -29.90700 0.06816 0.17958 0.00021 MINI INTERN> 8.41922 50.20711 0.00000 41.13484 7.00344 MINI EXTERN> -118.86982 -95.35935 0.00000 0.00000 0.00000 MINI CONSTR> 77.55756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -29.95841 0.05141 0.32116 0.00022 MINI INTERN> 8.41617 50.19481 0.00000 41.11124 6.99926 MINI EXTERN> -118.92740 -95.36780 0.00000 0.00000 0.00000 MINI CONSTR> 77.61530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20922 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -30.01111 0.05270 0.36889 0.00023 MINI INTERN> 8.42732 50.16691 0.00000 41.09245 6.99444 MINI EXTERN> -118.97571 -95.38398 0.00000 0.00000 0.00000 MINI CONSTR> 77.66746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -30.06637 0.05526 0.33496 0.00024 MINI INTERN> 8.41304 50.14314 0.00000 41.07176 6.98994 MINI EXTERN> -119.01394 -95.38533 0.00000 0.00000 0.00000 MINI CONSTR> 77.71504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20922 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -30.11723 0.05085 0.41830 0.00025 MINI INTERN> 8.42900 50.11307 0.00000 41.05245 6.98503 MINI EXTERN> -119.06355 -95.40234 0.00000 0.00000 0.00000 MINI CONSTR> 77.76911 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -30.17046 0.05323 0.37962 0.00026 MINI INTERN> 8.42033 50.08949 0.00000 41.03373 6.98073 MINI EXTERN> -119.10065 -95.40777 0.00000 0.00000 0.00000 MINI CONSTR> 77.81368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20920 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -30.23909 0.06863 0.12510 0.00011 MINI INTERN> 8.40461 50.02550 0.00000 41.01584 6.97326 MINI EXTERN> -119.11115 -95.40380 0.00000 0.00000 0.00000 MINI CONSTR> 77.85665 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -30.27047 0.03138 0.41011 0.00028 MINI INTERN> 8.41858 50.04235 0.00000 40.99534 6.97192 MINI EXTERN> -119.18250 -95.42433 0.00000 0.00000 0.00000 MINI CONSTR> 77.90818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20919 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -30.34231 0.07184 0.12972 0.00012 MINI INTERN> 8.39994 49.97363 0.00000 40.97790 6.96406 MINI EXTERN> -119.18920 -95.41923 0.00000 0.00000 0.00000 MINI CONSTR> 77.95058 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -30.36905 0.02675 0.42220 0.00030 MINI INTERN> 8.40575 50.00024 0.00000 40.95584 6.96344 MINI EXTERN> -119.26053 -95.43416 0.00000 0.00000 0.00000 MINI CONSTR> 78.00036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20917 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -30.44785 0.07880 0.13483 0.00013 MINI INTERN> 8.39488 49.92122 0.00000 40.93872 6.95459 MINI EXTERN> -119.26893 -95.43497 0.00000 0.00000 0.00000 MINI CONSTR> 78.04664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -30.46844 0.02059 0.45301 0.00032 MINI INTERN> 8.40909 49.95013 0.00000 40.91859 6.95466 MINI EXTERN> -119.34193 -95.45374 0.00000 0.00000 0.00000 MINI CONSTR> 78.09475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20915 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -30.55229 0.08385 0.14785 0.00014 MINI INTERN> 8.39036 49.86849 0.00000 40.89953 6.94502 MINI EXTERN> -119.34726 -95.45041 0.00000 0.00000 0.00000 MINI CONSTR> 78.14198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -30.59713 0.04484 0.12116 0.00014 MINI INTERN> 8.38671 49.85159 0.00000 40.88362 6.94159 MINI EXTERN> -119.38364 -95.45863 0.00000 0.00000 0.00000 MINI CONSTR> 78.18163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20914 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -30.64449 0.04736 0.12536 0.00015 MINI INTERN> 8.38448 49.82740 0.00000 40.86598 6.93719 MINI EXTERN> -119.41873 -95.46556 0.00000 0.00000 0.00000 MINI CONSTR> 78.22475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -30.69173 0.04724 0.12546 0.00015 MINI INTERN> 8.38129 49.80437 0.00000 40.84834 6.93291 MINI EXTERN> -119.45407 -95.47218 0.00000 0.00000 0.00000 MINI CONSTR> 78.26760 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20911 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -30.74069 0.04896 0.20772 0.00016 MINI INTERN> 8.38714 49.76898 0.00000 40.82881 6.92699 MINI EXTERN> -119.48844 -95.48019 0.00000 0.00000 0.00000 MINI CONSTR> 78.31601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -30.78777 0.04708 0.17165 0.00016 MINI INTERN> 8.37808 49.75187 0.00000 40.81166 6.92340 MINI EXTERN> -119.52413 -95.48522 0.00000 0.00000 0.00000 MINI CONSTR> 78.35659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20911 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -30.83215 0.04438 0.18802 0.00017 MINI INTERN> 8.37795 49.72728 0.00000 40.79519 6.91894 MINI EXTERN> -119.55681 -95.49240 0.00000 0.00000 0.00000 MINI CONSTR> 78.39771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -30.87794 0.04580 0.19483 0.00018 MINI INTERN> 8.37878 49.70466 0.00000 40.77875 6.91467 MINI EXTERN> -119.59259 -95.50172 0.00000 0.00000 0.00000 MINI CONSTR> 78.43950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20911 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -30.91810 0.04016 0.26372 0.00018 MINI INTERN> 8.37842 49.67674 0.00000 40.76146 6.90966 MINI EXTERN> -119.62051 -95.50441 0.00000 0.00000 0.00000 MINI CONSTR> 78.48055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -30.96123 0.04312 0.29781 0.00019 MINI INTERN> 8.38643 49.65543 0.00000 40.74619 6.90556 MINI EXTERN> -119.65867 -95.51791 0.00000 0.00000 0.00000 MINI CONSTR> 78.52174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20911 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -31.00305 0.04183 0.30338 0.00020 MINI INTERN> 8.38328 49.63183 0.00000 40.73057 6.90115 MINI EXTERN> -119.68783 -95.52246 0.00000 0.00000 0.00000 MINI CONSTR> 78.56041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -31.04533 0.04228 0.30769 0.00020 MINI INTERN> 8.37620 49.60905 0.00000 40.71418 6.89676 MINI EXTERN> -119.71646 -95.52437 0.00000 0.00000 0.00000 MINI CONSTR> 78.59930 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20910 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -31.08855 0.04322 0.33465 0.00021 MINI INTERN> 8.38222 49.58702 0.00000 40.69858 6.89246 MINI EXTERN> -119.75336 -95.53591 0.00000 0.00000 0.00000 MINI CONSTR> 78.64043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -31.13136 0.04282 0.31249 0.00022 MINI INTERN> 8.37015 49.56817 0.00000 40.68275 6.88858 MINI EXTERN> -119.78159 -95.53650 0.00000 0.00000 0.00000 MINI CONSTR> 78.67708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20910 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -31.17225 0.04089 0.35346 0.00023 MINI INTERN> 8.38222 49.55228 0.00000 40.66907 6.88520 MINI EXTERN> -119.82363 -95.55367 0.00000 0.00000 0.00000 MINI CONSTR> 78.71627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -31.22576 0.05351 0.11134 0.00010 MINI INTERN> 8.35196 49.55437 0.00000 40.65410 6.88420 MINI EXTERN> -119.86353 -95.55639 0.00000 0.00000 0.00000 MINI CONSTR> 78.74954 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20909 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -31.25067 0.02492 0.36608 0.00025 MINI INTERN> 8.36398 49.50781 0.00000 40.63827 6.87630 MINI EXTERN> -119.87345 -95.55260 0.00000 0.00000 0.00000 MINI CONSTR> 78.78901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -31.30777 0.05710 0.11511 0.00011 MINI INTERN> 8.34777 49.51523 0.00000 40.62522 6.87632 MINI EXTERN> -119.92639 -95.56908 0.00000 0.00000 0.00000 MINI CONSTR> 78.82315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20907 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -31.32969 0.02192 0.37419 0.00026 MINI INTERN> 8.36628 49.46436 0.00000 40.61169 6.86779 MINI EXTERN> -119.93312 -95.56808 0.00000 0.00000 0.00000 MINI CONSTR> 78.86139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -31.39376 0.06407 0.11553 0.00011 MINI INTERN> 8.34326 49.47347 0.00000 40.59569 6.86787 MINI EXTERN> -119.99171 -95.58226 0.00000 0.00000 0.00000 MINI CONSTR> 78.89992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20905 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -31.41139 0.01763 0.40563 0.00028 MINI INTERN> 8.36308 49.42274 0.00000 40.58128 6.85901 MINI EXTERN> -119.99631 -95.57877 0.00000 0.00000 0.00000 MINI CONSTR> 78.93758 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -31.47720 0.06580 0.13681 0.00012 MINI INTERN> 8.33835 49.43556 0.00000 40.56726 6.85980 MINI EXTERN> -120.05775 -95.59534 0.00000 0.00000 0.00000 MINI CONSTR> 78.97493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20905 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -31.48855 0.01135 0.43342 0.00030 MINI INTERN> 8.37295 49.37909 0.00000 40.55497 6.85047 MINI EXTERN> -120.05885 -95.59669 0.00000 0.00000 0.00000 MINI CONSTR> 79.00952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -31.55876 0.07021 0.15479 0.00013 MINI INTERN> 8.33417 49.39742 0.00000 40.54026 6.85166 MINI EXTERN> -120.12185 -95.60828 0.00000 0.00000 0.00000 MINI CONSTR> 79.04786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20905 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -31.59527 0.03651 0.10333 0.00014 MINI INTERN> 8.33256 49.37299 0.00000 40.52885 6.84726 MINI EXTERN> -120.14281 -95.61196 0.00000 0.00000 0.00000 MINI CONSTR> 79.07785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -31.63715 0.04189 0.11290 0.00014 MINI INTERN> 8.33025 49.35451 0.00000 40.51546 6.84316 MINI EXTERN> -120.17663 -95.61888 0.00000 0.00000 0.00000 MINI CONSTR> 79.11498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20904 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -31.67777 0.04062 0.19018 0.00015 MINI INTERN> 8.32722 49.34227 0.00000 40.50177 6.83953 MINI EXTERN> -120.21627 -95.62646 0.00000 0.00000 0.00000 MINI CONSTR> 79.15418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -31.71889 0.04112 0.13308 0.00015 MINI INTERN> 8.32615 49.31687 0.00000 40.48998 6.83482 MINI EXTERN> -120.24169 -95.63214 0.00000 0.00000 0.00000 MINI CONSTR> 79.18712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20903 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -31.75756 0.03866 0.16750 0.00016 MINI INTERN> 8.32123 49.30110 0.00000 40.47733 6.83091 MINI EXTERN> -120.27377 -95.63662 0.00000 0.00000 0.00000 MINI CONSTR> 79.22227 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -31.79131 0.03376 0.23614 0.00016 MINI INTERN> 8.32468 49.28893 0.00000 40.46690 6.82759 MINI EXTERN> -120.30884 -95.64614 0.00000 0.00000 0.00000 MINI CONSTR> 79.25557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20903 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -31.82733 0.03602 0.25754 0.00017 MINI INTERN> 8.31666 49.27094 0.00000 40.45448 6.82344 MINI EXTERN> -120.33437 -95.64630 0.00000 0.00000 0.00000 MINI CONSTR> 79.28783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -31.86323 0.03590 0.25694 0.00018 MINI INTERN> 8.31809 49.25552 0.00000 40.44457 6.81991 MINI EXTERN> -120.36571 -95.65469 0.00000 0.00000 0.00000 MINI CONSTR> 79.31907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20900 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -31.90064 0.03741 0.28114 0.00018 MINI INTERN> 8.32322 49.23560 0.00000 40.43464 6.81561 MINI EXTERN> -120.39760 -95.66449 0.00000 0.00000 0.00000 MINI CONSTR> 79.35238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -31.93585 0.03521 0.28352 0.00019 MINI INTERN> 8.31754 49.22122 0.00000 40.42394 6.81200 MINI EXTERN> -120.42598 -95.66762 0.00000 0.00000 0.00000 MINI CONSTR> 79.38305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20901 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -31.97217 0.03633 0.30935 0.00020 MINI INTERN> 8.31141 49.20313 0.00000 40.41242 6.80768 MINI EXTERN> -120.45336 -95.66905 0.00000 0.00000 0.00000 MINI CONSTR> 79.41560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -32.00848 0.03630 0.28755 0.00020 MINI INTERN> 8.31565 49.18461 0.00000 40.40440 6.80387 MINI EXTERN> -120.48240 -95.67911 0.00000 0.00000 0.00000 MINI CONSTR> 79.44450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20901 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -32.04319 0.03471 0.32734 0.00021 MINI INTERN> 8.30629 49.16236 0.00000 40.39225 6.79898 MINI EXTERN> -120.50322 -95.67530 0.00000 0.00000 0.00000 MINI CONSTR> 79.47544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -32.08881 0.04562 0.10330 0.00009 MINI INTERN> 8.31043 49.12384 0.00000 40.38459 6.79329 MINI EXTERN> -120.51818 -95.68374 0.00000 0.00000 0.00000 MINI CONSTR> 79.50096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20898 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -32.11074 0.02193 0.33148 0.00023 MINI INTERN> 8.31485 49.13494 0.00000 40.37730 6.79221 MINI EXTERN> -120.56735 -95.69584 0.00000 0.00000 0.00000 MINI CONSTR> 79.53315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -32.15951 0.04877 0.10827 0.00010 MINI INTERN> 8.30761 49.08779 0.00000 40.36691 6.78508 MINI EXTERN> -120.57256 -95.69379 0.00000 0.00000 0.00000 MINI CONSTR> 79.55943 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20898 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -32.17747 0.01797 0.35888 0.00024 MINI INTERN> 8.30347 49.10232 0.00000 40.35833 6.78426 MINI EXTERN> -120.61788 -95.69832 0.00000 0.00000 0.00000 MINI CONSTR> 79.59034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -32.20666 0.02918 0.43185 0.00025 MINI INTERN> 8.33020 49.07443 0.00000 40.35339 6.77925 MINI EXTERN> -120.64687 -95.71579 0.00000 0.00000 0.00000 MINI CONSTR> 79.61873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20899 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -32.26376 0.05710 0.12024 0.00011 MINI INTERN> 8.30309 49.03423 0.00000 40.34229 6.77270 MINI EXTERN> -120.65261 -95.70794 0.00000 0.00000 0.00000 MINI CONSTR> 79.64448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -32.27708 0.01332 0.38343 0.00027 MINI INTERN> 8.30480 49.05516 0.00000 40.33546 6.77284 MINI EXTERN> -120.70301 -95.71627 0.00000 0.00000 0.00000 MINI CONSTR> 79.67394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20899 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -32.33766 0.06058 0.12354 0.00012 MINI INTERN> 8.30062 48.99693 0.00000 40.32615 6.76397 MINI EXTERN> -120.71037 -95.71850 0.00000 0.00000 0.00000 MINI CONSTR> 79.70356 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -32.33766 0.06058 0.12354 0.00014 STPD INTERN> 8.30062 48.99693 0.00000 40.32615 6.76397 STPD EXTERN> -120.71037 -95.71850 0.00000 0.00000 0.00000 STPD CONSTR> 79.70356 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20899 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20899 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -32.33766 0.06058 0.12354 0.00000 MINI INTERN> 8.30062 48.99693 0.00000 40.32615 6.76397 MINI EXTERN> -120.71037 -95.71850 0.00000 0.00000 0.00000 MINI CONSTR> 79.70356 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -34.01502 1.67736 1.23929 0.16155 MINI INTERN> 8.78680 47.46524 0.00000 40.02040 6.45238 MINI EXTERN> -123.64688 -96.00546 0.00000 0.00000 0.00000 MINI CONSTR> 82.91249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -34.89511 0.88010 0.45114 0.04523 MINI INTERN> 8.12270 46.86622 0.00000 40.03364 6.31092 MINI EXTERN> -125.83176 -96.03144 0.00000 0.00000 0.00000 MINI CONSTR> 85.63461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -35.20597 0.31085 0.56607 0.04090 MINI INTERN> 8.19180 46.68838 0.00000 39.61898 6.26540 MINI EXTERN> -126.15754 -96.13985 0.00000 0.00000 0.00000 MINI CONSTR> 86.32686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -35.63291 0.42694 0.84546 0.08863 MINI INTERN> 8.26946 46.31585 0.00000 38.88834 6.22401 MINI EXTERN> -125.88794 -96.35501 0.00000 0.00000 0.00000 MINI CONSTR> 86.91237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -35.93384 0.30093 0.50365 0.05477 MINI INTERN> 8.09469 46.44447 0.00000 38.44741 6.16377 MINI EXTERN> -125.90205 -96.43577 0.00000 0.00000 0.00000 MINI CONSTR> 87.25364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -36.15452 0.22068 0.36935 0.04117 MINI INTERN> 8.04106 46.32797 0.00000 38.27322 6.18230 MINI EXTERN> -126.02550 -96.33002 0.00000 0.00000 0.00000 MINI CONSTR> 87.37644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -36.34577 0.19124 0.54675 0.03985 MINI INTERN> 8.03231 46.10530 0.00000 38.28248 6.17283 MINI EXTERN> -125.93719 -96.27438 0.00000 0.00000 0.00000 MINI CONSTR> 87.27289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -36.55862 0.21285 0.45974 0.03438 MINI INTERN> 7.86999 46.08370 0.00000 38.24118 6.12880 MINI EXTERN> -125.69110 -96.28122 0.00000 0.00000 0.00000 MINI CONSTR> 87.09004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -36.71475 0.15613 0.42934 0.03792 MINI INTERN> 7.85347 45.89606 0.00000 38.31740 6.11683 MINI EXTERN> -125.45455 -96.32483 0.00000 0.00000 0.00000 MINI CONSTR> 86.88088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -36.89159 0.17684 0.38119 0.03409 MINI INTERN> 7.87133 45.95139 0.00000 38.48131 6.10417 MINI EXTERN> -125.62918 -96.28271 0.00000 0.00000 0.00000 MINI CONSTR> 86.61210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -37.01546 0.12387 0.35414 0.03312 MINI INTERN> 7.90988 46.20504 0.00000 38.49674 6.07562 MINI EXTERN> -125.82777 -96.24759 0.00000 0.00000 0.00000 MINI CONSTR> 86.37263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -37.19783 0.18237 0.40789 0.05029 MINI INTERN> 8.12942 46.61233 0.00000 38.45769 6.14240 MINI EXTERN> -126.06620 -96.41549 0.00000 0.00000 0.00000 MINI CONSTR> 85.94201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -37.34019 0.14236 0.35836 0.03321 MINI INTERN> 8.13908 46.93279 0.00000 38.32352 6.17796 MINI EXTERN> -125.85116 -96.63599 0.00000 0.00000 0.00000 MINI CONSTR> 85.57362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -37.42449 0.08430 0.31237 0.02329 MINI INTERN> 8.07018 47.03743 0.00000 38.35236 6.18002 MINI EXTERN> -125.61536 -96.77047 0.00000 0.00000 0.00000 MINI CONSTR> 85.32135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -37.49759 0.07310 0.29516 0.01866 MINI INTERN> 8.08628 46.99383 0.00000 38.38323 6.19166 MINI EXTERN> -125.41878 -96.79991 0.00000 0.00000 0.00000 MINI CONSTR> 85.06611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -37.57325 0.07565 0.27950 0.02263 MINI INTERN> 8.01135 47.14322 0.00000 38.54545 6.14230 MINI EXTERN> -125.46259 -96.70792 0.00000 0.00000 0.00000 MINI CONSTR> 84.75495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -37.66767 0.09442 0.37421 0.03708 MINI INTERN> 7.95861 47.34433 0.00000 38.67450 6.30626 MINI EXTERN> -125.58689 -96.68153 0.00000 0.00000 0.00000 MINI CONSTR> 84.31705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -37.80441 0.13674 0.44814 0.04864 MINI INTERN> 7.94669 47.37982 0.00000 38.77549 6.44887 MINI EXTERN> -125.20510 -96.81338 0.00000 0.00000 0.00000 MINI CONSTR> 83.66319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -37.97810 0.17369 0.55244 0.07275 MINI INTERN> 8.03347 47.36728 0.00000 39.10168 6.53194 MINI EXTERN> -124.77425 -97.14080 0.00000 0.00000 0.00000 MINI CONSTR> 82.90258 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -38.15198 0.17388 0.55543 0.04785 MINI INTERN> 8.15194 47.69640 0.00000 39.10647 6.56427 MINI EXTERN> -124.43779 -97.49098 0.00000 0.00000 0.00000 MINI CONSTR> 82.25771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -38.15198 0.17388 0.55543 0.02000 CONJ INTERN> 8.15194 47.69640 0.00000 39.10647 6.56427 CONJ EXTERN> -124.43779 -97.49098 0.00000 0.00000 0.00000 CONJ CONSTR> 82.25771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "8400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.48064 ( PROT LYS 1 HT2 ) 0.48064 ( PROT LYS 1 N ) 0.60080 ( PROT LYS 1 HT3 ) 0.48064 ( PROT LYS 1 CA ) 0.60080 ( PROT LYS 1 CB ) 0.48064 ( PROT LYS 1 CG ) 0.48064 ( PROT LYS 1 CD ) 0.48064 ( PROT LYS 1 CE ) 0.48064 ( PROT LYS 1 NZ ) 0.48064 ( PROT LYS 1 HZ1 ) 0.48064 ( PROT LYS 1 HZ2 ) 0.48064 ( PROT LYS 1 HZ3 ) 0.48064 ( PROT LYS 1 C ) 0.60080 ( PROT LYS 1 O ) 0.60080 ( PROT MET 2 N ) 0.60080 ( PROT MET 2 H ) 0.48064 ( PROT MET 2 CA ) 0.60080 ( PROT MET 2 CB ) 0.48064 ( PROT MET 2 CG ) 0.48064 ( PROT MET 2 SD ) 0.48064 ( PROT MET 2 CE ) 0.48064 ( PROT MET 2 C ) 0.60080 ( PROT MET 2 O ) 0.60080 ( PROT LYS 3 N ) 0.60080 ( PROT LYS 3 H ) 0.48064 ( PROT LYS 3 CA ) 0.60080 ( PROT LYS 3 CB ) 0.48064 ( PROT LYS 3 CG ) 0.48064 ( PROT LYS 3 CD ) 0.48064 ( PROT LYS 3 CE ) 0.48064 ( PROT LYS 3 NZ ) 0.48064 ( PROT LYS 3 HZ1 ) 0.48064 ( PROT LYS 3 HZ2 ) 0.48064 ( PROT LYS 3 HZ3 ) 0.48064 ( PROT LYS 3 C ) 0.60080 ( PROT LYS 3 O ) 0.60080 ( PROT ALA 4 N ) 0.60080 ( PROT ALA 4 H ) 0.48064 ( PROT ALA 4 CA ) 0.60080 ( PROT ALA 4 CB ) 0.48064 ( PROT ALA 4 C ) 0.60080 ( PROT ALA 4 O ) 0.60080 ( PROT VAL 5 N ) 0.60080 ( PROT VAL 5 H ) 0.48064 ( PROT VAL 5 CA ) 0.60080 ( PROT VAL 5 CB ) 0.48064 ( PROT VAL 5 CG1 ) 0.48064 ( PROT VAL 5 CG2 ) 0.48064 ( PROT VAL 5 C ) 0.60080 ( PROT VAL 5 O ) 0.60080 ( PROT MET 6 N ) 0.60080 ( PROT MET 6 H ) 0.48064 ( PROT MET 6 CA ) 0.60080 ( PROT MET 6 CB ) 0.48064 ( PROT MET 6 CG ) 0.48064 ( PROT MET 6 SD ) 0.48064 ( PROT MET 6 CE ) 0.48064 ( PROT MET 6 C ) 0.60080 ( PROT MET 6 O ) 0.60080 ( PROT ILE 7 N ) 0.60080 ( PROT ILE 7 H ) 0.48064 ( PROT ILE 7 CA ) 0.60080 ( PROT ILE 7 CB ) 0.48064 ( PROT ILE 7 CG2 ) 0.48064 ( PROT ILE 7 CG1 ) 0.48064 ( PROT ILE 7 CD ) 0.48064 ( PROT ILE 7 C ) 0.60080 ( PROT ILE 7 O ) 0.60080 ( PROT GLY 8 N ) 0.60080 ( PROT GLY 8 H ) 0.48064 ( PROT GLY 8 CA ) 0.60080 ( PROT GLY 8 C ) 0.60080 ( PROT GLY 8 O ) 0.60080 ( PROT ALA 9 N ) 0.60080 ( PROT ALA 9 H ) 0.48064 ( PROT ALA 9 CA ) 0.60080 ( PROT ALA 9 CB ) 0.48064 ( PROT ALA 9 C ) 0.60080 ( PROT ALA 9 O ) 0.60080 ( PROT CYS 10 N ) 0.60080 ( PROT CYS 10 H ) 0.48064 ( PROT CYS 10 CA ) 0.60080 ( PROT CYS 10 CB ) 0.48064 ( PROT CYS 10 SG ) 0.48064 ( PROT CYS 10 C ) 0.60080 ( PROT CYS 10 O ) 0.60080 ( PROT PHE 11 N ) 0.60080 ( PROT PHE 11 H ) 0.48064 ( PROT PHE 11 CA ) 0.60080 ( PROT PHE 11 CB ) 0.48064 ( PROT PHE 11 CG ) 0.48064 ( PROT PHE 11 CD1 ) 0.48064 ( PROT PHE 11 CD2 ) 0.48064 ( PROT PHE 11 CE1 ) 0.48064 ( PROT PHE 11 CE2 ) 0.48064 ( PROT PHE 11 CZ ) 0.48064 ( PROT PHE 11 C ) 0.60080 ( PROT PHE 11 O ) 0.60080 ( PROT LEU 12 N ) 0.60080 ( PROT LEU 12 H ) 0.48064 ( PROT LEU 12 CA ) 0.60080 ( PROT LEU 12 CB ) 0.48064 ( PROT LEU 12 CG ) 0.48064 ( PROT LEU 12 CD1 ) 0.48064 ( PROT LEU 12 CD2 ) 0.48064 ( PROT LEU 12 C ) 0.60080 ( PROT LEU 12 O ) 0.60080 ( PROT ILE 13 N ) 0.60080 ( PROT ILE 13 H ) 0.48064 ( PROT ILE 13 CA ) 0.60080 ( PROT ILE 13 CB ) 0.48064 ( PROT ILE 13 CG2 ) 0.48064 ( PROT ILE 13 CG1 ) 0.48064 ( PROT ILE 13 CD ) 0.48064 ( PROT ILE 13 C ) 0.60080 ( PROT ILE 13 O ) 0.60080 ( PROT ASH 14 N ) 0.60080 ( PROT ASH 14 H ) 0.48064 ( PROT ASH 14 CA ) 0.60080 ( PROT ASH 14 CB ) 0.48064 ( PROT ASH 14 CG ) 0.48064 ( PROT ASH 14 OD1 ) 0.48064 ( PROT ASH 14 OD2 ) 0.48064 ( PROT ASH 14 HD2 ) 0.48064 ( PROT ASH 14 C ) 0.60080 ( PROT ASH 14 O ) 0.60080 ( PROT PHE 15 N ) 0.60080 ( PROT PHE 15 H ) 0.48064 ( PROT PHE 15 CA ) 0.60080 ( PROT PHE 15 CB ) 0.48064 ( PROT PHE 15 CG ) 0.48064 ( PROT PHE 15 CD1 ) 0.48064 ( PROT PHE 15 CD2 ) 0.48064 ( PROT PHE 15 CE1 ) 0.48064 ( PROT PHE 15 CE2 ) 0.48064 ( PROT PHE 15 CZ ) 0.48064 ( PROT PHE 15 C ) 0.60080 ( PROT PHE 15 O ) 0.60080 ( PROT MET 16 N ) 0.60080 ( PROT MET 16 H ) 0.48064 ( PROT MET 16 CA ) 0.60080 ( PROT MET 16 CB ) 0.48064 ( PROT MET 16 CG ) 0.48064 ( PROT MET 16 SD ) 0.48064 ( PROT MET 16 CE ) 0.48064 ( PROT MET 16 C ) 0.60080 ( PROT MET 16 O ) 0.60080 ( PROT PHE 17 N ) 0.60080 ( PROT PHE 17 H ) 0.48064 ( PROT PHE 17 CA ) 0.60080 ( PROT PHE 17 CB ) 0.48064 ( PROT PHE 17 CG ) 0.48064 ( PROT PHE 17 CD1 ) 0.48064 ( PROT PHE 17 CD2 ) 0.48064 ( PROT PHE 17 CE1 ) 0.48064 ( PROT PHE 17 CE2 ) 0.48064 ( PROT PHE 17 CZ ) 0.48064 ( PROT PHE 17 C ) 0.60080 ( PROT PHE 17 O ) 0.60080 ( PROT PHE 18 N ) 0.60080 ( PROT PHE 18 H ) 0.48064 ( PROT PHE 18 CA ) 0.60080 ( PROT PHE 18 CB ) 0.48064 ( PROT PHE 18 CG ) 0.48064 ( PROT PHE 18 CD1 ) 0.48064 ( PROT PHE 18 CD2 ) 0.48064 ( PROT PHE 18 CE1 ) 0.48064 ( PROT PHE 18 CE2 ) 0.48064 ( PROT PHE 18 CZ ) 0.48064 ( PROT PHE 18 C ) 0.60080 ( PROT PHE 18 O ) 0.60080 ( PROT GLU 19 N ) 0.60080 ( PROT GLU 19 H ) 0.48064 ( PROT GLU 19 CA ) 0.60080 ( PROT GLU 19 CB ) 0.48064 ( PROT GLU 19 CG ) 0.48064 ( PROT GLU 19 CD ) 0.48064 ( PROT GLU 19 OE1 ) 0.48064 ( PROT GLU 19 OE2 ) 0.48064 ( PROT GLU 19 C ) 0.60080 ( PROT GLU 19 O ) 0.60080 ( PROT SER 20 N ) 0.60080 ( PROT SER 20 H ) 0.48064 ( PROT SER 20 CA ) 0.60080 ( PROT SER 20 CB ) 0.48064 ( PROT SER 20 OG ) 0.48064 ( PROT SER 20 HG ) 0.48064 ( PROT SER 20 C ) 0.60080 ( PROT SER 20 O ) 0.60080 ( PROT THR 21 N ) 0.60080 ( PROT THR 21 H ) 0.48064 ( PROT THR 21 CA ) 0.60080 ( PROT THR 21 CB ) 0.48064 ( PROT THR 21 OG1 ) 0.48064 ( PROT THR 21 HG1 ) 0.48064 ( PROT THR 21 CG2 ) 0.48064 ( PROT THR 21 C ) 0.60080 ( PROT THR 21 O ) 0.60080 ( PROT GLY 22 N ) 0.60080 ( PROT GLY 22 H ) 0.48064 ( PROT GLY 22 CA ) 0.60080 ( PROT GLY 22 C ) 0.60080 ( PROT GLY 22 O ) 0.60080 ( PROT SER 23 N ) 0.60080 ( PROT SER 23 H ) 0.48064 ( PROT SER 23 CA ) 0.60080 ( PROT SER 23 CB ) 0.48064 ( PROT SER 23 OG ) 0.48064 ( PROT SER 23 HG ) 0.48064 ( PROT SER 23 C ) 0.60080 ( PROT SER 23 O ) 0.60080 ( PROT GLN 24 N ) 0.60080 ( PROT GLN 24 H ) 0.48064 ( PROT GLN 24 CA ) 0.60080 ( PROT GLN 24 CB ) 0.48064 ( PROT GLN 24 CG ) 0.48064 ( PROT GLN 24 CD ) 0.48064 ( PROT GLN 24 OE1 ) 0.48064 ( PROT GLN 24 NE2 ) 0.48064 ( PROT GLN 24 HE21 ) 0.48064 ( PROT GLN 24 HE22 ) 0.48064 ( PROT GLN 24 C ) 0.60080 ( PROT GLN 24 O ) 0.60080 ( PROT GLU 25 N ) 0.60080 ( PROT GLU 25 H ) 0.48064 ( PROT GLU 25 CA ) 0.60080 ( PROT GLU 25 CB ) 0.48064 ( PROT GLU 25 CG ) 0.48064 ( PROT GLU 25 CD ) 0.48064 ( PROT GLU 25 OE1 ) 0.48064 ( PROT GLU 25 OE2 ) 0.48064 ( PROT GLU 25 C ) 0.60080 ( PROT GLU 25 O ) 0.60080 ( PROT GLN 26 N ) 0.60080 ( PROT GLN 26 H ) 0.48064 ( PROT GLN 26 CA ) 0.60080 ( PROT GLN 26 CB ) 0.48064 ( PROT GLN 26 CG ) 0.48064 ( PROT GLN 26 CD ) 0.48064 ( PROT GLN 26 OE1 ) 0.48064 ( PROT GLN 26 NE2 ) 0.48064 ( PROT GLN 26 HE21 ) 0.48064 ( PROT GLN 26 HE22 ) 0.48064 ( PROT GLN 26 C ) 0.60080 ( PROT GLN 26 O ) 0.60080 ( PROT LYS 27 N ) 0.60080 ( PROT LYS 27 H ) 0.48064 ( PROT LYS 27 CA ) 0.60080 ( PROT LYS 27 CB ) 0.48064 ( PROT LYS 27 CG ) 0.48064 ( PROT LYS 27 CD ) 0.48064 ( PROT LYS 27 CE ) 0.48064 ( PROT LYS 27 NZ ) 0.48064 ( PROT LYS 27 HZ1 ) 0.48064 ( PROT LYS 27 HZ2 ) 0.48064 ( PROT LYS 27 HZ3 ) 0.48064 ( PROT LYS 27 C ) 0.60080 ( PROT LYS 27 O ) 0.60080 ( PROT SER 28 N ) 0.60080 ( PROT SER 28 H ) 0.48064 ( PROT SER 28 CA ) 0.60080 ( PROT SER 28 CB ) 0.48064 ( PROT SER 28 OG ) 0.48064 ( PROT SER 28 HG ) 0.48064 ( PROT SER 28 C ) 0.60080 ( PROT SER 28 O ) 0.60080 ( PROT GLY 29 N ) 0.60080 ( PROT GLY 29 H ) 0.48064 ( PROT GLY 29 CA ) 0.60080 ( PROT GLY 29 C ) 0.60080 ( PROT GLY 29 O ) 0.60080 ( PROT VAL 30 N ) 0.60080 ( PROT VAL 30 H ) 0.48064 ( PROT VAL 30 CA ) 0.60080 ( PROT VAL 30 CB ) 0.48064 ( PROT VAL 30 CG1 ) 0.48064 ( PROT VAL 30 CG2 ) 0.48064 ( PROT VAL 30 C ) 0.60080 ( PROT VAL 30 O ) 0.60080 ( PROT TRP 31 N ) 0.60080 ( PROT TRP 31 H ) 0.48064 ( PROT TRP 31 CA ) 0.60080 ( PROT TRP 31 CB ) 0.48064 ( PROT TRP 31 CG ) 0.48064 ( PROT TRP 31 CD2 ) 0.48064 ( PROT TRP 31 CE2 ) 0.48064 ( PROT TRP 31 CE3 ) 0.48064 ( PROT TRP 31 CD1 ) 0.48064 ( PROT TRP 31 NE1 ) 0.48064 ( PROT TRP 31 HE1 ) 0.48064 ( PROT TRP 31 CZ2 ) 0.48064 ( PROT TRP 31 CZ3 ) 0.48064 ( PROT TRP 31 CH2 ) 0.48064 ( PROT TRP 31 C ) 0.60080 ( PROT TRP 31 OT1 ) 0.48064 ( PROT TRP 31 OT2 ) 0.48064 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.62798 7.22307 -13.21643 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00283 0.00636 -0.00349 ROTATION MATRIX 0.999995 0.002489 0.002161 -0.002484 0.999994 -0.002312 -0.002167 0.002306 0.999995 AXIS OF ROTATION IS -0.573728 -0.537641 0.617882 ANGLE IS 0.23 TOTAL SQUARE DIFF IS 101.8312 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.585548 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.5855" Parameter: A <- "0.5855" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.53863 7.27062 -13.42538 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.01040 -0.01507 -0.01498 ROTATION MATRIX 0.999597 0.019586 0.020547 -0.019098 0.999537 -0.023694 -0.021001 0.023292 0.999508 AXIS OF ROTATION IS -0.637609 -0.563808 0.524953 ANGLE IS 2.11 CENTER OF ROTATION 13.977237 6.855824-13.331217 SHIFT IS 0.007267 TOTAL SQUARE DIFF IS 5.1022 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.405692 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.5855" RDCMND substituted energy or value "?RMS" to " 0.4057" Parameter: A <- "0.5855 0.4057" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *8400 0.5855 0.4057 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 82.26" Parameter: H <- "82.26" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -120.40969 82.25771 0.77708 ENER INTERN> 8.15194 47.69640 0.00000 39.10647 6.56427 ENER EXTERN> -124.43779 -97.49098 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -120.41" Parameter: B <- "-120.41" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -97.49" Parameter: C <- "-97.49" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -124.44" Parameter: C <- " -221.93" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -221.93" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 8.15" Parameter: D <- "8.15" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 47.70" Parameter: D <- " 55.85" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 39.11" Parameter: D <- " 94.96" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.56" Parameter: D <- " 101.52" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 101.52" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 8400 ENER= -120.41 GRMS= 0.78 ELEC= -97.49 VDW= -124.44 RDTITL> *EXTERNAL= -221.93 INTERNAL= 101.52 USER= 0.00 HARM= 82.26 RDTITL> *BOND= 8.15 ANGL= 47.70 DIHE= 39.11 IMPR= 6.56 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "8400" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_8400.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_8400.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 8400 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 8400 ENER= -120.41 GRMS= 0.78 ELEC= -97.49 VDW= -124.44 RDTITL> *EXTERNAL= -221.93 INTERNAL= 101.52 USER= 0.00 HARM= 82.26 RDTITL> *BOND= 8.15 ANGL= 47.70 DIHE= 39.11 IMPR= 6.56 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "8400" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_8400.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_8400.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 8400 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 8400 ENER= -120.41 GRMS= 0.78 ELEC= -97.49 VDW= -124.44 RDTITL> *EXTERNAL= -221.93 INTERNAL= 101.52 USER= 0.00 HARM= 82.26 RDTITL> *BOND= 8.15 ANGL= 47.70 DIHE= 39.11 IMPR= 6.56 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 8400 0.5855 0.4057 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "8400" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20899 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20882 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -63.89154 -56.51815 0.59209 0.02000 MINI INTERN> 8.15194 47.69640 0.00000 39.10647 6.56427 MINI EXTERN> -124.43779 -97.49098 0.00000 0.00000 0.00000 MINI CONSTR> 56.51815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -56.32020 -7.57134 7.51578 0.00360 MINI INTERN> 15.76394 48.62463 0.00000 39.30421 6.67639 MINI EXTERN> -128.56515 -95.69555 0.00000 0.00000 0.00000 MINI CONSTR> 57.57133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20879 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -65.33563 9.01543 0.61593 0.00065 MINI INTERN> 8.18257 47.80165 0.00000 39.27418 6.41530 MINI EXTERN> -128.49236 -96.25248 0.00000 0.00000 0.00000 MINI CONSTR> 57.73550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -65.58773 0.25210 0.23970 0.00028 MINI INTERN> 8.13567 47.69354 0.00000 39.22678 6.39051 MINI EXTERN> -128.61456 -96.30013 0.00000 0.00000 0.00000 MINI CONSTR> 57.88046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20879 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -65.71646 0.12872 0.50388 0.00029 MINI INTERN> 8.14910 47.63974 0.00000 39.19861 6.37702 MINI EXTERN> -128.79072 -96.30307 0.00000 0.00000 0.00000 MINI CONSTR> 58.01285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -65.84927 0.13281 0.51124 0.00030 MINI INTERN> 8.14754 47.59821 0.00000 39.17619 6.36641 MINI EXTERN> -128.95891 -96.30670 0.00000 0.00000 0.00000 MINI CONSTR> 58.12799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20878 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -65.97781 0.12854 0.53980 0.00031 MINI INTERN> 8.14980 47.55495 0.00000 39.15203 6.35607 MINI EXTERN> -129.12512 -96.30879 0.00000 0.00000 0.00000 MINI CONSTR> 58.24325 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -66.09649 0.11868 0.59534 0.00032 MINI INTERN> 8.15431 47.51397 0.00000 39.12688 6.34646 MINI EXTERN> -129.28264 -96.30997 0.00000 0.00000 0.00000 MINI CONSTR> 58.35450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20875 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -66.20814 0.11166 0.57373 0.00034 MINI INTERN> 8.14753 47.48188 0.00000 39.10491 6.33881 MINI EXTERN> -129.41784 -96.31243 0.00000 0.00000 0.00000 MINI CONSTR> 58.44899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -66.32179 0.11364 0.59576 0.00035 MINI INTERN> 8.14847 47.44081 0.00000 39.07943 6.33036 MINI EXTERN> -129.55811 -96.31476 0.00000 0.00000 0.00000 MINI CONSTR> 58.55200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20876 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -66.46974 0.14795 0.18650 0.00015 MINI INTERN> 8.12907 47.39738 0.00000 39.06295 6.32288 MINI EXTERN> -129.69583 -96.32949 0.00000 0.00000 0.00000 MINI CONSTR> 58.64329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -66.52682 0.05708 0.65694 0.00037 MINI INTERN> 8.15103 47.36467 0.00000 39.02878 6.31535 MINI EXTERN> -129.80810 -96.32066 0.00000 0.00000 0.00000 MINI CONSTR> 58.74211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20869 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -66.62999 0.10316 0.67318 0.00039 MINI INTERN> 8.15117 47.32401 0.00000 39.00244 6.30810 MINI EXTERN> -129.92711 -96.32468 0.00000 0.00000 0.00000 MINI CONSTR> 58.83608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -66.73175 0.10177 0.69805 0.00040 MINI INTERN> 8.15303 47.28092 0.00000 38.97495 6.30094 MINI EXTERN> -130.04339 -96.32890 0.00000 0.00000 0.00000 MINI CONSTR> 58.93069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20869 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -66.82817 0.09642 0.73605 0.00042 MINI INTERN> 8.15693 47.23794 0.00000 38.94697 6.29408 MINI EXTERN> -130.15428 -96.33321 0.00000 0.00000 0.00000 MINI CONSTR> 59.02340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -66.99080 0.16263 0.23433 0.00018 MINI INTERN> 8.12253 47.19657 0.00000 38.93071 6.28664 MINI EXTERN> -130.27414 -96.36100 0.00000 0.00000 0.00000 MINI CONSTR> 59.10789 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20868 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -67.07380 0.08300 0.16991 0.00019 MINI INTERN> 8.11436 47.16117 0.00000 38.90744 6.28150 MINI EXTERN> -130.35287 -96.36399 0.00000 0.00000 0.00000 MINI CONSTR> 59.17858 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -67.17077 0.09697 0.16998 0.00019 MINI INTERN> 8.11131 47.12160 0.00000 38.87959 6.27505 MINI EXTERN> -130.45165 -96.37210 0.00000 0.00000 0.00000 MINI CONSTR> 59.26542 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20868 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -67.26549 0.09472 0.17360 0.00020 MINI INTERN> 8.10849 47.08264 0.00000 38.85166 6.26876 MINI EXTERN> -130.54678 -96.38093 0.00000 0.00000 0.00000 MINI CONSTR> 59.35067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -67.35697 0.09148 0.31600 0.00021 MINI INTERN> 8.11666 47.04881 0.00000 38.82218 6.26156 MINI EXTERN> -130.65165 -96.39715 0.00000 0.00000 0.00000 MINI CONSTR> 59.44261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20867 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -67.44790 0.09092 0.21448 0.00022 MINI INTERN> 8.10364 47.00874 0.00000 38.79521 6.25645 MINI EXTERN> -130.72821 -96.40126 0.00000 0.00000 0.00000 MINI CONSTR> 59.51754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -67.54024 0.09235 0.21132 0.00022 MINI INTERN> 8.09874 46.96921 0.00000 38.76555 6.25053 MINI EXTERN> -130.81528 -96.41020 0.00000 0.00000 0.00000 MINI CONSTR> 59.60120 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20865 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -67.63227 0.09203 0.21946 0.00023 MINI INTERN> 8.09583 46.92905 0.00000 38.73563 6.24457 MINI EXTERN> -130.90235 -96.42061 0.00000 0.00000 0.00000 MINI CONSTR> 59.68560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -67.72063 0.08837 0.25124 0.00024 MINI INTERN> 8.09360 46.89138 0.00000 38.70556 6.23869 MINI EXTERN> -130.98673 -96.43177 0.00000 0.00000 0.00000 MINI CONSTR> 59.76864 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20861 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -67.78945 0.06881 0.38775 0.00025 MINI INTERN> 8.10074 46.86384 0.00000 38.67792 6.23308 MINI EXTERN> -131.06394 -96.44542 0.00000 0.00000 0.00000 MINI CONSTR> 59.84432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -67.87438 0.08493 0.39834 0.00026 MINI INTERN> 8.09874 46.82445 0.00000 38.64793 6.22773 MINI EXTERN> -131.14227 -96.45498 0.00000 0.00000 0.00000 MINI CONSTR> 59.92403 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20862 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -67.95680 0.08243 0.42493 0.00027 MINI INTERN> 8.09783 46.78635 0.00000 38.61740 6.22246 MINI EXTERN> -131.21975 -96.46490 0.00000 0.00000 0.00000 MINI CONSTR> 60.00379 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -68.03324 0.07644 0.46788 0.00028 MINI INTERN> 8.09944 46.75066 0.00000 38.58766 6.21736 MINI EXTERN> -131.29366 -96.47548 0.00000 0.00000 0.00000 MINI CONSTR> 60.08077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20861 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -68.10606 0.07282 0.44393 0.00029 MINI INTERN> 8.09440 46.71736 0.00000 38.56266 6.21289 MINI EXTERN> -131.35349 -96.48572 0.00000 0.00000 0.00000 MINI CONSTR> 60.14583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -68.18265 0.07658 0.46207 0.00030 MINI INTERN> 8.09166 46.68251 0.00000 38.53328 6.20807 MINI EXTERN> -131.42270 -96.49599 0.00000 0.00000 0.00000 MINI CONSTR> 60.22053 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20861 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -68.25992 0.07727 0.46961 0.00031 MINI INTERN> 8.08802 46.64716 0.00000 38.50383 6.20331 MINI EXTERN> -131.49074 -96.50644 0.00000 0.00000 0.00000 MINI CONSTR> 60.29493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -68.35914 0.09922 0.14893 0.00013 MINI INTERN> 8.06599 46.59426 0.00000 38.48013 6.19850 MINI EXTERN> -131.53877 -96.51887 0.00000 0.00000 0.00000 MINI CONSTR> 60.35962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20861 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -68.39295 0.03381 0.51555 0.00033 MINI INTERN> 8.08651 46.58547 0.00000 38.45025 6.19455 MINI EXTERN> -131.61038 -96.52827 0.00000 0.00000 0.00000 MINI CONSTR> 60.42892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -68.46323 0.07027 0.53136 0.00034 MINI INTERN> 8.08527 46.55260 0.00000 38.42164 6.19018 MINI EXTERN> -131.67289 -96.53928 0.00000 0.00000 0.00000 MINI CONSTR> 60.49926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20860 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -68.53170 0.06847 0.55585 0.00036 MINI INTERN> 8.08421 46.52161 0.00000 38.39263 6.18591 MINI EXTERN> -131.73521 -96.55069 0.00000 0.00000 0.00000 MINI CONSTR> 60.56985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -68.64305 0.11135 0.17644 0.00015 MINI INTERN> 8.05666 46.46056 0.00000 38.36915 6.18007 MINI EXTERN> -131.77501 -96.56986 0.00000 0.00000 0.00000 MINI CONSTR> 60.63538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20859 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -68.70077 0.05771 0.13380 0.00016 MINI INTERN> 8.05091 46.43774 0.00000 38.34626 6.17677 MINI EXTERN> -131.82322 -96.57922 0.00000 0.00000 0.00000 MINI CONSTR> 60.68999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -68.76832 0.06755 0.13227 0.00017 MINI INTERN> 8.04822 46.40619 0.00000 38.31878 6.17246 MINI EXTERN> -131.87831 -96.59219 0.00000 0.00000 0.00000 MINI CONSTR> 60.75654 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20859 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -68.83577 0.06745 0.13295 0.00017 MINI INTERN> 8.04586 46.37419 0.00000 38.29101 6.16813 MINI EXTERN> -131.93283 -96.60560 0.00000 0.00000 0.00000 MINI CONSTR> 60.82347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -68.90212 0.06635 0.25193 0.00018 MINI INTERN> 8.05553 46.33050 0.00000 38.26125 6.16272 MINI EXTERN> -131.98541 -96.62359 0.00000 0.00000 0.00000 MINI CONSTR> 60.89687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20858 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -68.96476 0.06264 0.16739 0.00019 MINI INTERN> 8.04479 46.30876 0.00000 38.23666 6.15949 MINI EXTERN> -132.03510 -96.63361 0.00000 0.00000 0.00000 MINI CONSTR> 60.95424 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -69.02821 0.06345 0.16671 0.00019 MINI INTERN> 8.04265 46.27828 0.00000 38.20966 6.15541 MINI EXTERN> -132.08543 -96.64712 0.00000 0.00000 0.00000 MINI CONSTR> 61.01835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20855 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -69.09121 0.06300 0.17764 0.00020 MINI INTERN> 8.04198 46.24639 0.00000 38.18239 6.15123 MINI EXTERN> -132.13501 -96.66125 0.00000 0.00000 0.00000 MINI CONSTR> 61.08306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -69.14231 0.05110 0.31361 0.00021 MINI INTERN> 8.05641 46.20642 0.00000 38.15635 6.14645 MINI EXTERN> -132.17610 -96.67814 0.00000 0.00000 0.00000 MINI CONSTR> 61.14629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20855 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -69.20083 0.05852 0.31460 0.00021 MINI INTERN> 8.05625 46.17627 0.00000 38.13062 6.14264 MINI EXTERN> -132.22196 -96.69139 0.00000 0.00000 0.00000 MINI CONSTR> 61.20674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -69.25925 0.05842 0.32595 0.00022 MINI INTERN> 8.05381 46.14852 0.00000 38.10401 6.13888 MINI EXTERN> -132.26752 -96.70551 0.00000 0.00000 0.00000 MINI CONSTR> 61.26856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20854 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -69.31474 0.05549 0.35738 0.00023 MINI INTERN> 8.06809 46.10626 0.00000 38.07844 6.13453 MINI EXTERN> -132.31315 -96.71889 0.00000 0.00000 0.00000 MINI CONSTR> 61.32999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -69.36434 0.04960 0.39236 0.00024 MINI INTERN> 8.05004 46.09969 0.00000 38.05308 6.13183 MINI EXTERN> -132.35156 -96.73378 0.00000 0.00000 0.00000 MINI CONSTR> 61.38635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20853 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -69.41474 0.05040 0.36462 0.00025 MINI INTERN> 8.05564 46.06719 0.00000 38.03218 6.12841 MINI EXTERN> -132.39003 -96.74446 0.00000 0.00000 0.00000 MINI CONSTR> 61.43631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -69.46842 0.05367 0.38109 0.00026 MINI INTERN> 8.06330 46.03206 0.00000 38.00716 6.12447 MINI EXTERN> -132.43296 -96.75787 0.00000 0.00000 0.00000 MINI CONSTR> 61.49543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20849 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -69.52157 0.05316 0.39484 0.00027 MINI INTERN> 8.03475 46.03430 0.00000 37.98040 6.12220 MINI EXTERN> -132.47383 -96.77266 0.00000 0.00000 0.00000 MINI CONSTR> 61.55326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -69.58767 0.06610 0.12321 0.00011 MINI INTERN> 8.00965 46.02794 0.00000 37.95938 6.12057 MINI EXTERN> -132.53031 -96.77579 0.00000 0.00000 0.00000 MINI CONSTR> 61.60091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20850 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -69.61117 0.02350 0.42310 0.00029 MINI INTERN> 8.05731 45.96528 0.00000 37.93795 6.11499 MINI EXTERN> -132.54422 -96.79733 0.00000 0.00000 0.00000 MINI CONSTR> 61.65485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -69.66060 0.04943 0.43967 0.00030 MINI INTERN> 8.06950 45.92797 0.00000 37.91422 6.11112 MINI EXTERN> -132.58436 -96.81006 0.00000 0.00000 0.00000 MINI CONSTR> 61.71100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20848 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -69.70440 0.04380 0.49561 0.00031 MINI INTERN> 8.02631 45.95256 0.00000 37.88790 6.11004 MINI EXTERN> -132.62146 -96.82557 0.00000 0.00000 0.00000 MINI CONSTR> 61.76580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -69.78241 0.07800 0.14891 0.00013 MINI INTERN> 7.99994 45.93900 0.00000 37.86656 6.10814 MINI EXTERN> -132.68325 -96.82747 0.00000 0.00000 0.00000 MINI CONSTR> 61.81466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20846 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -69.82330 0.04090 0.11066 0.00014 MINI INTERN> 8.00111 45.91326 0.00000 37.84795 6.10522 MINI EXTERN> -132.70938 -96.83955 0.00000 0.00000 0.00000 MINI CONSTR> 61.85808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -69.87149 0.04819 0.11053 0.00014 MINI INTERN> 8.00049 45.88883 0.00000 37.82473 6.10203 MINI EXTERN> -132.74632 -96.85299 0.00000 0.00000 0.00000 MINI CONSTR> 61.91173 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20846 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -69.91764 0.04615 0.11876 0.00015 MINI INTERN> 7.99626 45.86997 0.00000 37.80195 6.09918 MINI EXTERN> -132.78288 -96.86593 0.00000 0.00000 0.00000 MINI CONSTR> 61.96380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -69.96087 0.04323 0.21545 0.00015 MINI INTERN> 7.99120 45.85956 0.00000 37.77771 6.09669 MINI EXTERN> -132.82674 -96.87788 0.00000 0.00000 0.00000 MINI CONSTR> 62.01859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20845 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -70.00604 0.04516 0.13807 0.00016 MINI INTERN> 7.99116 45.83047 0.00000 37.75803 6.09352 MINI EXTERN> -132.85251 -96.89137 0.00000 0.00000 0.00000 MINI CONSTR> 62.06467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -70.05170 0.04566 0.13898 0.00016 MINI INTERN> 7.99194 45.80579 0.00000 37.73555 6.09041 MINI EXTERN> -132.88740 -96.90479 0.00000 0.00000 0.00000 MINI CONSTR> 62.11680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20843 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -70.09493 0.04323 0.17417 0.00017 MINI INTERN> 7.98162 45.79556 0.00000 37.71264 6.08799 MINI EXTERN> -132.92290 -96.91826 0.00000 0.00000 0.00000 MINI CONSTR> 62.16842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -70.12844 0.03351 0.26007 0.00018 MINI INTERN> 7.98132 45.78484 0.00000 37.69251 6.08582 MINI EXTERN> -132.95856 -96.92864 0.00000 0.00000 0.00000 MINI CONSTR> 62.21428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20842 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -70.16883 0.04039 0.28126 0.00018 MINI INTERN> 7.99736 45.74822 0.00000 37.67227 6.08233 MINI EXTERN> -132.99153 -96.94050 0.00000 0.00000 0.00000 MINI CONSTR> 62.26302 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -70.20536 0.03654 0.30227 0.00019 MINI INTERN> 7.97749 45.75134 0.00000 37.65151 6.08076 MINI EXTERN> -133.02175 -96.95306 0.00000 0.00000 0.00000 MINI CONSTR> 62.30835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20840 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -70.24290 0.03753 0.28656 0.00020 MINI INTERN> 7.98480 45.72302 0.00000 37.63369 6.07786 MINI EXTERN> -133.04897 -96.96399 0.00000 0.00000 0.00000 MINI CONSTR> 62.35070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -70.28006 0.03717 0.33803 0.00020 MINI INTERN> 7.96742 45.72372 0.00000 37.61125 6.07605 MINI EXTERN> -133.08063 -96.97810 0.00000 0.00000 0.00000 MINI CONSTR> 62.40023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20838 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -70.31648 0.03641 0.31253 0.00021 MINI INTERN> 7.97660 45.69429 0.00000 37.59430 6.07317 MINI EXTERN> -133.10746 -96.98821 0.00000 0.00000 0.00000 MINI CONSTR> 62.44083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -70.35513 0.03866 0.32779 0.00022 MINI INTERN> 7.99022 45.66080 0.00000 37.57454 6.06988 MINI EXTERN> -133.13881 -97.00038 0.00000 0.00000 0.00000 MINI CONSTR> 62.48862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -70.40417 0.04904 0.10634 0.00010 MINI INTERN> 7.98340 45.62227 0.00000 37.55753 6.06623 MINI EXTERN> -133.14553 -97.01675 0.00000 0.00000 0.00000 MINI CONSTR> 62.52869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -70.42262 0.01845 0.35134 0.00024 MINI INTERN> 7.97078 45.64664 0.00000 37.53695 6.06603 MINI EXTERN> -133.19223 -97.02402 0.00000 0.00000 0.00000 MINI CONSTR> 62.57323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -70.47538 0.05276 0.11066 0.00010 MINI INTERN> 7.98062 45.58662 0.00000 37.52033 6.06134 MINI EXTERN> -133.19884 -97.04050 0.00000 0.00000 0.00000 MINI CONSTR> 62.61505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -70.48922 0.01384 0.37963 0.00025 MINI INTERN> 7.98914 45.59463 0.00000 37.50146 6.06048 MINI EXTERN> -133.24712 -97.04592 0.00000 0.00000 0.00000 MINI CONSTR> 62.65811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -70.54485 0.05563 0.12226 0.00011 MINI INTERN> 7.97978 45.54961 0.00000 37.48366 6.05640 MINI EXTERN> -133.25061 -97.06425 0.00000 0.00000 0.00000 MINI CONSTR> 62.70057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -70.55400 0.00915 0.40234 0.00027 MINI INTERN> 7.97627 45.57542 0.00000 37.46482 6.05650 MINI EXTERN> -133.29967 -97.06915 0.00000 0.00000 0.00000 MINI CONSTR> 62.74180 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -70.61421 0.06021 0.13186 0.00012 MINI INTERN> 7.97806 45.51355 0.00000 37.44670 6.05148 MINI EXTERN> -133.30257 -97.08829 0.00000 0.00000 0.00000 MINI CONSTR> 62.78686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -70.64402 0.02980 0.09438 0.00012 MINI INTERN> 7.97275 45.50443 0.00000 37.43144 6.04986 MINI EXTERN> -133.32762 -97.09720 0.00000 0.00000 0.00000 MINI CONSTR> 62.82233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20836 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -70.67951 0.03549 0.09569 0.00013 MINI INTERN> 7.97083 45.48690 0.00000 37.41239 6.04738 MINI EXTERN> -133.35417 -97.10970 0.00000 0.00000 0.00000 MINI CONSTR> 62.86686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -70.71344 0.03393 0.18517 0.00013 MINI INTERN> 7.98059 45.45614 0.00000 37.39220 6.04393 MINI EXTERN> -133.37645 -97.12458 0.00000 0.00000 0.00000 MINI CONSTR> 62.91475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -70.74689 0.03345 0.11911 0.00014 MINI INTERN> 7.97036 45.44944 0.00000 37.37568 6.04236 MINI EXTERN> -133.40343 -97.13436 0.00000 0.00000 0.00000 MINI CONSTR> 62.95305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -70.77978 0.03288 0.13525 0.00014 MINI INTERN> 7.97683 45.42486 0.00000 37.35789 6.03960 MINI EXTERN> -133.42865 -97.14608 0.00000 0.00000 0.00000 MINI CONSTR> 62.99576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20835 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -70.80637 0.02659 0.21695 0.00015 MINI INTERN> 7.97982 45.40583 0.00000 37.34069 6.03699 MINI EXTERN> -133.44664 -97.15894 0.00000 0.00000 0.00000 MINI CONSTR> 63.03587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -70.84138 0.03501 0.12857 0.00015 MINI INTERN> 7.96889 45.39874 0.00000 37.32417 6.03546 MINI EXTERN> -133.47471 -97.16856 0.00000 0.00000 0.00000 MINI CONSTR> 63.07462 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20833 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -70.86772 0.02634 0.23324 0.00016 MINI INTERN> 7.98025 45.37162 0.00000 37.30647 6.03233 MINI EXTERN> -133.49331 -97.18176 0.00000 0.00000 0.00000 MINI CONSTR> 63.11669 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -70.89850 0.03078 0.24464 0.00016 MINI INTERN> 7.97502 45.35983 0.00000 37.28868 6.03021 MINI EXTERN> -133.51644 -97.19367 0.00000 0.00000 0.00000 MINI CONSTR> 63.15788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20832 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -70.92645 0.02795 0.27623 0.00017 MINI INTERN> 7.99276 45.32733 0.00000 37.27276 6.02718 MINI EXTERN> -133.54013 -97.20405 0.00000 0.00000 0.00000 MINI CONSTR> 63.19769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -70.95423 0.02778 0.25544 0.00018 MINI INTERN> 7.97770 45.32608 0.00000 37.25764 6.02586 MINI EXTERN> -133.55929 -97.21448 0.00000 0.00000 0.00000 MINI CONSTR> 63.23226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20832 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -70.98277 0.02853 0.29262 0.00018 MINI INTERN> 7.98553 45.30262 0.00000 37.23997 6.02308 MINI EXTERN> -133.58193 -97.22642 0.00000 0.00000 0.00000 MINI CONSTR> 63.27438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -71.00997 0.02720 0.27777 0.00019 MINI INTERN> 7.97778 45.29491 0.00000 37.22545 6.02151 MINI EXTERN> -133.60216 -97.23620 0.00000 0.00000 0.00000 MINI CONSTR> 63.30874 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20832 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -71.03956 0.02960 0.28527 0.00020 MINI INTERN> 7.98436 45.27197 0.00000 37.20874 6.01889 MINI EXTERN> -133.62553 -97.24716 0.00000 0.00000 0.00000 MINI CONSTR> 63.34916 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -71.07741 0.03785 0.09218 0.00008 MINI INTERN> 7.95210 45.28747 0.00000 37.19447 6.01916 MINI EXTERN> -133.66112 -97.25378 0.00000 0.00000 0.00000 MINI CONSTR> 63.38429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20832 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -71.09067 0.01326 0.30962 0.00021 MINI INTERN> 7.97998 45.24758 0.00000 37.17835 6.01498 MINI EXTERN> -133.66468 -97.26812 0.00000 0.00000 0.00000 MINI CONSTR> 63.42126 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -71.11857 0.02790 0.31738 0.00022 MINI INTERN> 7.98138 45.23052 0.00000 37.16194 6.01269 MINI EXTERN> -133.68625 -97.27906 0.00000 0.00000 0.00000 MINI CONSTR> 63.46022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20832 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -71.15976 0.04119 0.09865 0.00009 MINI INTERN> 7.94805 45.24517 0.00000 37.14812 6.01310 MINI EXTERN> -133.72539 -97.28515 0.00000 0.00000 0.00000 MINI CONSTR> 63.49635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -71.16809 0.00833 0.34238 0.00023 MINI INTERN> 7.98118 45.20295 0.00000 37.13224 6.00865 MINI EXTERN> -133.72516 -97.29956 0.00000 0.00000 0.00000 MINI CONSTR> 63.53163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20831 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -71.21366 0.04557 0.10515 0.00010 MINI INTERN> 7.94532 45.21737 0.00000 37.11758 6.00910 MINI EXTERN> -133.76780 -97.30600 0.00000 0.00000 0.00000 MINI CONSTR> 63.57077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -71.23675 0.02309 0.08306 0.00011 MINI INTERN> 7.94589 45.20194 0.00000 37.10454 6.00711 MINI EXTERN> -133.78277 -97.31522 0.00000 0.00000 0.00000 MINI CONSTR> 63.60175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20830 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -71.26319 0.02644 0.08596 0.00011 MINI INTERN> 7.94581 45.18701 0.00000 37.08954 6.00508 MINI EXTERN> -133.80386 -97.32543 0.00000 0.00000 0.00000 MINI CONSTR> 63.63866 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -71.28817 0.02498 0.15568 0.00011 MINI INTERN> 7.93951 45.18282 0.00000 37.07425 6.00375 MINI EXTERN> -133.83069 -97.33543 0.00000 0.00000 0.00000 MINI CONSTR> 63.67762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20829 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -71.31087 0.02271 0.08159 0.00012 MINI INTERN> 7.94329 45.16157 0.00000 37.06218 6.00140 MINI EXTERN> -133.84027 -97.34437 0.00000 0.00000 0.00000 MINI CONSTR> 63.70533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -71.31087 0.02271 0.08159 0.00014 STPD INTERN> 7.94329 45.16157 0.00000 37.06218 6.00140 STPD EXTERN> -133.84027 -97.34437 0.00000 0.00000 0.00000 STPD CONSTR> 63.70533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20829 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20829 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -71.31087 0.02271 0.08159 0.00000 MINI INTERN> 7.94329 45.16157 0.00000 37.06218 6.00140 MINI EXTERN> -133.84027 -97.34437 0.00000 0.00000 0.00000 MINI CONSTR> 63.70533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -73.33037 2.01949 0.26306 0.19239 MINI INTERN> 7.89358 43.43339 0.00000 35.25387 5.76857 MINI EXTERN> -137.19831 -98.52437 0.00000 0.00000 0.00000 MINI CONSTR> 70.04291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -73.48761 0.15724 0.24506 0.02481 MINI INTERN> 7.86791 43.33620 0.00000 35.17046 5.71328 MINI EXTERN> -137.11618 -99.00621 0.00000 0.00000 0.00000 MINI CONSTR> 70.54693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -73.89212 0.40451 0.62979 0.11479 MINI INTERN> 7.65754 42.95137 0.00000 34.74261 5.87529 MINI EXTERN> -136.60346 -99.96790 0.00000 0.00000 0.00000 MINI CONSTR> 71.45242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -74.41905 0.52693 0.49260 0.10354 MINI INTERN> 7.64648 43.01445 0.00000 33.62841 5.89697 MINI EXTERN> -136.93886 -100.44114 0.00000 0.00000 0.00000 MINI CONSTR> 72.77464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -74.57147 0.15242 0.28846 0.04020 MINI INTERN> 7.73890 42.96528 0.00000 33.52028 5.80125 MINI EXTERN> -137.20815 -100.59088 0.00000 0.00000 0.00000 MINI CONSTR> 73.20185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -74.66491 0.09344 0.21545 0.02729 MINI INTERN> 7.81897 42.79566 0.00000 33.49941 5.70841 MINI EXTERN> -137.37918 -100.54733 0.00000 0.00000 0.00000 MINI CONSTR> 73.43915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -74.72735 0.06244 0.22225 0.01722 MINI INTERN> 7.83339 42.74615 0.00000 33.42764 5.78294 MINI EXTERN> -137.54685 -100.50324 0.00000 0.00000 0.00000 MINI CONSTR> 73.53262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -74.79102 0.06366 0.22238 0.02438 MINI INTERN> 7.77704 42.78323 0.00000 33.37887 5.72447 MINI EXTERN> -137.49057 -100.48158 0.00000 0.00000 0.00000 MINI CONSTR> 73.51754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -74.83530 0.04428 0.17733 0.01511 MINI INTERN> 7.80228 42.86293 0.00000 33.34782 5.72916 MINI EXTERN> -137.22416 -100.76389 0.00000 0.00000 0.00000 MINI CONSTR> 73.41057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -74.87747 0.04218 0.19266 0.01904 MINI INTERN> 7.75566 42.81954 0.00000 33.36849 5.70556 MINI EXTERN> -136.64467 -101.06958 0.00000 0.00000 0.00000 MINI CONSTR> 73.18753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -74.92872 0.05125 0.21338 0.02133 MINI INTERN> 7.75880 42.74055 0.00000 33.42053 5.76548 MINI EXTERN> -136.47115 -100.98437 0.00000 0.00000 0.00000 MINI CONSTR> 72.84144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -74.97493 0.04621 0.18043 0.01865 MINI INTERN> 7.75733 42.78562 0.00000 33.54983 5.75929 MINI EXTERN> -136.85281 -100.46550 0.00000 0.00000 0.00000 MINI CONSTR> 72.49131 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -75.01585 0.04092 0.19653 0.01635 MINI INTERN> 7.78359 42.93359 0.00000 33.75497 5.72448 MINI EXTERN> -137.11724 -100.22030 0.00000 0.00000 0.00000 MINI CONSTR> 72.12506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -75.06430 0.04845 0.16742 0.02706 MINI INTERN> 7.79752 42.91264 0.00000 33.98347 5.77732 MINI EXTERN> -136.98120 -100.18912 0.00000 0.00000 0.00000 MINI CONSTR> 71.63507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -75.10525 0.04096 0.18250 0.02025 MINI INTERN> 7.84598 43.11113 0.00000 34.15367 5.82432 MINI EXTERN> -136.87862 -100.34663 0.00000 0.00000 0.00000 MINI CONSTR> 71.18489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -75.14793 0.04268 0.15938 0.02341 MINI INTERN> 7.90252 43.45975 0.00000 34.32293 5.81595 MINI EXTERN> -136.65787 -100.68397 0.00000 0.00000 0.00000 MINI CONSTR> 70.69277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -75.18482 0.03689 0.14523 0.02092 MINI INTERN> 7.86647 43.62211 0.00000 34.42527 5.78034 MINI EXTERN> -136.43450 -100.70723 0.00000 0.00000 0.00000 MINI CONSTR> 70.26272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -75.21030 0.02548 0.12901 0.01577 MINI INTERN> 7.83741 43.63219 0.00000 34.41579 5.78835 MINI EXTERN> -136.09258 -100.76332 0.00000 0.00000 0.00000 MINI CONSTR> 69.97185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -75.23136 0.02107 0.11470 0.01446 MINI INTERN> 7.86103 43.59387 0.00000 34.32919 5.81033 MINI EXTERN> -135.84055 -100.72980 0.00000 0.00000 0.00000 MINI CONSTR> 69.74456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -75.24989 0.01853 0.11061 0.01153 MINI INTERN> 7.91883 43.63729 0.00000 34.27241 5.81813 MINI EXTERN> -135.74137 -100.71667 0.00000 0.00000 0.00000 MINI CONSTR> 69.56149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -75.24989 0.01853 0.11061 0.02000 CONJ INTERN> 7.91883 43.63729 0.00000 34.27241 5.81813 CONJ EXTERN> -135.74137 -100.71667 0.00000 0.00000 0.00000 CONJ CONSTR> 69.56149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "9000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.31241 ( PROT LYS 1 HT2 ) 0.31241 ( PROT LYS 1 N ) 0.39052 ( PROT LYS 1 HT3 ) 0.31241 ( PROT LYS 1 CA ) 0.39052 ( PROT LYS 1 CB ) 0.31241 ( PROT LYS 1 CG ) 0.31241 ( PROT LYS 1 CD ) 0.31241 ( PROT LYS 1 CE ) 0.31241 ( PROT LYS 1 NZ ) 0.31241 ( PROT LYS 1 HZ1 ) 0.31241 ( PROT LYS 1 HZ2 ) 0.31241 ( PROT LYS 1 HZ3 ) 0.31241 ( PROT LYS 1 C ) 0.39052 ( PROT LYS 1 O ) 0.39052 ( PROT MET 2 N ) 0.39052 ( PROT MET 2 H ) 0.31241 ( PROT MET 2 CA ) 0.39052 ( PROT MET 2 CB ) 0.31241 ( PROT MET 2 CG ) 0.31241 ( PROT MET 2 SD ) 0.31241 ( PROT MET 2 CE ) 0.31241 ( PROT MET 2 C ) 0.39052 ( PROT MET 2 O ) 0.39052 ( PROT LYS 3 N ) 0.39052 ( PROT LYS 3 H ) 0.31241 ( PROT LYS 3 CA ) 0.39052 ( PROT LYS 3 CB ) 0.31241 ( PROT LYS 3 CG ) 0.31241 ( PROT LYS 3 CD ) 0.31241 ( PROT LYS 3 CE ) 0.31241 ( PROT LYS 3 NZ ) 0.31241 ( PROT LYS 3 HZ1 ) 0.31241 ( PROT LYS 3 HZ2 ) 0.31241 ( PROT LYS 3 HZ3 ) 0.31241 ( PROT LYS 3 C ) 0.39052 ( PROT LYS 3 O ) 0.39052 ( PROT ALA 4 N ) 0.39052 ( PROT ALA 4 H ) 0.31241 ( PROT ALA 4 CA ) 0.39052 ( PROT ALA 4 CB ) 0.31241 ( PROT ALA 4 C ) 0.39052 ( PROT ALA 4 O ) 0.39052 ( PROT VAL 5 N ) 0.39052 ( PROT VAL 5 H ) 0.31241 ( PROT VAL 5 CA ) 0.39052 ( PROT VAL 5 CB ) 0.31241 ( PROT VAL 5 CG1 ) 0.31241 ( PROT VAL 5 CG2 ) 0.31241 ( PROT VAL 5 C ) 0.39052 ( PROT VAL 5 O ) 0.39052 ( PROT MET 6 N ) 0.39052 ( PROT MET 6 H ) 0.31241 ( PROT MET 6 CA ) 0.39052 ( PROT MET 6 CB ) 0.31241 ( PROT MET 6 CG ) 0.31241 ( PROT MET 6 SD ) 0.31241 ( PROT MET 6 CE ) 0.31241 ( PROT MET 6 C ) 0.39052 ( PROT MET 6 O ) 0.39052 ( PROT ILE 7 N ) 0.39052 ( PROT ILE 7 H ) 0.31241 ( PROT ILE 7 CA ) 0.39052 ( PROT ILE 7 CB ) 0.31241 ( PROT ILE 7 CG2 ) 0.31241 ( PROT ILE 7 CG1 ) 0.31241 ( PROT ILE 7 CD ) 0.31241 ( PROT ILE 7 C ) 0.39052 ( PROT ILE 7 O ) 0.39052 ( PROT GLY 8 N ) 0.39052 ( PROT GLY 8 H ) 0.31241 ( PROT GLY 8 CA ) 0.39052 ( PROT GLY 8 C ) 0.39052 ( PROT GLY 8 O ) 0.39052 ( PROT ALA 9 N ) 0.39052 ( PROT ALA 9 H ) 0.31241 ( PROT ALA 9 CA ) 0.39052 ( PROT ALA 9 CB ) 0.31241 ( PROT ALA 9 C ) 0.39052 ( PROT ALA 9 O ) 0.39052 ( PROT CYS 10 N ) 0.39052 ( PROT CYS 10 H ) 0.31241 ( PROT CYS 10 CA ) 0.39052 ( PROT CYS 10 CB ) 0.31241 ( PROT CYS 10 SG ) 0.31241 ( PROT CYS 10 C ) 0.39052 ( PROT CYS 10 O ) 0.39052 ( PROT PHE 11 N ) 0.39052 ( PROT PHE 11 H ) 0.31241 ( PROT PHE 11 CA ) 0.39052 ( PROT PHE 11 CB ) 0.31241 ( PROT PHE 11 CG ) 0.31241 ( PROT PHE 11 CD1 ) 0.31241 ( PROT PHE 11 CD2 ) 0.31241 ( PROT PHE 11 CE1 ) 0.31241 ( PROT PHE 11 CE2 ) 0.31241 ( PROT PHE 11 CZ ) 0.31241 ( PROT PHE 11 C ) 0.39052 ( PROT PHE 11 O ) 0.39052 ( PROT LEU 12 N ) 0.39052 ( PROT LEU 12 H ) 0.31241 ( PROT LEU 12 CA ) 0.39052 ( PROT LEU 12 CB ) 0.31241 ( PROT LEU 12 CG ) 0.31241 ( PROT LEU 12 CD1 ) 0.31241 ( PROT LEU 12 CD2 ) 0.31241 ( PROT LEU 12 C ) 0.39052 ( PROT LEU 12 O ) 0.39052 ( PROT ILE 13 N ) 0.39052 ( PROT ILE 13 H ) 0.31241 ( PROT ILE 13 CA ) 0.39052 ( PROT ILE 13 CB ) 0.31241 ( PROT ILE 13 CG2 ) 0.31241 ( PROT ILE 13 CG1 ) 0.31241 ( PROT ILE 13 CD ) 0.31241 ( PROT ILE 13 C ) 0.39052 ( PROT ILE 13 O ) 0.39052 ( PROT ASH 14 N ) 0.39052 ( PROT ASH 14 H ) 0.31241 ( PROT ASH 14 CA ) 0.39052 ( PROT ASH 14 CB ) 0.31241 ( PROT ASH 14 CG ) 0.31241 ( PROT ASH 14 OD1 ) 0.31241 ( PROT ASH 14 OD2 ) 0.31241 ( PROT ASH 14 HD2 ) 0.31241 ( PROT ASH 14 C ) 0.39052 ( PROT ASH 14 O ) 0.39052 ( PROT PHE 15 N ) 0.39052 ( PROT PHE 15 H ) 0.31241 ( PROT PHE 15 CA ) 0.39052 ( PROT PHE 15 CB ) 0.31241 ( PROT PHE 15 CG ) 0.31241 ( PROT PHE 15 CD1 ) 0.31241 ( PROT PHE 15 CD2 ) 0.31241 ( PROT PHE 15 CE1 ) 0.31241 ( PROT PHE 15 CE2 ) 0.31241 ( PROT PHE 15 CZ ) 0.31241 ( PROT PHE 15 C ) 0.39052 ( PROT PHE 15 O ) 0.39052 ( PROT MET 16 N ) 0.39052 ( PROT MET 16 H ) 0.31241 ( PROT MET 16 CA ) 0.39052 ( PROT MET 16 CB ) 0.31241 ( PROT MET 16 CG ) 0.31241 ( PROT MET 16 SD ) 0.31241 ( PROT MET 16 CE ) 0.31241 ( PROT MET 16 C ) 0.39052 ( PROT MET 16 O ) 0.39052 ( PROT PHE 17 N ) 0.39052 ( PROT PHE 17 H ) 0.31241 ( PROT PHE 17 CA ) 0.39052 ( PROT PHE 17 CB ) 0.31241 ( PROT PHE 17 CG ) 0.31241 ( PROT PHE 17 CD1 ) 0.31241 ( PROT PHE 17 CD2 ) 0.31241 ( PROT PHE 17 CE1 ) 0.31241 ( PROT PHE 17 CE2 ) 0.31241 ( PROT PHE 17 CZ ) 0.31241 ( PROT PHE 17 C ) 0.39052 ( PROT PHE 17 O ) 0.39052 ( PROT PHE 18 N ) 0.39052 ( PROT PHE 18 H ) 0.31241 ( PROT PHE 18 CA ) 0.39052 ( PROT PHE 18 CB ) 0.31241 ( PROT PHE 18 CG ) 0.31241 ( PROT PHE 18 CD1 ) 0.31241 ( PROT PHE 18 CD2 ) 0.31241 ( PROT PHE 18 CE1 ) 0.31241 ( PROT PHE 18 CE2 ) 0.31241 ( PROT PHE 18 CZ ) 0.31241 ( PROT PHE 18 C ) 0.39052 ( PROT PHE 18 O ) 0.39052 ( PROT GLU 19 N ) 0.39052 ( PROT GLU 19 H ) 0.31241 ( PROT GLU 19 CA ) 0.39052 ( PROT GLU 19 CB ) 0.31241 ( PROT GLU 19 CG ) 0.31241 ( PROT GLU 19 CD ) 0.31241 ( PROT GLU 19 OE1 ) 0.31241 ( PROT GLU 19 OE2 ) 0.31241 ( PROT GLU 19 C ) 0.39052 ( PROT GLU 19 O ) 0.39052 ( PROT SER 20 N ) 0.39052 ( PROT SER 20 H ) 0.31241 ( PROT SER 20 CA ) 0.39052 ( PROT SER 20 CB ) 0.31241 ( PROT SER 20 OG ) 0.31241 ( PROT SER 20 HG ) 0.31241 ( PROT SER 20 C ) 0.39052 ( PROT SER 20 O ) 0.39052 ( PROT THR 21 N ) 0.39052 ( PROT THR 21 H ) 0.31241 ( PROT THR 21 CA ) 0.39052 ( PROT THR 21 CB ) 0.31241 ( PROT THR 21 OG1 ) 0.31241 ( PROT THR 21 HG1 ) 0.31241 ( PROT THR 21 CG2 ) 0.31241 ( PROT THR 21 C ) 0.39052 ( PROT THR 21 O ) 0.39052 ( PROT GLY 22 N ) 0.39052 ( PROT GLY 22 H ) 0.31241 ( PROT GLY 22 CA ) 0.39052 ( PROT GLY 22 C ) 0.39052 ( PROT GLY 22 O ) 0.39052 ( PROT SER 23 N ) 0.39052 ( PROT SER 23 H ) 0.31241 ( PROT SER 23 CA ) 0.39052 ( PROT SER 23 CB ) 0.31241 ( PROT SER 23 OG ) 0.31241 ( PROT SER 23 HG ) 0.31241 ( PROT SER 23 C ) 0.39052 ( PROT SER 23 O ) 0.39052 ( PROT GLN 24 N ) 0.39052 ( PROT GLN 24 H ) 0.31241 ( PROT GLN 24 CA ) 0.39052 ( PROT GLN 24 CB ) 0.31241 ( PROT GLN 24 CG ) 0.31241 ( PROT GLN 24 CD ) 0.31241 ( PROT GLN 24 OE1 ) 0.31241 ( PROT GLN 24 NE2 ) 0.31241 ( PROT GLN 24 HE21 ) 0.31241 ( PROT GLN 24 HE22 ) 0.31241 ( PROT GLN 24 C ) 0.39052 ( PROT GLN 24 O ) 0.39052 ( PROT GLU 25 N ) 0.39052 ( PROT GLU 25 H ) 0.31241 ( PROT GLU 25 CA ) 0.39052 ( PROT GLU 25 CB ) 0.31241 ( PROT GLU 25 CG ) 0.31241 ( PROT GLU 25 CD ) 0.31241 ( PROT GLU 25 OE1 ) 0.31241 ( PROT GLU 25 OE2 ) 0.31241 ( PROT GLU 25 C ) 0.39052 ( PROT GLU 25 O ) 0.39052 ( PROT GLN 26 N ) 0.39052 ( PROT GLN 26 H ) 0.31241 ( PROT GLN 26 CA ) 0.39052 ( PROT GLN 26 CB ) 0.31241 ( PROT GLN 26 CG ) 0.31241 ( PROT GLN 26 CD ) 0.31241 ( PROT GLN 26 OE1 ) 0.31241 ( PROT GLN 26 NE2 ) 0.31241 ( PROT GLN 26 HE21 ) 0.31241 ( PROT GLN 26 HE22 ) 0.31241 ( PROT GLN 26 C ) 0.39052 ( PROT GLN 26 O ) 0.39052 ( PROT LYS 27 N ) 0.39052 ( PROT LYS 27 H ) 0.31241 ( PROT LYS 27 CA ) 0.39052 ( PROT LYS 27 CB ) 0.31241 ( PROT LYS 27 CG ) 0.31241 ( PROT LYS 27 CD ) 0.31241 ( PROT LYS 27 CE ) 0.31241 ( PROT LYS 27 NZ ) 0.31241 ( PROT LYS 27 HZ1 ) 0.31241 ( PROT LYS 27 HZ2 ) 0.31241 ( PROT LYS 27 HZ3 ) 0.31241 ( PROT LYS 27 C ) 0.39052 ( PROT LYS 27 O ) 0.39052 ( PROT SER 28 N ) 0.39052 ( PROT SER 28 H ) 0.31241 ( PROT SER 28 CA ) 0.39052 ( PROT SER 28 CB ) 0.31241 ( PROT SER 28 OG ) 0.31241 ( PROT SER 28 HG ) 0.31241 ( PROT SER 28 C ) 0.39052 ( PROT SER 28 O ) 0.39052 ( PROT GLY 29 N ) 0.39052 ( PROT GLY 29 H ) 0.31241 ( PROT GLY 29 CA ) 0.39052 ( PROT GLY 29 C ) 0.39052 ( PROT GLY 29 O ) 0.39052 ( PROT VAL 30 N ) 0.39052 ( PROT VAL 30 H ) 0.31241 ( PROT VAL 30 CA ) 0.39052 ( PROT VAL 30 CB ) 0.31241 ( PROT VAL 30 CG1 ) 0.31241 ( PROT VAL 30 CG2 ) 0.31241 ( PROT VAL 30 C ) 0.39052 ( PROT VAL 30 O ) 0.39052 ( PROT TRP 31 N ) 0.39052 ( PROT TRP 31 H ) 0.31241 ( PROT TRP 31 CA ) 0.39052 ( PROT TRP 31 CB ) 0.31241 ( PROT TRP 31 CG ) 0.31241 ( PROT TRP 31 CD2 ) 0.31241 ( PROT TRP 31 CE2 ) 0.31241 ( PROT TRP 31 CE3 ) 0.31241 ( PROT TRP 31 CD1 ) 0.31241 ( PROT TRP 31 NE1 ) 0.31241 ( PROT TRP 31 HE1 ) 0.31241 ( PROT TRP 31 CZ2 ) 0.31241 ( PROT TRP 31 CZ3 ) 0.31241 ( PROT TRP 31 CH2 ) 0.31241 ( PROT TRP 31 C ) 0.39052 ( PROT TRP 31 OT1 ) 0.31241 ( PROT TRP 31 OT2 ) 0.31241 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.62670 7.22369 -13.21593 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00411 0.00573 -0.00399 ROTATION MATRIX 0.999996 0.002102 0.001876 -0.002099 0.999996 -0.002019 -0.001880 0.002015 0.999996 AXIS OF ROTATION IS -0.582126 -0.541953 0.606148 ANGLE IS 0.20 TOTAL SQUARE DIFF IS 132.9680 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.669107 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.6691" Parameter: A <- "0.6691" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.55669 7.27905 -13.43606 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.02847 -0.02350 -0.00429 ROTATION MATRIX 0.999642 0.018297 0.019526 -0.017854 0.999584 -0.022631 -0.019932 0.022275 0.999553 AXIS OF ROTATION IS -0.642797 -0.564821 0.517483 ANGLE IS 2.00 CENTER OF ROTATION 13.959950 6.766670-13.466044 SHIFT IS 0.029351 TOTAL SQUARE DIFF IS 7.5475 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.493425 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.6691" RDCMND substituted energy or value "?RMS" to " 0.4934" Parameter: A <- "0.6691 0.4934" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *9000 0.6691 0.4934 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 69.56" Parameter: H <- "69.56" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -144.81138 69.56149 0.42344 ENER INTERN> 7.91883 43.63729 0.00000 34.27241 5.81813 ENER EXTERN> -135.74137 -100.71667 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -144.81" Parameter: B <- "-144.81" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -100.72" Parameter: C <- "-100.72" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -135.74" Parameter: C <- " -236.46" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -236.46" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.92" Parameter: D <- "7.92" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 43.64" Parameter: D <- " 51.56" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 34.27" Parameter: D <- " 85.83" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.82" Parameter: D <- " 91.65" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 91.65" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 9000 ENER= -144.81 GRMS= 0.42 ELEC= -100.72 VDW= -135.74 RDTITL> *EXTERNAL= -236.46 INTERNAL= 91.65 USER= 0.00 HARM= 69.56 RDTITL> *BOND= 7.92 ANGL= 43.64 DIHE= 34.27 IMPR= 5.82 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20829 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20787 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -97.74451 -47.06687 0.18971 0.02000 MINI INTERN> 7.91883 43.63729 0.00000 34.27241 5.81813 MINI EXTERN> -135.74137 -100.71667 0.00000 0.00000 0.00000 MINI CONSTR> 47.06687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -92.69193 -5.05258 6.26213 0.00360 MINI INTERN> 14.29546 43.60949 0.00000 35.19211 5.90628 MINI EXTERN> -142.56638 -97.82448 0.00000 0.00000 0.00000 MINI CONSTR> 48.69559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20782 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -97.48715 4.79522 2.69035 0.00156 MINI INTERN> 8.26628 44.33655 0.00000 35.13302 5.86808 MINI EXTERN> -141.10829 -98.69998 0.00000 0.00000 0.00000 MINI CONSTR> 48.71720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -98.66510 1.17795 0.15414 0.00028 MINI INTERN> 8.04925 43.43861 0.00000 35.02049 5.85217 MINI EXTERN> -140.87354 -98.88968 0.00000 0.00000 0.00000 MINI CONSTR> 48.73761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20780 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -98.71887 0.05377 0.40570 0.00029 MINI INTERN> 7.99603 43.37985 0.00000 34.93931 5.84181 MINI EXTERN> -140.53757 -99.12614 0.00000 0.00000 0.00000 MINI CONSTR> 48.78785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -98.79621 0.07734 0.12385 0.00013 MINI INTERN> 8.01825 43.31292 0.00000 34.87136 5.84117 MINI EXTERN> -140.40101 -99.27265 0.00000 0.00000 0.00000 MINI CONSTR> 48.83375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20779 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -98.81391 0.01771 0.47762 0.00031 MINI INTERN> 7.94178 43.34031 0.00000 34.83377 5.83657 MINI EXTERN> -140.30799 -99.34590 0.00000 0.00000 0.00000 MINI CONSTR> 48.88755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -98.88905 0.07514 0.15029 0.00013 MINI INTERN> 8.00757 43.25042 0.00000 34.78208 5.83468 MINI EXTERN> -140.26586 -99.43501 0.00000 0.00000 0.00000 MINI CONSTR> 48.93706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20779 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -98.92879 0.03973 0.10856 0.00014 MINI INTERN> 7.98357 43.23923 0.00000 34.75242 5.83246 MINI EXTERN> -140.24248 -99.47768 0.00000 0.00000 0.00000 MINI CONSTR> 48.98368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -98.97185 0.04306 0.11710 0.00014 MINI INTERN> 7.98149 43.21294 0.00000 34.71774 5.83037 MINI EXTERN> -140.23247 -99.52152 0.00000 0.00000 0.00000 MINI CONSTR> 49.03960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20778 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -99.01307 0.04122 0.20080 0.00015 MINI INTERN> 8.00554 43.17120 0.00000 34.68103 5.82853 MINI EXTERN> -140.23775 -99.56251 0.00000 0.00000 0.00000 MINI CONSTR> 49.10088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -99.05334 0.04027 0.16125 0.00016 MINI INTERN> 7.97722 43.16753 0.00000 34.65593 5.82712 MINI EXTERN> -140.24894 -99.58526 0.00000 0.00000 0.00000 MINI CONSTR> 49.15304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20774 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -99.08762 0.03428 0.23310 0.00016 MINI INTERN> 8.00541 43.12730 0.00000 34.62713 5.82573 MINI EXTERN> -140.27019 -99.61121 0.00000 0.00000 0.00000 MINI CONSTR> 49.20821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -99.12886 0.04125 0.17373 0.00017 MINI INTERN> 7.96951 43.12835 0.00000 34.60540 5.82416 MINI EXTERN> -140.29231 -99.62541 0.00000 0.00000 0.00000 MINI CONSTR> 49.26143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20773 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -99.15961 0.03075 0.25242 0.00017 MINI INTERN> 7.98740 43.10205 0.00000 34.57915 5.82365 MINI EXTERN> -140.32034 -99.64589 0.00000 0.00000 0.00000 MINI CONSTR> 49.31436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -99.19382 0.03421 0.28739 0.00018 MINI INTERN> 8.01378 43.05791 0.00000 34.55706 5.82124 MINI EXTERN> -140.35355 -99.65918 0.00000 0.00000 0.00000 MINI CONSTR> 49.36892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20771 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -99.22797 0.03415 0.28854 0.00019 MINI INTERN> 8.00751 43.04715 0.00000 34.53437 5.82068 MINI EXTERN> -140.38481 -99.67355 0.00000 0.00000 0.00000 MINI CONSTR> 49.42067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -99.26316 0.03519 0.27815 0.00019 MINI INTERN> 7.98552 43.04629 0.00000 34.51377 5.81985 MINI EXTERN> -140.41657 -99.68396 0.00000 0.00000 0.00000 MINI CONSTR> 49.47195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20769 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -99.29668 0.03352 0.30937 0.00020 MINI INTERN> 8.01018 43.00042 0.00000 34.49551 5.81663 MINI EXTERN> -140.45497 -99.69028 0.00000 0.00000 0.00000 MINI CONSTR> 49.52582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -99.33123 0.03454 0.29044 0.00021 MINI INTERN> 7.99986 42.99535 0.00000 34.47281 5.81658 MINI EXTERN> -140.48974 -99.70348 0.00000 0.00000 0.00000 MINI CONSTR> 49.57739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20768 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -99.37541 0.04418 0.09980 0.00009 MINI INTERN> 7.92473 43.01178 0.00000 34.46517 5.81207 MINI EXTERN> -140.52126 -99.69417 0.00000 0.00000 0.00000 MINI CONSTR> 49.62627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -99.39443 0.01902 0.33652 0.00022 MINI INTERN> 8.01303 42.95022 0.00000 34.43291 5.81357 MINI EXTERN> -140.56486 -99.72066 0.00000 0.00000 0.00000 MINI CONSTR> 49.68135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20768 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -99.42383 0.02940 0.38390 0.00023 MINI INTERN> 7.95093 42.99009 0.00000 34.41350 5.81374 MINI EXTERN> -140.59759 -99.72700 0.00000 0.00000 0.00000 MINI CONSTR> 49.73249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -99.45689 0.03306 0.36035 0.00024 MINI INTERN> 7.99139 42.94210 0.00000 34.39131 5.81261 MINI EXTERN> -140.63774 -99.73994 0.00000 0.00000 0.00000 MINI CONSTR> 49.78339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20768 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -99.50776 0.05088 0.11236 0.00010 MINI INTERN> 7.91396 42.94597 0.00000 34.38831 5.80586 MINI EXTERN> -140.67217 -99.72267 0.00000 0.00000 0.00000 MINI CONSTR> 49.83297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -99.53688 0.02912 0.09580 0.00011 MINI INTERN> 7.91606 42.93065 0.00000 34.36996 5.80509 MINI EXTERN> -140.70570 -99.73084 0.00000 0.00000 0.00000 MINI CONSTR> 49.87791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20765 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -99.56776 0.03088 0.09768 0.00011 MINI INTERN> 7.91433 42.91474 0.00000 34.35189 5.80355 MINI EXTERN> -140.74221 -99.73689 0.00000 0.00000 0.00000 MINI CONSTR> 49.92683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -99.59918 0.03142 0.09377 0.00012 MINI INTERN> 7.91531 42.89749 0.00000 34.33283 5.80221 MINI EXTERN> -140.77948 -99.74403 0.00000 0.00000 0.00000 MINI CONSTR> 49.97650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20764 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -99.63129 0.03211 0.09776 0.00012 MINI INTERN> 7.91007 42.88435 0.00000 34.31371 5.80070 MINI EXTERN> -140.81765 -99.75034 0.00000 0.00000 0.00000 MINI CONSTR> 50.02787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -99.66240 0.03111 0.16641 0.00012 MINI INTERN> 7.89546 42.87436 0.00000 34.29700 5.79778 MINI EXTERN> -140.85780 -99.75169 0.00000 0.00000 0.00000 MINI CONSTR> 50.08249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20765 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -99.69034 0.02794 0.09425 0.00013 MINI INTERN> 7.90835 42.85490 0.00000 34.27748 5.79809 MINI EXTERN> -140.88821 -99.76326 0.00000 0.00000 0.00000 MINI CONSTR> 50.12230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -99.71961 0.02926 0.19448 0.00013 MINI INTERN> 7.88188 42.85530 0.00000 34.26151 5.79504 MINI EXTERN> -140.92747 -99.76296 0.00000 0.00000 0.00000 MINI CONSTR> 50.17711 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20764 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -99.74976 0.03016 0.14728 0.00014 MINI INTERN> 7.89872 42.82618 0.00000 34.24289 5.79391 MINI EXTERN> -140.96180 -99.77124 0.00000 0.00000 0.00000 MINI CONSTR> 50.22158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -99.77515 0.02538 0.20940 0.00014 MINI INTERN> 7.87861 42.82714 0.00000 34.22723 5.79193 MINI EXTERN> -140.99539 -99.77342 0.00000 0.00000 0.00000 MINI CONSTR> 50.26875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20763 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -99.80654 0.03140 0.15668 0.00015 MINI INTERN> 7.89935 42.79528 0.00000 34.20729 5.79099 MINI EXTERN> -141.03073 -99.78320 0.00000 0.00000 0.00000 MINI CONSTR> 50.31447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -99.82948 0.02293 0.22550 0.00015 MINI INTERN> 7.88890 42.78784 0.00000 34.19319 5.78855 MINI EXTERN> -141.06283 -99.78409 0.00000 0.00000 0.00000 MINI CONSTR> 50.35896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20762 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -99.85538 0.02590 0.25648 0.00016 MINI INTERN> 7.86440 42.79722 0.00000 34.17493 5.78785 MINI EXTERN> -141.09477 -99.79011 0.00000 0.00000 0.00000 MINI CONSTR> 50.40510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -99.88246 0.02708 0.23821 0.00017 MINI INTERN> 7.88094 42.76578 0.00000 34.15929 5.78568 MINI EXTERN> -141.12732 -99.79445 0.00000 0.00000 0.00000 MINI CONSTR> 50.44761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20761 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -99.90721 0.02475 0.29410 0.00017 MINI INTERN> 7.85602 42.77836 0.00000 34.13968 5.78528 MINI EXTERN> -141.15988 -99.80189 0.00000 0.00000 0.00000 MINI CONSTR> 50.49521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -99.93342 0.02621 0.26802 0.00018 MINI INTERN> 7.86000 42.75961 0.00000 34.12408 5.78377 MINI EXTERN> -141.18940 -99.80671 0.00000 0.00000 0.00000 MINI CONSTR> 50.53522 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20760 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -99.95973 0.02631 0.27414 0.00019 MINI INTERN> 7.89441 42.71356 0.00000 34.10762 5.78122 MINI EXTERN> -141.22391 -99.81182 0.00000 0.00000 0.00000 MINI CONSTR> 50.57920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -99.99319 0.03346 0.08689 0.00008 MINI INTERN> 7.91028 42.69790 0.00000 34.08224 5.78396 MINI EXTERN> -141.25237 -99.83262 0.00000 0.00000 0.00000 MINI CONSTR> 50.61743 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20759 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -100.00844 0.01525 0.29352 0.00020 MINI INTERN> 7.85655 42.71973 0.00000 34.07493 5.77881 MINI EXTERN> -141.28230 -99.82048 0.00000 0.00000 0.00000 MINI CONSTR> 50.66434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -100.03278 0.02434 0.33031 0.00021 MINI INTERN> 7.90138 42.66892 0.00000 34.05689 5.77659 MINI EXTERN> -141.31744 -99.82805 0.00000 0.00000 0.00000 MINI CONSTR> 50.70894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20758 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -100.05765 0.02487 0.32752 0.00021 MINI INTERN> 7.84689 42.70316 0.00000 34.04011 5.77614 MINI EXTERN> -141.34397 -99.83191 0.00000 0.00000 0.00000 MINI CONSTR> 50.75194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -100.09741 0.03976 0.10163 0.00009 MINI INTERN> 7.91329 42.64290 0.00000 34.01080 5.77882 MINI EXTERN> -141.37779 -99.85818 0.00000 0.00000 0.00000 MINI CONSTR> 50.79274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20757 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -100.10498 0.00756 0.34504 0.00023 MINI INTERN> 7.84284 42.68170 0.00000 34.00703 5.77340 MINI EXTERN> -141.40224 -99.84240 0.00000 0.00000 0.00000 MINI CONSTR> 50.83470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -100.14618 0.04120 0.12020 0.00010 MINI INTERN> 7.91407 42.61900 0.00000 33.97584 5.77661 MINI EXTERN> -141.43671 -99.87128 0.00000 0.00000 0.00000 MINI CONSTR> 50.87629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20756 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -100.16796 0.02178 0.08568 0.00010 MINI INTERN> 7.90500 42.61046 0.00000 33.96406 5.77454 MINI EXTERN> -141.46086 -99.87240 0.00000 0.00000 0.00000 MINI CONSTR> 50.91124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -100.19326 0.02530 0.13816 0.00011 MINI INTERN> 7.91785 42.59287 0.00000 33.94183 5.77426 MINI EXTERN> -141.49388 -99.88384 0.00000 0.00000 0.00000 MINI CONSTR> 50.95765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20755 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -100.21527 0.02200 0.08384 0.00011 MINI INTERN> 7.90277 42.58701 0.00000 33.93139 5.77181 MINI EXTERN> -141.51695 -99.88306 0.00000 0.00000 0.00000 MINI CONSTR> 50.99175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -100.23924 0.02398 0.16333 0.00011 MINI INTERN> 7.92753 42.56186 0.00000 33.90803 5.77172 MINI EXTERN> -141.55064 -99.89613 0.00000 0.00000 0.00000 MINI CONSTR> 51.03839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20755 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -100.26325 0.02401 0.12357 0.00012 MINI INTERN> 7.90713 42.56334 0.00000 33.89406 5.77010 MINI EXTERN> -141.57557 -99.89861 0.00000 0.00000 0.00000 MINI CONSTR> 51.07630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -100.28540 0.02215 0.14074 0.00012 MINI INTERN> 7.91435 42.54740 0.00000 33.87684 5.76905 MINI EXTERN> -141.60321 -99.90566 0.00000 0.00000 0.00000 MINI CONSTR> 51.11583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20754 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -100.30875 0.02335 0.13859 0.00013 MINI INTERN> 7.91786 42.53079 0.00000 33.86077 5.76737 MINI EXTERN> -141.63107 -99.91042 0.00000 0.00000 0.00000 MINI CONSTR> 51.15595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -100.32846 0.01972 0.19205 0.00013 MINI INTERN> 7.92506 42.52052 0.00000 33.84174 5.76720 MINI EXTERN> -141.65806 -99.92017 0.00000 0.00000 0.00000 MINI CONSTR> 51.19525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20753 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -100.35193 0.02346 0.20444 0.00014 MINI INTERN> 7.93659 42.49624 0.00000 33.82511 5.76516 MINI EXTERN> -141.68753 -99.92458 0.00000 0.00000 0.00000 MINI CONSTR> 51.23708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -100.37286 0.02093 0.22105 0.00014 MINI INTERN> 7.92714 42.49800 0.00000 33.80692 5.76499 MINI EXTERN> -141.71291 -99.93288 0.00000 0.00000 0.00000 MINI CONSTR> 51.27588 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20749 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -100.39411 0.02125 0.23528 0.00015 MINI INTERN> 7.94309 42.47190 0.00000 33.79118 5.76311 MINI EXTERN> -141.74042 -99.93771 0.00000 0.00000 0.00000 MINI CONSTR> 51.31474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -100.41561 0.02151 0.22045 0.00015 MINI INTERN> 7.92602 42.47599 0.00000 33.77575 5.76237 MINI EXTERN> -141.76337 -99.94305 0.00000 0.00000 0.00000 MINI CONSTR> 51.35067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20748 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -100.43673 0.02112 0.24661 0.00016 MINI INTERN> 7.94463 42.44432 0.00000 33.76125 5.75965 MINI EXTERN> -141.79151 -99.94533 0.00000 0.00000 0.00000 MINI CONSTR> 51.39024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -100.45855 0.02182 0.22876 0.00016 MINI INTERN> 7.93250 42.44789 0.00000 33.74323 5.75967 MINI EXTERN> -141.81538 -99.95396 0.00000 0.00000 0.00000 MINI CONSTR> 51.42750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20749 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -100.48046 0.02191 0.23728 0.00017 MINI INTERN> 7.93612 42.43355 0.00000 33.72607 5.75833 MINI EXTERN> -141.84229 -99.95968 0.00000 0.00000 0.00000 MINI CONSTR> 51.46744 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -100.50905 0.02858 0.07897 0.00007 MINI INTERN> 7.87804 42.44620 0.00000 33.72140 5.75319 MINI EXTERN> -141.86282 -99.94835 0.00000 0.00000 0.00000 MINI CONSTR> 51.50329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20749 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -100.52034 0.01129 0.26825 0.00018 MINI INTERN> 7.94633 42.40560 0.00000 33.69322 5.75592 MINI EXTERN> -141.89300 -99.97126 0.00000 0.00000 0.00000 MINI CONSTR> 51.54286 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -100.54060 0.02027 0.29568 0.00019 MINI INTERN> 7.91636 42.42159 0.00000 33.67656 5.75520 MINI EXTERN> -141.91655 -99.97570 0.00000 0.00000 0.00000 MINI CONSTR> 51.58194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20747 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -100.57227 0.03167 0.09082 0.00008 MINI INTERN> 7.87140 42.41552 0.00000 33.67460 5.74864 MINI EXTERN> -141.93730 -99.96188 0.00000 0.00000 0.00000 MINI CONSTR> 51.61676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -100.57887 0.00660 0.30375 0.00020 MINI INTERN> 7.93218 42.39019 0.00000 33.64487 5.75303 MINI EXTERN> -141.96441 -99.98779 0.00000 0.00000 0.00000 MINI CONSTR> 51.65306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20747 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -100.61194 0.03307 0.10629 0.00009 MINI INTERN> 7.86347 42.39927 0.00000 33.64480 5.74572 MINI EXTERN> -141.98405 -99.97017 0.00000 0.00000 0.00000 MINI CONSTR> 51.68901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -100.62955 0.01760 0.07698 0.00009 MINI INTERN> 7.87477 42.38273 0.00000 33.63004 5.74521 MINI EXTERN> -142.00467 -99.97683 0.00000 0.00000 0.00000 MINI CONSTR> 51.71921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20747 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -100.64890 0.01936 0.08035 0.00010 MINI INTERN> 7.87152 42.37418 0.00000 33.61541 5.74377 MINI EXTERN> -142.02737 -99.98085 0.00000 0.00000 0.00000 MINI CONSTR> 51.75444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -100.66914 0.02023 0.12602 0.00010 MINI INTERN> 7.85725 42.37102 0.00000 33.60125 5.74132 MINI EXTERN> -142.05193 -99.98209 0.00000 0.00000 0.00000 MINI CONSTR> 51.79404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20745 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -100.68695 0.01782 0.07492 0.00010 MINI INTERN> 7.87357 42.35206 0.00000 33.58550 5.74133 MINI EXTERN> -142.07227 -99.99055 0.00000 0.00000 0.00000 MINI CONSTR> 51.82341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -100.70604 0.01909 0.15386 0.00011 MINI INTERN> 7.85754 42.34777 0.00000 33.57295 5.73798 MINI EXTERN> -142.09693 -99.98906 0.00000 0.00000 0.00000 MINI CONSTR> 51.86369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20744 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -100.72539 0.01935 0.11602 0.00011 MINI INTERN> 7.85600 42.34178 0.00000 33.55691 5.73774 MINI EXTERN> -142.11775 -99.99617 0.00000 0.00000 0.00000 MINI CONSTR> 51.89610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -100.74198 0.01659 0.16704 0.00011 MINI INTERN> 7.85248 42.33087 0.00000 33.54482 5.73514 MINI EXTERN> -142.13978 -99.99653 0.00000 0.00000 0.00000 MINI CONSTR> 51.93101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20744 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -100.76194 0.01995 0.12707 0.00012 MINI INTERN> 7.85115 42.32526 0.00000 33.52791 5.73511 MINI EXTERN> -142.16097 -100.00454 0.00000 0.00000 0.00000 MINI CONSTR> 51.96414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -100.77723 0.01529 0.17672 0.00012 MINI INTERN> 7.84148 42.32077 0.00000 33.51645 5.73277 MINI EXTERN> -142.18117 -100.00464 0.00000 0.00000 0.00000 MINI CONSTR> 51.99711 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20743 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -100.79461 0.01739 0.20561 0.00013 MINI INTERN> 7.85903 42.29420 0.00000 33.50227 5.73066 MINI EXTERN> -142.20476 -100.00816 0.00000 0.00000 0.00000 MINI CONSTR> 52.03216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -100.81135 0.01673 0.21023 0.00013 MINI INTERN> 7.85187 42.28965 0.00000 33.48918 5.72919 MINI EXTERN> -142.22458 -100.01085 0.00000 0.00000 0.00000 MINI CONSTR> 52.06419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20743 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -100.82891 0.01757 0.19605 0.00014 MINI INTERN> 7.83637 42.29456 0.00000 33.47491 5.72860 MINI EXTERN> -142.24327 -100.01557 0.00000 0.00000 0.00000 MINI CONSTR> 52.09548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -100.84483 0.01592 0.24296 0.00014 MINI INTERN> 7.85672 42.26567 0.00000 33.46116 5.72617 MINI EXTERN> -142.26694 -100.01832 0.00000 0.00000 0.00000 MINI CONSTR> 52.13070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20743 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -100.86185 0.01702 0.22227 0.00015 MINI INTERN> 7.85296 42.25950 0.00000 33.44801 5.72524 MINI EXTERN> -142.28533 -100.02231 0.00000 0.00000 0.00000 MINI CONSTR> 52.16008 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -100.88446 0.02261 0.07159 0.00006 MINI INTERN> 7.87499 42.24305 0.00000 33.42589 5.72801 MINI EXTERN> -142.30584 -100.04003 0.00000 0.00000 0.00000 MINI CONSTR> 52.18947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20742 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -100.89457 0.01011 0.23412 0.00016 MINI INTERN> 7.84390 42.24698 0.00000 33.42145 5.72238 MINI EXTERN> -142.32463 -100.02844 0.00000 0.00000 0.00000 MINI CONSTR> 52.22378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -100.91846 0.02389 0.07606 0.00007 MINI INTERN> 7.87668 42.22270 0.00000 33.39760 5.72557 MINI EXTERN> -142.34642 -100.04854 0.00000 0.00000 0.00000 MINI CONSTR> 52.25396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20742 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -100.92588 0.00742 0.26114 0.00017 MINI INTERN> 7.81961 42.25390 0.00000 33.39276 5.72110 MINI EXTERN> -142.36179 -100.03789 0.00000 0.00000 0.00000 MINI CONSTR> 52.28643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -100.94048 0.01459 0.29258 0.00018 MINI INTERN> 7.86594 42.20254 0.00000 33.38020 5.71832 MINI EXTERN> -142.38521 -100.04059 0.00000 0.00000 0.00000 MINI CONSTR> 52.31833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20742 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -100.96775 0.02727 0.08062 0.00008 MINI INTERN> 7.87645 42.19499 0.00000 33.35644 5.72192 MINI EXTERN> -142.40506 -100.06055 0.00000 0.00000 0.00000 MINI CONSTR> 52.34805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -100.98297 0.01522 0.06820 0.00008 MINI INTERN> 7.86897 42.19057 0.00000 33.34509 5.72038 MINI EXTERN> -142.42223 -100.06235 0.00000 0.00000 0.00000 MINI CONSTR> 52.37660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20742 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -100.99935 0.01638 0.07039 0.00008 MINI INTERN> 7.87070 42.17998 0.00000 33.33111 5.71918 MINI EXTERN> -142.44191 -100.06656 0.00000 0.00000 0.00000 MINI CONSTR> 52.40816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -101.01581 0.01646 0.06768 0.00008 MINI INTERN> 7.86880 42.17140 0.00000 33.31764 5.71777 MINI EXTERN> -142.46130 -100.06987 0.00000 0.00000 0.00000 MINI CONSTR> 52.43975 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20741 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -101.03299 0.01718 0.06747 0.00009 MINI INTERN> 7.86814 42.16185 0.00000 33.30317 5.71641 MINI EXTERN> -142.48173 -100.07378 0.00000 0.00000 0.00000 MINI CONSTR> 52.47295 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -101.05093 0.01794 0.11629 0.00009 MINI INTERN> 7.88457 42.14323 0.00000 33.28350 5.71611 MINI EXTERN> -142.50622 -100.08279 0.00000 0.00000 0.00000 MINI CONSTR> 52.51066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20740 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -101.06743 0.01650 0.08339 0.00009 MINI INTERN> 7.87246 42.14034 0.00000 33.27226 5.71419 MINI EXTERN> -142.52368 -100.08360 0.00000 0.00000 0.00000 MINI CONSTR> 52.54060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -101.08217 0.01475 0.07173 0.00010 MINI INTERN> 7.86962 42.13210 0.00000 33.26097 5.71257 MINI EXTERN> -142.54069 -100.08552 0.00000 0.00000 0.00000 MINI CONSTR> 52.56878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20740 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -101.09721 0.01503 0.14739 0.00010 MINI INTERN> 7.89103 42.11336 0.00000 33.24131 5.71289 MINI EXTERN> -142.56368 -100.09577 0.00000 0.00000 0.00000 MINI CONSTR> 52.60365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -101.11491 0.01770 0.08607 0.00011 MINI INTERN> 7.87310 42.11175 0.00000 33.23139 5.71035 MINI EXTERN> -142.58064 -100.09455 0.00000 0.00000 0.00000 MINI CONSTR> 52.63369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20737 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -101.13193 0.01702 0.09833 0.00011 MINI INTERN> 7.87724 42.09928 0.00000 33.21566 5.70917 MINI EXTERN> -142.60187 -100.09936 0.00000 0.00000 0.00000 MINI CONSTR> 52.66796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -101.14509 0.01317 0.16265 0.00011 MINI INTERN> 7.89349 42.08407 0.00000 33.19840 5.70922 MINI EXTERN> -142.62238 -100.10742 0.00000 0.00000 0.00000 MINI CONSTR> 52.69953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20736 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -101.16112 0.01603 0.17067 0.00012 MINI INTERN> 7.90068 42.06777 0.00000 33.18422 5.70762 MINI EXTERN> -142.64275 -100.11077 0.00000 0.00000 0.00000 MINI CONSTR> 52.73209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -101.16112 0.01603 0.17067 0.00014 STPD INTERN> 7.90068 42.06777 0.00000 33.18422 5.70762 STPD EXTERN> -142.64275 -100.11077 0.00000 0.00000 0.00000 STPD CONSTR> 52.73209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20736 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20736 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -101.16112 0.01603 0.17067 0.00000 MINI INTERN> 7.90068 42.06777 0.00000 33.18422 5.70762 MINI EXTERN> -142.64275 -100.11077 0.00000 0.00000 0.00000 MINI CONSTR> 52.73209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -102.81123 1.65011 0.17723 0.15424 MINI INTERN> 7.84918 40.53880 0.00000 30.78443 5.50585 MINI EXTERN> -146.68214 -100.50422 0.00000 0.00000 0.00000 MINI CONSTR> 59.69687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -102.84359 0.03235 0.10373 0.00890 MINI INTERN> 7.74799 40.57186 0.00000 30.71673 5.46442 MINI EXTERN> -146.52455 -100.62210 0.00000 0.00000 0.00000 MINI CONSTR> 59.80206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -102.90807 0.06448 0.17538 0.03605 MINI INTERN> 7.59252 40.12088 0.00000 30.47394 5.43118 MINI EXTERN> -145.74310 -100.55911 0.00000 0.00000 0.00000 MINI CONSTR> 59.77564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -103.01397 0.10590 0.16454 0.05049 MINI INTERN> 7.61764 40.10954 0.00000 30.33213 5.39271 MINI EXTERN> -145.63429 -100.53541 0.00000 0.00000 0.00000 MINI CONSTR> 59.70370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -103.09385 0.07988 0.16616 0.02917 MINI INTERN> 7.64741 40.06891 0.00000 30.21923 5.37605 MINI EXTERN> -145.78154 -100.30726 0.00000 0.00000 0.00000 MINI CONSTR> 59.68335 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -103.14113 0.04728 0.10999 0.02827 MINI INTERN> 7.70181 40.03741 0.00000 30.19353 5.38743 MINI EXTERN> -146.01308 -100.14640 0.00000 0.00000 0.00000 MINI CONSTR> 59.69817 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -103.17182 0.03069 0.10847 0.01589 MINI INTERN> 7.68009 40.09245 0.00000 30.12613 5.38757 MINI EXTERN> -146.06083 -100.12099 0.00000 0.00000 0.00000 MINI CONSTR> 59.72375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -103.20075 0.02893 0.11337 0.01739 MINI INTERN> 7.68043 40.14758 0.00000 30.08777 5.42830 MINI EXTERN> -146.18809 -100.12081 0.00000 0.00000 0.00000 MINI CONSTR> 59.76407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -103.23316 0.03240 0.10309 0.02802 MINI INTERN> 7.73249 40.10360 0.00000 30.06888 5.41920 MINI EXTERN> -146.22906 -100.14880 0.00000 0.00000 0.00000 MINI CONSTR> 59.82054 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -103.25847 0.02531 0.09078 0.01756 MINI INTERN> 7.68273 40.03221 0.00000 30.04660 5.44455 MINI EXTERN> -146.32047 -99.99968 0.00000 0.00000 0.00000 MINI CONSTR> 59.85558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -103.27865 0.02017 0.08111 0.01546 MINI INTERN> 7.67676 40.00207 0.00000 30.07284 5.44544 MINI EXTERN> -146.23070 -100.09935 0.00000 0.00000 0.00000 MINI CONSTR> 59.85429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -103.29055 0.01190 0.06294 0.01254 MINI INTERN> 7.69216 40.01396 0.00000 30.07642 5.47199 MINI EXTERN> -146.17404 -100.20073 0.00000 0.00000 0.00000 MINI CONSTR> 59.82969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -103.30284 0.01229 0.06341 0.01193 MINI INTERN> 7.70914 40.04542 0.00000 30.05192 5.47109 MINI EXTERN> -146.18012 -100.17798 0.00000 0.00000 0.00000 MINI CONSTR> 59.77770 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -103.31152 0.00869 0.05154 0.00817 MINI INTERN> 7.70374 40.02997 0.00000 30.07501 5.47807 MINI EXTERN> -146.12216 -100.19410 0.00000 0.00000 0.00000 MINI CONSTR> 59.71793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -103.31856 0.00703 0.04971 0.00925 MINI INTERN> 7.69000 40.05697 0.00000 30.07423 5.49432 MINI EXTERN> -146.03726 -100.23903 0.00000 0.00000 0.00000 MINI CONSTR> 59.64221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -103.32511 0.00655 0.04991 0.00836 MINI INTERN> 7.70086 40.03788 0.00000 30.10700 5.49247 MINI EXTERN> -145.95078 -100.26897 0.00000 0.00000 0.00000 MINI CONSTR> 59.55642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -103.33222 0.00711 0.04901 0.00990 MINI INTERN> 7.71902 40.05875 0.00000 30.10952 5.50799 MINI EXTERN> -145.88880 -100.29661 0.00000 0.00000 0.00000 MINI CONSTR> 59.45792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -103.33866 0.00644 0.04793 0.01206 MINI INTERN> 7.71866 40.12524 0.00000 30.16770 5.50760 MINI EXTERN> -145.91856 -100.31006 0.00000 0.00000 0.00000 MINI CONSTR> 59.37076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -103.34470 0.00604 0.04512 0.01111 MINI INTERN> 7.69564 40.15418 0.00000 30.25862 5.50497 MINI EXTERN> -145.96410 -100.28297 0.00000 0.00000 0.00000 MINI CONSTR> 59.28895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -103.35061 0.00591 0.04762 0.00974 MINI INTERN> 7.69127 40.13870 0.00000 30.31702 5.52654 MINI EXTERN> -145.95612 -100.27379 0.00000 0.00000 0.00000 MINI CONSTR> 59.20576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -103.35061 0.00591 0.04762 0.02000 CONJ INTERN> 7.69127 40.13870 0.00000 30.31702 5.52654 CONJ EXTERN> -145.95612 -100.27379 0.00000 0.00000 0.00000 CONJ CONSTR> 59.20576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "9600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.20307 ( PROT LYS 1 HT2 ) 0.20307 ( PROT LYS 1 N ) 0.25384 ( PROT LYS 1 HT3 ) 0.20307 ( PROT LYS 1 CA ) 0.25384 ( PROT LYS 1 CB ) 0.20307 ( PROT LYS 1 CG ) 0.20307 ( PROT LYS 1 CD ) 0.20307 ( PROT LYS 1 CE ) 0.20307 ( PROT LYS 1 NZ ) 0.20307 ( PROT LYS 1 HZ1 ) 0.20307 ( PROT LYS 1 HZ2 ) 0.20307 ( PROT LYS 1 HZ3 ) 0.20307 ( PROT LYS 1 C ) 0.25384 ( PROT LYS 1 O ) 0.25384 ( PROT MET 2 N ) 0.25384 ( PROT MET 2 H ) 0.20307 ( PROT MET 2 CA ) 0.25384 ( PROT MET 2 CB ) 0.20307 ( PROT MET 2 CG ) 0.20307 ( PROT MET 2 SD ) 0.20307 ( PROT MET 2 CE ) 0.20307 ( PROT MET 2 C ) 0.25384 ( PROT MET 2 O ) 0.25384 ( PROT LYS 3 N ) 0.25384 ( PROT LYS 3 H ) 0.20307 ( PROT LYS 3 CA ) 0.25384 ( PROT LYS 3 CB ) 0.20307 ( PROT LYS 3 CG ) 0.20307 ( PROT LYS 3 CD ) 0.20307 ( PROT LYS 3 CE ) 0.20307 ( PROT LYS 3 NZ ) 0.20307 ( PROT LYS 3 HZ1 ) 0.20307 ( PROT LYS 3 HZ2 ) 0.20307 ( PROT LYS 3 HZ3 ) 0.20307 ( PROT LYS 3 C ) 0.25384 ( PROT LYS 3 O ) 0.25384 ( PROT ALA 4 N ) 0.25384 ( PROT ALA 4 H ) 0.20307 ( PROT ALA 4 CA ) 0.25384 ( PROT ALA 4 CB ) 0.20307 ( PROT ALA 4 C ) 0.25384 ( PROT ALA 4 O ) 0.25384 ( PROT VAL 5 N ) 0.25384 ( PROT VAL 5 H ) 0.20307 ( PROT VAL 5 CA ) 0.25384 ( PROT VAL 5 CB ) 0.20307 ( PROT VAL 5 CG1 ) 0.20307 ( PROT VAL 5 CG2 ) 0.20307 ( PROT VAL 5 C ) 0.25384 ( PROT VAL 5 O ) 0.25384 ( PROT MET 6 N ) 0.25384 ( PROT MET 6 H ) 0.20307 ( PROT MET 6 CA ) 0.25384 ( PROT MET 6 CB ) 0.20307 ( PROT MET 6 CG ) 0.20307 ( PROT MET 6 SD ) 0.20307 ( PROT MET 6 CE ) 0.20307 ( PROT MET 6 C ) 0.25384 ( PROT MET 6 O ) 0.25384 ( PROT ILE 7 N ) 0.25384 ( PROT ILE 7 H ) 0.20307 ( PROT ILE 7 CA ) 0.25384 ( PROT ILE 7 CB ) 0.20307 ( PROT ILE 7 CG2 ) 0.20307 ( PROT ILE 7 CG1 ) 0.20307 ( PROT ILE 7 CD ) 0.20307 ( PROT ILE 7 C ) 0.25384 ( PROT ILE 7 O ) 0.25384 ( PROT GLY 8 N ) 0.25384 ( PROT GLY 8 H ) 0.20307 ( PROT GLY 8 CA ) 0.25384 ( PROT GLY 8 C ) 0.25384 ( PROT GLY 8 O ) 0.25384 ( PROT ALA 9 N ) 0.25384 ( PROT ALA 9 H ) 0.20307 ( PROT ALA 9 CA ) 0.25384 ( PROT ALA 9 CB ) 0.20307 ( PROT ALA 9 C ) 0.25384 ( PROT ALA 9 O ) 0.25384 ( PROT CYS 10 N ) 0.25384 ( PROT CYS 10 H ) 0.20307 ( PROT CYS 10 CA ) 0.25384 ( PROT CYS 10 CB ) 0.20307 ( PROT CYS 10 SG ) 0.20307 ( PROT CYS 10 C ) 0.25384 ( PROT CYS 10 O ) 0.25384 ( PROT PHE 11 N ) 0.25384 ( PROT PHE 11 H ) 0.20307 ( PROT PHE 11 CA ) 0.25384 ( PROT PHE 11 CB ) 0.20307 ( PROT PHE 11 CG ) 0.20307 ( PROT PHE 11 CD1 ) 0.20307 ( PROT PHE 11 CD2 ) 0.20307 ( PROT PHE 11 CE1 ) 0.20307 ( PROT PHE 11 CE2 ) 0.20307 ( PROT PHE 11 CZ ) 0.20307 ( PROT PHE 11 C ) 0.25384 ( PROT PHE 11 O ) 0.25384 ( PROT LEU 12 N ) 0.25384 ( PROT LEU 12 H ) 0.20307 ( PROT LEU 12 CA ) 0.25384 ( PROT LEU 12 CB ) 0.20307 ( PROT LEU 12 CG ) 0.20307 ( PROT LEU 12 CD1 ) 0.20307 ( PROT LEU 12 CD2 ) 0.20307 ( PROT LEU 12 C ) 0.25384 ( PROT LEU 12 O ) 0.25384 ( PROT ILE 13 N ) 0.25384 ( PROT ILE 13 H ) 0.20307 ( PROT ILE 13 CA ) 0.25384 ( PROT ILE 13 CB ) 0.20307 ( PROT ILE 13 CG2 ) 0.20307 ( PROT ILE 13 CG1 ) 0.20307 ( PROT ILE 13 CD ) 0.20307 ( PROT ILE 13 C ) 0.25384 ( PROT ILE 13 O ) 0.25384 ( PROT ASH 14 N ) 0.25384 ( PROT ASH 14 H ) 0.20307 ( PROT ASH 14 CA ) 0.25384 ( PROT ASH 14 CB ) 0.20307 ( PROT ASH 14 CG ) 0.20307 ( PROT ASH 14 OD1 ) 0.20307 ( PROT ASH 14 OD2 ) 0.20307 ( PROT ASH 14 HD2 ) 0.20307 ( PROT ASH 14 C ) 0.25384 ( PROT ASH 14 O ) 0.25384 ( PROT PHE 15 N ) 0.25384 ( PROT PHE 15 H ) 0.20307 ( PROT PHE 15 CA ) 0.25384 ( PROT PHE 15 CB ) 0.20307 ( PROT PHE 15 CG ) 0.20307 ( PROT PHE 15 CD1 ) 0.20307 ( PROT PHE 15 CD2 ) 0.20307 ( PROT PHE 15 CE1 ) 0.20307 ( PROT PHE 15 CE2 ) 0.20307 ( PROT PHE 15 CZ ) 0.20307 ( PROT PHE 15 C ) 0.25384 ( PROT PHE 15 O ) 0.25384 ( PROT MET 16 N ) 0.25384 ( PROT MET 16 H ) 0.20307 ( PROT MET 16 CA ) 0.25384 ( PROT MET 16 CB ) 0.20307 ( PROT MET 16 CG ) 0.20307 ( PROT MET 16 SD ) 0.20307 ( PROT MET 16 CE ) 0.20307 ( PROT MET 16 C ) 0.25384 ( PROT MET 16 O ) 0.25384 ( PROT PHE 17 N ) 0.25384 ( PROT PHE 17 H ) 0.20307 ( PROT PHE 17 CA ) 0.25384 ( PROT PHE 17 CB ) 0.20307 ( PROT PHE 17 CG ) 0.20307 ( PROT PHE 17 CD1 ) 0.20307 ( PROT PHE 17 CD2 ) 0.20307 ( PROT PHE 17 CE1 ) 0.20307 ( PROT PHE 17 CE2 ) 0.20307 ( PROT PHE 17 CZ ) 0.20307 ( PROT PHE 17 C ) 0.25384 ( PROT PHE 17 O ) 0.25384 ( PROT PHE 18 N ) 0.25384 ( PROT PHE 18 H ) 0.20307 ( PROT PHE 18 CA ) 0.25384 ( PROT PHE 18 CB ) 0.20307 ( PROT PHE 18 CG ) 0.20307 ( PROT PHE 18 CD1 ) 0.20307 ( PROT PHE 18 CD2 ) 0.20307 ( PROT PHE 18 CE1 ) 0.20307 ( PROT PHE 18 CE2 ) 0.20307 ( PROT PHE 18 CZ ) 0.20307 ( PROT PHE 18 C ) 0.25384 ( PROT PHE 18 O ) 0.25384 ( PROT GLU 19 N ) 0.25384 ( PROT GLU 19 H ) 0.20307 ( PROT GLU 19 CA ) 0.25384 ( PROT GLU 19 CB ) 0.20307 ( PROT GLU 19 CG ) 0.20307 ( PROT GLU 19 CD ) 0.20307 ( PROT GLU 19 OE1 ) 0.20307 ( PROT GLU 19 OE2 ) 0.20307 ( PROT GLU 19 C ) 0.25384 ( PROT GLU 19 O ) 0.25384 ( PROT SER 20 N ) 0.25384 ( PROT SER 20 H ) 0.20307 ( PROT SER 20 CA ) 0.25384 ( PROT SER 20 CB ) 0.20307 ( PROT SER 20 OG ) 0.20307 ( PROT SER 20 HG ) 0.20307 ( PROT SER 20 C ) 0.25384 ( PROT SER 20 O ) 0.25384 ( PROT THR 21 N ) 0.25384 ( PROT THR 21 H ) 0.20307 ( PROT THR 21 CA ) 0.25384 ( PROT THR 21 CB ) 0.20307 ( PROT THR 21 OG1 ) 0.20307 ( PROT THR 21 HG1 ) 0.20307 ( PROT THR 21 CG2 ) 0.20307 ( PROT THR 21 C ) 0.25384 ( PROT THR 21 O ) 0.25384 ( PROT GLY 22 N ) 0.25384 ( PROT GLY 22 H ) 0.20307 ( PROT GLY 22 CA ) 0.25384 ( PROT GLY 22 C ) 0.25384 ( PROT GLY 22 O ) 0.25384 ( PROT SER 23 N ) 0.25384 ( PROT SER 23 H ) 0.20307 ( PROT SER 23 CA ) 0.25384 ( PROT SER 23 CB ) 0.20307 ( PROT SER 23 OG ) 0.20307 ( PROT SER 23 HG ) 0.20307 ( PROT SER 23 C ) 0.25384 ( PROT SER 23 O ) 0.25384 ( PROT GLN 24 N ) 0.25384 ( PROT GLN 24 H ) 0.20307 ( PROT GLN 24 CA ) 0.25384 ( PROT GLN 24 CB ) 0.20307 ( PROT GLN 24 CG ) 0.20307 ( PROT GLN 24 CD ) 0.20307 ( PROT GLN 24 OE1 ) 0.20307 ( PROT GLN 24 NE2 ) 0.20307 ( PROT GLN 24 HE21 ) 0.20307 ( PROT GLN 24 HE22 ) 0.20307 ( PROT GLN 24 C ) 0.25384 ( PROT GLN 24 O ) 0.25384 ( PROT GLU 25 N ) 0.25384 ( PROT GLU 25 H ) 0.20307 ( PROT GLU 25 CA ) 0.25384 ( PROT GLU 25 CB ) 0.20307 ( PROT GLU 25 CG ) 0.20307 ( PROT GLU 25 CD ) 0.20307 ( PROT GLU 25 OE1 ) 0.20307 ( PROT GLU 25 OE2 ) 0.20307 ( PROT GLU 25 C ) 0.25384 ( PROT GLU 25 O ) 0.25384 ( PROT GLN 26 N ) 0.25384 ( PROT GLN 26 H ) 0.20307 ( PROT GLN 26 CA ) 0.25384 ( PROT GLN 26 CB ) 0.20307 ( PROT GLN 26 CG ) 0.20307 ( PROT GLN 26 CD ) 0.20307 ( PROT GLN 26 OE1 ) 0.20307 ( PROT GLN 26 NE2 ) 0.20307 ( PROT GLN 26 HE21 ) 0.20307 ( PROT GLN 26 HE22 ) 0.20307 ( PROT GLN 26 C ) 0.25384 ( PROT GLN 26 O ) 0.25384 ( PROT LYS 27 N ) 0.25384 ( PROT LYS 27 H ) 0.20307 ( PROT LYS 27 CA ) 0.25384 ( PROT LYS 27 CB ) 0.20307 ( PROT LYS 27 CG ) 0.20307 ( PROT LYS 27 CD ) 0.20307 ( PROT LYS 27 CE ) 0.20307 ( PROT LYS 27 NZ ) 0.20307 ( PROT LYS 27 HZ1 ) 0.20307 ( PROT LYS 27 HZ2 ) 0.20307 ( PROT LYS 27 HZ3 ) 0.20307 ( PROT LYS 27 C ) 0.25384 ( PROT LYS 27 O ) 0.25384 ( PROT SER 28 N ) 0.25384 ( PROT SER 28 H ) 0.20307 ( PROT SER 28 CA ) 0.25384 ( PROT SER 28 CB ) 0.20307 ( PROT SER 28 OG ) 0.20307 ( PROT SER 28 HG ) 0.20307 ( PROT SER 28 C ) 0.25384 ( PROT SER 28 O ) 0.25384 ( PROT GLY 29 N ) 0.25384 ( PROT GLY 29 H ) 0.20307 ( PROT GLY 29 CA ) 0.25384 ( PROT GLY 29 C ) 0.25384 ( PROT GLY 29 O ) 0.25384 ( PROT VAL 30 N ) 0.25384 ( PROT VAL 30 H ) 0.20307 ( PROT VAL 30 CA ) 0.25384 ( PROT VAL 30 CB ) 0.20307 ( PROT VAL 30 CG1 ) 0.20307 ( PROT VAL 30 CG2 ) 0.20307 ( PROT VAL 30 C ) 0.25384 ( PROT VAL 30 O ) 0.25384 ( PROT TRP 31 N ) 0.25384 ( PROT TRP 31 H ) 0.20307 ( PROT TRP 31 CA ) 0.25384 ( PROT TRP 31 CB ) 0.20307 ( PROT TRP 31 CG ) 0.20307 ( PROT TRP 31 CD2 ) 0.20307 ( PROT TRP 31 CE2 ) 0.20307 ( PROT TRP 31 CE3 ) 0.20307 ( PROT TRP 31 CD1 ) 0.20307 ( PROT TRP 31 NE1 ) 0.20307 ( PROT TRP 31 HE1 ) 0.20307 ( PROT TRP 31 CZ2 ) 0.20307 ( PROT TRP 31 CZ3 ) 0.20307 ( PROT TRP 31 CH2 ) 0.20307 ( PROT TRP 31 C ) 0.25384 ( PROT TRP 31 OT1 ) 0.20307 ( PROT TRP 31 OT2 ) 0.20307 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.62631 7.22310 -13.21582 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00449 0.00633 -0.00410 ROTATION MATRIX 1.000000 0.000800 0.000548 -0.000800 1.000000 -0.000432 -0.000548 0.000431 1.000000 AXIS OF ROTATION IS -0.406607 -0.516476 0.753607 ANGLE IS 0.06 TOTAL SQUARE DIFF IS 174.4407 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.766383 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.7664" Parameter: A <- "0.7664" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.56402 7.28883 -13.44579 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.03580 -0.03328 0.00544 ROTATION MATRIX 0.999675 0.017425 0.018620 -0.017003 0.999601 -0.022554 -0.019006 0.022230 0.999572 AXIS OF ROTATION IS -0.659829 -0.554367 0.507250 ANGLE IS 1.94 CENTER OF ROTATION 13.954647 6.842999-13.380729 SHIFT IS 0.044831 TOTAL SQUARE DIFF IS 11.1382 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.599414 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.7664" RDCMND substituted energy or value "?RMS" to " 0.5994" Parameter: A <- "0.7664 0.5994" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *9600 0.7664 0.5994 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 59.21" Parameter: H <- "59.21" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -162.55637 59.20576 0.30574 ENER INTERN> 7.69127 40.13870 0.00000 30.31702 5.52654 ENER EXTERN> -145.95612 -100.27379 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -162.56" Parameter: B <- "-162.56" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -100.27" Parameter: C <- "-100.27" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -145.96" Parameter: C <- " -246.23" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -246.23" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.69" Parameter: D <- "7.69" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 40.14" Parameter: D <- " 47.83" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 30.32" Parameter: D <- " 78.15" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.53" Parameter: D <- " 83.68" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 83.68" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 9600 ENER= -162.56 GRMS= 0.31 ELEC= -100.27 VDW= -145.96 RDTITL> *EXTERNAL= -246.23 INTERNAL= 83.68 USER= 0.00 HARM= 59.21 RDTITL> *BOND= 7.69 ANGL= 40.14 DIHE= 30.32 IMPR= 5.53 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "9600" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_9600.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_9600.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 9600 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 9600 ENER= -162.56 GRMS= 0.31 ELEC= -100.27 VDW= -145.96 RDTITL> *EXTERNAL= -246.23 INTERNAL= 83.68 USER= 0.00 HARM= 59.21 RDTITL> *BOND= 7.69 ANGL= 40.14 DIHE= 30.32 IMPR= 5.53 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "9600" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_9600.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_9600.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 9600 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 9600 ENER= -162.56 GRMS= 0.31 ELEC= -100.27 VDW= -145.96 RDTITL> *EXTERNAL= -246.23 INTERNAL= 83.68 USER= 0.00 HARM= 59.21 RDTITL> *BOND= 7.69 ANGL= 40.14 DIHE= 30.32 IMPR= 5.53 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 9600 0.7664 0.5994 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "9600" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20736 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20650 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -122.85838 -39.69799 0.12093 0.02000 MINI INTERN> 7.69127 40.13870 0.00000 30.31702 5.52654 MINI EXTERN> -145.95612 -100.27379 0.00000 0.00000 0.00000 MINI CONSTR> 39.69799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -114.69060 -8.16778 7.80183 0.00360 MINI INTERN> 15.44156 41.86298 0.00000 31.18181 5.50081 MINI EXTERN> -151.82959 -97.95455 0.00000 0.00000 0.00000 MINI CONSTR> 41.10639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20639 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -123.33484 8.64425 0.81239 0.00065 MINI INTERN> 8.08848 40.38215 0.00000 30.96725 5.55164 MINI EXTERN> -151.15842 -98.26971 0.00000 0.00000 0.00000 MINI CONSTR> 41.10375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -123.45393 0.11909 0.50274 0.00028 MINI INTERN> 8.01811 40.18384 0.00000 30.85964 5.57202 MINI EXTERN> -150.61767 -98.57844 0.00000 0.00000 0.00000 MINI CONSTR> 41.10856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20637 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -123.49727 0.04334 0.49150 0.00029 MINI INTERN> 7.98045 40.08123 0.00000 30.80188 5.56537 MINI EXTERN> -150.25201 -98.79364 0.00000 0.00000 0.00000 MINI CONSTR> 41.11945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -123.56388 0.06661 0.16353 0.00013 MINI INTERN> 7.87637 40.04570 0.00000 30.76603 5.55194 MINI EXTERN> -149.96350 -98.97662 0.00000 0.00000 0.00000 MINI CONSTR> 41.13619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20636 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -123.59444 0.03056 0.13061 0.00013 MINI INTERN> 7.85231 40.00910 0.00000 30.72502 5.54997 MINI EXTERN> -149.78528 -99.10204 0.00000 0.00000 0.00000 MINI CONSTR> 41.15648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -123.62238 0.02794 0.14118 0.00013 MINI INTERN> 7.82975 39.98167 0.00000 30.68793 5.54681 MINI EXTERN> -149.64280 -99.20733 0.00000 0.00000 0.00000 MINI CONSTR> 41.18158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20637 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -123.64373 0.02135 0.21203 0.00014 MINI INTERN> 7.80647 39.96684 0.00000 30.65859 5.54301 MINI EXTERN> -149.53953 -99.28715 0.00000 0.00000 0.00000 MINI CONSTR> 41.20804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -123.66839 0.02466 0.22160 0.00014 MINI INTERN> 7.79187 39.94628 0.00000 30.62947 5.54026 MINI EXTERN> -149.46182 -99.35238 0.00000 0.00000 0.00000 MINI CONSTR> 41.23795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20637 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -123.69163 0.02324 0.23877 0.00015 MINI INTERN> 7.77837 39.93042 0.00000 30.60358 5.53749 MINI EXTERN> -149.40632 -99.40469 0.00000 0.00000 0.00000 MINI CONSTR> 41.26953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -123.71366 0.02203 0.22836 0.00016 MINI INTERN> 7.77072 39.91759 0.00000 30.58092 5.53633 MINI EXTERN> -149.37561 -99.44225 0.00000 0.00000 0.00000 MINI CONSTR> 41.29863 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20637 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -123.73606 0.02240 0.23994 0.00016 MINI INTERN> 7.75948 39.90588 0.00000 30.55956 5.53395 MINI EXTERN> -149.34984 -99.47715 0.00000 0.00000 0.00000 MINI CONSTR> 41.33207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -123.75899 0.02293 0.24784 0.00017 MINI INTERN> 7.74916 39.89493 0.00000 30.53953 5.53140 MINI EXTERN> -149.33479 -99.50651 0.00000 0.00000 0.00000 MINI CONSTR> 41.36730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20634 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -123.78221 0.02321 0.25094 0.00017 MINI INTERN> 7.74123 39.88407 0.00000 30.52035 5.52895 MINI EXTERN> -149.32967 -99.53064 0.00000 0.00000 0.00000 MINI CONSTR> 41.40350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -123.81225 0.03004 0.07842 0.00007 MINI INTERN> 7.78716 39.84967 0.00000 30.48630 5.53587 MINI EXTERN> -149.36353 -99.54400 0.00000 0.00000 0.00000 MINI CONSTR> 41.43627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20633 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -123.82296 0.01071 0.27338 0.00019 MINI INTERN> 7.72628 39.86847 0.00000 30.48822 5.52507 MINI EXTERN> -149.33587 -99.56665 0.00000 0.00000 0.00000 MINI CONSTR> 41.47152 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -123.84439 0.02143 0.28064 0.00019 MINI INTERN> 7.72349 39.85746 0.00000 30.47255 5.52300 MINI EXTERN> -149.34786 -99.58069 0.00000 0.00000 0.00000 MINI CONSTR> 41.50766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20632 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -123.86479 0.02040 0.30411 0.00020 MINI INTERN> 7.72412 39.84917 0.00000 30.45373 5.52152 MINI EXTERN> -149.36469 -99.59299 0.00000 0.00000 0.00000 MINI CONSTR> 41.54434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -123.89751 0.03271 0.09842 0.00009 MINI INTERN> 7.78471 39.80544 0.00000 30.41936 5.53187 MINI EXTERN> -149.41578 -99.60034 0.00000 0.00000 0.00000 MINI CONSTR> 41.57723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20630 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -123.90228 0.00477 0.31253 0.00022 MINI INTERN> 7.70588 39.83985 0.00000 30.43198 5.51829 MINI EXTERN> -149.39249 -99.61562 0.00000 0.00000 0.00000 MINI CONSTR> 41.60983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -123.93776 0.03548 0.10862 0.00009 MINI INTERN> 7.78500 39.78539 0.00000 30.39070 5.52989 MINI EXTERN> -149.45464 -99.62030 0.00000 0.00000 0.00000 MINI CONSTR> 41.64620 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20631 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -123.95557 0.01781 0.07221 0.00010 MINI INTERN> 7.77065 39.78278 0.00000 30.38350 5.52668 MINI EXTERN> -149.46639 -99.62765 0.00000 0.00000 0.00000 MINI CONSTR> 41.67486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -123.97688 0.02131 0.07584 0.00010 MINI INTERN> 7.77204 39.77169 0.00000 30.36913 5.52571 MINI EXTERN> -149.49049 -99.63683 0.00000 0.00000 0.00000 MINI CONSTR> 41.71187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20628 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -123.99591 0.01903 0.14420 0.00010 MINI INTERN> 7.79135 39.75474 0.00000 30.34964 5.52766 MINI EXTERN> -149.52258 -99.64618 0.00000 0.00000 0.00000 MINI CONSTR> 41.74946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -124.01587 0.01996 0.10174 0.00011 MINI INTERN> 7.77203 39.75694 0.00000 30.34163 5.52477 MINI EXTERN> -149.53877 -99.65368 0.00000 0.00000 0.00000 MINI CONSTR> 41.78121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20626 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -124.03360 0.01773 0.12632 0.00011 MINI INTERN> 7.78135 39.74402 0.00000 30.32757 5.52469 MINI EXTERN> -149.56480 -99.66049 0.00000 0.00000 0.00000 MINI CONSTR> 41.81406 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -124.04977 0.01617 0.16711 0.00012 MINI INTERN> 7.80207 39.72258 0.00000 30.31332 5.52483 MINI EXTERN> -149.59251 -99.66631 0.00000 0.00000 0.00000 MINI CONSTR> 41.84625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20626 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -124.06747 0.01770 0.18694 0.00012 MINI INTERN> 7.78525 39.73052 0.00000 30.30207 5.52394 MINI EXTERN> -149.61355 -99.67486 0.00000 0.00000 0.00000 MINI CONSTR> 41.87917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -124.08444 0.01697 0.19085 0.00012 MINI INTERN> 7.80016 39.71241 0.00000 30.28924 5.52352 MINI EXTERN> -149.63999 -99.68000 0.00000 0.00000 0.00000 MINI CONSTR> 41.91024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20625 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -124.10150 0.01706 0.19861 0.00013 MINI INTERN> 7.81771 39.68957 0.00000 30.27789 5.52243 MINI EXTERN> -149.66599 -99.68485 0.00000 0.00000 0.00000 MINI CONSTR> 41.94174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -124.11847 0.01697 0.21041 0.00013 MINI INTERN> 7.80836 39.69317 0.00000 30.26594 5.52208 MINI EXTERN> -149.68932 -99.69216 0.00000 0.00000 0.00000 MINI CONSTR> 41.97347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20625 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -124.13577 0.01730 0.19981 0.00014 MINI INTERN> 7.82107 39.67201 0.00000 30.25697 5.52038 MINI EXTERN> -149.71260 -99.69695 0.00000 0.00000 0.00000 MINI CONSTR> 42.00336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -124.15237 0.01660 0.22179 0.00014 MINI INTERN> 7.78839 39.69386 0.00000 30.24787 5.51938 MINI EXTERN> -149.73078 -99.70601 0.00000 0.00000 0.00000 MINI CONSTR> 42.03493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20625 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -124.16919 0.01683 0.21424 0.00015 MINI INTERN> 7.80575 39.67419 0.00000 30.23543 5.51916 MINI EXTERN> -149.75812 -99.71075 0.00000 0.00000 0.00000 MINI CONSTR> 42.06515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -124.19089 0.02170 0.07020 0.00006 MINI INTERN> 7.75034 39.69154 0.00000 30.24166 5.51256 MINI EXTERN> -149.76019 -99.71938 0.00000 0.00000 0.00000 MINI CONSTR> 42.09257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20623 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -124.20064 0.00975 0.24089 0.00016 MINI INTERN> 7.81730 39.65494 0.00000 30.21311 5.51822 MINI EXTERN> -149.80756 -99.72256 0.00000 0.00000 0.00000 MINI CONSTR> 42.12592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -124.21542 0.01477 0.27684 0.00017 MINI INTERN> 7.83706 39.62306 0.00000 30.20911 5.51451 MINI EXTERN> -149.82774 -99.72781 0.00000 0.00000 0.00000 MINI CONSTR> 42.15639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20623 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -124.23220 0.01678 0.26225 0.00017 MINI INTERN> 7.85150 39.61231 0.00000 30.19263 5.51618 MINI EXTERN> -149.85860 -99.73295 0.00000 0.00000 0.00000 MINI CONSTR> 42.18673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -124.25809 0.02589 0.08138 0.00007 MINI INTERN> 7.73936 39.67158 0.00000 30.20397 5.50855 MINI EXTERN> -149.85040 -99.74681 0.00000 0.00000 0.00000 MINI CONSTR> 42.21566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20623 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -124.26306 0.00497 0.28360 0.00019 MINI INTERN> 7.85761 39.59425 0.00000 30.17419 5.51417 MINI EXTERN> -149.90379 -99.74554 0.00000 0.00000 0.00000 MINI CONSTR> 42.24604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -124.29020 0.02714 0.09327 0.00008 MINI INTERN> 7.73313 39.66216 0.00000 30.18677 5.50635 MINI EXTERN> -149.89319 -99.76065 0.00000 0.00000 0.00000 MINI CONSTR> 42.27523 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20621 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -124.30508 0.01488 0.06728 0.00008 MINI INTERN> 7.74606 39.64876 0.00000 30.17497 5.50689 MINI EXTERN> -149.91741 -99.76567 0.00000 0.00000 0.00000 MINI CONSTR> 42.30133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -124.32168 0.01660 0.07147 0.00009 MINI INTERN> 7.74176 39.64465 0.00000 30.16637 5.50570 MINI EXTERN> -149.93918 -99.77308 0.00000 0.00000 0.00000 MINI CONSTR> 42.33210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20621 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -124.33858 0.01690 0.11347 0.00009 MINI INTERN> 7.72504 39.64781 0.00000 30.16047 5.50325 MINI EXTERN> -149.95878 -99.78206 0.00000 0.00000 0.00000 MINI CONSTR> 42.36569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -124.35459 0.01601 0.09248 0.00009 MINI INTERN> 7.72935 39.64066 0.00000 30.14907 5.50349 MINI EXTERN> -149.98263 -99.78843 0.00000 0.00000 0.00000 MINI CONSTR> 42.39391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20620 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -124.36991 0.01532 0.10109 0.00010 MINI INTERN> 7.72437 39.63696 0.00000 30.14180 5.50212 MINI EXTERN> -150.00213 -99.79584 0.00000 0.00000 0.00000 MINI CONSTR> 42.42282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -124.38584 0.01593 0.10338 0.00010 MINI INTERN> 7.72923 39.62598 0.00000 30.13278 5.50119 MINI EXTERN> -150.02480 -99.80268 0.00000 0.00000 0.00000 MINI CONSTR> 42.45246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20619 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -124.40075 0.01491 0.11861 0.00010 MINI INTERN> 7.71767 39.62826 0.00000 30.12595 5.49983 MINI EXTERN> -150.04292 -99.81077 0.00000 0.00000 0.00000 MINI CONSTR> 42.48123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -124.41491 0.01415 0.15557 0.00011 MINI INTERN> 7.70163 39.63434 0.00000 30.11998 5.49816 MINI EXTERN> -150.06027 -99.81941 0.00000 0.00000 0.00000 MINI CONSTR> 42.51066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20618 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -124.43072 0.01581 0.16516 0.00011 MINI INTERN> 7.71673 39.61514 0.00000 30.11027 5.49736 MINI EXTERN> -150.08518 -99.82575 0.00000 0.00000 0.00000 MINI CONSTR> 42.54071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -124.44533 0.01461 0.17186 0.00011 MINI INTERN> 7.69582 39.62617 0.00000 30.10380 5.49615 MINI EXTERN> -150.10145 -99.83476 0.00000 0.00000 0.00000 MINI CONSTR> 42.56893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20614 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -124.46113 0.01580 0.18033 0.00012 MINI INTERN> 7.70295 39.61362 0.00000 30.09482 5.49520 MINI EXTERN> -150.12483 -99.84207 0.00000 0.00000 0.00000 MINI CONSTR> 42.59919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -124.47550 0.01437 0.19655 0.00012 MINI INTERN> 7.68602 39.62410 0.00000 30.08626 5.49484 MINI EXTERN> -150.14353 -99.85083 0.00000 0.00000 0.00000 MINI CONSTR> 42.62764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20613 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -124.49039 0.01489 0.18319 0.00013 MINI INTERN> 7.69894 39.60481 0.00000 30.07909 5.49352 MINI EXTERN> -150.16346 -99.85735 0.00000 0.00000 0.00000 MINI CONSTR> 42.65406 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -124.50482 0.01442 0.20711 0.00013 MINI INTERN> 7.68904 39.61386 0.00000 30.06692 5.49454 MINI EXTERN> -150.18631 -99.86564 0.00000 0.00000 0.00000 MINI CONSTR> 42.68277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20613 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -124.51971 0.01490 0.19510 0.00014 MINI INTERN> 7.68313 39.60868 0.00000 30.06218 5.49252 MINI EXTERN> -150.20222 -99.87392 0.00000 0.00000 0.00000 MINI CONSTR> 42.70992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -124.53847 0.01876 0.06609 0.00006 MINI INTERN> 7.75418 39.55183 0.00000 30.04057 5.49607 MINI EXTERN> -150.23981 -99.87606 0.00000 0.00000 0.00000 MINI CONSTR> 42.73475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20613 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -124.54687 0.00839 0.22336 0.00015 MINI INTERN> 7.67268 39.60648 0.00000 30.04780 5.49070 MINI EXTERN> -150.23805 -99.89041 0.00000 0.00000 0.00000 MINI CONSTR> 42.76392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -124.55977 0.01290 0.25500 0.00015 MINI INTERN> 7.72557 39.55621 0.00000 30.03789 5.48973 MINI EXTERN> -150.26497 -99.89517 0.00000 0.00000 0.00000 MINI CONSTR> 42.79097 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20612 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -124.57454 0.01477 0.23989 0.00016 MINI INTERN> 7.68579 39.57945 0.00000 30.03545 5.48753 MINI EXTERN> -150.27464 -99.90616 0.00000 0.00000 0.00000 MINI CONSTR> 42.81804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -124.58733 0.01279 0.27261 0.00016 MINI INTERN> 7.66619 39.59999 0.00000 30.02289 5.48925 MINI EXTERN> -150.29541 -99.91549 0.00000 0.00000 0.00000 MINI CONSTR> 42.84526 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20611 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -124.60200 0.01467 0.25563 0.00017 MINI INTERN> 7.65580 39.59449 0.00000 30.02177 5.48592 MINI EXTERN> -150.30690 -99.92499 0.00000 0.00000 0.00000 MINI CONSTR> 42.87191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -124.62608 0.02407 0.08223 0.00007 MINI INTERN> 7.76259 39.51331 0.00000 29.99061 5.49249 MINI EXTERN> -150.35840 -99.92541 0.00000 0.00000 0.00000 MINI CONSTR> 42.89873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20610 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -124.63930 0.01322 0.06367 0.00008 MINI INTERN> 7.74781 39.51811 0.00000 29.98646 5.49110 MINI EXTERN> -150.37120 -99.93401 0.00000 0.00000 0.00000 MINI CONSTR> 42.92243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -124.65381 0.01451 0.06702 0.00008 MINI INTERN> 7.75138 39.51036 0.00000 29.97795 5.49064 MINI EXTERN> -150.39095 -99.94270 0.00000 0.00000 0.00000 MINI CONSTR> 42.94951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20610 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -124.66814 0.01433 0.06741 0.00008 MINI INTERN> 7.75245 39.50392 0.00000 29.97038 5.48993 MINI EXTERN> -150.40935 -99.95155 0.00000 0.00000 0.00000 MINI CONSTR> 42.97608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -124.68282 0.01469 0.11271 0.00009 MINI INTERN> 7.77286 39.48689 0.00000 29.95699 5.49077 MINI EXTERN> -150.43562 -99.96051 0.00000 0.00000 0.00000 MINI CONSTR> 43.00580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20609 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -124.69730 0.01448 0.08749 0.00009 MINI INTERN> 7.76337 39.48547 0.00000 29.95304 5.48902 MINI EXTERN> -150.44923 -99.96990 0.00000 0.00000 0.00000 MINI CONSTR> 43.03093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -124.71103 0.01372 0.09752 0.00009 MINI INTERN> 7.76890 39.47774 0.00000 29.94406 5.48895 MINI EXTERN> -150.46879 -99.97872 0.00000 0.00000 0.00000 MINI CONSTR> 43.05684 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20609 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -124.72508 0.01406 0.10342 0.00010 MINI INTERN> 7.76562 39.47657 0.00000 29.93601 5.48865 MINI EXTERN> -150.48655 -99.98841 0.00000 0.00000 0.00000 MINI CONSTR> 43.08302 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -124.73872 0.01363 0.11328 0.00010 MINI INTERN> 7.77551 39.46434 0.00000 29.92759 5.48832 MINI EXTERN> -150.50593 -99.99727 0.00000 0.00000 0.00000 MINI CONSTR> 43.10872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20607 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -124.75156 0.01285 0.14876 0.00010 MINI INTERN> 7.78728 39.45392 0.00000 29.91705 5.48876 MINI EXTERN> -150.52709 -100.00653 0.00000 0.00000 0.00000 MINI CONSTR> 43.13506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -124.76609 0.01453 0.15733 0.00011 MINI INTERN> 7.79288 39.44131 0.00000 29.91110 5.48726 MINI EXTERN> -150.54385 -100.01684 0.00000 0.00000 0.00000 MINI CONSTR> 43.16204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20607 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -124.77951 0.01342 0.16454 0.00011 MINI INTERN> 7.79286 39.44073 0.00000 29.90120 5.48786 MINI EXTERN> -150.56287 -100.02671 0.00000 0.00000 0.00000 MINI CONSTR> 43.18743 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -124.79380 0.01429 0.17615 0.00011 MINI INTERN> 7.80124 39.42711 0.00000 29.89443 5.48670 MINI EXTERN> -150.58035 -100.03720 0.00000 0.00000 0.00000 MINI CONSTR> 43.21427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20606 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -124.80725 0.01344 0.18171 0.00012 MINI INTERN> 7.79668 39.42964 0.00000 29.88546 5.48708 MINI EXTERN> -150.59776 -100.04762 0.00000 0.00000 0.00000 MINI CONSTR> 43.23927 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -124.82127 0.01402 0.17503 0.00012 MINI INTERN> 7.80119 39.41868 0.00000 29.87992 5.48588 MINI EXTERN> -150.61300 -100.05757 0.00000 0.00000 0.00000 MINI CONSTR> 43.26363 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20606 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -124.83470 0.01343 0.19713 0.00013 MINI INTERN> 7.77011 39.44151 0.00000 29.87401 5.48548 MINI EXTERN> -150.62456 -100.07040 0.00000 0.00000 0.00000 MINI CONSTR> 43.28917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -124.84877 0.01407 0.18566 0.00013 MINI INTERN> 7.79178 39.42021 0.00000 29.86460 5.48554 MINI EXTERN> -150.64491 -100.07969 0.00000 0.00000 0.00000 MINI CONSTR> 43.31370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20604 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -124.86658 0.01781 0.06451 0.00006 MINI INTERN> 7.72607 39.45173 0.00000 29.87321 5.48013 MINI EXTERN> -150.64046 -100.09358 0.00000 0.00000 0.00000 MINI CONSTR> 43.33632 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -124.87500 0.00842 0.21244 0.00014 MINI INTERN> 7.79343 39.41292 0.00000 29.84945 5.48507 MINI EXTERN> -150.67693 -100.10169 0.00000 0.00000 0.00000 MINI CONSTR> 43.36274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20604 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -124.89439 0.01939 0.06773 0.00006 MINI INTERN> 7.72201 39.44561 0.00000 29.86008 5.47889 MINI EXTERN> -150.66989 -100.11626 0.00000 0.00000 0.00000 MINI CONSTR> 43.38517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -124.90197 0.00758 0.21961 0.00015 MINI INTERN> 7.82045 39.38282 0.00000 29.83383 5.48438 MINI EXTERN> -150.71181 -100.12267 0.00000 0.00000 0.00000 MINI CONSTR> 43.41103 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20603 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -124.92347 0.02151 0.07079 0.00007 MINI INTERN> 7.71968 39.43809 0.00000 29.84622 5.47773 MINI EXTERN> -150.70024 -100.14052 0.00000 0.00000 0.00000 MINI CONSTR> 43.43556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -124.92979 0.00631 0.23770 0.00016 MINI INTERN> 7.81208 39.38394 0.00000 29.81863 5.48396 MINI EXTERN> -150.74149 -100.14786 0.00000 0.00000 0.00000 MINI CONSTR> 43.46095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20603 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -124.95282 0.02303 0.07716 0.00007 MINI INTERN> 7.71580 39.43194 0.00000 29.83258 5.47653 MINI EXTERN> -150.72958 -100.16586 0.00000 0.00000 0.00000 MINI CONSTR> 43.48577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -124.95753 0.00471 0.25835 0.00018 MINI INTERN> 7.81135 39.37790 0.00000 29.80387 5.48323 MINI EXTERN> -150.77072 -100.17353 0.00000 0.00000 0.00000 MINI CONSTR> 43.51038 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20603 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -124.98170 0.02418 0.09125 0.00008 MINI INTERN> 7.70681 39.43038 0.00000 29.81966 5.47528 MINI EXTERN> -150.75655 -100.19198 0.00000 0.00000 0.00000 MINI CONSTR> 43.53470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -124.99473 0.01303 0.06691 0.00008 MINI INTERN> 7.72130 39.41626 0.00000 29.81111 5.47561 MINI EXTERN> -150.77188 -100.20225 0.00000 0.00000 0.00000 MINI CONSTR> 43.55513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20603 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -125.00934 0.01461 0.06949 0.00008 MINI INTERN> 7.71751 39.41508 0.00000 29.80450 5.47506 MINI EXTERN> -150.78489 -100.21570 0.00000 0.00000 0.00000 MINI CONSTR> 43.57909 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -125.02428 0.01494 0.06658 0.00008 MINI INTERN> 7.72043 39.40901 0.00000 29.79681 5.47479 MINI EXTERN> -150.79937 -100.22907 0.00000 0.00000 0.00000 MINI CONSTR> 43.60313 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20602 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -125.04042 0.01614 0.11499 0.00009 MINI INTERN> 7.69505 39.42267 0.00000 29.79318 5.47289 MINI EXTERN> -150.80875 -100.24670 0.00000 0.00000 0.00000 MINI CONSTR> 43.63122 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -125.05573 0.01531 0.09157 0.00009 MINI INTERN> 7.71173 39.40588 0.00000 29.78389 5.47308 MINI EXTERN> -150.82511 -100.25923 0.00000 0.00000 0.00000 MINI CONSTR> 43.65403 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20601 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -125.07050 0.01477 0.10013 0.00009 MINI INTERN> 7.70317 39.40844 0.00000 29.77793 5.47233 MINI EXTERN> -150.83594 -100.27392 0.00000 0.00000 0.00000 MINI CONSTR> 43.67748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -125.08601 0.01551 0.10367 0.00010 MINI INTERN> 7.69744 39.41029 0.00000 29.77017 5.47218 MINI EXTERN> -150.84851 -100.28902 0.00000 0.00000 0.00000 MINI CONSTR> 43.70145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20599 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -125.10103 0.01502 0.11493 0.00010 MINI INTERN> 7.69319 39.40858 0.00000 29.76439 5.47118 MINI EXTERN> -150.85913 -100.30409 0.00000 0.00000 0.00000 MINI CONSTR> 43.72484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -125.11777 0.01674 0.10208 0.00011 MINI INTERN> 7.70007 39.39991 0.00000 29.75517 5.47125 MINI EXTERN> -150.87399 -100.31929 0.00000 0.00000 0.00000 MINI CONSTR> 43.74912 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20599 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -125.13231 0.01454 0.15859 0.00011 MINI INTERN> 7.67607 39.41471 0.00000 29.75124 5.46965 MINI EXTERN> -150.88092 -100.33712 0.00000 0.00000 0.00000 MINI CONSTR> 43.77406 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -125.14871 0.01640 0.17143 0.00011 MINI INTERN> 7.69439 39.39545 0.00000 29.74246 5.46919 MINI EXTERN> -150.89614 -100.35249 0.00000 0.00000 0.00000 MINI CONSTR> 43.79844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20599 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -125.16454 0.01584 0.17409 0.00012 MINI INTERN> 7.67518 39.40739 0.00000 29.73644 5.46845 MINI EXTERN> -150.90394 -100.36951 0.00000 0.00000 0.00000 MINI CONSTR> 43.82146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -125.16454 0.01584 0.17409 0.00014 STPD INTERN> 7.67518 39.40739 0.00000 29.73644 5.46845 STPD EXTERN> -150.90394 -100.36951 0.00000 0.00000 0.00000 STPD CONSTR> 43.82146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20599 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20599 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -125.16454 0.01584 0.17409 0.00000 MINI INTERN> 7.67518 39.40739 0.00000 29.73644 5.46845 MINI EXTERN> -150.90394 -100.36951 0.00000 0.00000 0.00000 MINI CONSTR> 43.82146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -125.63901 0.47446 1.35976 0.07716 MINI INTERN> 8.15899 39.26324 0.00000 29.11107 5.45880 MINI EXTERN> -151.47955 -101.14325 0.00000 0.00000 0.00000 MINI CONSTR> 44.99169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -126.01747 0.37846 2.01984 0.09128 MINI INTERN> 8.52748 39.39088 0.00000 28.36638 5.48538 MINI EXTERN> -152.27525 -101.64480 0.00000 0.00000 0.00000 MINI CONSTR> 46.13246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -126.31673 0.29927 1.74091 0.05222 MINI INTERN> 8.67073 39.35175 0.00000 27.94697 5.47635 MINI EXTERN> -152.92858 -101.90338 0.00000 0.00000 0.00000 MINI CONSTR> 47.06941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -126.56034 0.24361 1.17197 0.05639 MINI INTERN> 8.07532 39.74130 0.00000 27.78078 5.47472 MINI EXTERN> -153.56598 -101.94472 0.00000 0.00000 0.00000 MINI CONSTR> 47.87824 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -126.66401 0.10367 0.62276 0.01335 MINI INTERN> 7.80114 39.94858 0.00000 27.72737 5.51350 MINI EXTERN> -153.97486 -101.89719 0.00000 0.00000 0.00000 MINI CONSTR> 48.21746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -126.82001 0.15600 0.72671 0.03976 MINI INTERN> 8.00444 39.49850 0.00000 27.77963 5.68144 MINI EXTERN> -154.50840 -101.99182 0.00000 0.00000 0.00000 MINI CONSTR> 48.71619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -126.91941 0.09940 0.74343 0.02095 MINI INTERN> 7.91382 39.35848 0.00000 27.82075 5.72246 MINI EXTERN> -154.55225 -102.21735 0.00000 0.00000 0.00000 MINI CONSTR> 49.03469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -127.03577 0.11636 0.67167 0.02312 MINI INTERN> 8.11153 39.02168 0.00000 27.76126 5.66721 MINI EXTERN> -154.62173 -102.37896 0.00000 0.00000 0.00000 MINI CONSTR> 49.40325 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -127.13626 0.10049 0.60618 0.02133 MINI INTERN> 7.86411 38.98470 0.00000 27.72052 5.44473 MINI EXTERN> -154.46510 -102.40349 0.00000 0.00000 0.00000 MINI CONSTR> 49.71826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -127.24017 0.10392 0.64896 0.02625 MINI INTERN> 7.82382 38.72264 0.00000 27.57865 5.39097 MINI EXTERN> -154.41390 -102.39037 0.00000 0.00000 0.00000 MINI CONSTR> 50.04801 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -127.39435 0.15418 0.89187 0.04801 MINI INTERN> 7.88369 38.34900 0.00000 27.24626 5.45681 MINI EXTERN> -154.39589 -102.47406 0.00000 0.00000 0.00000 MINI CONSTR> 50.53984 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -127.52799 0.13364 0.85793 0.03113 MINI INTERN> 7.74302 38.37812 0.00000 26.78012 5.64224 MINI EXTERN> -154.71709 -102.33005 0.00000 0.00000 0.00000 MINI CONSTR> 50.97566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -127.64785 0.11986 0.67042 0.02246 MINI INTERN> 7.88774 38.31586 0.00000 26.45472 5.65603 MINI EXTERN> -155.37886 -101.95658 0.00000 0.00000 0.00000 MINI CONSTR> 51.37325 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -127.73607 0.08822 0.54660 0.01850 MINI INTERN> 7.64157 38.58550 0.00000 26.50523 5.47900 MINI EXTERN> -155.92098 -101.69238 0.00000 0.00000 0.00000 MINI CONSTR> 51.66599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -127.79560 0.05953 0.50114 0.01431 MINI INTERN> 7.70232 38.60727 0.00000 26.56977 5.33824 MINI EXTERN> -156.27715 -101.59703 0.00000 0.00000 0.00000 MINI CONSTR> 51.86099 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -127.86863 0.07304 0.55591 0.02174 MINI INTERN> 7.65072 38.58000 0.00000 26.52180 5.29536 MINI EXTERN> -156.41416 -101.59432 0.00000 0.00000 0.00000 MINI CONSTR> 52.09197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -127.91197 0.04334 0.41655 0.00942 MINI INTERN> 7.85313 38.28989 0.00000 26.40975 5.31022 MINI EXTERN> -156.43021 -101.56858 0.00000 0.00000 0.00000 MINI CONSTR> 52.22382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -127.95683 0.04486 0.41133 0.01315 MINI INTERN> 7.90944 38.08502 0.00000 26.34949 5.32100 MINI EXTERN> -156.44233 -101.52528 0.00000 0.00000 0.00000 MINI CONSTR> 52.34584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -127.99598 0.03915 0.46842 0.01270 MINI INTERN> 7.71461 38.18723 0.00000 26.34475 5.27998 MINI EXTERN> -156.47898 -101.47986 0.00000 0.00000 0.00000 MINI CONSTR> 52.43629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -128.03457 0.03859 0.44840 0.01041 MINI INTERN> 7.75192 38.08319 0.00000 26.36109 5.24268 MINI EXTERN> -156.47429 -101.51311 0.00000 0.00000 0.00000 MINI CONSTR> 52.51395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -128.03457 0.03859 0.44840 0.02000 CONJ INTERN> 7.75192 38.08319 0.00000 26.36109 5.24268 CONJ EXTERN> -156.47429 -101.51311 0.00000 0.00000 0.00000 CONJ CONSTR> 52.51395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "10200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.13199 ( PROT LYS 1 HT2 ) 0.13199 ( PROT LYS 1 N ) 0.16499 ( PROT LYS 1 HT3 ) 0.13199 ( PROT LYS 1 CA ) 0.16499 ( PROT LYS 1 CB ) 0.13199 ( PROT LYS 1 CG ) 0.13199 ( PROT LYS 1 CD ) 0.13199 ( PROT LYS 1 CE ) 0.13199 ( PROT LYS 1 NZ ) 0.13199 ( PROT LYS 1 HZ1 ) 0.13199 ( PROT LYS 1 HZ2 ) 0.13199 ( PROT LYS 1 HZ3 ) 0.13199 ( PROT LYS 1 C ) 0.16499 ( PROT LYS 1 O ) 0.16499 ( PROT MET 2 N ) 0.16499 ( PROT MET 2 H ) 0.13199 ( PROT MET 2 CA ) 0.16499 ( PROT MET 2 CB ) 0.13199 ( PROT MET 2 CG ) 0.13199 ( PROT MET 2 SD ) 0.13199 ( PROT MET 2 CE ) 0.13199 ( PROT MET 2 C ) 0.16499 ( PROT MET 2 O ) 0.16499 ( PROT LYS 3 N ) 0.16499 ( PROT LYS 3 H ) 0.13199 ( PROT LYS 3 CA ) 0.16499 ( PROT LYS 3 CB ) 0.13199 ( PROT LYS 3 CG ) 0.13199 ( PROT LYS 3 CD ) 0.13199 ( PROT LYS 3 CE ) 0.13199 ( PROT LYS 3 NZ ) 0.13199 ( PROT LYS 3 HZ1 ) 0.13199 ( PROT LYS 3 HZ2 ) 0.13199 ( PROT LYS 3 HZ3 ) 0.13199 ( PROT LYS 3 C ) 0.16499 ( PROT LYS 3 O ) 0.16499 ( PROT ALA 4 N ) 0.16499 ( PROT ALA 4 H ) 0.13199 ( PROT ALA 4 CA ) 0.16499 ( PROT ALA 4 CB ) 0.13199 ( PROT ALA 4 C ) 0.16499 ( PROT ALA 4 O ) 0.16499 ( PROT VAL 5 N ) 0.16499 ( PROT VAL 5 H ) 0.13199 ( PROT VAL 5 CA ) 0.16499 ( PROT VAL 5 CB ) 0.13199 ( PROT VAL 5 CG1 ) 0.13199 ( PROT VAL 5 CG2 ) 0.13199 ( PROT VAL 5 C ) 0.16499 ( PROT VAL 5 O ) 0.16499 ( PROT MET 6 N ) 0.16499 ( PROT MET 6 H ) 0.13199 ( PROT MET 6 CA ) 0.16499 ( PROT MET 6 CB ) 0.13199 ( PROT MET 6 CG ) 0.13199 ( PROT MET 6 SD ) 0.13199 ( PROT MET 6 CE ) 0.13199 ( PROT MET 6 C ) 0.16499 ( PROT MET 6 O ) 0.16499 ( PROT ILE 7 N ) 0.16499 ( PROT ILE 7 H ) 0.13199 ( PROT ILE 7 CA ) 0.16499 ( PROT ILE 7 CB ) 0.13199 ( PROT ILE 7 CG2 ) 0.13199 ( PROT ILE 7 CG1 ) 0.13199 ( PROT ILE 7 CD ) 0.13199 ( PROT ILE 7 C ) 0.16499 ( PROT ILE 7 O ) 0.16499 ( PROT GLY 8 N ) 0.16499 ( PROT GLY 8 H ) 0.13199 ( PROT GLY 8 CA ) 0.16499 ( PROT GLY 8 C ) 0.16499 ( PROT GLY 8 O ) 0.16499 ( PROT ALA 9 N ) 0.16499 ( PROT ALA 9 H ) 0.13199 ( PROT ALA 9 CA ) 0.16499 ( PROT ALA 9 CB ) 0.13199 ( PROT ALA 9 C ) 0.16499 ( PROT ALA 9 O ) 0.16499 ( PROT CYS 10 N ) 0.16499 ( PROT CYS 10 H ) 0.13199 ( PROT CYS 10 CA ) 0.16499 ( PROT CYS 10 CB ) 0.13199 ( PROT CYS 10 SG ) 0.13199 ( PROT CYS 10 C ) 0.16499 ( PROT CYS 10 O ) 0.16499 ( PROT PHE 11 N ) 0.16499 ( PROT PHE 11 H ) 0.13199 ( PROT PHE 11 CA ) 0.16499 ( PROT PHE 11 CB ) 0.13199 ( PROT PHE 11 CG ) 0.13199 ( PROT PHE 11 CD1 ) 0.13199 ( PROT PHE 11 CD2 ) 0.13199 ( PROT PHE 11 CE1 ) 0.13199 ( PROT PHE 11 CE2 ) 0.13199 ( PROT PHE 11 CZ ) 0.13199 ( PROT PHE 11 C ) 0.16499 ( PROT PHE 11 O ) 0.16499 ( PROT LEU 12 N ) 0.16499 ( PROT LEU 12 H ) 0.13199 ( PROT LEU 12 CA ) 0.16499 ( PROT LEU 12 CB ) 0.13199 ( PROT LEU 12 CG ) 0.13199 ( PROT LEU 12 CD1 ) 0.13199 ( PROT LEU 12 CD2 ) 0.13199 ( PROT LEU 12 C ) 0.16499 ( PROT LEU 12 O ) 0.16499 ( PROT ILE 13 N ) 0.16499 ( PROT ILE 13 H ) 0.13199 ( PROT ILE 13 CA ) 0.16499 ( PROT ILE 13 CB ) 0.13199 ( PROT ILE 13 CG2 ) 0.13199 ( PROT ILE 13 CG1 ) 0.13199 ( PROT ILE 13 CD ) 0.13199 ( PROT ILE 13 C ) 0.16499 ( PROT ILE 13 O ) 0.16499 ( PROT ASH 14 N ) 0.16499 ( PROT ASH 14 H ) 0.13199 ( PROT ASH 14 CA ) 0.16499 ( PROT ASH 14 CB ) 0.13199 ( PROT ASH 14 CG ) 0.13199 ( PROT ASH 14 OD1 ) 0.13199 ( PROT ASH 14 OD2 ) 0.13199 ( PROT ASH 14 HD2 ) 0.13199 ( PROT ASH 14 C ) 0.16499 ( PROT ASH 14 O ) 0.16499 ( PROT PHE 15 N ) 0.16499 ( PROT PHE 15 H ) 0.13199 ( PROT PHE 15 CA ) 0.16499 ( PROT PHE 15 CB ) 0.13199 ( PROT PHE 15 CG ) 0.13199 ( PROT PHE 15 CD1 ) 0.13199 ( PROT PHE 15 CD2 ) 0.13199 ( PROT PHE 15 CE1 ) 0.13199 ( PROT PHE 15 CE2 ) 0.13199 ( PROT PHE 15 CZ ) 0.13199 ( PROT PHE 15 C ) 0.16499 ( PROT PHE 15 O ) 0.16499 ( PROT MET 16 N ) 0.16499 ( PROT MET 16 H ) 0.13199 ( PROT MET 16 CA ) 0.16499 ( PROT MET 16 CB ) 0.13199 ( PROT MET 16 CG ) 0.13199 ( PROT MET 16 SD ) 0.13199 ( PROT MET 16 CE ) 0.13199 ( PROT MET 16 C ) 0.16499 ( PROT MET 16 O ) 0.16499 ( PROT PHE 17 N ) 0.16499 ( PROT PHE 17 H ) 0.13199 ( PROT PHE 17 CA ) 0.16499 ( PROT PHE 17 CB ) 0.13199 ( PROT PHE 17 CG ) 0.13199 ( PROT PHE 17 CD1 ) 0.13199 ( PROT PHE 17 CD2 ) 0.13199 ( PROT PHE 17 CE1 ) 0.13199 ( PROT PHE 17 CE2 ) 0.13199 ( PROT PHE 17 CZ ) 0.13199 ( PROT PHE 17 C ) 0.16499 ( PROT PHE 17 O ) 0.16499 ( PROT PHE 18 N ) 0.16499 ( PROT PHE 18 H ) 0.13199 ( PROT PHE 18 CA ) 0.16499 ( PROT PHE 18 CB ) 0.13199 ( PROT PHE 18 CG ) 0.13199 ( PROT PHE 18 CD1 ) 0.13199 ( PROT PHE 18 CD2 ) 0.13199 ( PROT PHE 18 CE1 ) 0.13199 ( PROT PHE 18 CE2 ) 0.13199 ( PROT PHE 18 CZ ) 0.13199 ( PROT PHE 18 C ) 0.16499 ( PROT PHE 18 O ) 0.16499 ( PROT GLU 19 N ) 0.16499 ( PROT GLU 19 H ) 0.13199 ( PROT GLU 19 CA ) 0.16499 ( PROT GLU 19 CB ) 0.13199 ( PROT GLU 19 CG ) 0.13199 ( PROT GLU 19 CD ) 0.13199 ( PROT GLU 19 OE1 ) 0.13199 ( PROT GLU 19 OE2 ) 0.13199 ( PROT GLU 19 C ) 0.16499 ( PROT GLU 19 O ) 0.16499 ( PROT SER 20 N ) 0.16499 ( PROT SER 20 H ) 0.13199 ( PROT SER 20 CA ) 0.16499 ( PROT SER 20 CB ) 0.13199 ( PROT SER 20 OG ) 0.13199 ( PROT SER 20 HG ) 0.13199 ( PROT SER 20 C ) 0.16499 ( PROT SER 20 O ) 0.16499 ( PROT THR 21 N ) 0.16499 ( PROT THR 21 H ) 0.13199 ( PROT THR 21 CA ) 0.16499 ( PROT THR 21 CB ) 0.13199 ( PROT THR 21 OG1 ) 0.13199 ( PROT THR 21 HG1 ) 0.13199 ( PROT THR 21 CG2 ) 0.13199 ( PROT THR 21 C ) 0.16499 ( PROT THR 21 O ) 0.16499 ( PROT GLY 22 N ) 0.16499 ( PROT GLY 22 H ) 0.13199 ( PROT GLY 22 CA ) 0.16499 ( PROT GLY 22 C ) 0.16499 ( PROT GLY 22 O ) 0.16499 ( PROT SER 23 N ) 0.16499 ( PROT SER 23 H ) 0.13199 ( PROT SER 23 CA ) 0.16499 ( PROT SER 23 CB ) 0.13199 ( PROT SER 23 OG ) 0.13199 ( PROT SER 23 HG ) 0.13199 ( PROT SER 23 C ) 0.16499 ( PROT SER 23 O ) 0.16499 ( PROT GLN 24 N ) 0.16499 ( PROT GLN 24 H ) 0.13199 ( PROT GLN 24 CA ) 0.16499 ( PROT GLN 24 CB ) 0.13199 ( PROT GLN 24 CG ) 0.13199 ( PROT GLN 24 CD ) 0.13199 ( PROT GLN 24 OE1 ) 0.13199 ( PROT GLN 24 NE2 ) 0.13199 ( PROT GLN 24 HE21 ) 0.13199 ( PROT GLN 24 HE22 ) 0.13199 ( PROT GLN 24 C ) 0.16499 ( PROT GLN 24 O ) 0.16499 ( PROT GLU 25 N ) 0.16499 ( PROT GLU 25 H ) 0.13199 ( PROT GLU 25 CA ) 0.16499 ( PROT GLU 25 CB ) 0.13199 ( PROT GLU 25 CG ) 0.13199 ( PROT GLU 25 CD ) 0.13199 ( PROT GLU 25 OE1 ) 0.13199 ( PROT GLU 25 OE2 ) 0.13199 ( PROT GLU 25 C ) 0.16499 ( PROT GLU 25 O ) 0.16499 ( PROT GLN 26 N ) 0.16499 ( PROT GLN 26 H ) 0.13199 ( PROT GLN 26 CA ) 0.16499 ( PROT GLN 26 CB ) 0.13199 ( PROT GLN 26 CG ) 0.13199 ( PROT GLN 26 CD ) 0.13199 ( PROT GLN 26 OE1 ) 0.13199 ( PROT GLN 26 NE2 ) 0.13199 ( PROT GLN 26 HE21 ) 0.13199 ( PROT GLN 26 HE22 ) 0.13199 ( PROT GLN 26 C ) 0.16499 ( PROT GLN 26 O ) 0.16499 ( PROT LYS 27 N ) 0.16499 ( PROT LYS 27 H ) 0.13199 ( PROT LYS 27 CA ) 0.16499 ( PROT LYS 27 CB ) 0.13199 ( PROT LYS 27 CG ) 0.13199 ( PROT LYS 27 CD ) 0.13199 ( PROT LYS 27 CE ) 0.13199 ( PROT LYS 27 NZ ) 0.13199 ( PROT LYS 27 HZ1 ) 0.13199 ( PROT LYS 27 HZ2 ) 0.13199 ( PROT LYS 27 HZ3 ) 0.13199 ( PROT LYS 27 C ) 0.16499 ( PROT LYS 27 O ) 0.16499 ( PROT SER 28 N ) 0.16499 ( PROT SER 28 H ) 0.13199 ( PROT SER 28 CA ) 0.16499 ( PROT SER 28 CB ) 0.13199 ( PROT SER 28 OG ) 0.13199 ( PROT SER 28 HG ) 0.13199 ( PROT SER 28 C ) 0.16499 ( PROT SER 28 O ) 0.16499 ( PROT GLY 29 N ) 0.16499 ( PROT GLY 29 H ) 0.13199 ( PROT GLY 29 CA ) 0.16499 ( PROT GLY 29 C ) 0.16499 ( PROT GLY 29 O ) 0.16499 ( PROT VAL 30 N ) 0.16499 ( PROT VAL 30 H ) 0.13199 ( PROT VAL 30 CA ) 0.16499 ( PROT VAL 30 CB ) 0.13199 ( PROT VAL 30 CG1 ) 0.13199 ( PROT VAL 30 CG2 ) 0.13199 ( PROT VAL 30 C ) 0.16499 ( PROT VAL 30 O ) 0.16499 ( PROT TRP 31 N ) 0.16499 ( PROT TRP 31 H ) 0.13199 ( PROT TRP 31 CA ) 0.16499 ( PROT TRP 31 CB ) 0.13199 ( PROT TRP 31 CG ) 0.13199 ( PROT TRP 31 CD2 ) 0.13199 ( PROT TRP 31 CE2 ) 0.13199 ( PROT TRP 31 CE3 ) 0.13199 ( PROT TRP 31 CD1 ) 0.13199 ( PROT TRP 31 NE1 ) 0.13199 ( PROT TRP 31 HE1 ) 0.13199 ( PROT TRP 31 CZ2 ) 0.13199 ( PROT TRP 31 CZ3 ) 0.13199 ( PROT TRP 31 CH2 ) 0.13199 ( PROT TRP 31 C ) 0.16499 ( PROT TRP 31 OT1 ) 0.13199 ( PROT TRP 31 OT2 ) 0.13199 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.61761 7.21849 -13.21469 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.01320 0.01094 -0.00523 ROTATION MATRIX 0.999978 -0.004312 -0.004954 0.004342 0.999973 0.006006 0.004928 -0.006027 0.999970 AXIS OF ROTATION IS 0.675468 0.554750 -0.485794 ANGLE IS 0.51 TOTAL SQUARE DIFF IS 237.6659 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 0.894551 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.8946" Parameter: A <- "0.8946" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.58095 7.30528 -13.45635 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.05272 -0.04973 0.01599 ROTATION MATRIX 0.999708 0.016673 0.017520 -0.016283 0.999622 -0.022137 -0.017882 0.021845 0.999601 AXIS OF ROTATION IS -0.672778 -0.541519 0.504110 ANGLE IS 1.87 CENTER OF ROTATION 14.056470 6.796626-13.298231 SHIFT IS 0.070460 TOTAL SQUARE DIFF IS 16.8115 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.736414 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.8946" RDCMND substituted energy or value "?RMS" to " 0.7364" Parameter: A <- "0.8946 0.7364" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *10200 0.8946 0.7364 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 52.51" Parameter: H <- "52.51" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -180.54852 52.51395 0.48741 ENER INTERN> 7.75192 38.08319 0.00000 26.36109 5.24268 ENER EXTERN> -156.47429 -101.51311 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -180.55" Parameter: B <- "-180.55" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -101.51" Parameter: C <- "-101.51" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -156.47" Parameter: C <- " -257.98" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -257.98" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.75" Parameter: D <- "7.75" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 38.08" Parameter: D <- " 45.83" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 26.36" Parameter: D <- " 72.19" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.24" Parameter: D <- " 77.43" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 77.43" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 10200 ENER= -180.55 GRMS= 0.49 ELEC= -101.51 VDW= -156.47 RDTITL> *EXTERNAL= -257.98 INTERNAL= 77.43 USER= 0.00 HARM= 52.51 RDTITL> *BOND= 7.75 ANGL= 38.08 DIHE= 26.36 IMPR= 5.24 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20599 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20512 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -145.61523 -34.93329 0.44991 0.02000 MINI INTERN> 7.75192 38.08319 0.00000 26.36109 5.24268 MINI EXTERN> -156.47429 -101.51311 0.00000 0.00000 0.00000 MINI CONSTR> 34.93329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -139.17499 -6.44024 6.14617 0.00360 MINI INTERN> 11.87236 40.67439 0.00000 27.05740 5.23034 MINI EXTERN> -157.40237 -101.68960 0.00000 0.00000 0.00000 MINI CONSTR> 35.08250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20514 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -145.92855 6.75356 0.63781 0.00065 MINI INTERN> 7.70904 38.38651 0.00000 26.54885 5.28226 MINI EXTERN> -157.39448 -101.56529 0.00000 0.00000 0.00000 MINI CONSTR> 35.10456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -146.03870 0.11015 0.29025 0.00028 MINI INTERN> 7.73864 38.18063 0.00000 26.51904 5.26769 MINI EXTERN> -157.32085 -101.55967 0.00000 0.00000 0.00000 MINI CONSTR> 35.13583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20513 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -146.07691 0.03821 0.17840 0.00012 MINI INTERN> 7.74998 38.15707 0.00000 26.51971 5.26776 MINI EXTERN> -157.37090 -101.56384 0.00000 0.00000 0.00000 MINI CONSTR> 35.16332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -146.09326 0.01635 0.06760 0.00005 MINI INTERN> 7.72514 38.17120 0.00000 26.51468 5.26788 MINI EXTERN> -157.38885 -101.56333 0.00000 0.00000 0.00000 MINI CONSTR> 35.18001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20513 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -146.09991 0.00665 0.23105 0.00013 MINI INTERN> 7.76235 38.13149 0.00000 26.51411 5.26527 MINI EXTERN> -157.41730 -101.55466 0.00000 0.00000 0.00000 MINI CONSTR> 35.19883 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -146.11254 0.01263 0.23716 0.00013 MINI INTERN> 7.76486 38.12490 0.00000 26.51062 5.26444 MINI EXTERN> -157.44475 -101.55033 0.00000 0.00000 0.00000 MINI CONSTR> 35.21774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20513 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -146.12490 0.01236 0.24687 0.00014 MINI INTERN> 7.76780 38.11796 0.00000 26.50678 5.26357 MINI EXTERN> -157.47271 -101.54530 0.00000 0.00000 0.00000 MINI CONSTR> 35.23700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -146.14475 0.01985 0.07489 0.00006 MINI INTERN> 7.72464 38.15709 0.00000 26.49959 5.26507 MINI EXTERN> -157.49631 -101.55029 0.00000 0.00000 0.00000 MINI CONSTR> 35.25546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20513 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -146.15508 0.01033 0.06046 0.00006 MINI INTERN> 7.72814 38.14939 0.00000 26.49631 5.26420 MINI EXTERN> -157.51787 -101.54600 0.00000 0.00000 0.00000 MINI CONSTR> 35.27074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -146.16688 0.01180 0.05975 0.00006 MINI INTERN> 7.72819 38.14601 0.00000 26.49170 5.26349 MINI EXTERN> -157.54281 -101.54231 0.00000 0.00000 0.00000 MINI CONSTR> 35.28885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20513 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -146.17867 0.01179 0.06012 0.00007 MINI INTERN> 7.72777 38.14318 0.00000 26.48675 5.26278 MINI EXTERN> -157.56752 -101.53876 0.00000 0.00000 0.00000 MINI CONSTR> 35.30714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -146.19031 0.01164 0.11179 0.00007 MINI INTERN> 7.71832 38.15367 0.00000 26.48004 5.26268 MINI EXTERN> -157.59342 -101.53895 0.00000 0.00000 0.00000 MINI CONSTR> 35.32734 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20514 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -146.20136 0.01105 0.07504 0.00007 MINI INTERN> 7.72380 38.14209 0.00000 26.47596 5.26151 MINI EXTERN> -157.61471 -101.53329 0.00000 0.00000 0.00000 MINI CONSTR> 35.34327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -146.21264 0.01127 0.07392 0.00007 MINI INTERN> 7.72416 38.13844 0.00000 26.47048 5.26069 MINI EXTERN> -157.63772 -101.52988 0.00000 0.00000 0.00000 MINI CONSTR> 35.36119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20514 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -146.22399 0.01135 0.07636 0.00008 MINI INTERN> 7.72420 38.13531 0.00000 26.46463 5.25986 MINI EXTERN> -157.66080 -101.52668 0.00000 0.00000 0.00000 MINI CONSTR> 35.37949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -146.23510 0.01111 0.08531 0.00008 MINI INTERN> 7.72344 38.13353 0.00000 26.45848 5.25908 MINI EXTERN> -157.68343 -101.52399 0.00000 0.00000 0.00000 MINI CONSTR> 35.39779 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20513 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -146.24389 0.00880 0.14024 0.00008 MINI INTERN> 7.71836 38.14126 0.00000 26.45180 5.25888 MINI EXTERN> -157.70380 -101.52542 0.00000 0.00000 0.00000 MINI CONSTR> 35.41503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -146.25455 0.01065 0.14161 0.00009 MINI INTERN> 7.71928 38.13693 0.00000 26.44575 5.25796 MINI EXTERN> -157.72508 -101.52197 0.00000 0.00000 0.00000 MINI CONSTR> 35.43258 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20514 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -146.26524 0.01069 0.14679 0.00009 MINI INTERN> 7.71953 38.13341 0.00000 26.43934 5.25705 MINI EXTERN> -157.74658 -101.51855 0.00000 0.00000 0.00000 MINI CONSTR> 35.45056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -146.27562 0.01038 0.15815 0.00009 MINI INTERN> 7.71878 38.13147 0.00000 26.43264 5.25621 MINI EXTERN> -157.76779 -101.51554 0.00000 0.00000 0.00000 MINI CONSTR> 35.46861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20513 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -146.28519 0.00958 0.17558 0.00010 MINI INTERN> 7.71753 38.13092 0.00000 26.42596 5.25545 MINI EXTERN> -157.78782 -101.51322 0.00000 0.00000 0.00000 MINI CONSTR> 35.48600 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -146.29442 0.00923 0.16592 0.00010 MINI INTERN> 7.71770 38.12652 0.00000 26.42053 5.25451 MINI EXTERN> -157.80442 -101.50991 0.00000 0.00000 0.00000 MINI CONSTR> 35.50066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20510 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -146.30429 0.00987 0.17276 0.00010 MINI INTERN> 7.71692 38.12418 0.00000 26.41380 5.25362 MINI EXTERN> -157.82389 -101.50678 0.00000 0.00000 0.00000 MINI CONSTR> 35.51785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -146.31430 0.01001 0.17585 0.00011 MINI INTERN> 7.71628 38.12118 0.00000 26.40700 5.25267 MINI EXTERN> -157.84318 -101.50332 0.00000 0.00000 0.00000 MINI CONSTR> 35.53507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20509 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -146.32726 0.01296 0.05571 0.00005 MINI INTERN> 7.72970 38.08848 0.00000 26.40323 5.24976 MINI EXTERN> -157.86017 -101.48845 0.00000 0.00000 0.00000 MINI CONSTR> 35.55019 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -146.33174 0.00448 0.19290 0.00012 MINI INTERN> 7.71474 38.11787 0.00000 26.39416 5.25102 MINI EXTERN> -157.87727 -101.49863 0.00000 0.00000 0.00000 MINI CONSTR> 35.56635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20508 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -146.34107 0.00933 0.19851 0.00012 MINI INTERN> 7.71398 38.11535 0.00000 26.38730 5.25009 MINI EXTERN> -157.89519 -101.49550 0.00000 0.00000 0.00000 MINI CONSTR> 35.58290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -146.35035 0.00928 0.20663 0.00012 MINI INTERN> 7.71311 38.11301 0.00000 26.38021 5.24914 MINI EXTERN> -157.91325 -101.49228 0.00000 0.00000 0.00000 MINI CONSTR> 35.59972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20507 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -146.36536 0.01501 0.06175 0.00005 MINI INTERN> 7.73013 38.07387 0.00000 26.37592 5.24575 MINI EXTERN> -157.92992 -101.47693 0.00000 0.00000 0.00000 MINI CONSTR> 35.61584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -146.37333 0.00797 0.05158 0.00006 MINI INTERN> 7.72780 38.07422 0.00000 26.36984 5.24513 MINI EXTERN> -157.94403 -101.47567 0.00000 0.00000 0.00000 MINI CONSTR> 35.62938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20507 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -146.38243 0.00910 0.05092 0.00006 MINI INTERN> 7.72742 38.07140 0.00000 26.36291 5.24419 MINI EXTERN> -157.96028 -101.47327 0.00000 0.00000 0.00000 MINI CONSTR> 35.64521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -146.39170 0.00927 0.05082 0.00006 MINI INTERN> 7.72720 38.06827 0.00000 26.35575 5.24320 MINI EXTERN> -157.97672 -101.47080 0.00000 0.00000 0.00000 MINI CONSTR> 35.66141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20507 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -146.40093 0.00924 0.05175 0.00006 MINI INTERN> 7.72729 38.06474 0.00000 26.34852 5.24218 MINI EXTERN> -157.99302 -101.46828 0.00000 0.00000 0.00000 MINI CONSTR> 35.67763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -146.40977 0.00883 0.10203 0.00006 MINI INTERN> 7.73458 38.05264 0.00000 26.34117 5.24056 MINI EXTERN> -158.01007 -101.46381 0.00000 0.00000 0.00000 MINI CONSTR> 35.69516 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20507 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -146.41860 0.00883 0.06444 0.00007 MINI INTERN> 7.72925 38.05587 0.00000 26.33438 5.24007 MINI EXTERN> -158.02412 -101.46319 0.00000 0.00000 0.00000 MINI CONSTR> 35.70914 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -146.42756 0.00897 0.06439 0.00007 MINI INTERN> 7.72893 38.05319 0.00000 26.32702 5.23912 MINI EXTERN> -158.03964 -101.46121 0.00000 0.00000 0.00000 MINI CONSTR> 35.72502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20507 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -146.43655 0.00898 0.06844 0.00007 MINI INTERN> 7.72914 38.04992 0.00000 26.31954 5.23813 MINI EXTERN> -158.05522 -101.45918 0.00000 0.00000 0.00000 MINI CONSTR> 35.74112 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -146.44516 0.00861 0.08144 0.00007 MINI INTERN> 7.73051 38.04557 0.00000 26.31216 5.23709 MINI EXTERN> -158.07037 -101.45710 0.00000 0.00000 0.00000 MINI CONSTR> 35.75698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20504 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -146.45186 0.00669 0.12512 0.00008 MINI INTERN> 7.73584 38.03795 0.00000 26.30564 5.23595 MINI EXTERN> -158.08374 -101.45480 0.00000 0.00000 0.00000 MINI CONSTR> 35.77131 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -146.46034 0.00848 0.12861 0.00008 MINI INTERN> 7.73560 38.03591 0.00000 26.29820 5.23509 MINI EXTERN> -158.09840 -101.45350 0.00000 0.00000 0.00000 MINI CONSTR> 35.78675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20504 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -146.46872 0.00838 0.13639 0.00008 MINI INTERN> 7.73563 38.03391 0.00000 26.29063 5.23425 MINI EXTERN> -158.11313 -101.45237 0.00000 0.00000 0.00000 MINI CONSTR> 35.80236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -146.47667 0.00795 0.14929 0.00009 MINI INTERN> 7.73627 38.03156 0.00000 26.28317 5.23340 MINI EXTERN> -158.12749 -101.45125 0.00000 0.00000 0.00000 MINI CONSTR> 35.81768 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20503 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -146.48430 0.00763 0.14265 0.00009 MINI INTERN> 7.73551 38.02934 0.00000 26.27666 5.23257 MINI EXTERN> -158.13978 -101.44953 0.00000 0.00000 0.00000 MINI CONSTR> 35.83093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -146.49225 0.00795 0.15002 0.00009 MINI INTERN> 7.73524 38.02793 0.00000 26.26922 5.23179 MINI EXTERN> -158.15372 -101.44863 0.00000 0.00000 0.00000 MINI CONSTR> 35.84592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20503 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -146.50045 0.00820 0.15538 0.00010 MINI INTERN> 7.73400 38.02771 0.00000 26.26151 5.23109 MINI EXTERN> -158.16807 -101.44798 0.00000 0.00000 0.00000 MINI CONSTR> 35.86128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -146.50883 0.00838 0.15797 0.00010 MINI INTERN> 7.73186 38.02822 0.00000 26.25368 5.23040 MINI EXTERN> -158.18253 -101.44723 0.00000 0.00000 0.00000 MINI CONSTR> 35.87677 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20502 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -146.51983 0.01099 0.04859 0.00004 MINI INTERN> 7.72242 38.02624 0.00000 26.24668 5.22880 MINI EXTERN> -158.19415 -101.44039 0.00000 0.00000 0.00000 MINI CONSTR> 35.89059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -146.52393 0.00411 0.17103 0.00011 MINI INTERN> 7.73012 38.02637 0.00000 26.23913 5.22890 MINI EXTERN> -158.20888 -101.44513 0.00000 0.00000 0.00000 MINI CONSTR> 35.90555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20502 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -146.53180 0.00787 0.17461 0.00011 MINI INTERN> 7.72832 38.02598 0.00000 26.23161 5.22814 MINI EXTERN> -158.22232 -101.44384 0.00000 0.00000 0.00000 MINI CONSTR> 35.92031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -146.53980 0.00800 0.17963 0.00011 MINI INTERN> 7.72604 38.02582 0.00000 26.22387 5.22734 MINI EXTERN> -158.23603 -101.44237 0.00000 0.00000 0.00000 MINI CONSTR> 35.93552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20501 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -146.54777 0.00797 0.18695 0.00012 MINI INTERN> 7.72403 38.02511 0.00000 26.21604 5.22647 MINI EXTERN> -158.24965 -101.44071 0.00000 0.00000 0.00000 MINI CONSTR> 35.95094 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -146.56070 0.01293 0.05596 0.00005 MINI INTERN> 7.72255 38.01107 0.00000 26.20845 5.22385 MINI EXTERN> -158.26030 -101.43209 0.00000 0.00000 0.00000 MINI CONSTR> 35.96576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20501 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -146.56757 0.00686 0.04658 0.00005 MINI INTERN> 7.72181 38.00980 0.00000 26.20210 5.22320 MINI EXTERN> -158.27115 -101.43147 0.00000 0.00000 0.00000 MINI CONSTR> 35.97814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -146.57544 0.00787 0.04607 0.00006 MINI INTERN> 7.72164 38.00721 0.00000 26.19458 5.22228 MINI EXTERN> -158.28370 -101.43012 0.00000 0.00000 0.00000 MINI CONSTR> 35.99267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20501 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -146.58349 0.00805 0.04602 0.00006 MINI INTERN> 7.72150 38.00449 0.00000 26.18683 5.22132 MINI EXTERN> -158.29648 -101.42871 0.00000 0.00000 0.00000 MINI CONSTR> 36.00757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -146.59155 0.00806 0.04676 0.00006 MINI INTERN> 7.72144 38.00164 0.00000 26.17900 5.22035 MINI EXTERN> -158.30927 -101.42726 0.00000 0.00000 0.00000 MINI CONSTR> 36.02255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20501 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -146.59945 0.00790 0.08991 0.00006 MINI INTERN> 7.72428 37.99572 0.00000 26.17015 5.21899 MINI EXTERN> -158.32326 -101.42427 0.00000 0.00000 0.00000 MINI CONSTR> 36.03893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -146.60714 0.00769 0.05854 0.00006 MINI INTERN> 7.72207 37.99533 0.00000 26.16349 5.21836 MINI EXTERN> -158.33417 -101.42411 0.00000 0.00000 0.00000 MINI CONSTR> 36.05189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20501 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -146.61405 0.00691 0.04664 0.00007 MINI INTERN> 7.72095 37.99408 0.00000 26.15699 5.21766 MINI EXTERN> -158.34460 -101.42354 0.00000 0.00000 0.00000 MINI CONSTR> 36.06441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -146.62131 0.00726 0.10698 0.00007 MINI INTERN> 7.72487 37.98775 0.00000 26.14799 5.21628 MINI EXTERN> -158.35853 -101.42036 0.00000 0.00000 0.00000 MINI CONSTR> 36.08069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20500 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -146.62955 0.00824 0.06228 0.00007 MINI INTERN> 7.72173 37.98777 0.00000 26.14121 5.21567 MINI EXTERN> -158.36936 -101.42046 0.00000 0.00000 0.00000 MINI CONSTR> 36.09388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -146.63604 0.00649 0.11542 0.00007 MINI INTERN> 7.72477 37.98312 0.00000 26.13286 5.21454 MINI EXTERN> -158.38225 -101.41792 0.00000 0.00000 0.00000 MINI CONSTR> 36.10884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20499 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -146.64348 0.00744 0.11719 0.00008 MINI INTERN> 7.72456 37.98094 0.00000 26.12524 5.21369 MINI EXTERN> -158.39409 -101.41675 0.00000 0.00000 0.00000 MINI CONSTR> 36.12292 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -146.65092 0.00744 0.12252 0.00008 MINI INTERN> 7.72451 37.97879 0.00000 26.11736 5.21284 MINI EXTERN> -158.40625 -101.41547 0.00000 0.00000 0.00000 MINI CONSTR> 36.13729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20499 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -146.65814 0.00722 0.13191 0.00008 MINI INTERN> 7.72471 37.97659 0.00000 26.10945 5.21200 MINI EXTERN> -158.41840 -101.41410 0.00000 0.00000 0.00000 MINI CONSTR> 36.15161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -146.66507 0.00693 0.12688 0.00009 MINI INTERN> 7.72409 37.97455 0.00000 26.10268 5.21118 MINI EXTERN> -158.42859 -101.41327 0.00000 0.00000 0.00000 MINI CONSTR> 36.16429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20499 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -146.67213 0.00706 0.13541 0.00009 MINI INTERN> 7.72412 37.97260 0.00000 26.09488 5.21037 MINI EXTERN> -158.44043 -101.41197 0.00000 0.00000 0.00000 MINI CONSTR> 36.17830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -146.67888 0.00675 0.15547 0.00009 MINI INTERN> 7.72501 37.97048 0.00000 26.08658 5.20956 MINI EXTERN> -158.45301 -101.41033 0.00000 0.00000 0.00000 MINI CONSTR> 36.19283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20499 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -146.68564 0.00675 0.14478 0.00010 MINI INTERN> 7.72397 37.96831 0.00000 26.08047 5.20870 MINI EXTERN> -158.46189 -101.40983 0.00000 0.00000 0.00000 MINI CONSTR> 36.20464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -146.69319 0.00755 0.14618 0.00010 MINI INTERN> 7.72357 37.96667 0.00000 26.07231 5.20794 MINI EXTERN> -158.47415 -101.40862 0.00000 0.00000 0.00000 MINI CONSTR> 36.21910 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20498 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -146.70293 0.00975 0.04639 0.00004 MINI INTERN> 7.71788 37.96451 0.00000 26.06764 5.20676 MINI EXTERN> -158.48004 -101.41142 0.00000 0.00000 0.00000 MINI CONSTR> 36.23174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -146.70627 0.00334 0.16015 0.00011 MINI INTERN> 7.72362 37.96274 0.00000 26.05776 5.20633 MINI EXTERN> -158.49555 -101.40644 0.00000 0.00000 0.00000 MINI CONSTR> 36.24527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20498 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -146.71338 0.00711 0.16455 0.00011 MINI INTERN> 7.72383 37.96088 0.00000 26.04970 5.20562 MINI EXTERN> -158.50749 -101.40520 0.00000 0.00000 0.00000 MINI CONSTR> 36.25926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -146.72052 0.00714 0.17066 0.00011 MINI INTERN> 7.72452 37.95892 0.00000 26.04133 5.20498 MINI EXTERN> -158.51995 -101.40384 0.00000 0.00000 0.00000 MINI CONSTR> 36.27352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20497 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -146.72744 0.00692 0.17994 0.00012 MINI INTERN> 7.72576 37.95670 0.00000 26.03287 5.20437 MINI EXTERN> -158.53252 -101.40240 0.00000 0.00000 0.00000 MINI CONSTR> 36.28776 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -146.73900 0.01156 0.05901 0.00005 MINI INTERN> 7.71606 37.95195 0.00000 26.03060 5.20194 MINI EXTERN> -158.53286 -101.40756 0.00000 0.00000 0.00000 MINI CONSTR> 36.30087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20495 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -146.74502 0.00603 0.04279 0.00005 MINI INTERN> 7.71685 37.95000 0.00000 26.02375 5.20149 MINI EXTERN> -158.54306 -101.40595 0.00000 0.00000 0.00000 MINI CONSTR> 36.31189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -146.75226 0.00724 0.04253 0.00005 MINI INTERN> 7.71659 37.94755 0.00000 26.01614 5.20057 MINI EXTERN> -158.55379 -101.40508 0.00000 0.00000 0.00000 MINI CONSTR> 36.32575 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20495 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -146.75962 0.00736 0.04270 0.00006 MINI INTERN> 7.71625 37.94507 0.00000 26.00842 5.19962 MINI EXTERN> -158.56458 -101.40425 0.00000 0.00000 0.00000 MINI CONSTR> 36.33986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -146.76692 0.00730 0.04390 0.00006 MINI INTERN> 7.71575 37.94263 0.00000 26.00081 5.19863 MINI EXTERN> -158.57511 -101.40355 0.00000 0.00000 0.00000 MINI CONSTR> 36.35392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20492 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -146.77377 0.00685 0.08809 0.00006 MINI INTERN> 7.71206 37.94088 0.00000 25.99465 5.19676 MINI EXTERN> -158.58219 -101.40482 0.00000 0.00000 0.00000 MINI CONSTR> 36.36888 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -146.78085 0.00708 0.05436 0.00006 MINI INTERN> 7.71385 37.93823 0.00000 25.98656 5.19652 MINI EXTERN> -158.59436 -101.40268 0.00000 0.00000 0.00000 MINI CONSTR> 36.38103 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20493 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -146.78804 0.00719 0.05473 0.00007 MINI INTERN> 7.71315 37.93608 0.00000 25.97899 5.19555 MINI EXTERN> -158.60473 -101.40197 0.00000 0.00000 0.00000 MINI CONSTR> 36.39489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -146.79524 0.00720 0.05879 0.00007 MINI INTERN> 7.71201 37.93409 0.00000 25.97151 5.19449 MINI EXTERN> -158.61478 -101.40147 0.00000 0.00000 0.00000 MINI CONSTR> 36.40892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20492 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -146.80109 0.00586 0.10626 0.00007 MINI INTERN> 7.70671 37.93420 0.00000 25.96620 5.19257 MINI EXTERN> -158.62046 -101.40299 0.00000 0.00000 0.00000 MINI CONSTR> 36.42267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -146.80787 0.00678 0.10668 0.00007 MINI INTERN> 7.70586 37.93233 0.00000 25.95900 5.19164 MINI EXTERN> -158.63012 -101.40238 0.00000 0.00000 0.00000 MINI CONSTR> 36.43581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20492 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -146.81471 0.00684 0.11051 0.00008 MINI INTERN> 7.70373 37.93136 0.00000 25.95194 5.19062 MINI EXTERN> -158.63972 -101.40195 0.00000 0.00000 0.00000 MINI CONSTR> 36.44931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -146.82113 0.00642 0.12405 0.00008 MINI INTERN> 7.70451 37.92803 0.00000 25.94460 5.18949 MINI EXTERN> -158.64889 -101.40155 0.00000 0.00000 0.00000 MINI CONSTR> 36.46268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20493 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -146.82732 0.00619 0.11867 0.00008 MINI INTERN> 7.70054 37.92931 0.00000 25.93839 5.18880 MINI EXTERN> -158.65755 -101.40114 0.00000 0.00000 0.00000 MINI CONSTR> 36.47433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -146.83348 0.00616 0.12845 0.00008 MINI INTERN> 7.70722 37.92072 0.00000 25.93126 5.18781 MINI EXTERN> -158.66749 -101.39994 0.00000 0.00000 0.00000 MINI CONSTR> 36.48694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20493 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -146.83968 0.00621 0.12783 0.00009 MINI INTERN> 7.69661 37.92858 0.00000 25.92461 5.18721 MINI EXTERN> -158.67543 -101.40024 0.00000 0.00000 0.00000 MINI CONSTR> 36.49898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -146.84751 0.00783 0.04250 0.00004 MINI INTERN> 7.71775 37.91261 0.00000 25.91276 5.18892 MINI EXTERN> -158.69588 -101.39350 0.00000 0.00000 0.00000 MINI CONSTR> 36.50984 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20492 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -146.85110 0.00359 0.14055 0.00009 MINI INTERN> 7.69618 37.92351 0.00000 25.91246 5.18517 MINI EXTERN> -158.69102 -101.39982 0.00000 0.00000 0.00000 MINI CONSTR> 36.52241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -146.85999 0.00889 0.04448 0.00004 MINI INTERN> 7.71820 37.90786 0.00000 25.89883 5.18742 MINI EXTERN> -158.71451 -101.39201 0.00000 0.00000 0.00000 MINI CONSTR> 36.53422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20491 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -146.86291 0.00292 0.15057 0.00010 MINI INTERN> 7.70097 37.91372 0.00000 25.89981 5.18314 MINI EXTERN> -158.70831 -101.39864 0.00000 0.00000 0.00000 MINI CONSTR> 36.54639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -146.86871 0.00579 0.16808 0.00011 MINI INTERN> 7.68755 37.92638 0.00000 25.89150 5.18311 MINI EXTERN> -158.71773 -101.39844 0.00000 0.00000 0.00000 MINI CONSTR> 36.55893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20491 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -146.87840 0.00969 0.04985 0.00005 MINI INTERN> 7.71996 37.89996 0.00000 25.87804 5.18523 MINI EXTERN> -158.74229 -101.38969 0.00000 0.00000 0.00000 MINI CONSTR> 36.57039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -146.88024 0.00184 0.16723 0.00011 MINI INTERN> 7.69022 37.91694 0.00000 25.88039 5.18066 MINI EXTERN> -158.73212 -101.39828 0.00000 0.00000 0.00000 MINI CONSTR> 36.58196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20490 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -146.89055 0.01031 0.05725 0.00005 MINI INTERN> 7.72137 37.89490 0.00000 25.86391 5.18389 MINI EXTERN> -158.76110 -101.38799 0.00000 0.00000 0.00000 MINI CONSTR> 36.59448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -146.89055 0.01031 0.05725 0.00006 STPD INTERN> 7.72137 37.89490 0.00000 25.86391 5.18389 STPD EXTERN> -158.76110 -101.38799 0.00000 0.00000 0.00000 STPD CONSTR> 36.59448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20490 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20490 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -146.89055 0.01031 0.05725 0.00000 MINI INTERN> 7.72137 37.89490 0.00000 25.86391 5.18389 MINI EXTERN> -158.76110 -101.38799 0.00000 0.00000 0.00000 MINI CONSTR> 36.59448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -148.01045 1.11990 0.49188 0.16068 MINI INTERN> 7.85816 37.02230 0.00000 23.75367 4.96011 MINI EXTERN> -162.19357 -100.62046 0.00000 0.00000 0.00000 MINI CONSTR> 41.20935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -148.11833 0.10788 0.16524 0.02171 MINI INTERN> 7.72732 37.16096 0.00000 23.58957 4.94509 MINI EXTERN> -162.46758 -100.78606 0.00000 0.00000 0.00000 MINI CONSTR> 41.71235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -148.15416 0.03583 0.19066 0.01129 MINI INTERN> 7.65844 37.15264 0.00000 23.51533 4.93716 MINI EXTERN> -162.30050 -100.96353 0.00000 0.00000 0.00000 MINI CONSTR> 41.84630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -148.22908 0.07492 0.19776 0.04644 MINI INTERN> 7.59360 36.91191 0.00000 23.28934 4.92100 MINI EXTERN> -162.02639 -100.99629 0.00000 0.00000 0.00000 MINI CONSTR> 42.07775 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -148.33342 0.10434 0.26166 0.06585 MINI INTERN> 7.55398 36.88336 0.00000 23.13425 4.89685 MINI EXTERN> -162.29497 -100.88393 0.00000 0.00000 0.00000 MINI CONSTR> 42.37704 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -148.42722 0.09381 0.21593 0.04874 MINI INTERN> 7.58008 36.76576 0.00000 22.94966 4.87280 MINI EXTERN> -162.46110 -100.77802 0.00000 0.00000 0.00000 MINI CONSTR> 42.64359 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -148.50432 0.07710 0.19465 0.03491 MINI INTERN> 7.58508 36.63713 0.00000 22.88087 4.87058 MINI EXTERN> -162.74575 -100.58657 0.00000 0.00000 0.00000 MINI CONSTR> 42.85433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -148.54551 0.04118 0.16269 0.01919 MINI INTERN> 7.61160 36.58275 0.00000 22.84492 4.87387 MINI EXTERN> -162.92950 -100.48266 0.00000 0.00000 0.00000 MINI CONSTR> 42.95351 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -148.57973 0.03423 0.16224 0.02168 MINI INTERN> 7.60032 36.59423 0.00000 22.78185 4.91012 MINI EXTERN> -163.08206 -100.39919 0.00000 0.00000 0.00000 MINI CONSTR> 43.01500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -148.61769 0.03796 0.15390 0.02534 MINI INTERN> 7.52075 36.59536 0.00000 22.76083 4.90636 MINI EXTERN> -163.11789 -100.34437 0.00000 0.00000 0.00000 MINI CONSTR> 43.06128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -148.65860 0.04091 0.16999 0.02834 MINI INTERN> 7.56797 36.59654 0.00000 22.73148 4.96627 MINI EXTERN> -163.10336 -100.50983 0.00000 0.00000 0.00000 MINI CONSTR> 43.09233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -148.70352 0.04493 0.18497 0.03115 MINI INTERN> 7.54137 36.54799 0.00000 22.72907 4.92533 MINI EXTERN> -163.09935 -100.45479 0.00000 0.00000 0.00000 MINI CONSTR> 43.10685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -148.75530 0.05177 0.20264 0.03232 MINI INTERN> 7.59249 36.38876 0.00000 22.69741 4.89451 MINI EXTERN> -163.12857 -100.30595 0.00000 0.00000 0.00000 MINI CONSTR> 43.10604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -148.79493 0.03963 0.16193 0.02353 MINI INTERN> 7.60024 36.42963 0.00000 22.72814 4.85698 MINI EXTERN> -163.09556 -100.40145 0.00000 0.00000 0.00000 MINI CONSTR> 43.08708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -148.83388 0.03895 0.17714 0.02679 MINI INTERN> 7.57051 36.40497 0.00000 22.76807 4.84536 MINI EXTERN> -162.82201 -100.64525 0.00000 0.00000 0.00000 MINI CONSTR> 43.04448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -148.86879 0.03491 0.16259 0.02290 MINI INTERN> 7.45502 36.43185 0.00000 22.73758 4.85235 MINI EXTERN> -162.59718 -100.73798 0.00000 0.00000 0.00000 MINI CONSTR> 42.98957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -148.90348 0.03469 0.14301 0.02453 MINI INTERN> 7.42049 36.41664 0.00000 22.66036 4.84749 MINI EXTERN> -162.45318 -100.71771 0.00000 0.00000 0.00000 MINI CONSTR> 42.92243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -148.94392 0.04044 0.16856 0.03466 MINI INTERN> 7.50752 36.55597 0.00000 22.64850 4.86368 MINI EXTERN> -162.47217 -100.88097 0.00000 0.00000 0.00000 MINI CONSTR> 42.83355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -148.98192 0.03800 0.15311 0.02503 MINI INTERN> 7.49545 36.57963 0.00000 22.68927 4.85830 MINI EXTERN> -162.45697 -100.89232 0.00000 0.00000 0.00000 MINI CONSTR> 42.74472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -149.01186 0.02995 0.14540 0.01861 MINI INTERN> 7.53522 36.67252 0.00000 22.67729 4.89703 MINI EXTERN> -162.41796 -101.04530 0.00000 0.00000 0.00000 MINI CONSTR> 42.66935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -149.01186 0.02995 0.14540 0.02000 CONJ INTERN> 7.53522 36.67252 0.00000 22.67729 4.89703 CONJ EXTERN> -162.41796 -101.04530 0.00000 0.00000 0.00000 CONJ CONSTR> 42.66935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "10800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.85797E-01 ( PROT LYS 1 HT2 ) 0.85797E-01 ( PROT LYS 1 N ) 0.10725 ( PROT LYS 1 HT3 ) 0.85797E-01 ( PROT LYS 1 CA ) 0.10725 ( PROT LYS 1 CB ) 0.85797E-01 ( PROT LYS 1 CG ) 0.85797E-01 ( PROT LYS 1 CD ) 0.85797E-01 ( PROT LYS 1 CE ) 0.85797E-01 ( PROT LYS 1 NZ ) 0.85797E-01 ( PROT LYS 1 HZ1 ) 0.85797E-01 ( PROT LYS 1 HZ2 ) 0.85797E-01 ( PROT LYS 1 HZ3 ) 0.85797E-01 ( PROT LYS 1 C ) 0.10725 ( PROT LYS 1 O ) 0.10725 ( PROT MET 2 N ) 0.10725 ( PROT MET 2 H ) 0.85797E-01 ( PROT MET 2 CA ) 0.10725 ( PROT MET 2 CB ) 0.85797E-01 ( PROT MET 2 CG ) 0.85797E-01 ( PROT MET 2 SD ) 0.85797E-01 ( PROT MET 2 CE ) 0.85797E-01 ( PROT MET 2 C ) 0.10725 ( PROT MET 2 O ) 0.10725 ( PROT LYS 3 N ) 0.10725 ( PROT LYS 3 H ) 0.85797E-01 ( PROT LYS 3 CA ) 0.10725 ( PROT LYS 3 CB ) 0.85797E-01 ( PROT LYS 3 CG ) 0.85797E-01 ( PROT LYS 3 CD ) 0.85797E-01 ( PROT LYS 3 CE ) 0.85797E-01 ( PROT LYS 3 NZ ) 0.85797E-01 ( PROT LYS 3 HZ1 ) 0.85797E-01 ( PROT LYS 3 HZ2 ) 0.85797E-01 ( PROT LYS 3 HZ3 ) 0.85797E-01 ( PROT LYS 3 C ) 0.10725 ( PROT LYS 3 O ) 0.10725 ( PROT ALA 4 N ) 0.10725 ( PROT ALA 4 H ) 0.85797E-01 ( PROT ALA 4 CA ) 0.10725 ( PROT ALA 4 CB ) 0.85797E-01 ( PROT ALA 4 C ) 0.10725 ( PROT ALA 4 O ) 0.10725 ( PROT VAL 5 N ) 0.10725 ( PROT VAL 5 H ) 0.85797E-01 ( PROT VAL 5 CA ) 0.10725 ( PROT VAL 5 CB ) 0.85797E-01 ( PROT VAL 5 CG1 ) 0.85797E-01 ( PROT VAL 5 CG2 ) 0.85797E-01 ( PROT VAL 5 C ) 0.10725 ( PROT VAL 5 O ) 0.10725 ( PROT MET 6 N ) 0.10725 ( PROT MET 6 H ) 0.85797E-01 ( PROT MET 6 CA ) 0.10725 ( PROT MET 6 CB ) 0.85797E-01 ( PROT MET 6 CG ) 0.85797E-01 ( PROT MET 6 SD ) 0.85797E-01 ( PROT MET 6 CE ) 0.85797E-01 ( PROT MET 6 C ) 0.10725 ( PROT MET 6 O ) 0.10725 ( PROT ILE 7 N ) 0.10725 ( PROT ILE 7 H ) 0.85797E-01 ( PROT ILE 7 CA ) 0.10725 ( PROT ILE 7 CB ) 0.85797E-01 ( PROT ILE 7 CG2 ) 0.85797E-01 ( PROT ILE 7 CG1 ) 0.85797E-01 ( PROT ILE 7 CD ) 0.85797E-01 ( PROT ILE 7 C ) 0.10725 ( PROT ILE 7 O ) 0.10725 ( PROT GLY 8 N ) 0.10725 ( PROT GLY 8 H ) 0.85797E-01 ( PROT GLY 8 CA ) 0.10725 ( PROT GLY 8 C ) 0.10725 ( PROT GLY 8 O ) 0.10725 ( PROT ALA 9 N ) 0.10725 ( PROT ALA 9 H ) 0.85797E-01 ( PROT ALA 9 CA ) 0.10725 ( PROT ALA 9 CB ) 0.85797E-01 ( PROT ALA 9 C ) 0.10725 ( PROT ALA 9 O ) 0.10725 ( PROT CYS 10 N ) 0.10725 ( PROT CYS 10 H ) 0.85797E-01 ( PROT CYS 10 CA ) 0.10725 ( PROT CYS 10 CB ) 0.85797E-01 ( PROT CYS 10 SG ) 0.85797E-01 ( PROT CYS 10 C ) 0.10725 ( PROT CYS 10 O ) 0.10725 ( PROT PHE 11 N ) 0.10725 ( PROT PHE 11 H ) 0.85797E-01 ( PROT PHE 11 CA ) 0.10725 ( PROT PHE 11 CB ) 0.85797E-01 ( PROT PHE 11 CG ) 0.85797E-01 ( PROT PHE 11 CD1 ) 0.85797E-01 ( PROT PHE 11 CD2 ) 0.85797E-01 ( PROT PHE 11 CE1 ) 0.85797E-01 ( PROT PHE 11 CE2 ) 0.85797E-01 ( PROT PHE 11 CZ ) 0.85797E-01 ( PROT PHE 11 C ) 0.10725 ( PROT PHE 11 O ) 0.10725 ( PROT LEU 12 N ) 0.10725 ( PROT LEU 12 H ) 0.85797E-01 ( PROT LEU 12 CA ) 0.10725 ( PROT LEU 12 CB ) 0.85797E-01 ( PROT LEU 12 CG ) 0.85797E-01 ( PROT LEU 12 CD1 ) 0.85797E-01 ( PROT LEU 12 CD2 ) 0.85797E-01 ( PROT LEU 12 C ) 0.10725 ( PROT LEU 12 O ) 0.10725 ( PROT ILE 13 N ) 0.10725 ( PROT ILE 13 H ) 0.85797E-01 ( PROT ILE 13 CA ) 0.10725 ( PROT ILE 13 CB ) 0.85797E-01 ( PROT ILE 13 CG2 ) 0.85797E-01 ( PROT ILE 13 CG1 ) 0.85797E-01 ( PROT ILE 13 CD ) 0.85797E-01 ( PROT ILE 13 C ) 0.10725 ( PROT ILE 13 O ) 0.10725 ( PROT ASH 14 N ) 0.10725 ( PROT ASH 14 H ) 0.85797E-01 ( PROT ASH 14 CA ) 0.10725 ( PROT ASH 14 CB ) 0.85797E-01 ( PROT ASH 14 CG ) 0.85797E-01 ( PROT ASH 14 OD1 ) 0.85797E-01 ( PROT ASH 14 OD2 ) 0.85797E-01 ( PROT ASH 14 HD2 ) 0.85797E-01 ( PROT ASH 14 C ) 0.10725 ( PROT ASH 14 O ) 0.10725 ( PROT PHE 15 N ) 0.10725 ( PROT PHE 15 H ) 0.85797E-01 ( PROT PHE 15 CA ) 0.10725 ( PROT PHE 15 CB ) 0.85797E-01 ( PROT PHE 15 CG ) 0.85797E-01 ( PROT PHE 15 CD1 ) 0.85797E-01 ( PROT PHE 15 CD2 ) 0.85797E-01 ( PROT PHE 15 CE1 ) 0.85797E-01 ( PROT PHE 15 CE2 ) 0.85797E-01 ( PROT PHE 15 CZ ) 0.85797E-01 ( PROT PHE 15 C ) 0.10725 ( PROT PHE 15 O ) 0.10725 ( PROT MET 16 N ) 0.10725 ( PROT MET 16 H ) 0.85797E-01 ( PROT MET 16 CA ) 0.10725 ( PROT MET 16 CB ) 0.85797E-01 ( PROT MET 16 CG ) 0.85797E-01 ( PROT MET 16 SD ) 0.85797E-01 ( PROT MET 16 CE ) 0.85797E-01 ( PROT MET 16 C ) 0.10725 ( PROT MET 16 O ) 0.10725 ( PROT PHE 17 N ) 0.10725 ( PROT PHE 17 H ) 0.85797E-01 ( PROT PHE 17 CA ) 0.10725 ( PROT PHE 17 CB ) 0.85797E-01 ( PROT PHE 17 CG ) 0.85797E-01 ( PROT PHE 17 CD1 ) 0.85797E-01 ( PROT PHE 17 CD2 ) 0.85797E-01 ( PROT PHE 17 CE1 ) 0.85797E-01 ( PROT PHE 17 CE2 ) 0.85797E-01 ( PROT PHE 17 CZ ) 0.85797E-01 ( PROT PHE 17 C ) 0.10725 ( PROT PHE 17 O ) 0.10725 ( PROT PHE 18 N ) 0.10725 ( PROT PHE 18 H ) 0.85797E-01 ( PROT PHE 18 CA ) 0.10725 ( PROT PHE 18 CB ) 0.85797E-01 ( PROT PHE 18 CG ) 0.85797E-01 ( PROT PHE 18 CD1 ) 0.85797E-01 ( PROT PHE 18 CD2 ) 0.85797E-01 ( PROT PHE 18 CE1 ) 0.85797E-01 ( PROT PHE 18 CE2 ) 0.85797E-01 ( PROT PHE 18 CZ ) 0.85797E-01 ( PROT PHE 18 C ) 0.10725 ( PROT PHE 18 O ) 0.10725 ( PROT GLU 19 N ) 0.10725 ( PROT GLU 19 H ) 0.85797E-01 ( PROT GLU 19 CA ) 0.10725 ( PROT GLU 19 CB ) 0.85797E-01 ( PROT GLU 19 CG ) 0.85797E-01 ( PROT GLU 19 CD ) 0.85797E-01 ( PROT GLU 19 OE1 ) 0.85797E-01 ( PROT GLU 19 OE2 ) 0.85797E-01 ( PROT GLU 19 C ) 0.10725 ( PROT GLU 19 O ) 0.10725 ( PROT SER 20 N ) 0.10725 ( PROT SER 20 H ) 0.85797E-01 ( PROT SER 20 CA ) 0.10725 ( PROT SER 20 CB ) 0.85797E-01 ( PROT SER 20 OG ) 0.85797E-01 ( PROT SER 20 HG ) 0.85797E-01 ( PROT SER 20 C ) 0.10725 ( PROT SER 20 O ) 0.10725 ( PROT THR 21 N ) 0.10725 ( PROT THR 21 H ) 0.85797E-01 ( PROT THR 21 CA ) 0.10725 ( PROT THR 21 CB ) 0.85797E-01 ( PROT THR 21 OG1 ) 0.85797E-01 ( PROT THR 21 HG1 ) 0.85797E-01 ( PROT THR 21 CG2 ) 0.85797E-01 ( PROT THR 21 C ) 0.10725 ( PROT THR 21 O ) 0.10725 ( PROT GLY 22 N ) 0.10725 ( PROT GLY 22 H ) 0.85797E-01 ( PROT GLY 22 CA ) 0.10725 ( PROT GLY 22 C ) 0.10725 ( PROT GLY 22 O ) 0.10725 ( PROT SER 23 N ) 0.10725 ( PROT SER 23 H ) 0.85797E-01 ( PROT SER 23 CA ) 0.10725 ( PROT SER 23 CB ) 0.85797E-01 ( PROT SER 23 OG ) 0.85797E-01 ( PROT SER 23 HG ) 0.85797E-01 ( PROT SER 23 C ) 0.10725 ( PROT SER 23 O ) 0.10725 ( PROT GLN 24 N ) 0.10725 ( PROT GLN 24 H ) 0.85797E-01 ( PROT GLN 24 CA ) 0.10725 ( PROT GLN 24 CB ) 0.85797E-01 ( PROT GLN 24 CG ) 0.85797E-01 ( PROT GLN 24 CD ) 0.85797E-01 ( PROT GLN 24 OE1 ) 0.85797E-01 ( PROT GLN 24 NE2 ) 0.85797E-01 ( PROT GLN 24 HE21 ) 0.85797E-01 ( PROT GLN 24 HE22 ) 0.85797E-01 ( PROT GLN 24 C ) 0.10725 ( PROT GLN 24 O ) 0.10725 ( PROT GLU 25 N ) 0.10725 ( PROT GLU 25 H ) 0.85797E-01 ( PROT GLU 25 CA ) 0.10725 ( PROT GLU 25 CB ) 0.85797E-01 ( PROT GLU 25 CG ) 0.85797E-01 ( PROT GLU 25 CD ) 0.85797E-01 ( PROT GLU 25 OE1 ) 0.85797E-01 ( PROT GLU 25 OE2 ) 0.85797E-01 ( PROT GLU 25 C ) 0.10725 ( PROT GLU 25 O ) 0.10725 ( PROT GLN 26 N ) 0.10725 ( PROT GLN 26 H ) 0.85797E-01 ( PROT GLN 26 CA ) 0.10725 ( PROT GLN 26 CB ) 0.85797E-01 ( PROT GLN 26 CG ) 0.85797E-01 ( PROT GLN 26 CD ) 0.85797E-01 ( PROT GLN 26 OE1 ) 0.85797E-01 ( PROT GLN 26 NE2 ) 0.85797E-01 ( PROT GLN 26 HE21 ) 0.85797E-01 ( PROT GLN 26 HE22 ) 0.85797E-01 ( PROT GLN 26 C ) 0.10725 ( PROT GLN 26 O ) 0.10725 ( PROT LYS 27 N ) 0.10725 ( PROT LYS 27 H ) 0.85797E-01 ( PROT LYS 27 CA ) 0.10725 ( PROT LYS 27 CB ) 0.85797E-01 ( PROT LYS 27 CG ) 0.85797E-01 ( PROT LYS 27 CD ) 0.85797E-01 ( PROT LYS 27 CE ) 0.85797E-01 ( PROT LYS 27 NZ ) 0.85797E-01 ( PROT LYS 27 HZ1 ) 0.85797E-01 ( PROT LYS 27 HZ2 ) 0.85797E-01 ( PROT LYS 27 HZ3 ) 0.85797E-01 ( PROT LYS 27 C ) 0.10725 ( PROT LYS 27 O ) 0.10725 ( PROT SER 28 N ) 0.10725 ( PROT SER 28 H ) 0.85797E-01 ( PROT SER 28 CA ) 0.10725 ( PROT SER 28 CB ) 0.85797E-01 ( PROT SER 28 OG ) 0.85797E-01 ( PROT SER 28 HG ) 0.85797E-01 ( PROT SER 28 C ) 0.10725 ( PROT SER 28 O ) 0.10725 ( PROT GLY 29 N ) 0.10725 ( PROT GLY 29 H ) 0.85797E-01 ( PROT GLY 29 CA ) 0.10725 ( PROT GLY 29 C ) 0.10725 ( PROT GLY 29 O ) 0.10725 ( PROT VAL 30 N ) 0.10725 ( PROT VAL 30 H ) 0.85797E-01 ( PROT VAL 30 CA ) 0.10725 ( PROT VAL 30 CB ) 0.85797E-01 ( PROT VAL 30 CG1 ) 0.85797E-01 ( PROT VAL 30 CG2 ) 0.85797E-01 ( PROT VAL 30 C ) 0.10725 ( PROT VAL 30 O ) 0.10725 ( PROT TRP 31 N ) 0.10725 ( PROT TRP 31 H ) 0.85797E-01 ( PROT TRP 31 CA ) 0.10725 ( PROT TRP 31 CB ) 0.85797E-01 ( PROT TRP 31 CG ) 0.85797E-01 ( PROT TRP 31 CD2 ) 0.85797E-01 ( PROT TRP 31 CE2 ) 0.85797E-01 ( PROT TRP 31 CE3 ) 0.85797E-01 ( PROT TRP 31 CD1 ) 0.85797E-01 ( PROT TRP 31 NE1 ) 0.85797E-01 ( PROT TRP 31 HE1 ) 0.85797E-01 ( PROT TRP 31 CZ2 ) 0.85797E-01 ( PROT TRP 31 CZ3 ) 0.85797E-01 ( PROT TRP 31 CH2 ) 0.85797E-01 ( PROT TRP 31 C ) 0.10725 ( PROT TRP 31 OT1 ) 0.85797E-01 ( PROT TRP 31 OT2 ) 0.85797E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.62746 7.22371 -13.21503 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.00334 0.00572 -0.00488 ROTATION MATRIX 1.000000 0.000770 0.000573 -0.000770 1.000000 -0.000417 -0.000573 0.000416 1.000000 AXIS OF ROTATION IS -0.397896 -0.547663 0.736032 ANGLE IS 0.06 TOTAL SQUARE DIFF IS 297.9174 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 1.001543 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.0015" Parameter: A <- "1.0015" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.58576 7.31379 -13.46419 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.05753 -0.05824 0.02384 ROTATION MATRIX 0.999828 0.012523 0.013716 -0.012264 0.999748 -0.018785 -0.013948 0.018614 0.999729 AXIS OF ROTATION IS -0.709523 -0.524827 0.470249 ANGLE IS 1.51 CENTER OF ROTATION 14.121362 6.899898-13.030165 SHIFT IS 0.082596 TOTAL SQUARE DIFF IS 21.7457 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.837541 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.0015" RDCMND substituted energy or value "?RMS" to " 0.8375" Parameter: A <- "1.0015 0.8375" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *10800 1.0015 0.8375 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 42.67" Parameter: H <- "42.67" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -191.68121 42.66935 0.21770 ENER INTERN> 7.53522 36.67252 0.00000 22.67729 4.89703 ENER EXTERN> -162.41796 -101.04530 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -191.68" Parameter: B <- "-191.68" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -101.05" Parameter: C <- "-101.05" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -162.42" Parameter: C <- " -263.47" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -263.47" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.54" Parameter: D <- "7.54" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 36.67" Parameter: D <- " 44.21" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 22.68" Parameter: D <- " 66.89" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.90" Parameter: D <- " 71.79" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 71.79" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 10800 ENER= -191.68 GRMS= 0.22 ELEC= -101.05 VDW= -162.42 RDTITL> *EXTERNAL= -263.47 INTERNAL= 71.79 USER= 0.00 HARM= 42.67 RDTITL> *BOND= 7.54 ANGL= 36.67 DIHE= 22.68 IMPR= 4.90 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "10800" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_10800.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_10800.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 10800 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 10800 ENER= -191.68 GRMS= 0.22 ELEC= -101.05 VDW= -162.42 RDTITL> *EXTERNAL= -263.47 INTERNAL= 71.79 USER= 0.00 HARM= 42.67 RDTITL> *BOND= 7.54 ANGL= 36.67 DIHE= 22.68 IMPR= 4.90 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "10800" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_10800.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_10800.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 10800 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 10800 ENER= -191.68 GRMS= 0.22 ELEC= -101.05 VDW= -162.42 RDTITL> *EXTERNAL= -263.47 INTERNAL= 71.79 USER= 0.00 HARM= 42.67 RDTITL> *BOND= 7.54 ANGL= 36.67 DIHE= 22.68 IMPR= 4.90 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 10800 1.0015 0.8375 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "10800" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20490 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20386 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -163.49368 -28.18753 0.15567 0.02000 MINI INTERN> 7.53522 36.67252 0.00000 22.67729 4.89703 MINI EXTERN> -162.41796 -101.04530 0.00000 0.00000 0.00000 MINI CONSTR> 28.18753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -162.40386 -1.08982 2.55462 0.00360 MINI INTERN> 8.58864 37.38606 0.00000 22.96975 4.81735 MINI EXTERN> -164.45187 -100.22391 0.00000 0.00000 0.00000 MINI CONSTR> 28.51013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20374 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -161.86656 -0.53730 3.21399 0.00156 MINI INTERN> 9.46886 36.72075 0.00000 22.76731 4.91377 MINI EXTERN> -163.67939 -100.58577 0.00000 0.00000 0.00000 MINI CONSTR> 28.52791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -163.46161 1.59505 1.21214 0.00067 MINI INTERN> 7.73739 36.88137 0.00000 22.85309 4.84292 MINI EXTERN> -163.65948 -100.65773 0.00000 0.00000 0.00000 MINI CONSTR> 28.54083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20374 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -163.73500 0.27338 0.11608 0.00012 MINI INTERN> 7.58797 36.74068 0.00000 22.82516 4.86403 MINI EXTERN> -163.61929 -100.68733 0.00000 0.00000 0.00000 MINI CONSTR> 28.55379 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -163.74718 0.01218 0.15182 0.00013 MINI INTERN> 7.59614 36.72137 0.00000 22.81906 4.86446 MINI EXTERN> -163.60497 -100.71457 0.00000 0.00000 0.00000 MINI CONSTR> 28.57133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20373 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -163.75698 0.00980 0.22340 0.00013 MINI INTERN> 7.57231 36.73419 0.00000 22.81359 4.86691 MINI EXTERN> -163.60399 -100.72994 0.00000 0.00000 0.00000 MINI CONSTR> 28.58995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -163.76688 0.00990 0.22422 0.00013 MINI INTERN> 7.57352 36.72592 0.00000 22.80765 4.86728 MINI EXTERN> -163.60989 -100.73527 0.00000 0.00000 0.00000 MINI CONSTR> 28.60391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20372 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -163.77641 0.00953 0.22946 0.00014 MINI INTERN> 7.58458 36.71024 0.00000 22.80202 4.86711 MINI EXTERN> -163.62263 -100.73712 0.00000 0.00000 0.00000 MINI CONSTR> 28.61938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -163.78570 0.00928 0.23170 0.00014 MINI INTERN> 7.59403 36.69782 0.00000 22.79559 4.86691 MINI EXTERN> -163.63711 -100.73765 0.00000 0.00000 0.00000 MINI CONSTR> 28.63471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20372 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -163.80259 0.01689 0.06415 0.00006 MINI INTERN> 7.58039 36.70481 0.00000 22.78611 4.86816 MINI EXTERN> -163.63580 -100.75583 0.00000 0.00000 0.00000 MINI CONSTR> 28.64959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -163.81142 0.00884 0.05095 0.00006 MINI INTERN> 7.57894 36.70426 0.00000 22.78109 4.86836 MINI EXTERN> -163.64958 -100.75799 0.00000 0.00000 0.00000 MINI CONSTR> 28.66350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20372 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -163.82140 0.00997 0.05186 0.00007 MINI INTERN> 7.57987 36.70068 0.00000 22.77514 4.86859 MINI EXTERN> -163.66583 -100.75975 0.00000 0.00000 0.00000 MINI CONSTR> 28.67990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -163.83127 0.00987 0.08742 0.00007 MINI INTERN> 7.57843 36.69840 0.00000 22.76862 4.86930 MINI EXTERN> -163.68223 -100.76149 0.00000 0.00000 0.00000 MINI CONSTR> 28.69770 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20373 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -163.84000 0.00873 0.07479 0.00007 MINI INTERN> 7.58228 36.69329 0.00000 22.76416 4.86923 MINI EXTERN> -163.69844 -100.76224 0.00000 0.00000 0.00000 MINI CONSTR> 28.71172 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -163.84908 0.00908 0.07303 0.00007 MINI INTERN> 7.58437 36.68984 0.00000 22.75913 4.86927 MINI EXTERN> -163.71601 -100.76261 0.00000 0.00000 0.00000 MINI CONSTR> 28.72694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20372 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -163.85768 0.00860 0.08584 0.00008 MINI INTERN> 7.58438 36.68800 0.00000 22.75438 4.86954 MINI EXTERN> -163.73309 -100.76298 0.00000 0.00000 0.00000 MINI CONSTR> 28.74209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -163.86521 0.00753 0.11839 0.00008 MINI INTERN> 7.59314 36.67894 0.00000 22.74969 4.86968 MINI EXTERN> -163.74965 -100.76380 0.00000 0.00000 0.00000 MINI CONSTR> 28.75680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20371 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -163.87387 0.00866 0.12490 0.00008 MINI INTERN> 7.58605 36.68429 0.00000 22.74487 4.87009 MINI EXTERN> -163.76767 -100.76350 0.00000 0.00000 0.00000 MINI CONSTR> 28.77200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -163.88171 0.00785 0.13690 0.00009 MINI INTERN> 7.60087 36.66956 0.00000 22.74069 4.86962 MINI EXTERN> -163.78578 -100.76311 0.00000 0.00000 0.00000 MINI CONSTR> 28.78643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20370 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -163.88959 0.00788 0.14352 0.00009 MINI INTERN> 7.59564 36.67371 0.00000 22.73619 4.86983 MINI EXTERN> -163.80268 -100.76289 0.00000 0.00000 0.00000 MINI CONSTR> 28.80061 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -163.89757 0.00798 0.13578 0.00009 MINI INTERN> 7.60141 36.66689 0.00000 22.73244 4.86937 MINI EXTERN> -163.81995 -100.76164 0.00000 0.00000 0.00000 MINI CONSTR> 28.81391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20370 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -163.90573 0.00816 0.14683 0.00010 MINI INTERN> 7.59544 36.67194 0.00000 22.72766 4.86972 MINI EXTERN> -163.83813 -100.76130 0.00000 0.00000 0.00000 MINI CONSTR> 28.82895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -163.91297 0.00724 0.16659 0.00010 MINI INTERN> 7.61290 36.65504 0.00000 22.72365 4.86916 MINI EXTERN> -163.85674 -100.76037 0.00000 0.00000 0.00000 MINI CONSTR> 28.84340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20370 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -163.92074 0.00777 0.15478 0.00010 MINI INTERN> 7.60870 36.65766 0.00000 22.71984 4.86899 MINI EXTERN> -163.87260 -100.75942 0.00000 0.00000 0.00000 MINI CONSTR> 28.85611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -163.93215 0.01141 0.04709 0.00004 MINI INTERN> 7.57946 36.68146 0.00000 22.71673 4.86813 MINI EXTERN> -163.89397 -100.75400 0.00000 0.00000 0.00000 MINI CONSTR> 28.87004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20367 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -163.93620 0.00405 0.17263 0.00011 MINI INTERN> 7.61912 36.64660 0.00000 22.71148 4.86855 MINI EXTERN> -163.90957 -100.75729 0.00000 0.00000 0.00000 MINI CONSTR> 28.88491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -163.94332 0.00713 0.18605 0.00012 MINI INTERN> 7.59650 36.66817 0.00000 22.70673 4.86923 MINI EXTERN> -163.92539 -100.75725 0.00000 0.00000 0.00000 MINI CONSTR> 28.89869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20367 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -163.95536 0.01204 0.05421 0.00005 MINI INTERN> 7.57803 36.68020 0.00000 22.70476 4.86762 MINI EXTERN> -163.94648 -100.75108 0.00000 0.00000 0.00000 MINI CONSTR> 28.91159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -163.95791 0.00255 0.18442 0.00012 MINI INTERN> 7.61330 36.65065 0.00000 22.69898 4.86855 MINI EXTERN> -163.95861 -100.75592 0.00000 0.00000 0.00000 MINI CONSTR> 28.92514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20366 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -163.97079 0.01288 0.06049 0.00005 MINI INTERN> 7.57672 36.67992 0.00000 22.69669 4.86723 MINI EXTERN> -163.98158 -100.74927 0.00000 0.00000 0.00000 MINI CONSTR> 28.93951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -163.97754 0.00675 0.04504 0.00006 MINI INTERN> 7.58154 36.67450 0.00000 22.69296 4.86729 MINI EXTERN> -163.99559 -100.74945 0.00000 0.00000 0.00000 MINI CONSTR> 28.95121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20366 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -163.98555 0.00801 0.04506 0.00006 MINI INTERN> 7.58247 36.67285 0.00000 22.68870 4.86707 MINI EXTERN> -164.01368 -100.74866 0.00000 0.00000 0.00000 MINI CONSTR> 28.96570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -163.99331 0.00776 0.04825 0.00006 MINI INTERN> 7.58052 36.67405 0.00000 22.68457 4.86685 MINI EXTERN> -164.03142 -100.74777 0.00000 0.00000 0.00000 MINI CONSTR> 28.97989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20365 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -164.00069 0.00738 0.08637 0.00006 MINI INTERN> 7.57225 36.68183 0.00000 22.68072 4.86626 MINI EXTERN> -164.05083 -100.74578 0.00000 0.00000 0.00000 MINI CONSTR> 28.99487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -164.00830 0.00761 0.05626 0.00006 MINI INTERN> 7.57829 36.67498 0.00000 22.67652 4.86636 MINI EXTERN> -164.06573 -100.74620 0.00000 0.00000 0.00000 MINI CONSTR> 29.00749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20364 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -164.01513 0.00682 0.04634 0.00007 MINI INTERN> 7.58275 36.67012 0.00000 22.67267 4.86629 MINI EXTERN> -164.08057 -100.74607 0.00000 0.00000 0.00000 MINI CONSTR> 29.01969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -164.02202 0.00690 0.10352 0.00007 MINI INTERN> 7.57097 36.68169 0.00000 22.66903 4.86551 MINI EXTERN> -164.10041 -100.74377 0.00000 0.00000 0.00000 MINI CONSTR> 29.03495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20365 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -164.02986 0.00784 0.06893 0.00007 MINI INTERN> 7.57431 36.67735 0.00000 22.66455 4.86578 MINI EXTERN> -164.11489 -100.74453 0.00000 0.00000 0.00000 MINI CONSTR> 29.04758 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -164.03565 0.00579 0.10950 0.00007 MINI INTERN> 7.56589 36.68582 0.00000 22.66126 4.86529 MINI EXTERN> -164.13131 -100.74308 0.00000 0.00000 0.00000 MINI CONSTR> 29.06047 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20364 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -164.04242 0.00677 0.12252 0.00008 MINI INTERN> 7.57558 36.67629 0.00000 22.65756 4.86471 MINI EXTERN> -164.14819 -100.74217 0.00000 0.00000 0.00000 MINI CONSTR> 29.07381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -164.04886 0.00644 0.12636 0.00008 MINI INTERN> 7.56660 36.68472 0.00000 22.65380 4.86466 MINI EXTERN> -164.16314 -100.74173 0.00000 0.00000 0.00000 MINI CONSTR> 29.08623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20362 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -164.05553 0.00667 0.12013 0.00008 MINI INTERN> 7.56553 36.68521 0.00000 22.64997 4.86461 MINI EXTERN> -164.17738 -100.74166 0.00000 0.00000 0.00000 MINI CONSTR> 29.09820 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -164.06245 0.00691 0.13709 0.00009 MINI INTERN> 7.56939 36.68143 0.00000 22.64604 4.86400 MINI EXTERN> -164.19480 -100.74090 0.00000 0.00000 0.00000 MINI CONSTR> 29.11238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20362 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -164.06902 0.00657 0.13077 0.00009 MINI INTERN> 7.56274 36.68736 0.00000 22.64211 4.86411 MINI EXTERN> -164.20852 -100.74105 0.00000 0.00000 0.00000 MINI CONSTR> 29.12423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -164.07582 0.00680 0.13865 0.00009 MINI INTERN> 7.57474 36.67555 0.00000 22.63830 4.86351 MINI EXTERN> -164.22492 -100.74047 0.00000 0.00000 0.00000 MINI CONSTR> 29.13747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20361 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -164.08443 0.00861 0.04437 0.00004 MINI INTERN> 7.59232 36.65695 0.00000 22.63260 4.86454 MINI EXTERN> -164.23647 -100.74293 0.00000 0.00000 0.00000 MINI CONSTR> 29.14857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -164.08806 0.00362 0.14771 0.00010 MINI INTERN> 7.56487 36.68482 0.00000 22.63097 4.86319 MINI EXTERN> -164.25355 -100.73989 0.00000 0.00000 0.00000 MINI CONSTR> 29.16153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20361 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -164.09775 0.00969 0.04592 0.00004 MINI INTERN> 7.59397 36.65481 0.00000 22.62462 4.86413 MINI EXTERN> -164.26650 -100.74255 0.00000 0.00000 0.00000 MINI CONSTR> 29.17378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -164.10070 0.00295 0.15750 0.00011 MINI INTERN> 7.55922 36.69000 0.00000 22.62327 4.86278 MINI EXTERN> -164.28270 -100.73970 0.00000 0.00000 0.00000 MINI CONSTR> 29.18643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -164.10731 0.00661 0.16662 0.00011 MINI INTERN> 7.56819 36.68122 0.00000 22.61945 4.86214 MINI EXTERN> -164.29876 -100.73934 0.00000 0.00000 0.00000 MINI CONSTR> 29.19978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -164.11768 0.01037 0.05469 0.00005 MINI INTERN> 7.59828 36.65015 0.00000 22.61227 4.86358 MINI EXTERN> -164.31165 -100.74227 0.00000 0.00000 0.00000 MINI CONSTR> 29.21196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -164.11928 0.00160 0.17600 0.00012 MINI INTERN> 7.55527 36.69362 0.00000 22.61186 4.86194 MINI EXTERN> -164.32621 -100.73949 0.00000 0.00000 0.00000 MINI CONSTR> 29.22375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -164.13045 0.01117 0.06102 0.00005 MINI INTERN> 7.60056 36.64771 0.00000 22.60423 4.86322 MINI EXTERN> -164.34060 -100.74219 0.00000 0.00000 0.00000 MINI CONSTR> 29.23662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -164.13609 0.00564 0.04113 0.00005 MINI INTERN> 7.59354 36.65353 0.00000 22.60160 4.86270 MINI EXTERN> -164.35255 -100.74174 0.00000 0.00000 0.00000 MINI CONSTR> 29.24682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -164.14290 0.00681 0.04214 0.00006 MINI INTERN> 7.59380 36.65312 0.00000 22.59732 4.86250 MINI EXTERN> -164.36781 -100.74177 0.00000 0.00000 0.00000 MINI CONSTR> 29.25994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -164.14933 0.00643 0.08066 0.00006 MINI INTERN> 7.60659 36.64210 0.00000 22.59178 4.86277 MINI EXTERN> -164.38416 -100.74224 0.00000 0.00000 0.00000 MINI CONSTR> 29.27383 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -164.15581 0.00648 0.05144 0.00006 MINI INTERN> 7.59937 36.64777 0.00000 22.58887 4.86217 MINI EXTERN> -164.39726 -100.74187 0.00000 0.00000 0.00000 MINI CONSTR> 29.28515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -164.16158 0.00577 0.04365 0.00006 MINI INTERN> 7.59545 36.65105 0.00000 22.58558 4.86185 MINI EXTERN> -164.40971 -100.74188 0.00000 0.00000 0.00000 MINI CONSTR> 29.29608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -164.16734 0.00576 0.09528 0.00006 MINI INTERN> 7.60998 36.63898 0.00000 22.57985 4.86227 MINI EXTERN> -164.42548 -100.74246 0.00000 0.00000 0.00000 MINI CONSTR> 29.30953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -164.17403 0.00669 0.06297 0.00007 MINI INTERN> 7.60483 36.64236 0.00000 22.57712 4.86150 MINI EXTERN> -164.43870 -100.74202 0.00000 0.00000 0.00000 MINI CONSTR> 29.32090 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -164.17897 0.00495 0.10067 0.00007 MINI INTERN> 7.61541 36.63366 0.00000 22.57239 4.86172 MINI EXTERN> -164.45220 -100.74247 0.00000 0.00000 0.00000 MINI CONSTR> 29.33252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -164.18475 0.00578 0.11280 0.00007 MINI INTERN> 7.60724 36.64184 0.00000 22.56816 4.86182 MINI EXTERN> -164.46536 -100.74297 0.00000 0.00000 0.00000 MINI CONSTR> 29.34451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -164.19025 0.00549 0.11613 0.00007 MINI INTERN> 7.61646 36.63319 0.00000 22.56435 4.86155 MINI EXTERN> -164.47842 -100.74303 0.00000 0.00000 0.00000 MINI CONSTR> 29.35565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -164.19595 0.00571 0.11052 0.00008 MINI INTERN> 7.61824 36.63104 0.00000 22.56104 4.86115 MINI EXTERN> -164.49084 -100.74302 0.00000 0.00000 0.00000 MINI CONSTR> 29.36644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -164.20172 0.00576 0.12902 0.00008 MINI INTERN> 7.61340 36.63653 0.00000 22.55638 4.86132 MINI EXTERN> -164.50497 -100.74345 0.00000 0.00000 0.00000 MINI CONSTR> 29.37907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -164.20735 0.00563 0.12012 0.00008 MINI INTERN> 7.62061 36.62912 0.00000 22.55315 4.86083 MINI EXTERN> -164.51726 -100.74336 0.00000 0.00000 0.00000 MINI CONSTR> 29.38957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -164.21333 0.00598 0.12648 0.00009 MINI INTERN> 7.61807 36.63191 0.00000 22.54881 4.86082 MINI EXTERN> -164.53122 -100.74357 0.00000 0.00000 0.00000 MINI CONSTR> 29.40186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -164.22114 0.00781 0.04051 0.00004 MINI INTERN> 7.59179 36.65260 0.00000 22.54838 4.85899 MINI EXTERN> -164.54214 -100.74344 0.00000 0.00000 0.00000 MINI CONSTR> 29.41267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -164.22430 0.00316 0.13808 0.00009 MINI INTERN> 7.61763 36.63281 0.00000 22.54107 4.86053 MINI EXTERN> -164.55676 -100.74406 0.00000 0.00000 0.00000 MINI CONSTR> 29.42448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -164.22953 0.00523 0.15256 0.00010 MINI INTERN> 7.63200 36.61889 0.00000 22.53834 4.85946 MINI EXTERN> -164.57068 -100.74329 0.00000 0.00000 0.00000 MINI CONSTR> 29.43575 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -164.23494 0.00541 0.15094 0.00010 MINI INTERN> 7.62027 36.63090 0.00000 22.53338 4.86021 MINI EXTERN> -164.58189 -100.74460 0.00000 0.00000 0.00000 MINI CONSTR> 29.44679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -164.24359 0.00865 0.04652 0.00004 MINI INTERN> 7.59027 36.65355 0.00000 22.53398 4.85784 MINI EXTERN> -164.59200 -100.74466 0.00000 0.00000 0.00000 MINI CONSTR> 29.45743 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -164.24536 0.00177 0.15898 0.00011 MINI INTERN> 7.62117 36.63036 0.00000 22.52607 4.85983 MINI EXTERN> -164.60588 -100.74525 0.00000 0.00000 0.00000 MINI CONSTR> 29.46833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -164.25441 0.00905 0.05479 0.00005 MINI INTERN> 7.58723 36.65625 0.00000 22.52703 4.85724 MINI EXTERN> -164.61604 -100.74543 0.00000 0.00000 0.00000 MINI CONSTR> 29.47932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -164.25924 0.00482 0.03957 0.00005 MINI INTERN> 7.59386 36.65009 0.00000 22.52337 4.85730 MINI EXTERN> -164.62680 -100.74557 0.00000 0.00000 0.00000 MINI CONSTR> 29.48850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -164.26461 0.00538 0.04162 0.00005 MINI INTERN> 7.59253 36.65125 0.00000 22.51991 4.85700 MINI EXTERN> -164.63868 -100.74596 0.00000 0.00000 0.00000 MINI CONSTR> 29.49934 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -164.27014 0.00552 0.06671 0.00005 MINI INTERN> 7.58485 36.65833 0.00000 22.51682 4.85632 MINI EXTERN> -164.65123 -100.74656 0.00000 0.00000 0.00000 MINI CONSTR> 29.51133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -164.27503 0.00489 0.03891 0.00005 MINI INTERN> 7.59460 36.64924 0.00000 22.51284 4.85659 MINI EXTERN> -164.66181 -100.74668 0.00000 0.00000 0.00000 MINI CONSTR> 29.52020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -164.28053 0.00550 0.07908 0.00005 MINI INTERN> 7.58451 36.65856 0.00000 22.51011 4.85558 MINI EXTERN> -164.67476 -100.74737 0.00000 0.00000 0.00000 MINI CONSTR> 29.53285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -164.28609 0.00557 0.05448 0.00006 MINI INTERN> 7.58761 36.65565 0.00000 22.50581 4.85585 MINI EXTERN> -164.68616 -100.74784 0.00000 0.00000 0.00000 MINI CONSTR> 29.54299 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -164.29114 0.00504 0.06674 0.00006 MINI INTERN> 7.58515 36.65788 0.00000 22.50276 4.85534 MINI EXTERN> -164.69768 -100.74827 0.00000 0.00000 0.00000 MINI CONSTR> 29.55369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -164.29572 0.00458 0.09050 0.00006 MINI INTERN> 7.58229 36.66067 0.00000 22.50002 4.85470 MINI EXTERN> -164.70888 -100.74873 0.00000 0.00000 0.00000 MINI CONSTR> 29.56421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -164.30162 0.00590 0.05940 0.00006 MINI INTERN> 7.58663 36.65646 0.00000 22.49546 4.85503 MINI EXTERN> -164.72056 -100.74925 0.00000 0.00000 0.00000 MINI CONSTR> 29.57461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -164.30587 0.00425 0.09566 0.00007 MINI INTERN> 7.57861 36.66421 0.00000 22.49310 4.85425 MINI EXTERN> -164.73127 -100.74990 0.00000 0.00000 0.00000 MINI CONSTR> 29.58513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -164.31086 0.00499 0.10961 0.00007 MINI INTERN> 7.58764 36.65573 0.00000 22.48979 4.85363 MINI EXTERN> -164.74367 -100.75008 0.00000 0.00000 0.00000 MINI CONSTR> 29.59609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -164.31562 0.00475 0.11207 0.00007 MINI INTERN> 7.58108 36.66198 0.00000 22.48670 4.85336 MINI EXTERN> -164.75411 -100.75073 0.00000 0.00000 0.00000 MINI CONSTR> 29.60609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -164.32058 0.00496 0.10611 0.00007 MINI INTERN> 7.57709 36.66577 0.00000 22.48318 4.85336 MINI EXTERN> -164.76437 -100.75140 0.00000 0.00000 0.00000 MINI CONSTR> 29.61579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -164.32558 0.00500 0.11636 0.00008 MINI INTERN> 7.58645 36.65693 0.00000 22.47983 4.85279 MINI EXTERN> -164.77655 -100.75166 0.00000 0.00000 0.00000 MINI CONSTR> 29.62663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -164.33055 0.00498 0.11751 0.00008 MINI INTERN> 7.57334 36.66978 0.00000 22.47582 4.85313 MINI EXTERN> -164.78655 -100.75289 0.00000 0.00000 0.00000 MINI CONSTR> 29.63682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -164.33682 0.00626 0.03775 0.00003 MINI INTERN> 7.60142 36.64295 0.00000 22.47022 4.85394 MINI EXTERN> -164.79889 -100.75218 0.00000 0.00000 0.00000 MINI CONSTR> 29.64573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -164.33976 0.00295 0.12505 0.00008 MINI INTERN> 7.57664 36.66643 0.00000 22.47024 4.85199 MINI EXTERN> -164.80804 -100.75358 0.00000 0.00000 0.00000 MINI CONSTR> 29.65656 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -164.34711 0.00735 0.03760 0.00004 MINI INTERN> 7.60159 36.64282 0.00000 22.46312 4.85342 MINI EXTERN> -164.82162 -100.75329 0.00000 0.00000 0.00000 MINI CONSTR> 29.66686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -164.34958 0.00247 0.13768 0.00009 MINI INTERN> 7.58210 36.66134 0.00000 22.46355 4.85116 MINI EXTERN> -164.83060 -100.75486 0.00000 0.00000 0.00000 MINI CONSTR> 29.67773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20359 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -164.35396 0.00438 0.15471 0.00009 MINI INTERN> 7.56724 36.67666 0.00000 22.45910 4.85178 MINI EXTERN> -164.84031 -100.75636 0.00000 0.00000 0.00000 MINI CONSTR> 29.68793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -164.36180 0.00785 0.04376 0.00004 MINI INTERN> 7.60486 36.64008 0.00000 22.45251 4.85284 MINI EXTERN> -164.85454 -100.75486 0.00000 0.00000 0.00000 MINI CONSTR> 29.69731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20359 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -164.36335 0.00154 0.14812 0.00010 MINI INTERN> 7.57387 36.66950 0.00000 22.45405 4.85034 MINI EXTERN> -164.86138 -100.75702 0.00000 0.00000 0.00000 MINI CONSTR> 29.70730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -164.37188 0.00854 0.04608 0.00004 MINI INTERN> 7.60554 36.63962 0.00000 22.44533 4.85239 MINI EXTERN> -164.87698 -100.75600 0.00000 0.00000 0.00000 MINI CONSTR> 29.71822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20359 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -164.37625 0.00437 0.03672 0.00005 MINI INTERN> 7.60271 36.64179 0.00000 22.44295 4.85187 MINI EXTERN> -164.88581 -100.75677 0.00000 0.00000 0.00000 MINI CONSTR> 29.72700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -164.38111 0.00486 0.03903 0.00005 MINI INTERN> 7.60369 36.64106 0.00000 22.43932 4.85172 MINI EXTERN> -164.89671 -100.75734 0.00000 0.00000 0.00000 MINI CONSTR> 29.73715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20358 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -164.38598 0.00487 0.06461 0.00005 MINI INTERN> 7.61154 36.63484 0.00000 22.43450 4.85196 MINI EXTERN> -164.90953 -100.75745 0.00000 0.00000 0.00000 MINI CONSTR> 29.74817 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -164.38598 0.00487 0.06461 0.00006 STPD INTERN> 7.61154 36.63484 0.00000 22.43450 4.85196 STPD EXTERN> -164.90953 -100.75745 0.00000 0.00000 0.00000 STPD CONSTR> 29.74817 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20358 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20358 ATOM PAIRS WERE FOUND FOR ATOM LIST 745 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -164.38598 0.00487 0.06461 0.00000 MINI INTERN> 7.61154 36.63484 0.00000 22.43450 4.85196 MINI EXTERN> -164.90953 -100.75745 0.00000 0.00000 0.00000 MINI CONSTR> 29.74817 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -164.95565 0.56967 0.56104 0.09638 MINI INTERN> 7.55379 36.64355 0.00000 21.74937 4.81260 MINI EXTERN> -167.19163 -100.53929 0.00000 0.00000 0.00000 MINI CONSTR> 32.01597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -165.18009 0.22444 0.23458 0.08654 MINI INTERN> 7.69970 36.78754 0.00000 21.47410 4.78355 MINI EXTERN> -168.13242 -100.83375 0.00000 0.00000 0.00000 MINI CONSTR> 33.04118 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -165.20468 0.02459 0.06353 0.00655 MINI INTERN> 7.69717 36.82405 0.00000 21.45520 4.79178 MINI EXTERN> -168.20481 -100.91437 0.00000 0.00000 0.00000 MINI CONSTR> 33.14630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -165.22925 0.02457 0.18043 0.01897 MINI INTERN> 7.63683 36.76269 0.00000 21.40116 4.76425 MINI EXTERN> -168.17102 -100.83556 0.00000 0.00000 0.00000 MINI CONSTR> 33.21240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -165.31225 0.08300 0.28500 0.06603 MINI INTERN> 7.57675 36.80745 0.00000 21.33949 4.73276 MINI EXTERN> -168.27531 -100.89765 0.00000 0.00000 0.00000 MINI CONSTR> 33.40428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -165.40897 0.09672 0.26113 0.04894 MINI INTERN> 7.57512 36.82759 0.00000 21.26651 4.71091 MINI EXTERN> -168.33507 -101.07734 0.00000 0.00000 0.00000 MINI CONSTR> 33.62331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -165.48274 0.07378 0.22463 0.04010 MINI INTERN> 7.61047 36.75909 0.00000 21.19055 4.69451 MINI EXTERN> -168.46305 -101.06421 0.00000 0.00000 0.00000 MINI CONSTR> 33.78990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -165.52734 0.04460 0.15298 0.02270 MINI INTERN> 7.60635 36.68292 0.00000 21.14545 4.70818 MINI EXTERN> -168.52200 -101.03553 0.00000 0.00000 0.00000 MINI CONSTR> 33.88729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -165.56176 0.03441 0.14051 0.02016 MINI INTERN> 7.62831 36.68443 0.00000 21.07436 4.72749 MINI EXTERN> -168.49160 -101.13894 0.00000 0.00000 0.00000 MINI CONSTR> 33.95419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -165.58759 0.02583 0.13928 0.01893 MINI INTERN> 7.59798 36.67932 0.00000 21.03884 4.70443 MINI EXTERN> -168.48383 -101.12508 0.00000 0.00000 0.00000 MINI CONSTR> 34.00075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -165.61823 0.03064 0.15165 0.02225 MINI INTERN> 7.61028 36.64202 0.00000 20.95289 4.70479 MINI EXTERN> -168.42042 -101.15927 0.00000 0.00000 0.00000 MINI CONSTR> 34.05147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -165.64847 0.03024 0.14116 0.02004 MINI INTERN> 7.59405 36.66947 0.00000 20.91761 4.68448 MINI EXTERN> -168.46927 -101.13962 0.00000 0.00000 0.00000 MINI CONSTR> 34.09480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -165.68571 0.03724 0.15478 0.03052 MINI INTERN> 7.58773 36.54683 0.00000 20.86073 4.65605 MINI EXTERN> -168.45061 -101.03134 0.00000 0.00000 0.00000 MINI CONSTR> 34.14491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -165.72323 0.03752 0.14825 0.02959 MINI INTERN> 7.58757 36.45328 0.00000 20.82737 4.66080 MINI EXTERN> -168.44980 -100.99359 0.00000 0.00000 0.00000 MINI CONSTR> 34.19113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -165.75214 0.02891 0.14022 0.02529 MINI INTERN> 7.63284 36.47069 0.00000 20.81829 4.65508 MINI EXTERN> -168.40672 -101.13869 0.00000 0.00000 0.00000 MINI CONSTR> 34.21636 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -165.77389 0.02174 0.12243 0.01710 MINI INTERN> 7.60612 36.46056 0.00000 20.80438 4.66219 MINI EXTERN> -168.30766 -101.22958 0.00000 0.00000 0.00000 MINI CONSTR> 34.23010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -165.79608 0.02219 0.11650 0.02053 MINI INTERN> 7.56817 36.34347 0.00000 20.81284 4.65274 MINI EXTERN> -168.15439 -101.25675 0.00000 0.00000 0.00000 MINI CONSTR> 34.23785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -165.81286 0.01678 0.10957 0.01403 MINI INTERN> 7.57480 36.35838 0.00000 20.83537 4.68180 MINI EXTERN> -168.13072 -101.37015 0.00000 0.00000 0.00000 MINI CONSTR> 34.23766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -165.83037 0.01751 0.11155 0.01740 MINI INTERN> 7.59665 36.35387 0.00000 20.89414 4.68305 MINI EXTERN> -168.19188 -101.39810 0.00000 0.00000 0.00000 MINI CONSTR> 34.23189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -165.84403 0.01367 0.08936 0.01043 MINI INTERN> 7.60586 36.31156 0.00000 20.92835 4.68341 MINI EXTERN> -168.23107 -101.36691 0.00000 0.00000 0.00000 MINI CONSTR> 34.22476 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -165.84403 0.01367 0.08936 0.02000 CONJ INTERN> 7.60586 36.31156 0.00000 20.92835 4.68341 CONJ EXTERN> -168.23107 -101.36691 0.00000 0.00000 0.00000 CONJ CONSTR> 34.22476 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "11400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.55768E-01 ( PROT LYS 1 HT2 ) 0.55768E-01 ( PROT LYS 1 N ) 0.69710E-01 ( PROT LYS 1 HT3 ) 0.55768E-01 ( PROT LYS 1 CA ) 0.69710E-01 ( PROT LYS 1 CB ) 0.55768E-01 ( PROT LYS 1 CG ) 0.55768E-01 ( PROT LYS 1 CD ) 0.55768E-01 ( PROT LYS 1 CE ) 0.55768E-01 ( PROT LYS 1 NZ ) 0.55768E-01 ( PROT LYS 1 HZ1 ) 0.55768E-01 ( PROT LYS 1 HZ2 ) 0.55768E-01 ( PROT LYS 1 HZ3 ) 0.55768E-01 ( PROT LYS 1 C ) 0.69710E-01 ( PROT LYS 1 O ) 0.69710E-01 ( PROT MET 2 N ) 0.69710E-01 ( PROT MET 2 H ) 0.55768E-01 ( PROT MET 2 CA ) 0.69710E-01 ( PROT MET 2 CB ) 0.55768E-01 ( PROT MET 2 CG ) 0.55768E-01 ( PROT MET 2 SD ) 0.55768E-01 ( PROT MET 2 CE ) 0.55768E-01 ( PROT MET 2 C ) 0.69710E-01 ( PROT MET 2 O ) 0.69710E-01 ( PROT LYS 3 N ) 0.69710E-01 ( PROT LYS 3 H ) 0.55768E-01 ( PROT LYS 3 CA ) 0.69710E-01 ( PROT LYS 3 CB ) 0.55768E-01 ( PROT LYS 3 CG ) 0.55768E-01 ( PROT LYS 3 CD ) 0.55768E-01 ( PROT LYS 3 CE ) 0.55768E-01 ( PROT LYS 3 NZ ) 0.55768E-01 ( PROT LYS 3 HZ1 ) 0.55768E-01 ( PROT LYS 3 HZ2 ) 0.55768E-01 ( PROT LYS 3 HZ3 ) 0.55768E-01 ( PROT LYS 3 C ) 0.69710E-01 ( PROT LYS 3 O ) 0.69710E-01 ( PROT ALA 4 N ) 0.69710E-01 ( PROT ALA 4 H ) 0.55768E-01 ( PROT ALA 4 CA ) 0.69710E-01 ( PROT ALA 4 CB ) 0.55768E-01 ( PROT ALA 4 C ) 0.69710E-01 ( PROT ALA 4 O ) 0.69710E-01 ( PROT VAL 5 N ) 0.69710E-01 ( PROT VAL 5 H ) 0.55768E-01 ( PROT VAL 5 CA ) 0.69710E-01 ( PROT VAL 5 CB ) 0.55768E-01 ( PROT VAL 5 CG1 ) 0.55768E-01 ( PROT VAL 5 CG2 ) 0.55768E-01 ( PROT VAL 5 C ) 0.69710E-01 ( PROT VAL 5 O ) 0.69710E-01 ( PROT MET 6 N ) 0.69710E-01 ( PROT MET 6 H ) 0.55768E-01 ( PROT MET 6 CA ) 0.69710E-01 ( PROT MET 6 CB ) 0.55768E-01 ( PROT MET 6 CG ) 0.55768E-01 ( PROT MET 6 SD ) 0.55768E-01 ( PROT MET 6 CE ) 0.55768E-01 ( PROT MET 6 C ) 0.69710E-01 ( PROT MET 6 O ) 0.69710E-01 ( PROT ILE 7 N ) 0.69710E-01 ( PROT ILE 7 H ) 0.55768E-01 ( PROT ILE 7 CA ) 0.69710E-01 ( PROT ILE 7 CB ) 0.55768E-01 ( PROT ILE 7 CG2 ) 0.55768E-01 ( PROT ILE 7 CG1 ) 0.55768E-01 ( PROT ILE 7 CD ) 0.55768E-01 ( PROT ILE 7 C ) 0.69710E-01 ( PROT ILE 7 O ) 0.69710E-01 ( PROT GLY 8 N ) 0.69710E-01 ( PROT GLY 8 H ) 0.55768E-01 ( PROT GLY 8 CA ) 0.69710E-01 ( PROT GLY 8 C ) 0.69710E-01 ( PROT GLY 8 O ) 0.69710E-01 ( PROT ALA 9 N ) 0.69710E-01 ( PROT ALA 9 H ) 0.55768E-01 ( PROT ALA 9 CA ) 0.69710E-01 ( PROT ALA 9 CB ) 0.55768E-01 ( PROT ALA 9 C ) 0.69710E-01 ( PROT ALA 9 O ) 0.69710E-01 ( PROT CYS 10 N ) 0.69710E-01 ( PROT CYS 10 H ) 0.55768E-01 ( PROT CYS 10 CA ) 0.69710E-01 ( PROT CYS 10 CB ) 0.55768E-01 ( PROT CYS 10 SG ) 0.55768E-01 ( PROT CYS 10 C ) 0.69710E-01 ( PROT CYS 10 O ) 0.69710E-01 ( PROT PHE 11 N ) 0.69710E-01 ( PROT PHE 11 H ) 0.55768E-01 ( PROT PHE 11 CA ) 0.69710E-01 ( PROT PHE 11 CB ) 0.55768E-01 ( PROT PHE 11 CG ) 0.55768E-01 ( PROT PHE 11 CD1 ) 0.55768E-01 ( PROT PHE 11 CD2 ) 0.55768E-01 ( PROT PHE 11 CE1 ) 0.55768E-01 ( PROT PHE 11 CE2 ) 0.55768E-01 ( PROT PHE 11 CZ ) 0.55768E-01 ( PROT PHE 11 C ) 0.69710E-01 ( PROT PHE 11 O ) 0.69710E-01 ( PROT LEU 12 N ) 0.69710E-01 ( PROT LEU 12 H ) 0.55768E-01 ( PROT LEU 12 CA ) 0.69710E-01 ( PROT LEU 12 CB ) 0.55768E-01 ( PROT LEU 12 CG ) 0.55768E-01 ( PROT LEU 12 CD1 ) 0.55768E-01 ( PROT LEU 12 CD2 ) 0.55768E-01 ( PROT LEU 12 C ) 0.69710E-01 ( PROT LEU 12 O ) 0.69710E-01 ( PROT ILE 13 N ) 0.69710E-01 ( PROT ILE 13 H ) 0.55768E-01 ( PROT ILE 13 CA ) 0.69710E-01 ( PROT ILE 13 CB ) 0.55768E-01 ( PROT ILE 13 CG2 ) 0.55768E-01 ( PROT ILE 13 CG1 ) 0.55768E-01 ( PROT ILE 13 CD ) 0.55768E-01 ( PROT ILE 13 C ) 0.69710E-01 ( PROT ILE 13 O ) 0.69710E-01 ( PROT ASH 14 N ) 0.69710E-01 ( PROT ASH 14 H ) 0.55768E-01 ( PROT ASH 14 CA ) 0.69710E-01 ( PROT ASH 14 CB ) 0.55768E-01 ( PROT ASH 14 CG ) 0.55768E-01 ( PROT ASH 14 OD1 ) 0.55768E-01 ( PROT ASH 14 OD2 ) 0.55768E-01 ( PROT ASH 14 HD2 ) 0.55768E-01 ( PROT ASH 14 C ) 0.69710E-01 ( PROT ASH 14 O ) 0.69710E-01 ( PROT PHE 15 N ) 0.69710E-01 ( PROT PHE 15 H ) 0.55768E-01 ( PROT PHE 15 CA ) 0.69710E-01 ( PROT PHE 15 CB ) 0.55768E-01 ( PROT PHE 15 CG ) 0.55768E-01 ( PROT PHE 15 CD1 ) 0.55768E-01 ( PROT PHE 15 CD2 ) 0.55768E-01 ( PROT PHE 15 CE1 ) 0.55768E-01 ( PROT PHE 15 CE2 ) 0.55768E-01 ( PROT PHE 15 CZ ) 0.55768E-01 ( PROT PHE 15 C ) 0.69710E-01 ( PROT PHE 15 O ) 0.69710E-01 ( PROT MET 16 N ) 0.69710E-01 ( PROT MET 16 H ) 0.55768E-01 ( PROT MET 16 CA ) 0.69710E-01 ( PROT MET 16 CB ) 0.55768E-01 ( PROT MET 16 CG ) 0.55768E-01 ( PROT MET 16 SD ) 0.55768E-01 ( PROT MET 16 CE ) 0.55768E-01 ( PROT MET 16 C ) 0.69710E-01 ( PROT MET 16 O ) 0.69710E-01 ( PROT PHE 17 N ) 0.69710E-01 ( PROT PHE 17 H ) 0.55768E-01 ( PROT PHE 17 CA ) 0.69710E-01 ( PROT PHE 17 CB ) 0.55768E-01 ( PROT PHE 17 CG ) 0.55768E-01 ( PROT PHE 17 CD1 ) 0.55768E-01 ( PROT PHE 17 CD2 ) 0.55768E-01 ( PROT PHE 17 CE1 ) 0.55768E-01 ( PROT PHE 17 CE2 ) 0.55768E-01 ( PROT PHE 17 CZ ) 0.55768E-01 ( PROT PHE 17 C ) 0.69710E-01 ( PROT PHE 17 O ) 0.69710E-01 ( PROT PHE 18 N ) 0.69710E-01 ( PROT PHE 18 H ) 0.55768E-01 ( PROT PHE 18 CA ) 0.69710E-01 ( PROT PHE 18 CB ) 0.55768E-01 ( PROT PHE 18 CG ) 0.55768E-01 ( PROT PHE 18 CD1 ) 0.55768E-01 ( PROT PHE 18 CD2 ) 0.55768E-01 ( PROT PHE 18 CE1 ) 0.55768E-01 ( PROT PHE 18 CE2 ) 0.55768E-01 ( PROT PHE 18 CZ ) 0.55768E-01 ( PROT PHE 18 C ) 0.69710E-01 ( PROT PHE 18 O ) 0.69710E-01 ( PROT GLU 19 N ) 0.69710E-01 ( PROT GLU 19 H ) 0.55768E-01 ( PROT GLU 19 CA ) 0.69710E-01 ( PROT GLU 19 CB ) 0.55768E-01 ( PROT GLU 19 CG ) 0.55768E-01 ( PROT GLU 19 CD ) 0.55768E-01 ( PROT GLU 19 OE1 ) 0.55768E-01 ( PROT GLU 19 OE2 ) 0.55768E-01 ( PROT GLU 19 C ) 0.69710E-01 ( PROT GLU 19 O ) 0.69710E-01 ( PROT SER 20 N ) 0.69710E-01 ( PROT SER 20 H ) 0.55768E-01 ( PROT SER 20 CA ) 0.69710E-01 ( PROT SER 20 CB ) 0.55768E-01 ( PROT SER 20 OG ) 0.55768E-01 ( PROT SER 20 HG ) 0.55768E-01 ( PROT SER 20 C ) 0.69710E-01 ( PROT SER 20 O ) 0.69710E-01 ( PROT THR 21 N ) 0.69710E-01 ( PROT THR 21 H ) 0.55768E-01 ( PROT THR 21 CA ) 0.69710E-01 ( PROT THR 21 CB ) 0.55768E-01 ( PROT THR 21 OG1 ) 0.55768E-01 ( PROT THR 21 HG1 ) 0.55768E-01 ( PROT THR 21 CG2 ) 0.55768E-01 ( PROT THR 21 C ) 0.69710E-01 ( PROT THR 21 O ) 0.69710E-01 ( PROT GLY 22 N ) 0.69710E-01 ( PROT GLY 22 H ) 0.55768E-01 ( PROT GLY 22 CA ) 0.69710E-01 ( PROT GLY 22 C ) 0.69710E-01 ( PROT GLY 22 O ) 0.69710E-01 ( PROT SER 23 N ) 0.69710E-01 ( PROT SER 23 H ) 0.55768E-01 ( PROT SER 23 CA ) 0.69710E-01 ( PROT SER 23 CB ) 0.55768E-01 ( PROT SER 23 OG ) 0.55768E-01 ( PROT SER 23 HG ) 0.55768E-01 ( PROT SER 23 C ) 0.69710E-01 ( PROT SER 23 O ) 0.69710E-01 ( PROT GLN 24 N ) 0.69710E-01 ( PROT GLN 24 H ) 0.55768E-01 ( PROT GLN 24 CA ) 0.69710E-01 ( PROT GLN 24 CB ) 0.55768E-01 ( PROT GLN 24 CG ) 0.55768E-01 ( PROT GLN 24 CD ) 0.55768E-01 ( PROT GLN 24 OE1 ) 0.55768E-01 ( PROT GLN 24 NE2 ) 0.55768E-01 ( PROT GLN 24 HE21 ) 0.55768E-01 ( PROT GLN 24 HE22 ) 0.55768E-01 ( PROT GLN 24 C ) 0.69710E-01 ( PROT GLN 24 O ) 0.69710E-01 ( PROT GLU 25 N ) 0.69710E-01 ( PROT GLU 25 H ) 0.55768E-01 ( PROT GLU 25 CA ) 0.69710E-01 ( PROT GLU 25 CB ) 0.55768E-01 ( PROT GLU 25 CG ) 0.55768E-01 ( PROT GLU 25 CD ) 0.55768E-01 ( PROT GLU 25 OE1 ) 0.55768E-01 ( PROT GLU 25 OE2 ) 0.55768E-01 ( PROT GLU 25 C ) 0.69710E-01 ( PROT GLU 25 O ) 0.69710E-01 ( PROT GLN 26 N ) 0.69710E-01 ( PROT GLN 26 H ) 0.55768E-01 ( PROT GLN 26 CA ) 0.69710E-01 ( PROT GLN 26 CB ) 0.55768E-01 ( PROT GLN 26 CG ) 0.55768E-01 ( PROT GLN 26 CD ) 0.55768E-01 ( PROT GLN 26 OE1 ) 0.55768E-01 ( PROT GLN 26 NE2 ) 0.55768E-01 ( PROT GLN 26 HE21 ) 0.55768E-01 ( PROT GLN 26 HE22 ) 0.55768E-01 ( PROT GLN 26 C ) 0.69710E-01 ( PROT GLN 26 O ) 0.69710E-01 ( PROT LYS 27 N ) 0.69710E-01 ( PROT LYS 27 H ) 0.55768E-01 ( PROT LYS 27 CA ) 0.69710E-01 ( PROT LYS 27 CB ) 0.55768E-01 ( PROT LYS 27 CG ) 0.55768E-01 ( PROT LYS 27 CD ) 0.55768E-01 ( PROT LYS 27 CE ) 0.55768E-01 ( PROT LYS 27 NZ ) 0.55768E-01 ( PROT LYS 27 HZ1 ) 0.55768E-01 ( PROT LYS 27 HZ2 ) 0.55768E-01 ( PROT LYS 27 HZ3 ) 0.55768E-01 ( PROT LYS 27 C ) 0.69710E-01 ( PROT LYS 27 O ) 0.69710E-01 ( PROT SER 28 N ) 0.69710E-01 ( PROT SER 28 H ) 0.55768E-01 ( PROT SER 28 CA ) 0.69710E-01 ( PROT SER 28 CB ) 0.55768E-01 ( PROT SER 28 OG ) 0.55768E-01 ( PROT SER 28 HG ) 0.55768E-01 ( PROT SER 28 C ) 0.69710E-01 ( PROT SER 28 O ) 0.69710E-01 ( PROT GLY 29 N ) 0.69710E-01 ( PROT GLY 29 H ) 0.55768E-01 ( PROT GLY 29 CA ) 0.69710E-01 ( PROT GLY 29 C ) 0.69710E-01 ( PROT GLY 29 O ) 0.69710E-01 ( PROT VAL 30 N ) 0.69710E-01 ( PROT VAL 30 H ) 0.55768E-01 ( PROT VAL 30 CA ) 0.69710E-01 ( PROT VAL 30 CB ) 0.55768E-01 ( PROT VAL 30 CG1 ) 0.55768E-01 ( PROT VAL 30 CG2 ) 0.55768E-01 ( PROT VAL 30 C ) 0.69710E-01 ( PROT VAL 30 O ) 0.69710E-01 ( PROT TRP 31 N ) 0.69710E-01 ( PROT TRP 31 H ) 0.55768E-01 ( PROT TRP 31 CA ) 0.69710E-01 ( PROT TRP 31 CB ) 0.55768E-01 ( PROT TRP 31 CG ) 0.55768E-01 ( PROT TRP 31 CD2 ) 0.55768E-01 ( PROT TRP 31 CE2 ) 0.55768E-01 ( PROT TRP 31 CE3 ) 0.55768E-01 ( PROT TRP 31 CD1 ) 0.55768E-01 ( PROT TRP 31 NE1 ) 0.55768E-01 ( PROT TRP 31 HE1 ) 0.55768E-01 ( PROT TRP 31 CZ2 ) 0.55768E-01 ( PROT TRP 31 CZ3 ) 0.55768E-01 ( PROT TRP 31 CH2 ) 0.55768E-01 ( PROT TRP 31 C ) 0.69710E-01 ( PROT TRP 31 OT1 ) 0.55768E-01 ( PROT TRP 31 OT2 ) 0.55768E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.61340 7.21266 -13.20953 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.01740 0.01677 -0.01039 ROTATION MATRIX 0.999991 -0.002746 -0.003231 0.002761 0.999985 0.004650 0.003218 -0.004659 0.999984 AXIS OF ROTATION IS 0.739199 0.512161 -0.437352 ANGLE IS 0.36 TOTAL SQUARE DIFF IS 367.8528 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 1.112907 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.1129" Parameter: A <- "1.1129" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.59404 7.31301 -13.47529 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.06581 -0.05746 0.03494 ROTATION MATRIX 0.999905 0.009131 0.010358 -0.008968 0.999836 -0.015751 -0.010500 0.015657 0.999822 AXIS OF ROTATION IS -0.750993 -0.498721 0.432767 ANGLE IS 1.20 CENTER OF ROTATION 13.917052 7.176988-12.963824 SHIFT IS 0.093198 TOTAL SQUARE DIFF IS 27.4579 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.941137 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.1129" RDCMND substituted energy or value "?RMS" to " 0.9411" Parameter: A <- "1.1129 0.9411" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *11400 1.1129 0.9411 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 34.22" Parameter: H <- "34.22" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -200.06879 34.22476 0.14485 ENER INTERN> 7.60586 36.31156 0.00000 20.92835 4.68341 ENER EXTERN> -168.23107 -101.36691 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -200.07" Parameter: B <- "-200.07" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -101.37" Parameter: C <- "-101.37" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -168.23" Parameter: C <- " -269.60" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -269.60" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.61" Parameter: D <- "7.61" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 36.31" Parameter: D <- " 43.92" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 20.93" Parameter: D <- " 64.85" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.68" Parameter: D <- " 69.53" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 69.53" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 11400 ENER= -200.07 GRMS= 0.14 ELEC= -101.37 VDW= -168.23 RDTITL> *EXTERNAL= -269.60 INTERNAL= 69.53 USER= 0.00 HARM= 34.22 RDTITL> *BOND= 7.61 ANGL= 36.31 DIHE= 20.93 IMPR= 4.68 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/10/16 22:28:33 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 297 atoms. *** LEVEL 2 WARNING *** BOMLEV IS 0 CHARMM> close unit 10 VCLOSE: Closing unit 10 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> minimize sd nstep @2 nprint @6 - CHARMM> ihbfrq 0 inbfrq 10 tolgrd 0.01 Parameter: 2 -> "500" Parameter: 6 -> "5" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20358 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20253 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -177.57465 -22.49415 0.09653 0.02000 MINI INTERN> 7.60586 36.31156 0.00000 20.92835 4.68341 MINI EXTERN> -168.23107 -101.36691 0.00000 0.00000 0.00000 MINI CONSTR> 22.49415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -176.58136 -0.99328 2.29762 0.00360 MINI INTERN> 8.13083 37.44922 0.00000 21.12269 4.74263 MINI EXTERN> -170.22363 -100.54404 0.00000 0.00000 0.00000 MINI CONSTR> 22.74094 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20250 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -175.86539 -0.71598 3.06080 0.00156 MINI INTERN> 9.57285 36.40573 0.00000 21.01005 4.64958 MINI EXTERN> -169.53277 -100.71698 0.00000 0.00000 0.00000 MINI CONSTR> 22.74616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -177.47449 1.60911 1.06261 0.00067 MINI INTERN> 7.84828 36.55408 0.00000 20.99345 4.66717 MINI EXTERN> -169.46977 -100.81890 0.00000 0.00000 0.00000 MINI CONSTR> 22.75119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20249 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -177.70066 0.22617 0.10978 0.00012 MINI INTERN> 7.70705 36.44603 0.00000 20.98446 4.66650 MINI EXTERN> -169.40180 -100.85893 0.00000 0.00000 0.00000 MINI CONSTR> 22.75603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -177.70693 0.00627 0.14923 0.00013 MINI INTERN> 7.69252 36.43817 0.00000 20.97233 4.66937 MINI EXTERN> -169.33745 -100.90491 0.00000 0.00000 0.00000 MINI CONSTR> 22.76303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20249 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -177.71773 0.01080 0.04520 0.00005 MINI INTERN> 7.69075 36.41745 0.00000 20.96122 4.67107 MINI EXTERN> -169.29080 -100.93789 0.00000 0.00000 0.00000 MINI CONSTR> 22.77047 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -177.72301 0.00528 0.04417 0.00006 MINI INTERN> 7.68637 36.40932 0.00000 20.95326 4.67230 MINI EXTERN> -169.26150 -100.96017 0.00000 0.00000 0.00000 MINI CONSTR> 22.77742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20248 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -177.72714 0.00413 0.08473 0.00006 MINI INTERN> 7.68827 36.39812 0.00000 20.94601 4.67313 MINI EXTERN> -169.24023 -100.97728 0.00000 0.00000 0.00000 MINI CONSTR> 22.78485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -177.73153 0.00439 0.07523 0.00006 MINI INTERN> 7.68080 36.39785 0.00000 20.93993 4.67398 MINI EXTERN> -169.22624 -100.98968 0.00000 0.00000 0.00000 MINI CONSTR> 22.79183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20249 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -177.73500 0.00346 0.10100 0.00006 MINI INTERN> 7.66436 36.40976 0.00000 20.93425 4.67518 MINI EXTERN> -169.21620 -101.00105 0.00000 0.00000 0.00000 MINI CONSTR> 22.79871 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -177.73914 0.00414 0.08644 0.00006 MINI INTERN> 7.67845 36.39159 0.00000 20.92987 4.67509 MINI EXTERN> -169.21213 -101.00769 0.00000 0.00000 0.00000 MINI CONSTR> 22.80568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20248 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -177.74226 0.00313 0.11009 0.00007 MINI INTERN> 7.65949 36.40618 0.00000 20.92542 4.67585 MINI EXTERN> -169.20921 -101.01234 0.00000 0.00000 0.00000 MINI CONSTR> 22.81235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -177.74687 0.00461 0.03436 0.00003 MINI INTERN> 7.66632 36.39614 0.00000 20.92241 4.67578 MINI EXTERN> -169.21028 -101.01536 0.00000 0.00000 0.00000 MINI CONSTR> 22.81812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20248 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -177.74796 0.00109 0.12860 0.00007 MINI INTERN> 7.65218 36.40943 0.00000 20.91870 4.67640 MINI EXTERN> -169.21034 -101.01858 0.00000 0.00000 0.00000 MINI CONSTR> 22.82426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -177.75306 0.00510 0.04215 0.00003 MINI INTERN> 7.66730 36.39166 0.00000 20.91600 4.67601 MINI EXTERN> -169.21401 -101.02038 0.00000 0.00000 0.00000 MINI CONSTR> 22.83034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20248 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -177.75563 0.00257 0.03037 0.00003 MINI INTERN> 7.66450 36.39311 0.00000 20.91356 4.67614 MINI EXTERN> -169.21652 -101.02166 0.00000 0.00000 0.00000 MINI CONSTR> 22.83523 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -177.75870 0.00307 0.03041 0.00003 MINI INTERN> 7.66410 36.39242 0.00000 20.91067 4.67621 MINI EXTERN> -169.22063 -101.02286 0.00000 0.00000 0.00000 MINI CONSTR> 22.84141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20248 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -177.76174 0.00304 0.03124 0.00003 MINI INTERN> 7.66407 36.39161 0.00000 20.90789 4.67623 MINI EXTERN> -169.22548 -101.02364 0.00000 0.00000 0.00000 MINI CONSTR> 22.84759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -177.76457 0.00283 0.06243 0.00004 MINI INTERN> 7.66905 36.38669 0.00000 20.90512 4.67612 MINI EXTERN> -169.23165 -101.02412 0.00000 0.00000 0.00000 MINI CONSTR> 22.85422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20247 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -177.76752 0.00295 0.03834 0.00004 MINI INTERN> 7.66526 36.38948 0.00000 20.90277 4.67619 MINI EXTERN> -169.23664 -101.02422 0.00000 0.00000 0.00000 MINI CONSTR> 22.85963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -177.77051 0.00298 0.03877 0.00004 MINI INTERN> 7.66522 36.38921 0.00000 20.90022 4.67617 MINI EXTERN> -169.24301 -101.02416 0.00000 0.00000 0.00000 MINI CONSTR> 22.86585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20246 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -177.77347 0.00296 0.04232 0.00004 MINI INTERN> 7.66575 36.38857 0.00000 20.89771 4.67611 MINI EXTERN> -169.24985 -101.02390 0.00000 0.00000 0.00000 MINI CONSTR> 22.87213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -177.77583 0.00236 0.07469 0.00004 MINI INTERN> 7.67033 36.38480 0.00000 20.89541 4.67598 MINI EXTERN> -169.25697 -101.02357 0.00000 0.00000 0.00000 MINI CONSTR> 22.87820 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20246 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -177.77863 0.00279 0.07553 0.00004 MINI INTERN> 7.67043 36.38476 0.00000 20.89311 4.67592 MINI EXTERN> -169.26394 -101.02305 0.00000 0.00000 0.00000 MINI CONSTR> 22.88415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -177.78144 0.00281 0.07849 0.00004 MINI INTERN> 7.67076 36.38467 0.00000 20.89078 4.67586 MINI EXTERN> -169.27131 -101.02246 0.00000 0.00000 0.00000 MINI CONSTR> 22.89026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20246 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -177.78418 0.00274 0.08453 0.00005 MINI INTERN> 7.67146 36.38442 0.00000 20.88846 4.67580 MINI EXTERN> -169.27890 -101.02183 0.00000 0.00000 0.00000 MINI CONSTR> 22.89641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -177.78675 0.00257 0.09291 0.00005 MINI INTERN> 7.67257 36.38388 0.00000 20.88626 4.67572 MINI EXTERN> -169.28643 -101.02109 0.00000 0.00000 0.00000 MINI CONSTR> 22.90236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20245 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -177.78924 0.00250 0.08774 0.00005 MINI INTERN> 7.67232 36.38399 0.00000 20.88440 4.67560 MINI EXTERN> -169.29301 -101.02001 0.00000 0.00000 0.00000 MINI CONSTR> 22.90746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -177.79191 0.00266 0.09199 0.00005 MINI INTERN> 7.67280 36.38407 0.00000 20.88220 4.67553 MINI EXTERN> -169.30076 -101.01920 0.00000 0.00000 0.00000 MINI CONSTR> 22.91345 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20245 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -177.79464 0.00273 0.09489 0.00005 MINI INTERN> 7.67293 36.38456 0.00000 20.87996 4.67547 MINI EXTERN> -169.30869 -101.01842 0.00000 0.00000 0.00000 MINI CONSTR> 22.91955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -177.79740 0.00276 0.09532 0.00006 MINI INTERN> 7.67272 36.38533 0.00000 20.87774 4.67542 MINI EXTERN> -169.31664 -101.01759 0.00000 0.00000 0.00000 MINI CONSTR> 22.92560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20245 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -177.80093 0.00353 0.03073 0.00002 MINI INTERN> 7.66311 36.39189 0.00000 20.87591 4.67516 MINI EXTERN> -169.32352 -101.01433 0.00000 0.00000 0.00000 MINI CONSTR> 22.93086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -177.80210 0.00117 0.10548 0.00006 MINI INTERN> 7.67451 36.38461 0.00000 20.87386 4.67519 MINI EXTERN> -169.33137 -101.01542 0.00000 0.00000 0.00000 MINI CONSTR> 22.93651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20244 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -177.80470 0.00259 0.10877 0.00006 MINI INTERN> 7.67446 36.38549 0.00000 20.87170 4.67516 MINI EXTERN> -169.33929 -101.01465 0.00000 0.00000 0.00000 MINI CONSTR> 22.94245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -177.80727 0.00257 0.11343 0.00006 MINI INTERN> 7.67419 36.38680 0.00000 20.86949 4.67516 MINI EXTERN> -169.34730 -101.01408 0.00000 0.00000 0.00000 MINI CONSTR> 22.94846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20244 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -177.81146 0.00419 0.03469 0.00003 MINI INTERN> 7.66460 36.39151 0.00000 20.86774 4.67453 MINI EXTERN> -169.35537 -101.00864 0.00000 0.00000 0.00000 MINI CONSTR> 22.95418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -177.81370 0.00224 0.02811 0.00003 MINI INTERN> 7.66533 36.39157 0.00000 20.86599 4.67450 MINI EXTERN> -169.36195 -101.00817 0.00000 0.00000 0.00000 MINI CONSTR> 22.95903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20244 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -177.81449 0.00079 0.12535 0.00007 MINI INTERN> 7.67368 36.39004 0.00000 20.86332 4.67510 MINI EXTERN> -169.37017 -101.01189 0.00000 0.00000 0.00000 MINI CONSTR> 22.96543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -177.81900 0.00451 0.04470 0.00003 MINI INTERN> 7.66604 36.39072 0.00000 20.86188 4.67395 MINI EXTERN> -169.37913 -101.00368 0.00000 0.00000 0.00000 MINI CONSTR> 22.97124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20243 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -177.82120 0.00220 0.02777 0.00003 MINI INTERN> 7.66652 36.39159 0.00000 20.86013 4.67408 MINI EXTERN> -169.38515 -101.00418 0.00000 0.00000 0.00000 MINI CONSTR> 22.97581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -177.82389 0.00268 0.02861 0.00003 MINI INTERN> 7.66706 36.39137 0.00000 20.85804 4.67389 MINI EXTERN> -169.39361 -101.00250 0.00000 0.00000 0.00000 MINI CONSTR> 22.98186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20243 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -177.82641 0.00252 0.05674 0.00003 MINI INTERN> 7.66886 36.38844 0.00000 20.85609 4.67325 MINI EXTERN> -169.40324 -100.99815 0.00000 0.00000 0.00000 MINI CONSTR> 22.98833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -177.82901 0.00260 0.03553 0.00004 MINI INTERN> 7.66865 36.39003 0.00000 20.85408 4.67341 MINI EXTERN> -169.41018 -100.99859 0.00000 0.00000 0.00000 MINI CONSTR> 22.99358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20243 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -177.83165 0.00264 0.03570 0.00004 MINI INTERN> 7.66945 36.38962 0.00000 20.85201 4.67323 MINI EXTERN> -169.41860 -100.99694 0.00000 0.00000 0.00000 MINI CONSTR> 22.99958 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -177.83430 0.00265 0.03799 0.00004 MINI INTERN> 7.67030 36.38903 0.00000 20.84993 4.67301 MINI EXTERN> -169.42720 -100.99504 0.00000 0.00000 0.00000 MINI CONSTR> 23.00567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20243 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -177.83685 0.00255 0.04493 0.00004 MINI INTERN> 7.67153 36.38780 0.00000 20.84793 4.67271 MINI EXTERN> -169.43582 -100.99267 0.00000 0.00000 0.00000 MINI CONSTR> 23.01168 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -177.83884 0.00199 0.06882 0.00004 MINI INTERN> 7.67430 36.38426 0.00000 20.84630 4.67217 MINI EXTERN> -169.44409 -100.98891 0.00000 0.00000 0.00000 MINI CONSTR> 23.01713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20241 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -177.84138 0.00254 0.07042 0.00004 MINI INTERN> 7.67508 36.38372 0.00000 20.84428 4.67197 MINI EXTERN> -169.45245 -100.98700 0.00000 0.00000 0.00000 MINI CONSTR> 23.02303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -177.84391 0.00253 0.07415 0.00004 MINI INTERN> 7.67605 36.38286 0.00000 20.84224 4.67173 MINI EXTERN> -169.46105 -100.98477 0.00000 0.00000 0.00000 MINI CONSTR> 23.02904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20241 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -177.84633 0.00242 0.08126 0.00005 MINI INTERN> 7.67734 36.38152 0.00000 20.84026 4.67144 MINI EXTERN> -169.46967 -100.98221 0.00000 0.00000 0.00000 MINI CONSTR> 23.03500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -177.84863 0.00230 0.07853 0.00005 MINI INTERN> 7.67735 36.38202 0.00000 20.83843 4.67135 MINI EXTERN> -169.47680 -100.98114 0.00000 0.00000 0.00000 MINI CONSTR> 23.04018 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20241 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -177.85098 0.00235 0.08293 0.00005 MINI INTERN> 7.67830 36.38115 0.00000 20.83650 4.67111 MINI EXTERN> -169.48495 -100.97896 0.00000 0.00000 0.00000 MINI CONSTR> 23.04587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -177.85340 0.00242 0.08621 0.00005 MINI INTERN> 7.67918 36.38035 0.00000 20.83452 4.67089 MINI EXTERN> -169.49329 -100.97674 0.00000 0.00000 0.00000 MINI CONSTR> 23.05170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20241 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -177.85586 0.00247 0.08767 0.00005 MINI INTERN> 7.67985 36.37982 0.00000 20.83251 4.67070 MINI EXTERN> -169.50160 -100.97470 0.00000 0.00000 0.00000 MINI CONSTR> 23.05755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -177.85906 0.00320 0.02788 0.00002 MINI INTERN> 7.67031 36.39592 0.00000 20.82972 4.67209 MINI EXTERN> -169.50535 -100.98446 0.00000 0.00000 0.00000 MINI CONSTR> 23.06273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20241 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -177.86018 0.00112 0.09629 0.00006 MINI INTERN> 7.68159 36.37832 0.00000 20.82890 4.67026 MINI EXTERN> -169.51675 -100.97070 0.00000 0.00000 0.00000 MINI CONSTR> 23.06819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -177.86251 0.00234 0.09895 0.00006 MINI INTERN> 7.68240 36.37756 0.00000 20.82697 4.67005 MINI EXTERN> -169.52484 -100.96852 0.00000 0.00000 0.00000 MINI CONSTR> 23.07387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20241 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -177.86487 0.00236 0.10258 0.00006 MINI INTERN> 7.68340 36.37648 0.00000 20.82500 4.66982 MINI EXTERN> -169.53320 -100.96604 0.00000 0.00000 0.00000 MINI CONSTR> 23.07967 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -177.86717 0.00230 0.10806 0.00006 MINI INTERN> 7.68465 36.37503 0.00000 20.82304 4.66956 MINI EXTERN> -169.54168 -100.96327 0.00000 0.00000 0.00000 MINI CONSTR> 23.08551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20240 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -177.87097 0.00380 0.03536 0.00003 MINI INTERN> 7.67056 36.39915 0.00000 20.81972 4.67153 MINI EXTERN> -169.54375 -100.97918 0.00000 0.00000 0.00000 MINI CONSTR> 23.09100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -177.87293 0.00196 0.02585 0.00003 MINI INTERN> 7.67259 36.39577 0.00000 20.81836 4.67111 MINI EXTERN> -169.55070 -100.97552 0.00000 0.00000 0.00000 MINI CONSTR> 23.09546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20239 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -177.87529 0.00236 0.02573 0.00003 MINI INTERN> 7.67292 36.39584 0.00000 20.81641 4.67095 MINI EXTERN> -169.55842 -100.97405 0.00000 0.00000 0.00000 MINI CONSTR> 23.10107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -177.87767 0.00238 0.02594 0.00003 MINI INTERN> 7.67313 36.39614 0.00000 20.81441 4.67080 MINI EXTERN> -169.56619 -100.97273 0.00000 0.00000 0.00000 MINI CONSTR> 23.10676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20237 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -177.88010 0.00242 0.04836 0.00003 MINI INTERN> 7.67003 36.40321 0.00000 20.81182 4.67116 MINI EXTERN> -169.57329 -100.97618 0.00000 0.00000 0.00000 MINI CONSTR> 23.11316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -177.88232 0.00222 0.03335 0.00003 MINI INTERN> 7.67222 36.39937 0.00000 20.81031 4.67071 MINI EXTERN> -169.58095 -100.97204 0.00000 0.00000 0.00000 MINI CONSTR> 23.11806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20237 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -177.88461 0.00229 0.03261 0.00003 MINI INTERN> 7.67261 36.39930 0.00000 20.80840 4.67053 MINI EXTERN> -169.58851 -100.97051 0.00000 0.00000 0.00000 MINI CONSTR> 23.12357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -177.88695 0.00234 0.03320 0.00004 MINI INTERN> 7.67279 36.39964 0.00000 20.80642 4.67038 MINI EXTERN> -169.59616 -100.96924 0.00000 0.00000 0.00000 MINI CONSTR> 23.12922 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20237 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -177.88927 0.00232 0.03659 0.00004 MINI INTERN> 7.67258 36.40082 0.00000 20.80438 4.67028 MINI EXTERN> -169.60366 -100.96857 0.00000 0.00000 0.00000 MINI CONSTR> 23.13491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -177.89111 0.00184 0.06413 0.00004 MINI INTERN> 7.66958 36.40798 0.00000 20.80213 4.67062 MINI EXTERN> -169.60935 -100.97243 0.00000 0.00000 0.00000 MINI CONSTR> 23.14035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20237 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -177.89331 0.00220 0.06489 0.00004 MINI INTERN> 7.66976 36.40833 0.00000 20.80025 4.67046 MINI EXTERN> -169.61659 -100.97124 0.00000 0.00000 0.00000 MINI CONSTR> 23.14573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -177.89552 0.00221 0.06736 0.00004 MINI INTERN> 7.66977 36.40906 0.00000 20.79832 4.67031 MINI EXTERN> -169.62392 -100.97030 0.00000 0.00000 0.00000 MINI CONSTR> 23.15124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20237 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -177.89769 0.00217 0.07234 0.00004 MINI INTERN> 7.66955 36.41033 0.00000 20.79635 4.67018 MINI EXTERN> -169.63116 -100.96972 0.00000 0.00000 0.00000 MINI CONSTR> 23.15678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -177.89973 0.00204 0.07936 0.00004 MINI INTERN> 7.66916 36.41201 0.00000 20.79441 4.67010 MINI EXTERN> -169.63806 -100.96950 0.00000 0.00000 0.00000 MINI CONSTR> 23.16216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20237 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -177.90171 0.00198 0.07509 0.00005 MINI INTERN> 7.66982 36.41110 0.00000 20.79282 4.66991 MINI EXTERN> -169.64455 -100.96760 0.00000 0.00000 0.00000 MINI CONSTR> 23.16678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -177.90382 0.00211 0.07875 0.00005 MINI INTERN> 7.66983 36.41186 0.00000 20.79093 4.66976 MINI EXTERN> -169.65169 -100.96669 0.00000 0.00000 0.00000 MINI CONSTR> 23.17217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20237 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -177.90599 0.00217 0.08137 0.00005 MINI INTERN> 7.67011 36.41207 0.00000 20.78903 4.66954 MINI EXTERN> -169.65913 -100.96529 0.00000 0.00000 0.00000 MINI CONSTR> 23.17767 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -177.90820 0.00221 0.08224 0.00005 MINI INTERN> 7.67073 36.41151 0.00000 20.78717 4.66928 MINI EXTERN> -169.66679 -100.96328 0.00000 0.00000 0.00000 MINI CONSTR> 23.18319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20237 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -177.91107 0.00286 0.02591 0.00002 MINI INTERN> 7.67958 36.39319 0.00000 20.78609 4.66822 MINI EXTERN> -169.67773 -100.94849 0.00000 0.00000 0.00000 MINI CONSTR> 23.18807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -177.91208 0.00101 0.08976 0.00005 MINI INTERN> 7.67098 36.41248 0.00000 20.78363 4.66898 MINI EXTERN> -169.68021 -100.96119 0.00000 0.00000 0.00000 MINI CONSTR> 23.19327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20236 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -177.91417 0.00209 0.09189 0.00006 MINI INTERN> 7.67176 36.41158 0.00000 20.78184 4.66870 MINI EXTERN> -169.68773 -100.95892 0.00000 0.00000 0.00000 MINI CONSTR> 23.19861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -177.91628 0.00211 0.09478 0.00006 MINI INTERN> 7.67291 36.40994 0.00000 20.78004 4.66837 MINI EXTERN> -169.69566 -100.95596 0.00000 0.00000 0.00000 MINI CONSTR> 23.20409 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20236 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -177.91836 0.00208 0.09918 0.00006 MINI INTERN> 7.67417 36.40812 0.00000 20.77822 4.66803 MINI EXTERN> -169.70370 -100.95280 0.00000 0.00000 0.00000 MINI CONSTR> 23.20961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -177.92177 0.00341 0.03146 0.00003 MINI INTERN> 7.68127 36.39302 0.00000 20.77663 4.66746 MINI EXTERN> -169.71368 -100.94133 0.00000 0.00000 0.00000 MINI CONSTR> 23.21487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20236 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -177.92356 0.00179 0.02418 0.00003 MINI INTERN> 7.68063 36.39449 0.00000 20.77508 4.66736 MINI EXTERN> -169.71924 -100.94108 0.00000 0.00000 0.00000 MINI CONSTR> 23.21920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -177.92569 0.00212 0.02395 0.00003 MINI INTERN> 7.68085 36.39461 0.00000 20.77320 4.66720 MINI EXTERN> -169.72634 -100.93974 0.00000 0.00000 0.00000 MINI CONSTR> 23.22453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20236 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -177.92786 0.00217 0.02391 0.00003 MINI INTERN> 7.68112 36.39465 0.00000 20.77127 4.66704 MINI EXTERN> -169.73363 -100.93831 0.00000 0.00000 0.00000 MINI CONSTR> 23.23000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -177.93004 0.00218 0.02425 0.00003 MINI INTERN> 7.68146 36.39458 0.00000 20.76932 4.66687 MINI EXTERN> -169.74098 -100.93680 0.00000 0.00000 0.00000 MINI CONSTR> 23.23551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20236 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -177.93217 0.00213 0.04795 0.00003 MINI INTERN> 7.68321 36.39265 0.00000 20.76718 4.66670 MINI EXTERN> -169.74916 -100.93434 0.00000 0.00000 0.00000 MINI CONSTR> 23.24157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -177.93423 0.00206 0.03095 0.00003 MINI INTERN> 7.68251 36.39387 0.00000 20.76552 4.66655 MINI EXTERN> -169.75532 -100.93363 0.00000 0.00000 0.00000 MINI CONSTR> 23.24627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20236 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -177.93633 0.00210 0.03099 0.00003 MINI INTERN> 7.68277 36.39391 0.00000 20.76364 4.66639 MINI EXTERN> -169.76237 -100.93226 0.00000 0.00000 0.00000 MINI CONSTR> 23.25160 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -177.93843 0.00211 0.03299 0.00004 MINI INTERN> 7.68315 36.39379 0.00000 20.76173 4.66623 MINI EXTERN> -169.76954 -100.93080 0.00000 0.00000 0.00000 MINI CONSTR> 23.25701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20236 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -177.94046 0.00203 0.03905 0.00004 MINI INTERN> 7.68373 36.39343 0.00000 20.75985 4.66607 MINI EXTERN> -169.77661 -100.92929 0.00000 0.00000 0.00000 MINI CONSTR> 23.26235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -177.94205 0.00159 0.05983 0.00004 MINI INTERN> 7.68500 36.39233 0.00000 20.75814 4.66594 MINI EXTERN> -169.78303 -100.92765 0.00000 0.00000 0.00000 MINI CONSTR> 23.26722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20236 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -177.94407 0.00202 0.06117 0.00004 MINI INTERN> 7.68529 36.39236 0.00000 20.75630 4.66578 MINI EXTERN> -169.78992 -100.92635 0.00000 0.00000 0.00000 MINI CONSTR> 23.27246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -177.94609 0.00202 0.06429 0.00004 MINI INTERN> 7.68567 36.39234 0.00000 20.75443 4.66563 MINI EXTERN> -169.79692 -100.92504 0.00000 0.00000 0.00000 MINI CONSTR> 23.27780 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20234 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -177.94803 0.00194 0.07025 0.00004 MINI INTERN> 7.68618 36.39221 0.00000 20.75258 4.66547 MINI EXTERN> -169.80386 -100.92371 0.00000 0.00000 0.00000 MINI CONSTR> 23.28311 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -177.94987 0.00185 0.06800 0.00004 MINI INTERN> 7.68630 36.39227 0.00000 20.75093 4.66532 MINI EXTERN> -169.80997 -100.92248 0.00000 0.00000 0.00000 MINI CONSTR> 23.28774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20233 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -177.95175 0.00188 0.07192 0.00005 MINI INTERN> 7.68671 36.39220 0.00000 20.74916 4.66517 MINI EXTERN> -169.81658 -100.92121 0.00000 0.00000 0.00000 MINI CONSTR> 23.29281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -177.95369 0.00194 0.07496 0.00005 MINI INTERN> 7.68706 36.39222 0.00000 20.74734 4.66502 MINI EXTERN> -169.82336 -100.91997 0.00000 0.00000 0.00000 MINI CONSTR> 23.29801 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20233 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -177.95568 0.00198 0.07667 0.00005 MINI INTERN> 7.68733 36.39231 0.00000 20.74551 4.66486 MINI EXTERN> -169.83019 -100.91875 0.00000 0.00000 0.00000 MINI CONSTR> 23.30326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -177.95568 0.00198 0.07667 0.00006 STPD INTERN> 7.68733 36.39231 0.00000 20.74551 4.66486 STPD EXTERN> -169.83019 -100.91875 0.00000 0.00000 0.00000 STPD CONSTR> 23.30326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep @7 nprint 5 - CHARMM> inbfrq 10 tolgrd 0.01 Parameter: 7 -> "100" NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20233 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20233 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -177.95568 0.00198 0.07667 0.00000 MINI INTERN> 7.68733 36.39231 0.00000 20.74551 4.66486 MINI EXTERN> -169.83019 -100.91875 0.00000 0.00000 0.00000 MINI CONSTR> 23.30326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -178.30532 0.34965 0.05032 0.02278 MINI INTERN> 7.79720 36.42941 0.00000 20.15899 4.61838 MINI EXTERN> -172.10852 -100.34349 0.00000 0.00000 0.00000 MINI CONSTR> 25.14271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -178.31245 0.00712 0.07772 0.00719 MINI INTERN> 7.79333 36.46888 0.00000 20.14834 4.60798 MINI EXTERN> -172.10120 -100.39953 0.00000 0.00000 0.00000 MINI CONSTR> 25.16975 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -178.37558 0.06313 0.14872 0.10011 MINI INTERN> 7.68698 36.13481 0.00000 20.08529 4.56721 MINI EXTERN> -172.02421 -100.20821 0.00000 0.00000 0.00000 MINI CONSTR> 25.38254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -178.42479 0.04921 0.13054 0.04920 MINI INTERN> 7.72744 36.07854 0.00000 20.04625 4.57415 MINI EXTERN> -172.24476 -100.15582 0.00000 0.00000 0.00000 MINI CONSTR> 25.54941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -178.45328 0.02849 0.07952 0.02164 MINI INTERN> 7.75805 36.13276 0.00000 19.95643 4.56481 MINI EXTERN> -172.31823 -100.19230 0.00000 0.00000 0.00000 MINI CONSTR> 25.64519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -178.46595 0.01267 0.06035 0.01610 MINI INTERN> 7.76399 36.12981 0.00000 19.88816 4.55996 MINI EXTERN> -172.26879 -100.22455 0.00000 0.00000 0.00000 MINI CONSTR> 25.68547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -178.47832 0.01237 0.07179 0.01683 MINI INTERN> 7.74853 36.11980 0.00000 19.81608 4.55447 MINI EXTERN> -172.22016 -100.21912 0.00000 0.00000 0.00000 MINI CONSTR> 25.72209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -178.49096 0.01264 0.07186 0.01234 MINI INTERN> 7.75200 36.10430 0.00000 19.77337 4.56286 MINI EXTERN> -172.27740 -100.16509 0.00000 0.00000 0.00000 MINI CONSTR> 25.75901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -178.50765 0.01670 0.06688 0.01996 MINI INTERN> 7.77715 36.02687 0.00000 19.73840 4.54323 MINI EXTERN> -172.32952 -100.06837 0.00000 0.00000 0.00000 MINI CONSTR> 25.80459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -178.52219 0.01454 0.07459 0.02167 MINI INTERN> 7.75122 36.07068 0.00000 19.66625 4.54022 MINI EXTERN> -172.31703 -100.07324 0.00000 0.00000 0.00000 MINI CONSTR> 25.83970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -178.53589 0.01370 0.07557 0.01925 MINI INTERN> 7.76348 36.01295 0.00000 19.60938 4.55891 MINI EXTERN> -172.16698 -100.18085 0.00000 0.00000 0.00000 MINI CONSTR> 25.86722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -178.54733 0.01143 0.06137 0.01664 MINI INTERN> 7.72290 36.04333 0.00000 19.56277 4.55271 MINI EXTERN> -172.12599 -100.19059 0.00000 0.00000 0.00000 MINI CONSTR> 25.88756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -178.55742 0.01010 0.06016 0.01738 MINI INTERN> 7.75824 36.07787 0.00000 19.58993 4.56660 MINI EXTERN> -172.22074 -100.23215 0.00000 0.00000 0.00000 MINI CONSTR> 25.90284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -178.56531 0.00789 0.05634 0.01145 MINI INTERN> 7.78560 36.03591 0.00000 19.61051 4.56142 MINI EXTERN> -172.34521 -100.12287 0.00000 0.00000 0.00000 MINI CONSTR> 25.90933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -178.57287 0.00756 0.04827 0.01323 MINI INTERN> 7.77448 36.04528 0.00000 19.63280 4.55423 MINI EXTERN> -172.40281 -100.08370 0.00000 0.00000 0.00000 MINI CONSTR> 25.90685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -178.58067 0.00780 0.05010 0.01404 MINI INTERN> 7.77151 36.03270 0.00000 19.62976 4.54689 MINI EXTERN> -172.29148 -100.16516 0.00000 0.00000 0.00000 MINI CONSTR> 25.89510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -178.58838 0.00770 0.05350 0.01552 MINI INTERN> 7.74707 36.01884 0.00000 19.60202 4.54518 MINI EXTERN> -172.20343 -100.17534 0.00000 0.00000 0.00000 MINI CONSTR> 25.87728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -178.59502 0.00664 0.04304 0.01402 MINI INTERN> 7.75546 36.03522 0.00000 19.58439 4.53575 MINI EXTERN> -172.15017 -100.21459 0.00000 0.00000 0.00000 MINI CONSTR> 25.85893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -178.60146 0.00644 0.05014 0.01403 MINI INTERN> 7.73707 36.02173 0.00000 19.58288 4.53561 MINI EXTERN> -172.12408 -100.19558 0.00000 0.00000 0.00000 MINI CONSTR> 25.84091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -178.60784 0.00638 0.04754 0.01356 MINI INTERN> 7.73241 36.04234 0.00000 19.57927 4.54027 MINI EXTERN> -172.15269 -100.17217 0.00000 0.00000 0.00000 MINI CONSTR> 25.82273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -178.60784 0.00638 0.04754 0.02000 CONJ INTERN> 7.73241 36.04234 0.00000 19.57927 4.54027 CONJ EXTERN> -172.15269 -100.17217 0.00000 0.00000 0.00000 CONJ CONSTR> 25.82273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "12000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.36249E-01 ( PROT LYS 1 HT2 ) 0.36249E-01 ( PROT LYS 1 N ) 0.45311E-01 ( PROT LYS 1 HT3 ) 0.36249E-01 ( PROT LYS 1 CA ) 0.45311E-01 ( PROT LYS 1 CB ) 0.36249E-01 ( PROT LYS 1 CG ) 0.36249E-01 ( PROT LYS 1 CD ) 0.36249E-01 ( PROT LYS 1 CE ) 0.36249E-01 ( PROT LYS 1 NZ ) 0.36249E-01 ( PROT LYS 1 HZ1 ) 0.36249E-01 ( PROT LYS 1 HZ2 ) 0.36249E-01 ( PROT LYS 1 HZ3 ) 0.36249E-01 ( PROT LYS 1 C ) 0.45311E-01 ( PROT LYS 1 O ) 0.45311E-01 ( PROT MET 2 N ) 0.45311E-01 ( PROT MET 2 H ) 0.36249E-01 ( PROT MET 2 CA ) 0.45311E-01 ( PROT MET 2 CB ) 0.36249E-01 ( PROT MET 2 CG ) 0.36249E-01 ( PROT MET 2 SD ) 0.36249E-01 ( PROT MET 2 CE ) 0.36249E-01 ( PROT MET 2 C ) 0.45311E-01 ( PROT MET 2 O ) 0.45311E-01 ( PROT LYS 3 N ) 0.45311E-01 ( PROT LYS 3 H ) 0.36249E-01 ( PROT LYS 3 CA ) 0.45311E-01 ( PROT LYS 3 CB ) 0.36249E-01 ( PROT LYS 3 CG ) 0.36249E-01 ( PROT LYS 3 CD ) 0.36249E-01 ( PROT LYS 3 CE ) 0.36249E-01 ( PROT LYS 3 NZ ) 0.36249E-01 ( PROT LYS 3 HZ1 ) 0.36249E-01 ( PROT LYS 3 HZ2 ) 0.36249E-01 ( PROT LYS 3 HZ3 ) 0.36249E-01 ( PROT LYS 3 C ) 0.45311E-01 ( PROT LYS 3 O ) 0.45311E-01 ( PROT ALA 4 N ) 0.45311E-01 ( PROT ALA 4 H ) 0.36249E-01 ( PROT ALA 4 CA ) 0.45311E-01 ( PROT ALA 4 CB ) 0.36249E-01 ( PROT ALA 4 C ) 0.45311E-01 ( PROT ALA 4 O ) 0.45311E-01 ( PROT VAL 5 N ) 0.45311E-01 ( PROT VAL 5 H ) 0.36249E-01 ( PROT VAL 5 CA ) 0.45311E-01 ( PROT VAL 5 CB ) 0.36249E-01 ( PROT VAL 5 CG1 ) 0.36249E-01 ( PROT VAL 5 CG2 ) 0.36249E-01 ( PROT VAL 5 C ) 0.45311E-01 ( PROT VAL 5 O ) 0.45311E-01 ( PROT MET 6 N ) 0.45311E-01 ( PROT MET 6 H ) 0.36249E-01 ( PROT MET 6 CA ) 0.45311E-01 ( PROT MET 6 CB ) 0.36249E-01 ( PROT MET 6 CG ) 0.36249E-01 ( PROT MET 6 SD ) 0.36249E-01 ( PROT MET 6 CE ) 0.36249E-01 ( PROT MET 6 C ) 0.45311E-01 ( PROT MET 6 O ) 0.45311E-01 ( PROT ILE 7 N ) 0.45311E-01 ( PROT ILE 7 H ) 0.36249E-01 ( PROT ILE 7 CA ) 0.45311E-01 ( PROT ILE 7 CB ) 0.36249E-01 ( PROT ILE 7 CG2 ) 0.36249E-01 ( PROT ILE 7 CG1 ) 0.36249E-01 ( PROT ILE 7 CD ) 0.36249E-01 ( PROT ILE 7 C ) 0.45311E-01 ( PROT ILE 7 O ) 0.45311E-01 ( PROT GLY 8 N ) 0.45311E-01 ( PROT GLY 8 H ) 0.36249E-01 ( PROT GLY 8 CA ) 0.45311E-01 ( PROT GLY 8 C ) 0.45311E-01 ( PROT GLY 8 O ) 0.45311E-01 ( PROT ALA 9 N ) 0.45311E-01 ( PROT ALA 9 H ) 0.36249E-01 ( PROT ALA 9 CA ) 0.45311E-01 ( PROT ALA 9 CB ) 0.36249E-01 ( PROT ALA 9 C ) 0.45311E-01 ( PROT ALA 9 O ) 0.45311E-01 ( PROT CYS 10 N ) 0.45311E-01 ( PROT CYS 10 H ) 0.36249E-01 ( PROT CYS 10 CA ) 0.45311E-01 ( PROT CYS 10 CB ) 0.36249E-01 ( PROT CYS 10 SG ) 0.36249E-01 ( PROT CYS 10 C ) 0.45311E-01 ( PROT CYS 10 O ) 0.45311E-01 ( PROT PHE 11 N ) 0.45311E-01 ( PROT PHE 11 H ) 0.36249E-01 ( PROT PHE 11 CA ) 0.45311E-01 ( PROT PHE 11 CB ) 0.36249E-01 ( PROT PHE 11 CG ) 0.36249E-01 ( PROT PHE 11 CD1 ) 0.36249E-01 ( PROT PHE 11 CD2 ) 0.36249E-01 ( PROT PHE 11 CE1 ) 0.36249E-01 ( PROT PHE 11 CE2 ) 0.36249E-01 ( PROT PHE 11 CZ ) 0.36249E-01 ( PROT PHE 11 C ) 0.45311E-01 ( PROT PHE 11 O ) 0.45311E-01 ( PROT LEU 12 N ) 0.45311E-01 ( PROT LEU 12 H ) 0.36249E-01 ( PROT LEU 12 CA ) 0.45311E-01 ( PROT LEU 12 CB ) 0.36249E-01 ( PROT LEU 12 CG ) 0.36249E-01 ( PROT LEU 12 CD1 ) 0.36249E-01 ( PROT LEU 12 CD2 ) 0.36249E-01 ( PROT LEU 12 C ) 0.45311E-01 ( PROT LEU 12 O ) 0.45311E-01 ( PROT ILE 13 N ) 0.45311E-01 ( PROT ILE 13 H ) 0.36249E-01 ( PROT ILE 13 CA ) 0.45311E-01 ( PROT ILE 13 CB ) 0.36249E-01 ( PROT ILE 13 CG2 ) 0.36249E-01 ( PROT ILE 13 CG1 ) 0.36249E-01 ( PROT ILE 13 CD ) 0.36249E-01 ( PROT ILE 13 C ) 0.45311E-01 ( PROT ILE 13 O ) 0.45311E-01 ( PROT ASH 14 N ) 0.45311E-01 ( PROT ASH 14 H ) 0.36249E-01 ( PROT ASH 14 CA ) 0.45311E-01 ( PROT ASH 14 CB ) 0.36249E-01 ( PROT ASH 14 CG ) 0.36249E-01 ( PROT ASH 14 OD1 ) 0.36249E-01 ( PROT ASH 14 OD2 ) 0.36249E-01 ( PROT ASH 14 HD2 ) 0.36249E-01 ( PROT ASH 14 C ) 0.45311E-01 ( PROT ASH 14 O ) 0.45311E-01 ( PROT PHE 15 N ) 0.45311E-01 ( PROT PHE 15 H ) 0.36249E-01 ( PROT PHE 15 CA ) 0.45311E-01 ( PROT PHE 15 CB ) 0.36249E-01 ( PROT PHE 15 CG ) 0.36249E-01 ( PROT PHE 15 CD1 ) 0.36249E-01 ( PROT PHE 15 CD2 ) 0.36249E-01 ( PROT PHE 15 CE1 ) 0.36249E-01 ( PROT PHE 15 CE2 ) 0.36249E-01 ( PROT PHE 15 CZ ) 0.36249E-01 ( PROT PHE 15 C ) 0.45311E-01 ( PROT PHE 15 O ) 0.45311E-01 ( PROT MET 16 N ) 0.45311E-01 ( PROT MET 16 H ) 0.36249E-01 ( PROT MET 16 CA ) 0.45311E-01 ( PROT MET 16 CB ) 0.36249E-01 ( PROT MET 16 CG ) 0.36249E-01 ( PROT MET 16 SD ) 0.36249E-01 ( PROT MET 16 CE ) 0.36249E-01 ( PROT MET 16 C ) 0.45311E-01 ( PROT MET 16 O ) 0.45311E-01 ( PROT PHE 17 N ) 0.45311E-01 ( PROT PHE 17 H ) 0.36249E-01 ( PROT PHE 17 CA ) 0.45311E-01 ( PROT PHE 17 CB ) 0.36249E-01 ( PROT PHE 17 CG ) 0.36249E-01 ( PROT PHE 17 CD1 ) 0.36249E-01 ( PROT PHE 17 CD2 ) 0.36249E-01 ( PROT PHE 17 CE1 ) 0.36249E-01 ( PROT PHE 17 CE2 ) 0.36249E-01 ( PROT PHE 17 CZ ) 0.36249E-01 ( PROT PHE 17 C ) 0.45311E-01 ( PROT PHE 17 O ) 0.45311E-01 ( PROT PHE 18 N ) 0.45311E-01 ( PROT PHE 18 H ) 0.36249E-01 ( PROT PHE 18 CA ) 0.45311E-01 ( PROT PHE 18 CB ) 0.36249E-01 ( PROT PHE 18 CG ) 0.36249E-01 ( PROT PHE 18 CD1 ) 0.36249E-01 ( PROT PHE 18 CD2 ) 0.36249E-01 ( PROT PHE 18 CE1 ) 0.36249E-01 ( PROT PHE 18 CE2 ) 0.36249E-01 ( PROT PHE 18 CZ ) 0.36249E-01 ( PROT PHE 18 C ) 0.45311E-01 ( PROT PHE 18 O ) 0.45311E-01 ( PROT GLU 19 N ) 0.45311E-01 ( PROT GLU 19 H ) 0.36249E-01 ( PROT GLU 19 CA ) 0.45311E-01 ( PROT GLU 19 CB ) 0.36249E-01 ( PROT GLU 19 CG ) 0.36249E-01 ( PROT GLU 19 CD ) 0.36249E-01 ( PROT GLU 19 OE1 ) 0.36249E-01 ( PROT GLU 19 OE2 ) 0.36249E-01 ( PROT GLU 19 C ) 0.45311E-01 ( PROT GLU 19 O ) 0.45311E-01 ( PROT SER 20 N ) 0.45311E-01 ( PROT SER 20 H ) 0.36249E-01 ( PROT SER 20 CA ) 0.45311E-01 ( PROT SER 20 CB ) 0.36249E-01 ( PROT SER 20 OG ) 0.36249E-01 ( PROT SER 20 HG ) 0.36249E-01 ( PROT SER 20 C ) 0.45311E-01 ( PROT SER 20 O ) 0.45311E-01 ( PROT THR 21 N ) 0.45311E-01 ( PROT THR 21 H ) 0.36249E-01 ( PROT THR 21 CA ) 0.45311E-01 ( PROT THR 21 CB ) 0.36249E-01 ( PROT THR 21 OG1 ) 0.36249E-01 ( PROT THR 21 HG1 ) 0.36249E-01 ( PROT THR 21 CG2 ) 0.36249E-01 ( PROT THR 21 C ) 0.45311E-01 ( PROT THR 21 O ) 0.45311E-01 ( PROT GLY 22 N ) 0.45311E-01 ( PROT GLY 22 H ) 0.36249E-01 ( PROT GLY 22 CA ) 0.45311E-01 ( PROT GLY 22 C ) 0.45311E-01 ( PROT GLY 22 O ) 0.45311E-01 ( PROT SER 23 N ) 0.45311E-01 ( PROT SER 23 H ) 0.36249E-01 ( PROT SER 23 CA ) 0.45311E-01 ( PROT SER 23 CB ) 0.36249E-01 ( PROT SER 23 OG ) 0.36249E-01 ( PROT SER 23 HG ) 0.36249E-01 ( PROT SER 23 C ) 0.45311E-01 ( PROT SER 23 O ) 0.45311E-01 ( PROT GLN 24 N ) 0.45311E-01 ( PROT GLN 24 H ) 0.36249E-01 ( PROT GLN 24 CA ) 0.45311E-01 ( PROT GLN 24 CB ) 0.36249E-01 ( PROT GLN 24 CG ) 0.36249E-01 ( PROT GLN 24 CD ) 0.36249E-01 ( PROT GLN 24 OE1 ) 0.36249E-01 ( PROT GLN 24 NE2 ) 0.36249E-01 ( PROT GLN 24 HE21 ) 0.36249E-01 ( PROT GLN 24 HE22 ) 0.36249E-01 ( PROT GLN 24 C ) 0.45311E-01 ( PROT GLN 24 O ) 0.45311E-01 ( PROT GLU 25 N ) 0.45311E-01 ( PROT GLU 25 H ) 0.36249E-01 ( PROT GLU 25 CA ) 0.45311E-01 ( PROT GLU 25 CB ) 0.36249E-01 ( PROT GLU 25 CG ) 0.36249E-01 ( PROT GLU 25 CD ) 0.36249E-01 ( PROT GLU 25 OE1 ) 0.36249E-01 ( PROT GLU 25 OE2 ) 0.36249E-01 ( PROT GLU 25 C ) 0.45311E-01 ( PROT GLU 25 O ) 0.45311E-01 ( PROT GLN 26 N ) 0.45311E-01 ( PROT GLN 26 H ) 0.36249E-01 ( PROT GLN 26 CA ) 0.45311E-01 ( PROT GLN 26 CB ) 0.36249E-01 ( PROT GLN 26 CG ) 0.36249E-01 ( PROT GLN 26 CD ) 0.36249E-01 ( PROT GLN 26 OE1 ) 0.36249E-01 ( PROT GLN 26 NE2 ) 0.36249E-01 ( PROT GLN 26 HE21 ) 0.36249E-01 ( PROT GLN 26 HE22 ) 0.36249E-01 ( PROT GLN 26 C ) 0.45311E-01 ( PROT GLN 26 O ) 0.45311E-01 ( PROT LYS 27 N ) 0.45311E-01 ( PROT LYS 27 H ) 0.36249E-01 ( PROT LYS 27 CA ) 0.45311E-01 ( PROT LYS 27 CB ) 0.36249E-01 ( PROT LYS 27 CG ) 0.36249E-01 ( PROT LYS 27 CD ) 0.36249E-01 ( PROT LYS 27 CE ) 0.36249E-01 ( PROT LYS 27 NZ ) 0.36249E-01 ( PROT LYS 27 HZ1 ) 0.36249E-01 ( PROT LYS 27 HZ2 ) 0.36249E-01 ( PROT LYS 27 HZ3 ) 0.36249E-01 ( PROT LYS 27 C ) 0.45311E-01 ( PROT LYS 27 O ) 0.45311E-01 ( PROT SER 28 N ) 0.45311E-01 ( PROT SER 28 H ) 0.36249E-01 ( PROT SER 28 CA ) 0.45311E-01 ( PROT SER 28 CB ) 0.36249E-01 ( PROT SER 28 OG ) 0.36249E-01 ( PROT SER 28 HG ) 0.36249E-01 ( PROT SER 28 C ) 0.45311E-01 ( PROT SER 28 O ) 0.45311E-01 ( PROT GLY 29 N ) 0.45311E-01 ( PROT GLY 29 H ) 0.36249E-01 ( PROT GLY 29 CA ) 0.45311E-01 ( PROT GLY 29 C ) 0.45311E-01 ( PROT GLY 29 O ) 0.45311E-01 ( PROT VAL 30 N ) 0.45311E-01 ( PROT VAL 30 H ) 0.36249E-01 ( PROT VAL 30 CA ) 0.45311E-01 ( PROT VAL 30 CB ) 0.36249E-01 ( PROT VAL 30 CG1 ) 0.36249E-01 ( PROT VAL 30 CG2 ) 0.36249E-01 ( PROT VAL 30 C ) 0.45311E-01 ( PROT VAL 30 O ) 0.45311E-01 ( PROT TRP 31 N ) 0.45311E-01 ( PROT TRP 31 H ) 0.36249E-01 ( PROT TRP 31 CA ) 0.45311E-01 ( PROT TRP 31 CB ) 0.36249E-01 ( PROT TRP 31 CG ) 0.36249E-01 ( PROT TRP 31 CD2 ) 0.36249E-01 ( PROT TRP 31 CE2 ) 0.36249E-01 ( PROT TRP 31 CE3 ) 0.36249E-01 ( PROT TRP 31 CD1 ) 0.36249E-01 ( PROT TRP 31 NE1 ) 0.36249E-01 ( PROT TRP 31 HE1 ) 0.36249E-01 ( PROT TRP 31 CZ2 ) 0.36249E-01 ( PROT TRP 31 CZ3 ) 0.36249E-01 ( PROT TRP 31 CH2 ) 0.36249E-01 ( PROT TRP 31 C ) 0.45311E-01 ( PROT TRP 31 OT1 ) 0.36249E-01 ( PROT TRP 31 OT2 ) 0.36249E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.60740 7.20935 -13.20475 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.02340 0.02008 -0.01517 ROTATION MATRIX 0.999993 -0.002346 -0.002914 0.002359 0.999986 0.004735 0.002903 -0.004742 0.999985 AXIS OF ROTATION IS 0.784891 0.481759 -0.389685 ANGLE IS 0.35 TOTAL SQUARE DIFF IS 427.3787 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 1.199577 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.1996" Parameter: A <- "1.1996" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.59444 7.31892 -13.48523 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.06621 -0.06337 0.04487 ROTATION MATRIX 0.999966 0.005131 0.006451 -0.005052 0.999911 -0.012313 -0.006513 0.012280 0.999903 AXIS OF ROTATION IS -0.830648 -0.437865 0.343946 ANGLE IS 0.85 TOTAL SQUARE DIFF IS 32.1793 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 1.018843 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.1996" RDCMND substituted energy or value "?RMS" to " 1.0188" Parameter: A <- "1.1996 1.0188" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *12000 1.1996 1.0188 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 25.82" Parameter: H <- "25.82" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -204.43057 25.82273 0.09618 ENER INTERN> 7.73241 36.04234 0.00000 19.57927 4.54027 ENER EXTERN> -172.15269 -100.17217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -204.43" Parameter: B <- "-204.43" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -100.17" Parameter: C <- "-100.17" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -172.15" Parameter: C <- " -272.32" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -272.32" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.73" Parameter: D <- "7.73" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 36.04" Parameter: D <- " 43.77" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 19.58" Parameter: D <- " 63.35" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.54" Parameter: D <- " 67.89" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 67.89" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 12000 ENER= -204.43 GRMS= 0.10 ELEC= -100.17 VDW= -172.15 RDTITL> *EXTERNAL= -272.32 INTERNAL= 67.89 USER= 0.00 HARM= 25.82 RDTITL> *BOND= 7.73 ANGL= 36.04 DIHE= 19.58 IMPR= 4.54 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "12000" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_12000.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_12000.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 12000 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 12000 ENER= -204.43 GRMS= 0.10 ELEC= -100.17 VDW= -172.15 RDTITL> *EXTERNAL= -272.32 INTERNAL= 67.89 USER= 0.00 HARM= 25.82 RDTITL> *BOND= 7.73 ANGL= 36.04 DIHE= 19.58 IMPR= 4.54 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "12000" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_12000.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_12000.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 12000 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 12000 ENER= -204.43 GRMS= 0.10 ELEC= -100.17 VDW= -172.15 RDTITL> *EXTERNAL= -272.32 INTERNAL= 67.89 USER= 0.00 HARM= 25.82 RDTITL> *BOND= 7.73 ANGL= 36.04 DIHE= 19.58 IMPR= 4.54 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 12000 1.1996 1.0188 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "12000" and "12000". IF test evaluated as false. Skipping command CHARMM> CHARMM> ! now do a minimization without any constraint CHARMM> cons harm clear CHARMM> ! check that constraint==0 CHARMM> scalar cons show ( PROT LYS 1 HT1 ) 0.0000 ( PROT LYS 1 HT2 ) 0.0000 ( PROT LYS 1 N ) 0.0000 ( PROT LYS 1 HT3 ) 0.0000 ( PROT LYS 1 CA ) 0.0000 ( PROT LYS 1 CB ) 0.0000 ( PROT LYS 1 CG ) 0.0000 ( PROT LYS 1 CD ) 0.0000 ( PROT LYS 1 CE ) 0.0000 ( PROT LYS 1 NZ ) 0.0000 ( PROT LYS 1 HZ1 ) 0.0000 ( PROT LYS 1 HZ2 ) 0.0000 ( PROT LYS 1 HZ3 ) 0.0000 ( PROT LYS 1 C ) 0.0000 ( PROT LYS 1 O ) 0.0000 ( PROT MET 2 N ) 0.0000 ( PROT MET 2 H ) 0.0000 ( PROT MET 2 CA ) 0.0000 ( PROT MET 2 CB ) 0.0000 ( PROT MET 2 CG ) 0.0000 ( PROT MET 2 SD ) 0.0000 ( PROT MET 2 CE ) 0.0000 ( PROT MET 2 C ) 0.0000 ( PROT MET 2 O ) 0.0000 ( PROT LYS 3 N ) 0.0000 ( PROT LYS 3 H ) 0.0000 ( PROT LYS 3 CA ) 0.0000 ( PROT LYS 3 CB ) 0.0000 ( PROT LYS 3 CG ) 0.0000 ( PROT LYS 3 CD ) 0.0000 ( PROT LYS 3 CE ) 0.0000 ( PROT LYS 3 NZ ) 0.0000 ( PROT LYS 3 HZ1 ) 0.0000 ( PROT LYS 3 HZ2 ) 0.0000 ( PROT LYS 3 HZ3 ) 0.0000 ( PROT LYS 3 C ) 0.0000 ( PROT LYS 3 O ) 0.0000 ( PROT ALA 4 N ) 0.0000 ( PROT ALA 4 H ) 0.0000 ( PROT ALA 4 CA ) 0.0000 ( PROT ALA 4 CB ) 0.0000 ( PROT ALA 4 C ) 0.0000 ( PROT ALA 4 O ) 0.0000 ( PROT VAL 5 N ) 0.0000 ( PROT VAL 5 H ) 0.0000 ( PROT VAL 5 CA ) 0.0000 ( PROT VAL 5 CB ) 0.0000 ( PROT VAL 5 CG1 ) 0.0000 ( PROT VAL 5 CG2 ) 0.0000 ( PROT VAL 5 C ) 0.0000 ( PROT VAL 5 O ) 0.0000 ( PROT MET 6 N ) 0.0000 ( PROT MET 6 H ) 0.0000 ( PROT MET 6 CA ) 0.0000 ( PROT MET 6 CB ) 0.0000 ( PROT MET 6 CG ) 0.0000 ( PROT MET 6 SD ) 0.0000 ( PROT MET 6 CE ) 0.0000 ( PROT MET 6 C ) 0.0000 ( PROT MET 6 O ) 0.0000 ( PROT ILE 7 N ) 0.0000 ( PROT ILE 7 H ) 0.0000 ( PROT ILE 7 CA ) 0.0000 ( PROT ILE 7 CB ) 0.0000 ( PROT ILE 7 CG2 ) 0.0000 ( PROT ILE 7 CG1 ) 0.0000 ( PROT ILE 7 CD ) 0.0000 ( PROT ILE 7 C ) 0.0000 ( PROT ILE 7 O ) 0.0000 ( PROT GLY 8 N ) 0.0000 ( PROT GLY 8 H ) 0.0000 ( PROT GLY 8 CA ) 0.0000 ( PROT GLY 8 C ) 0.0000 ( PROT GLY 8 O ) 0.0000 ( PROT ALA 9 N ) 0.0000 ( PROT ALA 9 H ) 0.0000 ( PROT ALA 9 CA ) 0.0000 ( PROT ALA 9 CB ) 0.0000 ( PROT ALA 9 C ) 0.0000 ( PROT ALA 9 O ) 0.0000 ( PROT CYS 10 N ) 0.0000 ( PROT CYS 10 H ) 0.0000 ( PROT CYS 10 CA ) 0.0000 ( PROT CYS 10 CB ) 0.0000 ( PROT CYS 10 SG ) 0.0000 ( PROT CYS 10 C ) 0.0000 ( PROT CYS 10 O ) 0.0000 ( PROT PHE 11 N ) 0.0000 ( PROT PHE 11 H ) 0.0000 ( PROT PHE 11 CA ) 0.0000 ( PROT PHE 11 CB ) 0.0000 ( PROT PHE 11 CG ) 0.0000 ( PROT PHE 11 CD1 ) 0.0000 ( PROT PHE 11 CD2 ) 0.0000 ( PROT PHE 11 CE1 ) 0.0000 ( PROT PHE 11 CE2 ) 0.0000 ( PROT PHE 11 CZ ) 0.0000 ( PROT PHE 11 C ) 0.0000 ( PROT PHE 11 O ) 0.0000 ( PROT LEU 12 N ) 0.0000 ( PROT LEU 12 H ) 0.0000 ( PROT LEU 12 CA ) 0.0000 ( PROT LEU 12 CB ) 0.0000 ( PROT LEU 12 CG ) 0.0000 ( PROT LEU 12 CD1 ) 0.0000 ( PROT LEU 12 CD2 ) 0.0000 ( PROT LEU 12 C ) 0.0000 ( PROT LEU 12 O ) 0.0000 ( PROT ILE 13 N ) 0.0000 ( PROT ILE 13 H ) 0.0000 ( PROT ILE 13 CA ) 0.0000 ( PROT ILE 13 CB ) 0.0000 ( PROT ILE 13 CG2 ) 0.0000 ( PROT ILE 13 CG1 ) 0.0000 ( PROT ILE 13 CD ) 0.0000 ( PROT ILE 13 C ) 0.0000 ( PROT ILE 13 O ) 0.0000 ( PROT ASH 14 N ) 0.0000 ( PROT ASH 14 H ) 0.0000 ( PROT ASH 14 CA ) 0.0000 ( PROT ASH 14 CB ) 0.0000 ( PROT ASH 14 CG ) 0.0000 ( PROT ASH 14 OD1 ) 0.0000 ( PROT ASH 14 OD2 ) 0.0000 ( PROT ASH 14 HD2 ) 0.0000 ( PROT ASH 14 C ) 0.0000 ( PROT ASH 14 O ) 0.0000 ( PROT PHE 15 N ) 0.0000 ( PROT PHE 15 H ) 0.0000 ( PROT PHE 15 CA ) 0.0000 ( PROT PHE 15 CB ) 0.0000 ( PROT PHE 15 CG ) 0.0000 ( PROT PHE 15 CD1 ) 0.0000 ( PROT PHE 15 CD2 ) 0.0000 ( PROT PHE 15 CE1 ) 0.0000 ( PROT PHE 15 CE2 ) 0.0000 ( PROT PHE 15 CZ ) 0.0000 ( PROT PHE 15 C ) 0.0000 ( PROT PHE 15 O ) 0.0000 ( PROT MET 16 N ) 0.0000 ( PROT MET 16 H ) 0.0000 ( PROT MET 16 CA ) 0.0000 ( PROT MET 16 CB ) 0.0000 ( PROT MET 16 CG ) 0.0000 ( PROT MET 16 SD ) 0.0000 ( PROT MET 16 CE ) 0.0000 ( PROT MET 16 C ) 0.0000 ( PROT MET 16 O ) 0.0000 ( PROT PHE 17 N ) 0.0000 ( PROT PHE 17 H ) 0.0000 ( PROT PHE 17 CA ) 0.0000 ( PROT PHE 17 CB ) 0.0000 ( PROT PHE 17 CG ) 0.0000 ( PROT PHE 17 CD1 ) 0.0000 ( PROT PHE 17 CD2 ) 0.0000 ( PROT PHE 17 CE1 ) 0.0000 ( PROT PHE 17 CE2 ) 0.0000 ( PROT PHE 17 CZ ) 0.0000 ( PROT PHE 17 C ) 0.0000 ( PROT PHE 17 O ) 0.0000 ( PROT PHE 18 N ) 0.0000 ( PROT PHE 18 H ) 0.0000 ( PROT PHE 18 CA ) 0.0000 ( PROT PHE 18 CB ) 0.0000 ( PROT PHE 18 CG ) 0.0000 ( PROT PHE 18 CD1 ) 0.0000 ( PROT PHE 18 CD2 ) 0.0000 ( PROT PHE 18 CE1 ) 0.0000 ( PROT PHE 18 CE2 ) 0.0000 ( PROT PHE 18 CZ ) 0.0000 ( PROT PHE 18 C ) 0.0000 ( PROT PHE 18 O ) 0.0000 ( PROT GLU 19 N ) 0.0000 ( PROT GLU 19 H ) 0.0000 ( PROT GLU 19 CA ) 0.0000 ( PROT GLU 19 CB ) 0.0000 ( PROT GLU 19 CG ) 0.0000 ( PROT GLU 19 CD ) 0.0000 ( PROT GLU 19 OE1 ) 0.0000 ( PROT GLU 19 OE2 ) 0.0000 ( PROT GLU 19 C ) 0.0000 ( PROT GLU 19 O ) 0.0000 ( PROT SER 20 N ) 0.0000 ( PROT SER 20 H ) 0.0000 ( PROT SER 20 CA ) 0.0000 ( PROT SER 20 CB ) 0.0000 ( PROT SER 20 OG ) 0.0000 ( PROT SER 20 HG ) 0.0000 ( PROT SER 20 C ) 0.0000 ( PROT SER 20 O ) 0.0000 ( PROT THR 21 N ) 0.0000 ( PROT THR 21 H ) 0.0000 ( PROT THR 21 CA ) 0.0000 ( PROT THR 21 CB ) 0.0000 ( PROT THR 21 OG1 ) 0.0000 ( PROT THR 21 HG1 ) 0.0000 ( PROT THR 21 CG2 ) 0.0000 ( PROT THR 21 C ) 0.0000 ( PROT THR 21 O ) 0.0000 ( PROT GLY 22 N ) 0.0000 ( PROT GLY 22 H ) 0.0000 ( PROT GLY 22 CA ) 0.0000 ( PROT GLY 22 C ) 0.0000 ( PROT GLY 22 O ) 0.0000 ( PROT SER 23 N ) 0.0000 ( PROT SER 23 H ) 0.0000 ( PROT SER 23 CA ) 0.0000 ( PROT SER 23 CB ) 0.0000 ( PROT SER 23 OG ) 0.0000 ( PROT SER 23 HG ) 0.0000 ( PROT SER 23 C ) 0.0000 ( PROT SER 23 O ) 0.0000 ( PROT GLN 24 N ) 0.0000 ( PROT GLN 24 H ) 0.0000 ( PROT GLN 24 CA ) 0.0000 ( PROT GLN 24 CB ) 0.0000 ( PROT GLN 24 CG ) 0.0000 ( PROT GLN 24 CD ) 0.0000 ( PROT GLN 24 OE1 ) 0.0000 ( PROT GLN 24 NE2 ) 0.0000 ( PROT GLN 24 HE21 ) 0.0000 ( PROT GLN 24 HE22 ) 0.0000 ( PROT GLN 24 C ) 0.0000 ( PROT GLN 24 O ) 0.0000 ( PROT GLU 25 N ) 0.0000 ( PROT GLU 25 H ) 0.0000 ( PROT GLU 25 CA ) 0.0000 ( PROT GLU 25 CB ) 0.0000 ( PROT GLU 25 CG ) 0.0000 ( PROT GLU 25 CD ) 0.0000 ( PROT GLU 25 OE1 ) 0.0000 ( PROT GLU 25 OE2 ) 0.0000 ( PROT GLU 25 C ) 0.0000 ( PROT GLU 25 O ) 0.0000 ( PROT GLN 26 N ) 0.0000 ( PROT GLN 26 H ) 0.0000 ( PROT GLN 26 CA ) 0.0000 ( PROT GLN 26 CB ) 0.0000 ( PROT GLN 26 CG ) 0.0000 ( PROT GLN 26 CD ) 0.0000 ( PROT GLN 26 OE1 ) 0.0000 ( PROT GLN 26 NE2 ) 0.0000 ( PROT GLN 26 HE21 ) 0.0000 ( PROT GLN 26 HE22 ) 0.0000 ( PROT GLN 26 C ) 0.0000 ( PROT GLN 26 O ) 0.0000 ( PROT LYS 27 N ) 0.0000 ( PROT LYS 27 H ) 0.0000 ( PROT LYS 27 CA ) 0.0000 ( PROT LYS 27 CB ) 0.0000 ( PROT LYS 27 CG ) 0.0000 ( PROT LYS 27 CD ) 0.0000 ( PROT LYS 27 CE ) 0.0000 ( PROT LYS 27 NZ ) 0.0000 ( PROT LYS 27 HZ1 ) 0.0000 ( PROT LYS 27 HZ2 ) 0.0000 ( PROT LYS 27 HZ3 ) 0.0000 ( PROT LYS 27 C ) 0.0000 ( PROT LYS 27 O ) 0.0000 ( PROT SER 28 N ) 0.0000 ( PROT SER 28 H ) 0.0000 ( PROT SER 28 CA ) 0.0000 ( PROT SER 28 CB ) 0.0000 ( PROT SER 28 OG ) 0.0000 ( PROT SER 28 HG ) 0.0000 ( PROT SER 28 C ) 0.0000 ( PROT SER 28 O ) 0.0000 ( PROT GLY 29 N ) 0.0000 ( PROT GLY 29 H ) 0.0000 ( PROT GLY 29 CA ) 0.0000 ( PROT GLY 29 C ) 0.0000 ( PROT GLY 29 O ) 0.0000 ( PROT VAL 30 N ) 0.0000 ( PROT VAL 30 H ) 0.0000 ( PROT VAL 30 CA ) 0.0000 ( PROT VAL 30 CB ) 0.0000 ( PROT VAL 30 CG1 ) 0.0000 ( PROT VAL 30 CG2 ) 0.0000 ( PROT VAL 30 C ) 0.0000 ( PROT VAL 30 O ) 0.0000 ( PROT TRP 31 N ) 0.0000 ( PROT TRP 31 H ) 0.0000 ( PROT TRP 31 CA ) 0.0000 ( PROT TRP 31 CB ) 0.0000 ( PROT TRP 31 CG ) 0.0000 ( PROT TRP 31 CD2 ) 0.0000 ( PROT TRP 31 CE2 ) 0.0000 ( PROT TRP 31 CE3 ) 0.0000 ( PROT TRP 31 CD1 ) 0.0000 ( PROT TRP 31 NE1 ) 0.0000 ( PROT TRP 31 HE1 ) 0.0000 ( PROT TRP 31 CZ2 ) 0.0000 ( PROT TRP 31 CZ3 ) 0.0000 ( PROT TRP 31 CH2 ) 0.0000 ( PROT TRP 31 C ) 0.0000 ( PROT TRP 31 OT1 ) 0.0000 ( PROT TRP 31 OT2 ) 0.0000 CHARMM> CHARMM> CHARMM> CHARMM> !write the structure after mini with constraints CHARMM> CHARMM> open unit 1 card write name ../coor/@output_intermediate.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../coor/mini_helix_allh_intermediate.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../coor/mini_helix_allh_intermediate.pdb CHARMM> write coor pdb unit 1 RDTITL> RDTITL> No title read. Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> ! 2000 conj grad. ! pour finir en beaute CHARMM> minimize conj nstep 2000 nprint 100 tolgrd 0.001 - CHARMM> inbfrq 10 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 20233 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20149 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 2000 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0010000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- MINI> 0 -204.43057 25.82273 0.09618 0.00000 MINI INTERN> 7.73241 36.04234 0.00000 19.57927 4.54027 MINI EXTERN> -172.15269 -100.17217 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -210.75678 6.32621 0.37530 0.19194 MINI INTERN> 8.62284 36.30221 0.00000 16.73168 4.31367 MINI EXTERN> -182.06136 -94.66582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19726 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -210.75678 6.32621 0.37530 0.00000 MINI INTERN> 8.62284 36.30221 0.00000 16.73168 4.31367 MINI EXTERN> -182.06136 -94.66582 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -213.12999 2.37321 0.12944 0.03343 MINI INTERN> 8.59196 35.87842 0.00000 16.52882 4.41240 MINI EXTERN> -182.08954 -96.45204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19758 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -213.12999 2.37321 0.12944 0.00000 MINI INTERN> 8.59196 35.87842 0.00000 16.52882 4.41240 MINI EXTERN> -182.08954 -96.45204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -213.75642 0.62644 0.15711 0.08293 MINI INTERN> 8.68122 36.03166 0.00000 16.51706 4.38893 MINI EXTERN> -182.91563 -96.45966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19745 ATOM PAIRS WERE FOUND FOR ATOM LIST 713 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -213.75642 0.62644 0.15711 0.00000 MINI INTERN> 8.68122 36.03166 0.00000 16.51706 4.38893 MINI EXTERN> -182.91563 -96.45966 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -214.28206 0.52564 0.11551 0.02935 MINI INTERN> 8.69492 36.49460 0.00000 16.54436 4.43865 MINI EXTERN> -183.27306 -97.18153 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19766 ATOM PAIRS WERE FOUND FOR ATOM LIST 719 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -214.28206 0.52564 0.11551 0.00000 MINI INTERN> 8.69492 36.49460 0.00000 16.54436 4.43865 MINI EXTERN> -183.27306 -97.18153 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -214.62502 0.34296 0.09618 0.01914 MINI INTERN> 8.74039 36.55242 0.00000 16.60281 4.43225 MINI EXTERN> -183.66314 -97.28975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19753 ATOM PAIRS WERE FOUND FOR ATOM LIST 716 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -214.62502 0.34296 0.09618 0.00000 MINI INTERN> 8.74039 36.55242 0.00000 16.60281 4.43225 MINI EXTERN> -183.66314 -97.28975 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -214.75392 0.12890 0.06034 0.01847 MINI INTERN> 8.73073 36.36876 0.00000 16.71610 4.45926 MINI EXTERN> -183.58460 -97.44417 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19754 ATOM PAIRS WERE FOUND FOR ATOM LIST 714 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -214.75392 0.12890 0.06034 0.00000 MINI INTERN> 8.73073 36.36876 0.00000 16.71610 4.45926 MINI EXTERN> -183.58460 -97.44417 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -214.84057 0.08665 0.06561 0.01590 MINI INTERN> 8.76633 36.42497 0.00000 16.83062 4.46522 MINI EXTERN> -183.89276 -97.43494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19755 ATOM PAIRS WERE FOUND FOR ATOM LIST 714 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -214.84057 0.08665 0.06561 0.00000 MINI INTERN> 8.76633 36.42497 0.00000 16.83062 4.46522 MINI EXTERN> -183.89276 -97.43494 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -214.90833 0.06777 0.05974 0.01597 MINI INTERN> 8.75564 36.32534 0.00000 16.90997 4.46975 MINI EXTERN> -183.85182 -97.51722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19757 ATOM PAIRS WERE FOUND FOR ATOM LIST 713 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -214.90833 0.06777 0.05974 0.00000 MINI INTERN> 8.75564 36.32534 0.00000 16.90997 4.46975 MINI EXTERN> -183.85182 -97.51722 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -214.96259 0.05426 0.04599 0.01309 MINI INTERN> 8.78394 36.35390 0.00000 17.00226 4.48200 MINI EXTERN> -184.05515 -97.52954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19762 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -214.96259 0.05426 0.04599 0.00000 MINI INTERN> 8.78394 36.35390 0.00000 17.00226 4.48200 MINI EXTERN> -184.05515 -97.52954 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -215.00705 0.04446 0.04982 0.01284 MINI INTERN> 8.77462 36.30318 0.00000 17.05186 4.48104 MINI EXTERN> -184.03163 -97.58612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19766 ATOM PAIRS WERE FOUND FOR ATOM LIST 715 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -215.00705 0.04446 0.04982 0.00000 MINI INTERN> 8.77462 36.30318 0.00000 17.05186 4.48104 MINI EXTERN> -184.03163 -97.58612 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -215.04388 0.03683 0.03524 0.01093 MINI INTERN> 8.79544 36.32615 0.00000 17.12631 4.49454 MINI EXTERN> -184.17429 -97.61204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19767 ATOM PAIRS WERE FOUND FOR ATOM LIST 714 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -215.04388 0.03683 0.03524 0.00000 MINI INTERN> 8.79544 36.32615 0.00000 17.12631 4.49454 MINI EXTERN> -184.17429 -97.61204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -215.07518 0.03130 0.06187 0.01109 MINI INTERN> 8.79412 36.29597 0.00000 17.16202 4.49065 MINI EXTERN> -184.16575 -97.65219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19772 ATOM PAIRS WERE FOUND FOR ATOM LIST 714 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -215.07518 0.03130 0.06187 0.00000 MINI INTERN> 8.79412 36.29597 0.00000 17.16202 4.49065 MINI EXTERN> -184.16575 -97.65219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -215.10158 0.02640 0.02789 0.00954 MINI INTERN> 8.80689 36.32558 0.00000 17.22125 4.50543 MINI EXTERN> -184.27187 -97.68886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19773 ATOM PAIRS WERE FOUND FOR ATOM LIST 714 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -215.10158 0.02640 0.02789 0.00000 MINI INTERN> 8.80689 36.32558 0.00000 17.22125 4.50543 MINI EXTERN> -184.27187 -97.68886 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -215.12397 0.02238 0.04063 0.00884 MINI INTERN> 8.79986 36.31616 0.00000 17.24618 4.49902 MINI EXTERN> -184.26669 -97.71849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19772 ATOM PAIRS WERE FOUND FOR ATOM LIST 710 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -215.12397 0.02238 0.04063 0.00000 MINI INTERN> 8.79986 36.31616 0.00000 17.24618 4.49902 MINI EXTERN> -184.26669 -97.71849 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -215.14315 0.01919 0.02121 0.00813 MINI INTERN> 8.81391 36.34632 0.00000 17.29245 4.51321 MINI EXTERN> -184.34783 -97.76121 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19775 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -215.14315 0.01919 0.02121 0.00000 MINI INTERN> 8.81391 36.34632 0.00000 17.29245 4.51321 MINI EXTERN> -184.34783 -97.76121 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -215.15976 0.01661 0.03876 0.00738 MINI INTERN> 8.80569 36.34286 0.00000 17.31393 4.50654 MINI EXTERN> -184.34350 -97.78528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19773 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -215.15976 0.01661 0.03876 0.00000 MINI INTERN> 8.80569 36.34286 0.00000 17.31393 4.50654 MINI EXTERN> -184.34350 -97.78528 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -215.17414 0.01439 0.01669 0.00667 MINI INTERN> 8.82061 36.37537 0.00000 17.35019 4.52014 MINI EXTERN> -184.40960 -97.83085 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19774 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -215.17414 0.01439 0.01669 0.00000 MINI INTERN> 8.82061 36.37537 0.00000 17.35019 4.52014 MINI EXTERN> -184.40960 -97.83085 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -215.18668 0.01253 0.03712 0.00617 MINI INTERN> 8.81561 36.37066 0.00000 17.36896 4.51397 MINI EXTERN> -184.40526 -97.85062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19773 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -215.18668 0.01253 0.03712 0.00000 MINI INTERN> 8.81561 36.37066 0.00000 17.36896 4.51397 MINI EXTERN> -184.40526 -97.85062 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -215.19757 0.01090 0.01460 0.00566 MINI INTERN> 8.82824 36.40523 0.00000 17.39762 4.52580 MINI EXTERN> -184.46170 -97.89277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19775 ATOM PAIRS WERE FOUND FOR ATOM LIST 709 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -215.19757 0.01090 0.01460 0.00000 MINI INTERN> 8.82824 36.40523 0.00000 17.39762 4.52580 MINI EXTERN> -184.46170 -97.89277 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -215.20703 0.00946 0.02615 0.00506 MINI INTERN> 8.82181 36.40041 0.00000 17.41565 4.52050 MINI EXTERN> -184.45548 -97.90994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 2000) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- CONJ> 2000 -215.20703 0.00946 0.02615 0.02000 CONJ INTERN> 8.82181 36.40041 0.00000 17.41565 4.52050 CONJ EXTERN> -184.45548 -97.90994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> minimize conj nstep 2000 nprint 100 tolgrd 0.001 - CHARMM> inbfrq 10 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 19775 atom pairs and 1259 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19778 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 2000 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0010000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- MINI> 0 -215.20703 0.00946 0.02615 0.00000 MINI INTERN> 8.82181 36.40041 0.00000 17.41565 4.52050 MINI EXTERN> -184.45548 -97.90994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -215.21535 0.00832 0.01257 0.00493 MINI INTERN> 8.83405 36.43796 0.00000 17.43863 4.53157 MINI EXTERN> -184.50435 -97.95321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19786 ATOM PAIRS WERE FOUND FOR ATOM LIST 709 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -215.21535 0.00832 0.01257 0.00000 MINI INTERN> 8.83405 36.43796 0.00000 17.43863 4.53157 MINI EXTERN> -184.50435 -97.95321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -215.22253 0.00718 0.02155 0.00425 MINI INTERN> 8.82766 36.43319 0.00000 17.45443 4.52757 MINI EXTERN> -184.49333 -97.97204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19783 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -215.22253 0.00718 0.02155 0.00000 MINI INTERN> 8.82766 36.43319 0.00000 17.45443 4.52757 MINI EXTERN> -184.49333 -97.97204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -215.22874 0.00621 0.01027 0.00414 MINI INTERN> 8.83827 36.46563 0.00000 17.47559 4.53783 MINI EXTERN> -184.53753 -98.00854 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19791 ATOM PAIRS WERE FOUND FOR ATOM LIST 710 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -215.22874 0.00621 0.01027 0.00000 MINI INTERN> 8.83827 36.46563 0.00000 17.47559 4.53783 MINI EXTERN> -184.53753 -98.00854 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -215.23419 0.00545 0.02585 0.00383 MINI INTERN> 8.83189 36.45599 0.00000 17.49209 4.53438 MINI EXTERN> -184.52618 -98.02236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19785 ATOM PAIRS WERE FOUND FOR ATOM LIST 710 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -215.23419 0.00545 0.02585 0.00000 MINI INTERN> 8.83189 36.45599 0.00000 17.49209 4.53438 MINI EXTERN> -184.52618 -98.02236 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -215.23896 0.00477 0.00990 0.00372 MINI INTERN> 8.84205 36.48721 0.00000 17.51120 4.54413 MINI EXTERN> -184.56611 -98.05743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19794 ATOM PAIRS WERE FOUND FOR ATOM LIST 709 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -215.23896 0.00477 0.00990 0.00000 MINI INTERN> 8.84205 36.48721 0.00000 17.51120 4.54413 MINI EXTERN> -184.56611 -98.05743 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -215.24323 0.00427 0.02338 0.00346 MINI INTERN> 8.83752 36.48261 0.00000 17.52735 4.54302 MINI EXTERN> -184.55076 -98.08297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19790 ATOM PAIRS WERE FOUND FOR ATOM LIST 710 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -215.24323 0.00427 0.02338 0.00000 MINI INTERN> 8.83752 36.48261 0.00000 17.52735 4.54302 MINI EXTERN> -184.55076 -98.08297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -215.24715 0.00392 0.00832 0.00332 MINI INTERN> 8.84564 36.52534 0.00000 17.54573 4.55522 MINI EXTERN> -184.58579 -98.13329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19795 ATOM PAIRS WERE FOUND FOR ATOM LIST 709 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -215.24715 0.00392 0.00832 0.00000 MINI INTERN> 8.84564 36.52534 0.00000 17.54573 4.55522 MINI EXTERN> -184.58579 -98.13329 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -215.25113 0.00398 0.04072 0.00348 MINI INTERN> 8.83808 36.54853 0.00000 17.56491 4.56014 MINI EXTERN> -184.56406 -98.19872 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19792 ATOM PAIRS WERE FOUND FOR ATOM LIST 710 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -215.25113 0.00398 0.04072 0.00000 MINI INTERN> 8.83808 36.54853 0.00000 17.56491 4.56014 MINI EXTERN> -184.56406 -98.19872 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -215.25587 0.00474 0.01102 0.00544 MINI INTERN> 8.85143 36.63838 0.00000 17.59614 4.58603 MINI EXTERN> -184.60013 -98.32771 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19796 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -215.25587 0.00474 0.01102 0.00000 MINI INTERN> 8.85143 36.63838 0.00000 17.59614 4.58603 MINI EXTERN> -184.60013 -98.32771 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -215.26219 0.00632 0.01490 0.00195 MINI INTERN> 8.84814 36.70283 0.00000 17.63375 4.60725 MINI EXTERN> -184.55197 -98.50218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19796 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -215.26219 0.00632 0.01490 0.00000 MINI INTERN> 8.84814 36.70283 0.00000 17.63375 4.60725 MINI EXTERN> -184.55197 -98.50218 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -215.26562 0.00343 0.00778 0.00254 MINI INTERN> 8.85620 36.74806 0.00000 17.63946 4.61784 MINI EXTERN> -184.58021 -98.54698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19801 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -215.26562 0.00343 0.00778 0.00000 MINI INTERN> 8.85620 36.74806 0.00000 17.63946 4.61784 MINI EXTERN> -184.58021 -98.54698 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -215.26817 0.00256 0.01564 0.00228 MINI INTERN> 8.85157 36.72807 0.00000 17.65662 4.61271 MINI EXTERN> -184.57382 -98.54334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19797 ATOM PAIRS WERE FOUND FOR ATOM LIST 713 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -215.26817 0.00256 0.01564 0.00000 MINI INTERN> 8.85157 36.72807 0.00000 17.65662 4.61271 MINI EXTERN> -184.57382 -98.54334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -215.27023 0.00206 0.00549 0.00203 MINI INTERN> 8.85866 36.74496 0.00000 17.66781 4.61801 MINI EXTERN> -184.60283 -98.55684 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19801 ATOM PAIRS WERE FOUND FOR ATOM LIST 713 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -215.27023 0.00206 0.00549 0.00000 MINI INTERN> 8.85866 36.74496 0.00000 17.66781 4.61801 MINI EXTERN> -184.60283 -98.55684 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -215.27193 0.00170 0.01021 0.00179 MINI INTERN> 8.85482 36.72024 0.00000 17.68550 4.61374 MINI EXTERN> -184.59054 -98.55568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19799 ATOM PAIRS WERE FOUND FOR ATOM LIST 713 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -215.27193 0.00170 0.01021 0.00000 MINI INTERN> 8.85482 36.72024 0.00000 17.68550 4.61374 MINI EXTERN> -184.59054 -98.55568 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -215.27335 0.00142 0.00432 0.00174 MINI INTERN> 8.86001 36.73522 0.00000 17.69363 4.61789 MINI EXTERN> -184.61719 -98.56291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19800 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -215.27335 0.00142 0.00432 0.00000 MINI INTERN> 8.86001 36.73522 0.00000 17.69363 4.61789 MINI EXTERN> -184.61719 -98.56291 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -215.27457 0.00122 0.01270 0.00167 MINI INTERN> 8.85633 36.71565 0.00000 17.70679 4.61411 MINI EXTERN> -184.60611 -98.56133 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19799 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -215.27457 0.00122 0.01270 0.00000 MINI INTERN> 8.85633 36.71565 0.00000 17.70679 4.61411 MINI EXTERN> -184.60611 -98.56133 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -215.27560 0.00103 0.00362 0.00147 MINI INTERN> 8.86115 36.72797 0.00000 17.71316 4.61753 MINI EXTERN> -184.62959 -98.56584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19800 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -215.27560 0.00103 0.00362 0.00000 MINI INTERN> 8.86115 36.72797 0.00000 17.71316 4.61753 MINI EXTERN> -184.62959 -98.56584 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -215.27650 0.00089 0.01430 0.00144 MINI INTERN> 8.85712 36.71283 0.00000 17.72324 4.61430 MINI EXTERN> -184.62046 -98.56353 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19799 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -215.27650 0.00089 0.01430 0.00000 MINI INTERN> 8.85712 36.71283 0.00000 17.72324 4.61430 MINI EXTERN> -184.62046 -98.56353 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -215.27726 0.00076 0.00299 0.00130 MINI INTERN> 8.86201 36.72242 0.00000 17.72875 4.61694 MINI EXTERN> -184.64020 -98.56716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43957 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19799 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -215.27726 0.00076 0.00299 0.00000 MINI INTERN> 8.86201 36.72242 0.00000 17.72875 4.61694 MINI EXTERN> -184.64020 -98.56716 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -215.27790 0.00064 0.00930 0.00115 MINI INTERN> 8.85825 36.71008 0.00000 17.73651 4.61408 MINI EXTERN> -184.63172 -98.56511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 2000) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- CONJ> 2000 -215.27790 0.00064 0.00930 0.02000 CONJ INTERN> 8.85825 36.71008 0.00000 17.73651 4.61408 CONJ EXTERN> -184.63172 -98.56511 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> CHARMM> open unit 18 card write name ../coor/@output_final.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../coor/mini_helix_allh_final.pdb:: OPNLGU> Unit 18 opened for WRITE access to ../coor/mini_helix_allh_final.pdb CHARMM> write coor pdb unit 18 RDTITL> RDTITL> No title read. Write CHARMM-pdb format CHARMM> CHARMM> open unit 19 card write name ../coor/@output_final.crd Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../coor/mini_helix_allh_final.crd:: OPNLGU> Unit 19 opened for WRITE access to ../coor/mini_helix_allh_final.crd CHARMM> write coor card unit 19 RDTITL> * HUMAN PHOSPHOLIPID SCRAMBLASE 1 FROM HUMAN_PLSCR1_B99990001.PDB RDTITL> * VCLOSE: Closing unit 19 with status "KEEP" CHARMM> close unit 19 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> CHARMM> CHARMM> CHARMM> CHARMM> FORMAT (F7.4) CHARMM> CHARMM> ! protein structural changes. CHARMM> CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 297 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.56332 7.16951 -13.17374 CENTER OF REFERENCE COORDINATE SET 13.63081 7.22943 -13.21992 NET TRANSLATION OF ROTATED ATOMS 0.06749 0.05992 -0.04618 ROTATION MATRIX 0.999947 -0.005885 -0.008448 0.006002 0.999885 0.013913 0.008365 -0.013963 0.999868 AXIS OF ROTATION IS 0.804342 0.485154 -0.343015 ANGLE IS 0.99 TOTAL SQUARE DIFF IS 941.7589 DENOMINATOR IS 297.0000 THUS RMS DIFF IS 1.780704 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.7807" Parameter: A <- "1.7807" CHARMM> set a @a ?RMS Parameter: A -> "1.7807" RDCMND substituted energy or value "?RMS" to " 1.7807" Parameter: A <- "1.7807 1.7807" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 297 CENTER OF ATOMS BEFORE TRANSLATION 13.54798 7.37968 -13.47837 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.01976 -0.12413 0.03802 ROTATION MATRIX 0.999940 -0.010073 -0.004314 0.010055 0.999941 -0.004158 0.004356 0.004115 0.999982 AXIS OF ROTATION IS -0.353183 0.370120 -0.859228 ANGLE IS 0.67 TOTAL SQUARE DIFF IS 62.7563 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 1.422813 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.7807 1.7807" RDCMND substituted energy or value "?RMS" to " 1.4228" Parameter: A <- "1.7807 1.7807 1.4228" CHARMM> !main chain - to compare with back CHARMM> !coor rms sele ( resname TIP3 ) end CHARMM> !set a @a ?RMS CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *12000 1.7807 1.7807 1.4228 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> stop ! phew VCLOSE: Closing unit 1 with status "KEEP" VCLOSE: Closing unit 18 with status "KEEP" $$$$$$ New timer profile $$$$$ List time 0.00 Other: 0.00 Electrostatic & VDW 15.23 Other: 0.00 Nonbond force 15.26 Other: 0.03 Bond energy 0.13 Other: 0.00 Angle energy 1.09 Other: 0.00 Dihedral energy 0.67 Other: 0.00 Restraints energy 0.00 Other: 0.00 INTRNL energy 1.94 Other: 0.05 Energy time 17.32 Other: 0.12 Total time 18.40 Other: 1.08 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47522 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL 2 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 63172 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 18.41 SECONDS CPU TIME: 0.00 SECONDS