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-2.6.32-358.23.2.el6.x86_64(x86_64)@kon Created on 3/17/14 at 17:25:34 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: 3/17/14 17:25:10 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 = 296 Number of groups = 112 Number of bonds = 301 Number of angles = 428 Number of dihedrals = 171 Number of impropers = 143 Number of cross-terms = 0 Number of HB acceptors = 44 Number of HB donors = 51 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: 3/17/14 17:25:10 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 754 exclusions and 501 interactions(1-4) found 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21229 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 21229 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21229 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 351929.01029 0.00000 133205.84102 ENER INTERN> 313.58055 198.21077 0.00000 9.94517 4.01769 ENER EXTERN> 351624.84650 -221.59038 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> 296 atoms have been selected out of 296 CHARMM> define water sele ( segid solv) end SELRPN> 0 atoms have been selected out of 296 CHARMM> define nonh sele ( .not. hydrogen ) end SELRPN> 245 atoms have been selected out of 296 CHARMM> define trace sele ( type ca ) end SELRPN> 31 atoms have been selected out of 296 CHARMM> define back sele ( type n .or. type ca .or. type c ) end SELRPN> 93 atoms have been selected out of 296 CHARMM> define main sele ( type n .or. type ca .or. type c .or. type o) end SELRPN> 123 atoms have been selected out of 296 CHARMM> define side sele ( (.not. main) ) end SELRPN> 173 atoms have been selected out of 296 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: 296 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 296 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 296 CHARMM> CHARMM> ! { quite tight on sidechains of pcna } CHARMM> SCALar CONSTraint SET 200. SELEct ( prot .AND. side ) END SELRPN> 173 atoms have been selected out of 296 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 ASP 14 N ) 250.00 ( PROT ASP 14 H ) 200.00 ( PROT ASP 14 CA ) 250.00 ( PROT ASP 14 CB ) 200.00 ( PROT ASP 14 CG ) 200.00 ( PROT ASP 14 OD1 ) 200.00 ( PROT ASP 14 OD2 ) 200.00 ( PROT ASP 14 C ) 250.00 ( PROT ASP 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: 3/17/14 17:25:10 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 21229 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21229 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 351929.01029 0.00000 133205.84102 0.02000 MINI INTERN> 313.58055 198.21077 0.00000 9.94517 4.01769 MINI EXTERN> 351624.84650 -221.59038 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 3518.41407 348410.59622 64.20637 0.02074 MINI INTERN> 604.92939 274.70583 0.00000 10.31476 107.21498 MINI EXTERN> 1955.56201 -122.30678 0.00000 0.00000 0.00000 MINI CONSTR> 687.99388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21204 ATOM PAIRS WERE FOUND FOR ATOM LIST 744 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 2559.00011 959.41396 11.80374 0.00896 MINI INTERN> 180.01937 161.23323 0.00000 12.58095 36.09456 MINI EXTERN> 1066.31978 -114.20020 0.00000 0.00000 0.00000 MINI CONSTR> 1216.95242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 2535.54096 23.45914 5.58449 0.00387 MINI INTERN> 102.83478 173.41305 0.00000 13.17417 41.53993 MINI EXTERN> 1021.02643 -115.64478 0.00000 0.00000 0.00000 MINI CONSTR> 1299.19738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21204 ATOM PAIRS WERE FOUND FOR ATOM LIST 748 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 2530.76225 4.77871 0.50470 0.00070 MINI INTERN> 119.36738 168.59178 0.00000 13.16957 40.60753 MINI EXTERN> 1016.00446 -114.49201 0.00000 0.00000 0.00000 MINI CONSTR> 1287.51354 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 2530.68679 0.07546 0.28099 0.00030 MINI INTERN> 116.89758 168.48837 0.00000 13.27316 40.53986 MINI EXTERN> 1020.01181 -114.90658 0.00000 0.00000 0.00000 MINI CONSTR> 1286.38259 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21204 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 2530.64621 0.04059 0.24508 0.00013 MINI INTERN> 118.27306 168.12930 0.00000 13.37842 40.57252 MINI EXTERN> 1017.62277 -114.65232 0.00000 0.00000 0.00000 MINI CONSTR> 1287.32245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 2530.62521 0.02099 0.29987 0.00013 MINI INTERN> 118.38282 168.00083 0.00000 13.45916 40.58600 MINI EXTERN> 1017.21385 -114.61624 0.00000 0.00000 0.00000 MINI CONSTR> 1287.59881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 2530.59908 0.02613 0.09253 0.00006 MINI INTERN> 117.20258 168.05192 0.00000 13.53035 40.58401 MINI EXTERN> 1018.79984 -114.80788 0.00000 0.00000 0.00000 MINI CONSTR> 1287.23826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 2530.58626 0.01283 0.07194 0.00006 MINI INTERN> 117.21362 167.96603 0.00000 13.59035 40.58903 MINI EXTERN> 1018.66423 -114.79605 0.00000 0.00000 0.00000 MINI CONSTR> 1287.35904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 2530.57630 0.00996 0.14712 0.00006 MINI INTERN> 116.77045 167.93667 0.00000 13.65869 40.59807 MINI EXTERN> 1019.14859 -114.86239 0.00000 0.00000 0.00000 MINI CONSTR> 1287.32623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 2530.56968 0.00662 0.16115 0.00006 MINI INTERN> 116.65213 167.88523 0.00000 13.70995 40.60423 MINI EXTERN> 1019.20446 -114.87462 0.00000 0.00000 0.00000 MINI CONSTR> 1287.38831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 2530.56520 0.00448 0.15651 0.00007 MINI INTERN> 116.61897 167.83647 0.00000 13.74794 40.60619 MINI EXTERN> 1019.18544 -114.87457 0.00000 0.00000 0.00000 MINI CONSTR> 1287.44475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 2530.55944 0.00575 0.04845 0.00003 MINI INTERN> 117.20281 167.69846 0.00000 13.78424 40.60289 MINI EXTERN> 1018.29812 -114.76695 0.00000 0.00000 0.00000 MINI CONSTR> 1287.73987 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 2530.55709 0.00235 0.04100 0.00003 MINI INTERN> 117.15403 167.66525 0.00000 13.81376 40.60568 MINI EXTERN> 1018.30439 -114.77082 0.00000 0.00000 0.00000 MINI CONSTR> 1287.78480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 2530.55583 0.00126 0.07001 0.00003 MINI INTERN> 117.24567 167.61593 0.00000 13.83901 40.60626 MINI EXTERN> 1018.12840 -114.75133 0.00000 0.00000 0.00000 MINI CONSTR> 1287.87190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 2530.55436 0.00147 0.02080 0.00001 MINI INTERN> 116.96717 167.63469 0.00000 13.85832 40.61218 MINI EXTERN> 1018.45941 -114.79560 0.00000 0.00000 0.00000 MINI CONSTR> 1287.81818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 2530.55368 0.00068 0.01627 0.00001 MINI INTERN> 116.96461 167.61346 0.00000 13.87372 40.61301 MINI EXTERN> 1018.43382 -114.79372 0.00000 0.00000 0.00000 MINI CONSTR> 1287.84878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 2530.55320 0.00048 0.03425 0.00001 MINI INTERN> 116.85928 167.60890 0.00000 13.89004 40.61590 MINI EXTERN> 1018.53921 -114.80877 0.00000 0.00000 0.00000 MINI CONSTR> 1287.84864 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 2530.55290 0.00030 0.03852 0.00002 MINI INTERN> 116.82879 167.59779 0.00000 13.90186 40.61704 MINI EXTERN> 1018.55610 -114.81193 0.00000 0.00000 0.00000 MINI CONSTR> 1287.86324 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 2530.55269 0.00021 0.03644 0.00002 MINI INTERN> 116.82428 167.58595 0.00000 13.91010 40.61710 MINI EXTERN> 1018.55065 -114.81158 0.00000 0.00000 0.00000 MINI CONSTR> 1287.87620 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> 101 2530.55255 0.00014 0.00879 0.00001 STPD INTERN> 116.93288 167.56728 0.00000 13.91066 40.61575 STPD EXTERN> 1018.40285 -114.79349 0.00000 0.00000 0.00000 STPD CONSTR> 1287.91661 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 21205 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 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 2530.55255 0.00014 0.00879 0.00000 MINI INTERN> 116.93288 167.56728 0.00000 13.91066 40.61575 MINI EXTERN> 1018.40285 -114.79349 0.00000 0.00000 0.00000 MINI CONSTR> 1287.91661 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 2530.55211 0.00044 0.00611 0.02000 CONJ INTERN> 116.89313 167.51233 0.00000 13.95246 40.61773 CONJ EXTERN> 1018.38322 -114.79425 0.00000 0.00000 0.00000 CONJ CONSTR> 1287.98749 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 ASP 14 N ) 162.50 ( PROT ASP 14 H ) 130.00 ( PROT ASP 14 CA ) 162.50 ( PROT ASP 14 CB ) 130.00 ( PROT ASP 14 CG ) 130.00 ( PROT ASP 14 OD1 ) 130.00 ( PROT ASP 14 OD2 ) 130.00 ( PROT ASP 14 C ) 162.50 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64193 7.24880 -13.21318 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00170 -0.00144 0.00172 ROTATION MATRIX 1.000000 -0.000026 -0.000064 0.000026 1.000000 0.000052 0.000064 -0.000052 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 6.0707 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.143210 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1432" Parameter: A <- "0.1432" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51740 7.24767 -13.42797 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01083 0.00787 -0.01238 ROTATION MATRIX 0.999945 0.007381 0.007500 -0.007321 0.999941 -0.008027 -0.007559 0.007972 0.999940 AXIS OF ROTATION IS -0.605204 -0.569630 0.556103 ANGLE IS 0.76 TOTAL SQUARE DIFF IS 0.0431 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.037287 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1432" RDCMND substituted energy or value "?RMS" to " 0.0373" Parameter: A <- "0.1432 0.0373" 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 0.1432 0.0373 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 " 1287.99" Parameter: H <- "1287.99" 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 1242.56462 1287.98749 35.25684 ENER INTERN> 116.89313 167.51233 0.00000 13.95246 40.61773 ENER EXTERN> 1018.38322 -114.79425 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 " 1242.56" Parameter: B <- "1242.56" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -114.79" Parameter: C <- "-114.79" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 1018.38" Parameter: C <- " 903.59" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 903.59" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 116.89" Parameter: D <- "116.89" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 167.51" Parameter: D <- " 284.40" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 13.95" Parameter: D <- " 298.35" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 40.62" Parameter: D <- " 338.97" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 338.97" 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= 1242.56 GRMS= 35.26 ELEC= -114.79 VDW= 1018.38 RDTITL> *EXTERNAL= 903.59 INTERNAL= 338.97 USER= 0.00 HARM= 1287.99 RDTITL> *BOND= 116.89 ANGL= 167.51 DIHE= 13.95 IMPR= 40.62 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21205 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21205 ATOM PAIRS WERE FOUND FOR ATOM LIST 749 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 2197.92069 -955.35608 15.00989 0.02000 MINI INTERN> 116.89313 167.51233 0.00000 13.95246 40.61773 MINI EXTERN> 1018.38322 -114.79425 0.00000 0.00000 0.00000 MINI CONSTR> 955.35608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 2081.89539 116.02531 16.61872 0.00864 MINI INTERN> 102.64290 177.48284 0.00000 16.73710 32.28074 MINI EXTERN> 835.30797 -116.31618 0.00000 0.00000 0.00000 MINI CONSTR> 1033.76001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21184 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 2032.20126 49.69413 1.39464 0.00156 MINI INTERN> 101.05313 165.32395 0.00000 16.11296 34.30273 MINI EXTERN> 788.65061 -112.17111 0.00000 0.00000 0.00000 MINI CONSTR> 1038.92899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 2030.13134 2.06992 0.56017 0.00067 MINI INTERN> 100.55966 164.63759 0.00000 16.35459 34.75801 MINI EXTERN> 781.78889 -112.22839 0.00000 0.00000 0.00000 MINI CONSTR> 1044.26100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21186 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 2029.86904 0.26230 0.28947 0.00029 MINI INTERN> 99.42735 163.77819 0.00000 16.67801 34.30400 MINI EXTERN> 784.79448 -112.32256 0.00000 0.00000 0.00000 MINI CONSTR> 1043.20958 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 2029.82711 0.04193 0.53015 0.00030 MINI INTERN> 100.16036 163.63529 0.00000 16.90413 34.24285 MINI EXTERN> 782.80123 -112.16887 0.00000 0.00000 0.00000 MINI CONSTR> 1044.25212 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21186 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 2029.75673 0.07038 0.15828 0.00013 MINI INTERN> 99.44646 163.23597 0.00000 17.04360 34.48524 MINI EXTERN> 782.92595 -112.32123 0.00000 0.00000 0.00000 MINI CONSTR> 1044.94074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 2029.73301 0.02373 0.17790 0.00013 MINI INTERN> 99.47263 163.02316 0.00000 17.18094 34.50671 MINI EXTERN> 782.56780 -112.30812 0.00000 0.00000 0.00000 MINI CONSTR> 1045.28989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21186 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 2029.71499 0.01802 0.07026 0.00006 MINI INTERN> 99.21704 162.93793 0.00000 17.27725 34.38481 MINI EXTERN> 783.20528 -112.31232 0.00000 0.00000 0.00000 MINI CONSTR> 1045.00500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 2029.70606 0.00893 0.07332 0.00006 MINI INTERN> 99.08307 162.84986 0.00000 17.35759 34.37677 MINI EXTERN> 783.26110 -112.32896 0.00000 0.00000 0.00000 MINI CONSTR> 1045.10661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21186 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 2029.70150 0.00456 0.09970 0.00006 MINI INTERN> 99.11216 162.73815 0.00000 17.42015 34.35449 MINI EXTERN> 783.24056 -112.31252 0.00000 0.00000 0.00000 MINI CONSTR> 1045.14852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 2029.69875 0.00275 0.10004 0.00006 MINI INTERN> 99.08025 162.67258 0.00000 17.46437 34.35114 MINI EXTERN> 783.24218 -112.31591 0.00000 0.00000 0.00000 MINI CONSTR> 1045.20414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21186 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 2029.69597 0.00278 0.04581 0.00003 MINI INTERN> 99.10702 162.67127 0.00000 17.49481 34.42432 MINI EXTERN> 782.70494 -112.31899 0.00000 0.00000 0.00000 MINI CONSTR> 1045.61260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 2029.69524 0.00073 0.05617 0.00003 MINI INTERN> 99.10832 162.63689 0.00000 17.51848 34.42241 MINI EXTERN> 782.66986 -112.31540 0.00000 0.00000 0.00000 MINI CONSTR> 1045.65468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21186 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 2029.69470 0.00054 0.05062 0.00003 MINI INTERN> 99.00284 162.63493 0.00000 17.53792 34.43096 MINI EXTERN> 782.73307 -112.33582 0.00000 0.00000 0.00000 MINI CONSTR> 1045.69081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 2029.69411 0.00059 0.01690 0.00001 MINI INTERN> 98.99002 162.60941 0.00000 17.55088 34.39747 MINI EXTERN> 782.87707 -112.33061 0.00000 0.00000 0.00000 MINI CONSTR> 1045.59987 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 2029.69401 0.00009 0.00764 0.00001 STPD INTERN> 98.99776 162.60752 0.00000 17.55457 34.40943 STPD EXTERN> 782.79806 -112.33124 0.00000 0.00000 0.00000 STPD CONSTR> 1045.65792 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 21186 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21186 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 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 2029.69401 0.00009 0.00764 0.00000 MINI INTERN> 98.99776 162.60752 0.00000 17.55457 34.40943 MINI EXTERN> 782.79806 -112.33124 0.00000 0.00000 0.00000 MINI CONSTR> 1045.65792 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 2029.69374 0.00028 0.00085 0.02000 CONJ INTERN> 98.96765 162.56486 0.00000 17.58943 34.40708 CONJ EXTERN> 782.77842 -112.33293 0.00000 0.00000 0.00000 CONJ CONSTR> 1045.71923 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 ASP 14 N ) 105.63 ( PROT ASP 14 H ) 84.500 ( PROT ASP 14 CA ) 105.63 ( PROT ASP 14 CB ) 84.500 ( PROT ASP 14 CG ) 84.500 ( PROT ASP 14 OD1 ) 84.500 ( PROT ASP 14 OD2 ) 84.500 ( PROT ASP 14 C ) 105.63 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64197 7.24877 -13.21326 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00174 -0.00141 0.00180 ROTATION MATRIX 1.000000 -0.000027 -0.000077 0.000027 1.000000 0.000060 0.000077 -0.000060 1.000000 AXIS OF ROTATION IS 0.595369 0.759536 -0.261993 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 7.5623 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.159838 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1598" Parameter: A <- "0.1598" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51628 7.24767 -13.42607 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01194 0.00788 -0.01428 ROTATION MATRIX 0.999918 0.008978 0.009157 -0.008888 0.999913 -0.009750 -0.009244 0.009668 0.999911 AXIS OF ROTATION IS -0.603644 -0.571990 0.555375 ANGLE IS 0.92 TOTAL SQUARE DIFF IS 0.0704 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.047671 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1598" RDCMND substituted energy or value "?RMS" to " 0.0477" Parameter: A <- "0.1598 0.0477" 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 0.1598 0.0477 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 " 1045.72" Parameter: H <- "1045.72" 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> 0 983.97451 1045.71923 25.65063 ENER INTERN> 98.96765 162.56486 0.00000 17.58943 34.40708 ENER EXTERN> 782.77842 -112.33293 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 " 983.97" Parameter: B <- "983.97" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -112.33" Parameter: C <- "-112.33" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 782.78" Parameter: C <- " 670.45" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 670.45" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 98.97" Parameter: D <- "98.97" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 162.56" Parameter: D <- " 261.53" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 17.59" Parameter: D <- " 279.12" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 34.41" Parameter: D <- " 313.53" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 313.53" 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= 1200 ENER= 983.97 GRMS= 25.65 ELEC= -112.33 VDW= 782.78 RDTITL> *EXTERNAL= 670.45 INTERNAL= 313.53 USER= 0.00 HARM= 1045.72 RDTITL> *BOND= 98.97 ANGL= 162.56 DIHE= 17.59 IMPR= 34.41 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= 983.97 GRMS= 25.65 ELEC= -112.33 VDW= 782.78 RDTITL> *EXTERNAL= 670.45 INTERNAL= 313.53 USER= 0.00 HARM= 1045.72 RDTITL> *BOND= 98.97 ANGL= 162.56 DIHE= 17.59 IMPR= 34.41 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= 983.97 GRMS= 25.65 ELEC= -112.33 VDW= 782.78 RDTITL> *EXTERNAL= 670.45 INTERNAL= 313.53 USER= 0.00 HARM= 1045.72 RDTITL> *BOND= 98.97 ANGL= 162.56 DIHE= 17.59 IMPR= 34.41 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 1200 0.1598 0.0477 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21186 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21186 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 1776.06178 -792.08727 11.19892 0.02000 MINI INTERN> 98.96765 162.56486 0.00000 17.58943 34.40708 MINI EXTERN> 782.77842 -112.33293 0.00000 0.00000 0.00000 MINI CONSTR> 792.08727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1670.47905 105.58273 14.91046 0.00864 MINI INTERN> 99.48636 148.31293 0.00000 19.64534 23.15778 MINI EXTERN> 673.99622 -108.92633 0.00000 0.00000 0.00000 MINI CONSTR> 814.80675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21172 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1631.35429 39.12476 5.36560 0.00373 MINI INTERN> 89.69051 164.89429 0.00000 20.67254 31.94218 MINI EXTERN> 577.23893 -111.17248 0.00000 0.00000 0.00000 MINI CONSTR> 858.08832 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1624.78805 6.56624 2.58706 0.00161 MINI INTERN> 88.05391 157.84588 0.00000 20.76691 26.12016 MINI EXTERN> 601.57423 -111.26390 0.00000 0.00000 0.00000 MINI CONSTR> 841.69087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21175 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1623.34363 1.44442 0.27667 0.00029 MINI INTERN> 85.08628 158.57130 0.00000 20.92859 27.42478 MINI EXTERN> 596.60012 -111.85163 0.00000 0.00000 0.00000 MINI CONSTR> 846.58420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1623.24871 0.09492 0.49721 0.00030 MINI INTERN> 83.90093 158.39679 0.00000 21.02789 27.27525 MINI EXTERN> 597.77795 -112.04689 0.00000 0.00000 0.00000 MINI CONSTR> 846.91679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21174 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1623.19317 0.05554 0.14907 0.00013 MINI INTERN> 85.16335 158.16346 0.00000 21.10535 27.59743 MINI EXTERN> 594.52899 -111.82473 0.00000 0.00000 0.00000 MINI CONSTR> 848.45933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1623.18225 0.01092 0.05582 0.00006 MINI INTERN> 84.88606 158.00596 0.00000 21.14372 27.44064 MINI EXTERN> 595.35715 -111.85683 0.00000 0.00000 0.00000 MINI CONSTR> 848.20554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21173 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1623.18052 0.00173 0.10774 0.00006 MINI INTERN> 85.02040 157.89355 0.00000 21.17694 27.43927 MINI EXTERN> 595.11349 -111.82477 0.00000 0.00000 0.00000 MINI CONSTR> 848.36165 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 1623.17807 0.00244 0.03425 0.00003 MINI INTERN> 84.93020 157.92148 0.00000 21.20139 27.48012 MINI EXTERN> 594.94318 -111.84270 0.00000 0.00000 0.00000 MINI CONSTR> 848.54441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21173 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 1623.17757 0.00050 0.01074 0.00001 MINI INTERN> 84.84608 157.91684 0.00000 21.21196 27.46523 MINI EXTERN> 595.06796 -111.85609 0.00000 0.00000 0.00000 MINI CONSTR> 848.52560 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> 53 1623.17741 0.00016 0.00962 0.00001 STPD INTERN> 84.83776 157.90932 0.00000 21.21863 27.46481 STPD EXTERN> 595.06108 -111.85686 0.00000 0.00000 0.00000 STPD CONSTR> 848.54267 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 21173 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21173 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 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 1623.17741 0.00016 0.00962 0.00000 MINI INTERN> 84.83776 157.90932 0.00000 21.21863 27.46481 MINI EXTERN> 595.06108 -111.85686 0.00000 0.00000 0.00000 MINI CONSTR> 848.54267 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 1623.17708 0.00033 0.00201 0.02000 CONJ INTERN> 84.82274 157.87277 0.00000 21.24800 27.46405 CONJ EXTERN> 595.00586 -111.85644 0.00000 0.00000 0.00000 CONJ CONSTR> 848.62009 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 ASP 14 N ) 68.656 ( PROT ASP 14 H ) 54.925 ( PROT ASP 14 CA ) 68.656 ( PROT ASP 14 CB ) 54.925 ( PROT ASP 14 CG ) 54.925 ( PROT ASP 14 OD1 ) 54.925 ( PROT ASP 14 OD2 ) 54.925 ( PROT ASP 14 C ) 68.656 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64191 7.24866 -13.21328 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00168 -0.00130 0.00182 ROTATION MATRIX 1.000000 -0.000030 -0.000096 0.000030 1.000000 0.000074 0.000096 -0.000074 1.000000 AXIS OF ROTATION IS 0.595116 0.765975 -0.243147 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 9.4246 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.178437 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1784" Parameter: A <- "0.1784" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51533 7.24794 -13.42391 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01289 0.00761 -0.01644 ROTATION MATRIX 0.999885 0.010590 0.010840 -0.010465 0.999879 -0.011494 -0.010961 0.011379 0.999875 AXIS OF ROTATION IS -0.602399 -0.574148 0.554499 ANGLE IS 1.09 CENTER OF ROTATION 13.796760 7.106606-13.283683 SHIFT IS -0.021250 TOTAL SQUARE DIFF IS 0.1087 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.059214 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1784" RDCMND substituted energy or value "?RMS" to " 0.0592" Parameter: A <- "0.1784 0.0592" 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 0.1784 0.0592 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 " 848.62" Parameter: H <- "848.62" 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> 0 774.55699 848.62009 18.64826 ENER INTERN> 84.82274 157.87277 0.00000 21.24800 27.46405 ENER EXTERN> 595.00586 -111.85644 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 " 774.56" Parameter: B <- "774.56" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -111.86" Parameter: C <- "-111.86" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 595.01" Parameter: C <- " 483.15" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 483.15" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 84.82" Parameter: D <- "84.82" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 157.87" Parameter: D <- " 242.69" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 21.25" Parameter: D <- " 263.94" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 27.46" Parameter: D <- " 291.40" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 291.40" 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= 774.56 GRMS= 18.65 ELEC= -111.86 VDW= 595.01 RDTITL> *EXTERNAL= 483.15 INTERNAL= 291.40 USER= 0.00 HARM= 848.62 RDTITL> *BOND= 84.82 ANGL= 157.87 DIHE= 21.25 IMPR= 27.46 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21173 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21173 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 1427.13944 -652.58245 8.28484 0.02000 MINI INTERN> 84.82274 157.87277 0.00000 21.24800 27.46405 MINI EXTERN> 595.00586 -111.85644 0.00000 0.00000 0.00000 MINI CONSTR> 652.58245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1360.35439 66.78505 17.37843 0.00864 MINI INTERN> 157.15691 149.39372 0.00000 23.56591 21.18863 MINI EXTERN> 417.40676 -102.56196 0.00000 0.00000 0.00000 MINI CONSTR> 694.20442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21159 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1310.28228 50.07210 7.00978 0.00373 MINI INTERN> 61.69774 161.37733 0.00000 24.75646 22.17791 MINI EXTERN> 470.77265 -115.50204 0.00000 0.00000 0.00000 MINI CONSTR> 685.00224 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1297.74909 12.53320 2.01266 0.00161 MINI INTERN> 76.52528 154.85070 0.00000 24.50284 21.52337 MINI EXTERN> 444.67871 -112.27645 0.00000 0.00000 0.00000 MINI CONSTR> 687.94463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21158 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1295.36606 2.38302 2.59693 0.00167 MINI INTERN> 75.73339 154.32518 0.00000 24.55817 21.47524 MINI EXTERN> 442.11889 -112.62175 0.00000 0.00000 0.00000 MINI CONSTR> 689.77694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1293.36972 1.99634 0.67066 0.00072 MINI INTERN> 72.08238 151.94158 0.00000 24.86323 21.24788 MINI EXTERN> 447.17157 -113.18166 0.00000 0.00000 0.00000 MINI CONSTR> 689.24475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21157 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1292.92930 0.44042 0.28491 0.00031 MINI INTERN> 72.27098 151.64836 0.00000 24.85715 21.21762 MINI EXTERN> 445.59097 -113.16942 0.00000 0.00000 0.00000 MINI CONSTR> 690.51365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1292.78997 0.13933 0.54377 0.00032 MINI INTERN> 72.41008 151.40168 0.00000 24.86552 21.20283 MINI EXTERN> 444.54714 -113.16136 0.00000 0.00000 0.00000 MINI CONSTR> 691.52408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21157 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1292.69653 0.09344 0.15501 0.00014 MINI INTERN> 71.65200 150.99670 0.00000 24.94793 21.17186 MINI EXTERN> 445.56617 -113.27316 0.00000 0.00000 0.00000 MINI CONSTR> 691.63502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 1292.67837 0.01816 0.22296 0.00014 MINI INTERN> 71.46611 150.83168 0.00000 24.97738 21.16225 MINI EXTERN> 445.62375 -113.29781 0.00000 0.00000 0.00000 MINI CONSTR> 691.91500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21157 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 1292.66319 0.01518 0.06203 0.00006 MINI INTERN> 71.63910 150.79832 0.00000 24.96828 21.15523 MINI EXTERN> 445.13474 -113.26307 0.00000 0.00000 0.00000 MINI CONSTR> 692.23060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 1292.65977 0.00342 0.02498 0.00003 MINI INTERN> 71.54508 150.74472 0.00000 24.98364 21.15733 MINI EXTERN> 445.16375 -113.27472 0.00000 0.00000 0.00000 MINI CONSTR> 692.33997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21157 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 1292.65848 0.00129 0.04108 0.00003 MINI INTERN> 71.49263 150.70855 0.00000 24.99497 21.16007 MINI EXTERN> 445.13458 -113.27937 0.00000 0.00000 0.00000 MINI CONSTR> 692.44705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 1292.65808 0.00040 0.04764 0.00003 MINI INTERN> 71.47193 150.69119 0.00000 25.00125 21.16192 MINI EXTERN> 445.09517 -113.27976 0.00000 0.00000 0.00000 MINI CONSTR> 692.51638 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 1292.65761 0.00047 0.00757 0.00001 STPD INTERN> 71.48972 150.66558 0.00000 25.00130 21.15278 STPD EXTERN> 445.10293 -113.27418 0.00000 0.00000 0.00000 STPD CONSTR> 692.51947 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 21157 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21157 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 1292.65761 0.00047 0.00757 0.00000 MINI INTERN> 71.48972 150.66558 0.00000 25.00130 21.15278 MINI EXTERN> 445.10293 -113.27418 0.00000 0.00000 0.00000 MINI CONSTR> 692.51947 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 1292.65739 0.00022 0.00397 0.02000 CONJ INTERN> 71.46026 150.63325 0.00000 25.01173 21.15255 CONJ EXTERN> 445.07134 -113.27442 0.00000 0.00000 0.00000 CONJ CONSTR> 692.60268 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 ASP 14 N ) 44.627 ( PROT ASP 14 H ) 35.701 ( PROT ASP 14 CA ) 44.627 ( PROT ASP 14 CB ) 35.701 ( PROT ASP 14 CG ) 35.701 ( PROT ASP 14 OD1 ) 35.701 ( PROT ASP 14 OD2 ) 35.701 ( PROT ASP 14 C ) 44.627 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64174 7.24845 -13.21323 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00151 -0.00108 0.00177 ROTATION MATRIX 1.000000 -0.000043 -0.000128 0.000043 1.000000 0.000103 0.000128 -0.000103 1.000000 AXIS OF ROTATION IS 0.605952 0.753420 -0.255306 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 11.8179 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.199813 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1998" Parameter: A <- "0.1998" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51450 7.24824 -13.42137 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01373 0.00731 -0.01898 ROTATION MATRIX 0.999846 0.012261 0.012581 -0.012094 0.999838 -0.013304 -0.012742 0.013150 0.999832 AXIS OF ROTATION IS -0.601502 -0.575792 0.553767 ANGLE IS 1.26 CENTER OF ROTATION 13.834231 7.078386-13.271433 SHIFT IS -0.022978 TOTAL SQUARE DIFF IS 0.1574 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.071263 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1998" RDCMND substituted energy or value "?RMS" to " 0.0713" Parameter: A <- "0.1998 0.0713" 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 0.1998 0.0713 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 " 692.60" Parameter: H <- "692.60" 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> 0 600.05471 692.60268 13.59305 ENER INTERN> 71.46026 150.63325 0.00000 25.01173 21.15255 ENER EXTERN> 445.07134 -113.27442 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 " 600.05" Parameter: B <- "600.05" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -113.27" Parameter: C <- "-113.27" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 445.07" Parameter: C <- " 331.80" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 331.80" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 71.46" Parameter: D <- "71.46" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 150.63" Parameter: D <- " 222.09" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 25.01" Parameter: D <- " 247.10" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 21.15" Parameter: D <- " 268.25" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 268.25" 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= 600.05 GRMS= 13.59 ELEC= -113.27 VDW= 445.07 RDTITL> *EXTERNAL= 331.80 INTERNAL= 268.25 USER= 0.00 HARM= 692.60 RDTITL> *BOND= 71.46 ANGL= 150.63 DIHE= 25.01 IMPR= 21.15 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= 600.05 GRMS= 13.59 ELEC= -113.27 VDW= 445.07 RDTITL> *EXTERNAL= 331.80 INTERNAL= 268.25 USER= 0.00 HARM= 692.60 RDTITL> *BOND= 71.46 ANGL= 150.63 DIHE= 25.01 IMPR= 21.15 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= 600.05 GRMS= 13.59 ELEC= -113.27 VDW= 445.07 RDTITL> *EXTERNAL= 331.80 INTERNAL= 268.25 USER= 0.00 HARM= 692.60 RDTITL> *BOND= 71.46 ANGL= 150.63 DIHE= 25.01 IMPR= 21.15 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 2400 0.1998 0.0713 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21157 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21157 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 1137.90158 -537.84687 6.10480 0.02000 MINI INTERN> 71.46026 150.63325 0.00000 25.01173 21.15255 MINI EXTERN> 445.07134 -113.27442 0.00000 0.00000 0.00000 MINI CONSTR> 537.84687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1092.91819 44.98339 16.46099 0.00864 MINI INTERN> 129.28311 142.56374 0.00000 27.20236 16.51567 MINI EXTERN> 315.40269 -106.86093 0.00000 0.00000 0.00000 MINI CONSTR> 568.81154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21137 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1044.61420 48.30400 6.33227 0.00373 MINI INTERN> 55.52471 150.87747 0.00000 29.34992 17.44963 MINI EXTERN> 343.31403 -116.55346 0.00000 0.00000 0.00000 MINI CONSTR> 564.65190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1036.31271 8.30148 6.21364 0.00387 MINI INTERN> 57.10081 145.49400 0.00000 29.63656 16.88969 MINI EXTERN> 339.78830 -116.42663 0.00000 0.00000 0.00000 MINI CONSTR> 563.82999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21135 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1026.75335 9.55936 2.57778 0.00167 MINI INTERN> 62.61167 142.86586 0.00000 28.80372 16.96486 MINI EXTERN> 322.73321 -115.01183 0.00000 0.00000 0.00000 MINI CONSTR> 567.78586 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1024.84454 1.90881 3.14959 0.00173 MINI INTERN> 64.42897 140.80789 0.00000 28.82693 16.97132 MINI EXTERN> 319.16277 -114.90839 0.00000 0.00000 0.00000 MINI CONSTR> 569.55505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21135 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1022.46828 2.37626 0.52126 0.00075 MINI INTERN> 57.75128 140.58371 0.00000 29.28883 16.91504 MINI EXTERN> 324.31927 -115.77576 0.00000 0.00000 0.00000 MINI CONSTR> 569.38590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1021.90305 0.56523 1.17615 0.00078 MINI INTERN> 56.34153 139.93183 0.00000 29.46457 16.90764 MINI EXTERN> 324.96303 -116.03784 0.00000 0.00000 0.00000 MINI CONSTR> 570.33228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21134 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1021.40106 0.50199 0.34240 0.00034 MINI INTERN> 57.65689 139.34129 0.00000 29.31342 16.92468 MINI EXTERN> 322.50379 -115.88062 0.00000 0.00000 0.00000 MINI CONSTR> 571.54161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 1021.22907 0.17199 0.32753 0.00035 MINI INTERN> 57.42524 139.05808 0.00000 29.33080 16.92781 MINI EXTERN> 322.22798 -115.94407 0.00000 0.00000 0.00000 MINI CONSTR> 572.20323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21133 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 1021.18064 0.04843 0.54455 0.00036 MINI INTERN> 57.66507 138.84603 0.00000 29.30955 16.93600 MINI EXTERN> 321.63664 -115.93733 0.00000 0.00000 0.00000 MINI CONSTR> 572.72467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 1021.09521 0.08543 0.21190 0.00016 MINI INTERN> 56.64075 138.90418 0.00000 29.40879 16.96649 MINI EXTERN> 322.31206 -116.07828 0.00000 0.00000 0.00000 MINI CONSTR> 572.94121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21134 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 1021.07516 0.02005 0.25437 0.00016 MINI INTERN> 56.70925 138.81470 0.00000 29.40888 16.98743 MINI EXTERN> 321.97330 -116.07856 0.00000 0.00000 0.00000 MINI CONSTR> 573.26017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 1021.05476 0.02041 0.06152 0.00007 MINI INTERN> 56.78254 138.61994 0.00000 29.39634 16.94548 MINI EXTERN> 322.01111 -116.07585 0.00000 0.00000 0.00000 MINI CONSTR> 573.37519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21133 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 1021.04861 0.00614 0.07988 0.00007 MINI INTERN> 56.89397 138.49616 0.00000 29.39871 16.94344 MINI EXTERN> 321.85997 -116.05940 0.00000 0.00000 0.00000 MINI CONSTR> 573.51576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 1021.04694 0.00167 0.12022 0.00007 MINI INTERN> 57.02259 138.39393 0.00000 29.39911 16.93933 MINI EXTERN> 321.73561 -116.03983 0.00000 0.00000 0.00000 MINI CONSTR> 573.59621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21133 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 1021.04310 0.00384 0.03652 0.00003 MINI INTERN> 56.67268 138.57101 0.00000 29.40331 16.95920 MINI EXTERN> 321.86692 -116.11318 0.00000 0.00000 0.00000 MINI CONSTR> 573.68316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 1021.04215 0.00096 0.05083 0.00003 MINI INTERN> 56.76122 138.50948 0.00000 29.40428 16.95953 MINI EXTERN> 321.76901 -116.09882 0.00000 0.00000 0.00000 MINI CONSTR> 573.73745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21133 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 1021.04112 0.00102 0.01372 0.00001 MINI INTERN> 56.69591 138.51569 0.00000 29.40210 16.95443 MINI EXTERN> 321.82435 -116.11696 0.00000 0.00000 0.00000 MINI CONSTR> 573.76561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 1021.04063 0.00049 0.01182 0.00002 MINI INTERN> 56.69789 138.50479 0.00000 29.40198 16.95460 MINI EXTERN> 321.80439 -116.12038 0.00000 0.00000 0.00000 MINI CONSTR> 573.79736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21133 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 1021.04031 0.00032 0.02190 0.00002 MINI INTERN> 56.70182 138.49016 0.00000 29.40101 16.95254 MINI EXTERN> 321.79584 -116.12430 0.00000 0.00000 0.00000 MINI CONSTR> 573.82325 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 1021.04012 0.00019 0.00813 0.00001 STPD INTERN> 56.68613 138.50039 0.00000 29.40164 16.95534 STPD EXTERN> 321.78925 -116.12859 0.00000 0.00000 0.00000 STPD CONSTR> 573.83596 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 21133 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21133 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 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 1021.04012 0.00019 0.00813 0.00000 MINI INTERN> 56.68613 138.50039 0.00000 29.40164 16.95534 MINI EXTERN> 321.78925 -116.12859 0.00000 0.00000 0.00000 MINI CONSTR> 573.83596 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 1021.03940 0.00073 0.00361 0.02000 CONJ INTERN> 56.67882 138.47299 0.00000 29.39966 16.95620 CONJ EXTERN> 321.72369 -116.15155 0.00000 0.00000 0.00000 CONJ CONSTR> 573.95959 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 ASP 14 N ) 29.007 ( PROT ASP 14 H ) 23.206 ( PROT ASP 14 CA ) 29.007 ( PROT ASP 14 CB ) 23.206 ( PROT ASP 14 CG ) 23.206 ( PROT ASP 14 OD1 ) 23.206 ( PROT ASP 14 OD2 ) 23.206 ( PROT ASP 14 C ) 29.007 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64145 7.24815 -13.21309 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00122 -0.00079 0.00163 ROTATION MATRIX 1.000000 -0.000060 -0.000169 0.000060 1.000000 0.000141 0.000169 -0.000141 1.000000 AXIS OF ROTATION IS 0.619451 0.740418 -0.260887 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 15.0338 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.225366 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2254" Parameter: A <- "0.2254" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51376 7.24807 -13.41847 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01447 0.00748 -0.02188 ROTATION MATRIX 0.999801 0.013913 0.014282 -0.013698 0.999792 -0.015084 -0.014489 0.014885 0.999784 AXIS OF ROTATION IS -0.600787 -0.576784 0.553512 ANGLE IS 1.43 CENTER OF ROTATION 13.861101 7.045803-13.274924 SHIFT IS -0.025117 TOTAL SQUARE DIFF IS 0.2161 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.083502 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2254" RDCMND substituted energy or value "?RMS" to " 0.0835" Parameter: A <- "0.2254 0.0835" 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 0.2254 0.0835 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 " 573.96" Parameter: H <- "573.96" 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> 0 447.07981 573.95959 9.98852 ENER INTERN> 56.67882 138.47299 0.00000 29.39966 16.95620 ENER EXTERN> 321.72369 -116.15155 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 " 447.08" Parameter: B <- "447.08" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -116.15" Parameter: C <- "-116.15" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 321.72" Parameter: C <- " 205.57" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 205.57" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 56.68" Parameter: D <- "56.68" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 138.47" Parameter: D <- " 195.15" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 29.40" Parameter: D <- " 224.55" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 16.96" Parameter: D <- " 241.51" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 241.51" 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= 447.08 GRMS= 9.99 ELEC= -116.15 VDW= 321.72 RDTITL> *EXTERNAL= 205.57 INTERNAL= 241.51 USER= 0.00 HARM= 573.96 RDTITL> *BOND= 56.68 ANGL= 138.47 DIHE= 29.40 IMPR= 16.96 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21133 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21133 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> 0 893.38564 -446.30583 4.48848 0.02000 MINI INTERN> 56.67882 138.47299 0.00000 29.39966 16.95620 MINI EXTERN> 321.72369 -116.15155 0.00000 0.00000 0.00000 MINI CONSTR> 446.30583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 860.07380 33.31184 13.69025 0.00864 MINI INTERN> 71.95430 133.18040 0.00000 32.11511 13.90026 MINI EXTERN> 255.56458 -116.00797 0.00000 0.00000 0.00000 MINI CONSTR> 469.36712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21113 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 820.42488 39.64892 5.35159 0.00373 MINI INTERN> 49.77607 135.66615 0.00000 33.85368 15.89724 MINI EXTERN> 227.79438 -117.22049 0.00000 0.00000 0.00000 MINI CONSTR> 474.65785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 809.61454 10.81034 1.60615 0.00161 MINI INTERN> 45.96860 130.22515 0.00000 33.98564 15.22970 MINI EXTERN> 228.24540 -117.70000 0.00000 0.00000 0.00000 MINI CONSTR> 473.66005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21109 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 805.27889 4.33565 2.95288 0.00167 MINI INTERN> 46.37341 128.05312 0.00000 34.19172 15.34748 MINI EXTERN> 224.79655 -117.82833 0.00000 0.00000 0.00000 MINI CONSTR> 474.34492 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 802.54150 2.73739 3.45034 0.00173 MINI INTERN> 46.30270 126.83607 0.00000 34.31887 15.45029 MINI EXTERN> 222.52087 -117.98233 0.00000 0.00000 0.00000 MINI CONSTR> 475.09503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21109 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 800.54904 1.99246 3.23211 0.00180 MINI INTERN> 45.63114 126.23914 0.00000 34.37972 15.54039 MINI EXTERN> 221.17622 -118.13647 0.00000 0.00000 0.00000 MINI CONSTR> 475.71890 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 797.85561 2.69343 1.20646 0.00078 MINI INTERN> 42.67201 126.21433 0.00000 34.38296 15.68663 MINI EXTERN> 221.14898 -118.64049 0.00000 0.00000 0.00000 MINI CONSTR> 476.39120 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21107 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 796.80254 1.05307 0.92855 0.00080 MINI INTERN> 42.46063 125.64310 0.00000 34.41062 15.71260 MINI EXTERN> 220.35627 -118.73166 0.00000 0.00000 0.00000 MINI CONSTR> 476.95100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 796.30420 0.49835 1.42181 0.00083 MINI INTERN> 42.16084 125.42989 0.00000 34.41576 15.74612 MINI EXTERN> 219.98698 -118.88451 0.00000 0.00000 0.00000 MINI CONSTR> 477.44913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21107 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 795.58998 0.71421 0.42797 0.00036 MINI INTERN> 42.50877 124.76141 0.00000 34.43996 15.72028 MINI EXTERN> 219.10398 -118.79730 0.00000 0.00000 0.00000 MINI CONSTR> 477.85288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 795.27153 0.31845 0.31559 0.00037 MINI INTERN> 42.36196 124.59963 0.00000 34.43403 15.73195 MINI EXTERN> 218.80250 -118.87083 0.00000 0.00000 0.00000 MINI CONSTR> 478.21229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21110 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 795.03985 0.23168 0.68766 0.00039 MINI INTERN> 42.54501 124.28673 0.00000 34.43221 15.72308 MINI EXTERN> 218.32921 -118.88510 0.00000 0.00000 0.00000 MINI CONSTR> 478.60872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 794.88240 0.15745 0.77506 0.00040 MINI INTERN> 42.55229 124.12959 0.00000 34.42149 15.72051 MINI EXTERN> 218.06371 -118.92948 0.00000 0.00000 0.00000 MINI CONSTR> 478.92428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21110 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 794.76665 0.11575 0.73127 0.00042 MINI INTERN> 42.52296 124.04938 0.00000 34.40749 15.72080 MINI EXTERN> 217.86750 -118.96808 0.00000 0.00000 0.00000 MINI CONSTR> 479.16661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 794.61032 0.15633 0.24626 0.00018 MINI INTERN> 42.06105 124.17539 0.00000 34.37861 15.74030 MINI EXTERN> 217.92831 -119.10973 0.00000 0.00000 0.00000 MINI CONSTR> 479.43638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 794.54350 0.06682 0.19650 0.00019 MINI INTERN> 42.06428 124.10187 0.00000 34.36459 15.73461 MINI EXTERN> 217.77792 -119.14214 0.00000 0.00000 0.00000 MINI CONSTR> 479.64236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 794.50287 0.04063 0.32584 0.00019 MINI INTERN> 42.00975 124.08667 0.00000 34.34616 15.73354 MINI EXTERN> 217.67098 -119.19096 0.00000 0.00000 0.00000 MINI CONSTR> 479.84673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 794.46904 0.03384 0.38407 0.00020 MINI INTERN> 42.01121 124.05200 0.00000 34.32826 15.72936 MINI EXTERN> 217.53219 -119.22366 0.00000 0.00000 0.00000 MINI CONSTR> 480.03969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 794.44143 0.02761 0.35676 0.00021 MINI INTERN> 41.99787 124.02043 0.00000 34.31653 15.72344 MINI EXTERN> 217.46460 -119.25241 0.00000 0.00000 0.00000 MINI CONSTR> 480.17098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 794.40209 0.03933 0.11594 0.00009 MINI INTERN> 42.10422 123.89981 0.00000 34.30950 15.70695 MINI EXTERN> 217.34580 -119.25511 0.00000 0.00000 0.00000 MINI CONSTR> 480.29093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 794.38530 0.01679 0.07298 0.00009 MINI INTERN> 42.09430 123.89205 0.00000 34.29665 15.70419 MINI EXTERN> 217.27165 -119.27833 0.00000 0.00000 0.00000 MINI CONSTR> 480.40479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 794.36942 0.01588 0.16295 0.00010 MINI INTERN> 42.10800 123.84977 0.00000 34.28302 15.69468 MINI EXTERN> 217.19823 -119.30843 0.00000 0.00000 0.00000 MINI CONSTR> 480.54415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 794.35625 0.01316 0.16805 0.00010 MINI INTERN> 42.10174 123.83514 0.00000 34.27014 15.68925 MINI EXTERN> 217.13458 -119.33451 0.00000 0.00000 0.00000 MINI CONSTR> 480.65992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 794.34537 0.01089 0.18555 0.00010 MINI INTERN> 42.09582 123.82143 0.00000 34.25791 15.68353 MINI EXTERN> 217.07677 -119.35961 0.00000 0.00000 0.00000 MINI CONSTR> 480.76951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 794.33586 0.00951 0.17593 0.00011 MINI INTERN> 42.10193 123.81081 0.00000 34.24704 15.67951 MINI EXTERN> 217.01318 -119.37720 0.00000 0.00000 0.00000 MINI CONSTR> 480.86059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 794.32293 0.01293 0.05205 0.00005 MINI INTERN> 42.11359 123.81866 0.00000 34.23238 15.67923 MINI EXTERN> 216.90171 -119.38994 0.00000 0.00000 0.00000 MINI CONSTR> 480.96730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 794.31930 0.00364 0.18825 0.00012 MINI INTERN> 42.09277 123.79429 0.00000 34.22559 15.66971 MINI EXTERN> 216.90834 -119.41803 0.00000 0.00000 0.00000 MINI CONSTR> 481.04662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 794.30684 0.01245 0.05654 0.00005 MINI INTERN> 42.12692 123.79960 0.00000 34.21045 15.67013 MINI EXTERN> 216.77442 -119.42602 0.00000 0.00000 0.00000 MINI CONSTR> 481.15134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 794.30067 0.00617 0.04428 0.00005 MINI INTERN> 42.12459 123.79158 0.00000 34.20262 15.66566 MINI EXTERN> 216.73659 -119.44174 0.00000 0.00000 0.00000 MINI CONSTR> 481.22137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21110 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 794.29397 0.00670 0.04345 0.00005 MINI INTERN> 42.12946 123.78386 0.00000 34.19286 15.66118 MINI EXTERN> 216.68042 -119.45814 0.00000 0.00000 0.00000 MINI CONSTR> 481.30433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 794.28798 0.00599 0.08682 0.00006 MINI INTERN> 42.15350 123.77803 0.00000 34.18086 15.65803 MINI EXTERN> 216.59262 -119.47167 0.00000 0.00000 0.00000 MINI CONSTR> 481.39659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21110 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 794.28204 0.00593 0.05323 0.00006 MINI INTERN> 42.14485 123.77075 0.00000 34.17400 15.65301 MINI EXTERN> 216.56448 -119.48758 0.00000 0.00000 0.00000 MINI CONSTR> 481.46253 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 794.27659 0.00545 0.06137 0.00006 MINI INTERN> 42.15346 123.76473 0.00000 34.16485 15.64903 MINI EXTERN> 216.50653 -119.50133 0.00000 0.00000 0.00000 MINI CONSTR> 481.53932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 794.27267 0.00392 0.09672 0.00006 MINI INTERN> 42.17097 123.76072 0.00000 34.15602 15.64634 MINI EXTERN> 216.44120 -119.51139 0.00000 0.00000 0.00000 MINI CONSTR> 481.60881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 794.26800 0.00467 0.10433 0.00006 MINI INTERN> 42.18041 123.75506 0.00000 34.14749 15.64266 MINI EXTERN> 216.38578 -119.52334 0.00000 0.00000 0.00000 MINI CONSTR> 481.67996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 794.26392 0.00409 0.11610 0.00007 MINI INTERN> 42.19039 123.75013 0.00000 34.13945 15.63924 MINI EXTERN> 216.33194 -119.53427 0.00000 0.00000 0.00000 MINI CONSTR> 481.74703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 794.26008 0.00384 0.10906 0.00007 MINI INTERN> 42.18900 123.74633 0.00000 34.13395 15.63551 MINI EXTERN> 216.30038 -119.54527 0.00000 0.00000 0.00000 MINI CONSTR> 481.80018 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 794.25598 0.00409 0.10979 0.00007 MINI INTERN> 42.19522 123.74125 0.00000 34.12659 15.63185 MINI EXTERN> 216.25327 -119.55610 0.00000 0.00000 0.00000 MINI CONSTR> 481.86392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 794.25089 0.00510 0.03479 0.00003 MINI INTERN> 42.14600 123.73581 0.00000 34.12614 15.62352 MINI EXTERN> 216.28976 -119.57732 0.00000 0.00000 0.00000 MINI CONSTR> 481.90698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 794.24949 0.00140 0.12051 0.00008 MINI INTERN> 42.20615 123.73373 0.00000 34.11429 15.62530 MINI EXTERN> 216.17061 -119.57473 0.00000 0.00000 0.00000 MINI CONSTR> 481.97414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 794.24620 0.00328 0.12697 0.00008 MINI INTERN> 42.21578 123.72864 0.00000 34.10736 15.62203 MINI EXTERN> 216.12268 -119.58348 0.00000 0.00000 0.00000 MINI CONSTR> 482.03319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 794.24086 0.00534 0.04300 0.00003 MINI INTERN> 42.14540 123.72522 0.00000 34.10964 15.61169 MINI EXTERN> 216.18660 -119.60902 0.00000 0.00000 0.00000 MINI CONSTR> 482.07133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 794.23825 0.00261 0.02856 0.00004 MINI INTERN> 42.15913 123.72210 0.00000 34.10401 15.60992 MINI EXTERN> 216.14111 -119.61363 0.00000 0.00000 0.00000 MINI CONSTR> 482.11561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21111 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 794.23519 0.00306 0.02858 0.00004 MINI INTERN> 42.16018 123.71882 0.00000 34.09874 15.60611 MINI EXTERN> 216.10584 -119.62316 0.00000 0.00000 0.00000 MINI CONSTR> 482.16865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 794.23247 0.00272 0.05921 0.00004 MINI INTERN> 42.14011 123.71682 0.00000 34.09570 15.60011 MINI EXTERN> 216.09732 -119.63792 0.00000 0.00000 0.00000 MINI CONSTR> 482.22033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 794.22969 0.00277 0.03559 0.00004 MINI INTERN> 42.15613 123.71333 0.00000 34.08968 15.59828 MINI EXTERN> 216.04704 -119.64209 0.00000 0.00000 0.00000 MINI CONSTR> 482.26732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 794.22709 0.00260 0.04045 0.00004 MINI INTERN> 42.15378 123.71087 0.00000 34.08534 15.59436 MINI EXTERN> 216.01812 -119.65132 0.00000 0.00000 0.00000 MINI CONSTR> 482.31593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 794.22517 0.00192 0.06583 0.00004 MINI INTERN> 42.13923 123.70978 0.00000 34.08295 15.58968 MINI EXTERN> 216.00873 -119.66234 0.00000 0.00000 0.00000 MINI CONSTR> 482.35715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 794.22286 0.00231 0.06967 0.00004 MINI INTERN> 42.13733 123.70792 0.00000 34.07896 15.58603 MINI EXTERN> 215.98054 -119.67067 0.00000 0.00000 0.00000 MINI CONSTR> 482.40276 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 794.22077 0.00210 0.07708 0.00005 MINI INTERN> 42.13327 123.70643 0.00000 34.07538 15.58230 MINI EXTERN> 215.95602 -119.67915 0.00000 0.00000 0.00000 MINI CONSTR> 482.44651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 794.21882 0.00195 0.07339 0.00005 MINI INTERN> 42.13684 123.70392 0.00000 34.07164 15.57964 MINI EXTERN> 215.92711 -119.68451 0.00000 0.00000 0.00000 MINI CONSTR> 482.48416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 794.21679 0.00203 0.07569 0.00005 MINI INTERN> 42.13558 123.70238 0.00000 34.06799 15.57630 MINI EXTERN> 215.90003 -119.69178 0.00000 0.00000 0.00000 MINI CONSTR> 482.52629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 794.21417 0.00261 0.02351 0.00002 MINI INTERN> 42.18726 123.69323 0.00000 34.05881 15.57741 MINI EXTERN> 215.81113 -119.68613 0.00000 0.00000 0.00000 MINI CONSTR> 482.57245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 794.21328 0.00090 0.08279 0.00005 MINI INTERN> 42.13237 123.69932 0.00000 34.06161 15.56997 MINI EXTERN> 215.85236 -119.70493 0.00000 0.00000 0.00000 MINI CONSTR> 482.60258 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 794.21153 0.00175 0.08564 0.00006 MINI INTERN> 42.13106 123.69794 0.00000 34.05836 15.56682 MINI EXTERN> 215.82733 -119.71147 0.00000 0.00000 0.00000 MINI CONSTR> 482.64149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 794.20876 0.00277 0.02541 0.00002 MINI INTERN> 42.19508 123.68578 0.00000 34.04792 15.56853 MINI EXTERN> 215.72467 -119.70269 0.00000 0.00000 0.00000 MINI CONSTR> 482.68947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 794.20730 0.00146 0.02116 0.00002 MINI INTERN> 42.19058 123.68490 0.00000 34.04573 15.56564 MINI EXTERN> 215.70881 -119.70860 0.00000 0.00000 0.00000 MINI CONSTR> 482.72023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 794.20568 0.00162 0.02070 0.00003 MINI INTERN> 42.19138 123.68288 0.00000 34.04259 15.56270 MINI EXTERN> 215.68349 -119.71391 0.00000 0.00000 0.00000 MINI CONSTR> 482.75655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 794.20408 0.00160 0.02067 0.00003 MINI INTERN> 42.19299 123.68071 0.00000 34.03937 15.55978 MINI EXTERN> 215.65704 -119.71897 0.00000 0.00000 0.00000 MINI CONSTR> 482.79315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 794.20257 0.00151 0.04039 0.00003 MINI INTERN> 42.21165 123.67517 0.00000 34.03415 15.55759 MINI EXTERN> 215.60896 -119.72025 0.00000 0.00000 0.00000 MINI CONSTR> 482.83529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 794.20110 0.00147 0.02568 0.00003 MINI INTERN> 42.20092 123.67558 0.00000 34.03273 15.55435 MINI EXTERN> 215.60015 -119.72729 0.00000 0.00000 0.00000 MINI CONSTR> 482.86466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 794.19965 0.00144 0.02669 0.00003 MINI INTERN> 42.20220 123.67352 0.00000 34.02979 15.55147 MINI EXTERN> 215.57505 -119.73183 0.00000 0.00000 0.00000 MINI CONSTR> 482.89945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 794.19829 0.00136 0.03138 0.00003 MINI INTERN> 42.20598 123.67103 0.00000 34.02667 15.54877 MINI EXTERN> 215.54745 -119.73559 0.00000 0.00000 0.00000 MINI CONSTR> 482.93398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 794.19726 0.00103 0.04790 0.00003 MINI INTERN> 42.21735 123.66718 0.00000 34.02308 15.54676 MINI EXTERN> 215.51385 -119.73687 0.00000 0.00000 0.00000 MINI CONSTR> 482.96590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 794.19599 0.00127 0.05031 0.00003 MINI INTERN> 42.21724 123.66546 0.00000 34.02057 15.54384 MINI EXTERN> 215.49142 -119.74100 0.00000 0.00000 0.00000 MINI CONSTR> 482.99846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 794.19481 0.00118 0.05523 0.00003 MINI INTERN> 42.21797 123.66370 0.00000 34.01803 15.54100 MINI EXTERN> 215.46833 -119.74474 0.00000 0.00000 0.00000 MINI CONSTR> 483.03051 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 794.19370 0.00110 0.05300 0.00004 MINI INTERN> 42.21746 123.66237 0.00000 34.01592 15.53865 MINI EXTERN> 215.44997 -119.74849 0.00000 0.00000 0.00000 MINI CONSTR> 483.05782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 794.19257 0.00113 0.05525 0.00004 MINI INTERN> 42.21647 123.66105 0.00000 34.01373 15.53586 MINI EXTERN> 215.42988 -119.75235 0.00000 0.00000 0.00000 MINI CONSTR> 483.08793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 794.19144 0.00113 0.05605 0.00004 MINI INTERN> 42.21372 123.66018 0.00000 34.01172 15.53301 MINI EXTERN> 215.41133 -119.75621 0.00000 0.00000 0.00000 MINI CONSTR> 483.11769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 794.19001 0.00143 0.01805 0.00002 MINI INTERN> 42.19489 123.66266 0.00000 34.01116 15.53054 MINI EXTERN> 215.41534 -119.76685 0.00000 0.00000 0.00000 MINI CONSTR> 483.14226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 794.18954 0.00047 0.06201 0.00004 MINI INTERN> 42.21526 123.65709 0.00000 34.00750 15.52827 MINI EXTERN> 215.37178 -119.76227 0.00000 0.00000 0.00000 MINI CONSTR> 483.17191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 794.18853 0.00101 0.06426 0.00004 MINI INTERN> 42.21272 123.65642 0.00000 34.00572 15.52545 MINI EXTERN> 215.35437 -119.76637 0.00000 0.00000 0.00000 MINI CONSTR> 483.20021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 794.18758 0.00095 0.06848 0.00004 MINI INTERN> 42.20692 123.65584 0.00000 34.00406 15.52259 MINI EXTERN> 215.33815 -119.76829 0.00000 0.00000 0.00000 MINI CONSTR> 483.22830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 794.18601 0.00157 0.02307 0.00002 MINI INTERN> 42.19690 123.65640 0.00000 34.00236 15.52129 MINI EXTERN> 215.33561 -119.78051 0.00000 0.00000 0.00000 MINI CONSTR> 483.25396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 794.18520 0.00080 0.01563 0.00002 MINI INTERN> 42.19833 123.65511 0.00000 34.00076 15.51926 MINI EXTERN> 215.31821 -119.78183 0.00000 0.00000 0.00000 MINI CONSTR> 483.27537 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 794.18425 0.00095 0.01568 0.00002 MINI INTERN> 42.19857 123.65359 0.00000 33.99865 15.51694 MINI EXTERN> 215.29844 -119.78478 0.00000 0.00000 0.00000 MINI CONSTR> 483.30285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 794.18335 0.00091 0.03043 0.00002 MINI INTERN> 42.19988 123.65153 0.00000 33.99605 15.51491 MINI EXTERN> 215.27782 -119.78982 0.00000 0.00000 0.00000 MINI CONSTR> 483.33297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 794.18247 0.00087 0.01988 0.00002 MINI INTERN> 42.19957 123.65036 0.00000 33.99450 15.51263 MINI EXTERN> 215.26031 -119.79083 0.00000 0.00000 0.00000 MINI CONSTR> 483.35593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 794.18165 0.00082 0.02411 0.00002 MINI INTERN> 42.20145 123.64895 0.00000 33.99246 15.51061 MINI EXTERN> 215.24152 -119.79479 0.00000 0.00000 0.00000 MINI CONSTR> 483.38146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 794.18099 0.00066 0.03548 0.00002 MINI INTERN> 42.20186 123.64718 0.00000 33.99046 15.50898 MINI EXTERN> 215.22498 -119.79763 0.00000 0.00000 0.00000 MINI CONSTR> 483.40516 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 794.18011 0.00089 0.02200 0.00002 MINI INTERN> 42.20077 123.64625 0.00000 33.98904 15.50660 MINI EXTERN> 215.20796 -119.79843 0.00000 0.00000 0.00000 MINI CONSTR> 483.42792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 794.17948 0.00062 0.03758 0.00003 MINI INTERN> 42.20329 123.64428 0.00000 33.98683 15.50510 MINI EXTERN> 215.19000 -119.80234 0.00000 0.00000 0.00000 MINI CONSTR> 483.45232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 794.17871 0.00077 0.04017 0.00003 MINI INTERN> 42.20470 123.64223 0.00000 33.98477 15.50311 MINI EXTERN> 215.17048 -119.80425 0.00000 0.00000 0.00000 MINI CONSTR> 483.47766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 794.17803 0.00069 0.04575 0.00003 MINI INTERN> 42.20770 123.64114 0.00000 33.98278 15.50128 MINI EXTERN> 215.15199 -119.80849 0.00000 0.00000 0.00000 MINI CONSTR> 483.50162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 794.17736 0.00067 0.04234 0.00003 MINI INTERN> 42.20607 123.63972 0.00000 33.98146 15.49948 MINI EXTERN> 215.13801 -119.80899 0.00000 0.00000 0.00000 MINI CONSTR> 483.52161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 794.17665 0.00071 0.04421 0.00003 MINI INTERN> 42.20723 123.63802 0.00000 33.97954 15.49759 MINI EXTERN> 215.11967 -119.81096 0.00000 0.00000 0.00000 MINI CONSTR> 483.54557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 794.17593 0.00072 0.04517 0.00003 MINI INTERN> 42.21007 123.63622 0.00000 33.97768 15.49566 MINI EXTERN> 215.10073 -119.81380 0.00000 0.00000 0.00000 MINI CONSTR> 483.56936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 794.17503 0.00090 0.01462 0.00001 MINI INTERN> 42.19766 123.63889 0.00000 33.97832 15.49207 MINI EXTERN> 215.09431 -119.81285 0.00000 0.00000 0.00000 MINI CONSTR> 483.58662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 794.17474 0.00029 0.04917 0.00003 MINI INTERN> 42.20866 123.63392 0.00000 33.97458 15.49229 MINI EXTERN> 215.07100 -119.81656 0.00000 0.00000 0.00000 MINI CONSTR> 483.61085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 794.17412 0.00062 0.05310 0.00003 MINI INTERN> 42.21439 123.63196 0.00000 33.97291 15.49043 MINI EXTERN> 215.05196 -119.82071 0.00000 0.00000 0.00000 MINI CONSTR> 483.63319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 794.17315 0.00097 0.01741 0.00001 MINI INTERN> 42.19598 123.63588 0.00000 33.97413 15.48643 MINI EXTERN> 215.04955 -119.81830 0.00000 0.00000 0.00000 MINI CONSTR> 483.64947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 794.17262 0.00053 0.01277 0.00002 MINI INTERN> 42.19770 123.63425 0.00000 33.97254 15.48529 MINI EXTERN> 215.03561 -119.81996 0.00000 0.00000 0.00000 MINI CONSTR> 483.66719 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 794.17201 0.00061 0.01318 0.00002 MINI INTERN> 42.19753 123.63318 0.00000 33.97116 15.48346 MINI EXTERN> 215.02059 -119.82185 0.00000 0.00000 0.00000 MINI CONSTR> 483.68794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 794.17143 0.00059 0.02235 0.00002 MINI INTERN> 42.19336 123.63316 0.00000 33.97030 15.48100 MINI EXTERN> 215.00746 -119.82300 0.00000 0.00000 0.00000 MINI CONSTR> 483.70913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 794.17091 0.00051 0.01249 0.00002 MINI INTERN> 42.19728 123.63102 0.00000 33.96849 15.48026 MINI EXTERN> 214.99289 -119.82497 0.00000 0.00000 0.00000 MINI CONSTR> 483.72594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 794.17033 0.00059 0.02573 0.00002 MINI INTERN> 42.19173 123.63135 0.00000 33.96782 15.47747 MINI EXTERN> 214.97986 -119.82607 0.00000 0.00000 0.00000 MINI CONSTR> 483.74816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 794.16975 0.00058 0.01592 0.00002 MINI INTERN> 42.19478 123.62937 0.00000 33.96599 15.47641 MINI EXTERN> 214.96410 -119.82811 0.00000 0.00000 0.00000 MINI CONSTR> 483.76720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 794.16919 0.00056 0.01876 0.00002 MINI INTERN> 42.19308 123.62824 0.00000 33.96477 15.47453 MINI EXTERN> 214.94992 -119.82889 0.00000 0.00000 0.00000 MINI CONSTR> 483.78753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 794.16876 0.00043 0.02923 0.00002 MINI INTERN> 42.18946 123.62850 0.00000 33.96416 15.47241 MINI EXTERN> 214.93930 -119.83024 0.00000 0.00000 0.00000 MINI CONSTR> 483.80517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 794.16823 0.00053 0.03009 0.00002 MINI INTERN> 42.19002 123.62774 0.00000 33.96282 15.47079 MINI EXTERN> 214.92501 -119.83278 0.00000 0.00000 0.00000 MINI CONSTR> 483.82464 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> 500 794.16823 0.00053 0.03009 0.00002 STPD INTERN> 42.19002 123.62774 0.00000 33.96282 15.47079 STPD EXTERN> 214.92501 -119.83278 0.00000 0.00000 0.00000 STPD CONSTR> 483.82464 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 21112 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21112 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> 0 794.16823 0.00053 0.03009 0.00000 MINI INTERN> 42.19002 123.62774 0.00000 33.96282 15.47079 MINI EXTERN> 214.92501 -119.83278 0.00000 0.00000 0.00000 MINI CONSTR> 483.82464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 794.14260 0.02563 0.04418 0.00937 MINI INTERN> 41.97939 123.41366 0.00000 33.85765 15.37755 MINI EXTERN> 213.57607 -119.85684 0.00000 0.00000 0.00000 MINI CONSTR> 485.79513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 794.13955 0.00305 0.02421 0.00402 MINI INTERN> 42.01895 123.48881 0.00000 33.83981 15.33765 MINI EXTERN> 213.46663 -119.85570 0.00000 0.00000 0.00000 MINI CONSTR> 485.84340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 794.13851 0.00105 0.01818 0.00164 MINI INTERN> 42.05382 123.50933 0.00000 33.83022 15.32709 MINI EXTERN> 213.46905 -119.85568 0.00000 0.00000 0.00000 MINI CONSTR> 485.80468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 794.13779 0.00071 0.01654 0.00231 MINI INTERN> 42.05762 123.48477 0.00000 33.82747 15.32371 MINI EXTERN> 213.40718 -119.85579 0.00000 0.00000 0.00000 MINI CONSTR> 485.89283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 794.13709 0.00070 0.01759 0.00248 MINI INTERN> 42.03193 123.46368 0.00000 33.82955 15.33120 MINI EXTERN> 213.33372 -119.85204 0.00000 0.00000 0.00000 MINI CONSTR> 485.99904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 794.13645 0.00064 0.01323 0.00216 MINI INTERN> 42.01142 123.46721 0.00000 33.83231 15.32940 MINI EXTERN> 213.30528 -119.83593 0.00000 0.00000 0.00000 MINI CONSTR> 486.02676 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> 33 794.13626 0.00019 0.00923 0.02000 CONJ INTERN> 42.02047 123.47882 0.00000 33.83029 15.32478 CONJ EXTERN> 213.30295 -119.82861 0.00000 0.00000 0.00000 CONJ CONSTR> 486.00755 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 ASP 14 N ) 18.855 ( PROT ASP 14 H ) 15.084 ( PROT ASP 14 CA ) 18.855 ( PROT ASP 14 CB ) 15.084 ( PROT ASP 14 CG ) 15.084 ( PROT ASP 14 OD1 ) 15.084 ( PROT ASP 14 OD2 ) 15.084 ( PROT ASP 14 C ) 18.855 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64112 7.24761 -13.21295 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00089 -0.00025 0.00149 ROTATION MATRIX 1.000000 -0.000093 -0.000234 0.000093 1.000000 0.000209 0.000234 -0.000209 1.000000 AXIS OF ROTATION IS 0.639508 0.714800 -0.283003 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 19.4159 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.256114 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2561" Parameter: A <- "0.2561" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51304 7.24823 -13.41585 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01519 0.00732 -0.02450 ROTATION MATRIX 0.999773 0.014856 0.015285 -0.014610 0.999763 -0.016112 -0.015520 0.015885 0.999753 AXIS OF ROTATION IS -0.600310 -0.577942 0.552821 ANGLE IS 1.53 CENTER OF ROTATION 13.900154 7.015037-13.263593 SHIFT IS -0.026895 TOTAL SQUARE DIFF IS 0.2931 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.097232 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2561" RDCMND substituted energy or value "?RMS" to " 0.0972" Parameter: A <- "0.2561 0.0972" 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 0.2561 0.0972 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 " 486.01" Parameter: H <- "486.01" 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> 0 308.12870 486.00755 7.44466 ENER INTERN> 42.02047 123.47882 0.00000 33.83029 15.32478 ENER EXTERN> 213.30295 -119.82861 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 " 308.13" Parameter: B <- "308.13" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -119.83" Parameter: C <- "-119.83" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 213.30" Parameter: C <- " 93.47" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 93.47" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 42.02" Parameter: D <- "42.02" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 123.48" Parameter: D <- " 165.50" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 33.83" Parameter: D <- " 199.33" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 15.32" Parameter: D <- " 214.65" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 214.65" 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= 3600 ENER= 308.13 GRMS= 7.44 ELEC= -119.83 VDW= 213.30 RDTITL> *EXTERNAL= 93.47 INTERNAL= 214.65 USER= 0.00 HARM= 486.01 RDTITL> *BOND= 42.02 ANGL= 123.48 DIHE= 33.83 IMPR= 15.32 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= 308.13 GRMS= 7.44 ELEC= -119.83 VDW= 213.30 RDTITL> *EXTERNAL= 93.47 INTERNAL= 214.65 USER= 0.00 HARM= 486.01 RDTITL> *BOND= 42.02 ANGL= 123.48 DIHE= 33.83 IMPR= 15.32 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= 308.13 GRMS= 7.44 ELEC= -119.83 VDW= 213.30 RDTITL> *EXTERNAL= 93.47 INTERNAL= 214.65 USER= 0.00 HARM= 486.01 RDTITL> *BOND= 42.02 ANGL= 123.48 DIHE= 33.83 IMPR= 15.32 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 3600 0.2561 0.0972 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21112 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21113 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> 0 678.51635 -370.38764 3.25837 0.02000 MINI INTERN> 42.02047 123.47882 0.00000 33.83029 15.32478 MINI EXTERN> 213.30295 -119.82861 0.00000 0.00000 0.00000 MINI CONSTR> 370.38764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 640.01749 38.49885 3.01327 0.00360 MINI INTERN> 36.89120 125.91240 0.00000 38.37461 15.21661 MINI EXTERN> 143.12823 -118.31937 0.00000 0.00000 0.00000 MINI CONSTR> 398.81381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21100 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 628.79459 11.22291 1.58622 0.00156 MINI INTERN> 34.45173 118.18943 0.00000 38.04319 15.22982 MINI EXTERN> 142.78792 -119.17599 0.00000 0.00000 0.00000 MINI CONSTR> 399.26848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 622.34211 6.45248 1.27213 0.00161 MINI INTERN> 32.95020 116.16384 0.00000 38.43893 15.34893 MINI EXTERN> 138.36592 -119.23149 0.00000 0.00000 0.00000 MINI CONSTR> 400.30577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21100 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 617.03868 5.30343 2.38333 0.00167 MINI INTERN> 34.07822 114.15397 0.00000 38.47104 15.73031 MINI EXTERN> 132.35768 -119.15609 0.00000 0.00000 0.00000 MINI CONSTR> 401.40356 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 613.10384 3.93484 1.73594 0.00173 MINI INTERN> 32.39543 113.04136 0.00000 38.67930 15.64244 MINI EXTERN> 130.87087 -119.22101 0.00000 0.00000 0.00000 MINI CONSTR> 401.69547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 611.24034 1.86351 2.64974 0.00180 MINI INTERN> 33.86169 111.99056 0.00000 38.57145 15.79738 MINI EXTERN> 127.97666 -119.09666 0.00000 0.00000 0.00000 MINI CONSTR> 402.13925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 608.33175 2.90858 0.81539 0.00078 MINI INTERN> 29.73194 111.68483 0.00000 38.98303 15.28706 MINI EXTERN> 130.08299 -119.34058 0.00000 0.00000 0.00000 MINI CONSTR> 401.90248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21100 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 606.88560 1.44615 0.63210 0.00080 MINI INTERN> 29.66901 111.25046 0.00000 38.94882 15.28902 MINI EXTERN> 128.89068 -119.30973 0.00000 0.00000 0.00000 MINI CONSTR> 402.14734 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 605.65623 1.22937 1.22019 0.00083 MINI INTERN> 28.92891 110.81653 0.00000 39.02327 15.08577 MINI EXTERN> 128.81775 -119.31882 0.00000 0.00000 0.00000 MINI CONSTR> 402.30282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 604.60279 1.05343 0.77428 0.00087 MINI INTERN> 29.11068 110.46228 0.00000 38.92044 15.11037 MINI EXTERN> 127.62442 -119.25176 0.00000 0.00000 0.00000 MINI CONSTR> 402.62637 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 604.07024 0.53255 1.29120 0.00090 MINI INTERN> 28.57847 110.31153 0.00000 38.95442 14.95795 MINI EXTERN> 127.71230 -119.24797 0.00000 0.00000 0.00000 MINI CONSTR> 402.80354 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 743 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 603.29123 0.77901 0.39622 0.00039 MINI INTERN> 29.29012 110.11350 0.00000 38.75037 15.12987 MINI EXTERN> 125.87619 -119.13641 0.00000 0.00000 0.00000 MINI CONSTR> 403.26759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 602.86900 0.42223 0.32939 0.00040 MINI INTERN> 29.16994 109.93407 0.00000 38.70898 15.06416 MINI EXTERN> 125.56488 -119.08740 0.00000 0.00000 0.00000 MINI CONSTR> 403.51436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21098 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 602.49256 0.37644 0.31537 0.00042 MINI INTERN> 29.09761 109.79000 0.00000 38.65087 15.01427 MINI EXTERN> 125.14698 -119.02576 0.00000 0.00000 0.00000 MINI CONSTR> 403.81860 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 602.22760 0.26496 0.62896 0.00043 MINI INTERN> 29.13578 109.79998 0.00000 38.56359 15.02601 MINI EXTERN> 124.48026 -118.97091 0.00000 0.00000 0.00000 MINI CONSTR> 404.19288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 602.00464 0.22296 0.69822 0.00045 MINI INTERN> 28.92417 109.78231 0.00000 38.51927 14.97416 MINI EXTERN> 124.26312 -118.93562 0.00000 0.00000 0.00000 MINI CONSTR> 404.47723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 601.83325 0.17139 0.71773 0.00046 MINI INTERN> 29.02102 109.64393 0.00000 38.45306 14.94784 MINI EXTERN> 123.85861 -118.85372 0.00000 0.00000 0.00000 MINI CONSTR> 404.76252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 601.67871 0.15455 0.70134 0.00048 MINI INTERN> 28.99636 109.52758 0.00000 38.40556 14.90212 MINI EXTERN> 123.60854 -118.78214 0.00000 0.00000 0.00000 MINI CONSTR> 405.02069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 601.56394 0.11477 0.83991 0.00050 MINI INTERN> 28.70764 109.51156 0.00000 38.38018 14.82626 MINI EXTERN> 123.63745 -118.74759 0.00000 0.00000 0.00000 MINI CONSTR> 405.24844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21101 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 601.36127 0.20266 0.23047 0.00022 MINI INTERN> 28.86048 109.01531 0.00000 38.34633 14.70361 MINI EXTERN> 123.60856 -118.60675 0.00000 0.00000 0.00000 MINI CONSTR> 405.43373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 601.27054 0.09073 0.17325 0.00022 MINI INTERN> 28.77438 109.01429 0.00000 38.30672 14.68403 MINI EXTERN> 123.38936 -118.55561 0.00000 0.00000 0.00000 MINI CONSTR> 405.65737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21100 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 601.18640 0.08415 0.32455 0.00023 MINI INTERN> 28.82837 108.80732 0.00000 38.25945 14.61781 MINI EXTERN> 123.23263 -118.45847 0.00000 0.00000 0.00000 MINI CONSTR> 405.89929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 601.10089 0.08550 0.23097 0.00024 MINI INTERN> 28.74566 108.81980 0.00000 38.21217 14.60532 MINI EXTERN> 122.98089 -118.40246 0.00000 0.00000 0.00000 MINI CONSTR> 406.13951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21101 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 601.04462 0.05627 0.34963 0.00025 MINI INTERN> 28.79459 108.66086 0.00000 38.17186 14.55596 MINI EXTERN> 122.83659 -118.31740 0.00000 0.00000 0.00000 MINI CONSTR> 406.34216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 600.99152 0.05310 0.44598 0.00026 MINI INTERN> 28.82010 108.58710 0.00000 38.12910 14.53058 MINI EXTERN> 122.60323 -118.24273 0.00000 0.00000 0.00000 MINI CONSTR> 406.56415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21098 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 600.93723 0.05429 0.41022 0.00027 MINI INTERN> 28.73506 108.56755 0.00000 38.09941 14.50593 MINI EXTERN> 122.47747 -118.18927 0.00000 0.00000 0.00000 MINI CONSTR> 406.74109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 600.86783 0.06941 0.12164 0.00012 MINI INTERN> 28.44275 108.79354 0.00000 38.06978 14.52907 MINI EXTERN> 122.27174 -118.17961 0.00000 0.00000 0.00000 MINI CONSTR> 406.94054 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21098 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 600.84696 0.02087 0.45556 0.00029 MINI INTERN> 28.65777 108.48205 0.00000 38.03281 14.45815 MINI EXTERN> 122.17083 -118.06162 0.00000 0.00000 0.00000 MINI CONSTR> 407.10696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 600.77730 0.06966 0.13458 0.00012 MINI INTERN> 28.34539 108.73697 0.00000 38.00142 14.48828 MINI EXTERN> 121.95770 -118.05927 0.00000 0.00000 0.00000 MINI CONSTR> 407.30682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21097 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 600.74117 0.03613 0.11104 0.00013 MINI INTERN> 28.34797 108.67088 0.00000 37.97195 14.46616 MINI EXTERN> 121.83169 -118.00019 0.00000 0.00000 0.00000 MINI CONSTR> 407.45272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 600.70377 0.03740 0.10850 0.00013 MINI INTERN> 28.31269 108.63508 0.00000 37.94092 14.44668 MINI EXTERN> 121.69521 -117.94180 0.00000 0.00000 0.00000 MINI CONSTR> 407.61499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21096 ATOM PAIRS WERE FOUND FOR ATOM LIST 742 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 600.66909 0.03468 0.18751 0.00014 MINI INTERN> 28.21762 108.67178 0.00000 37.90853 14.43972 MINI EXTERN> 121.52105 -117.88925 0.00000 0.00000 0.00000 MINI CONSTR> 407.79964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 600.63627 0.03282 0.15580 0.00014 MINI INTERN> 28.20617 108.61061 0.00000 37.88077 14.41674 MINI EXTERN> 121.41768 -117.83308 0.00000 0.00000 0.00000 MINI CONSTR> 407.93737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21097 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 600.61039 0.02588 0.21020 0.00015 MINI INTERN> 28.14826 108.62577 0.00000 37.85309 14.41063 MINI EXTERN> 121.27130 -117.78523 0.00000 0.00000 0.00000 MINI CONSTR> 408.08655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 600.57801 0.03237 0.14764 0.00015 MINI INTERN> 28.14701 108.54490 0.00000 37.82824 14.38430 MINI EXTERN> 121.17511 -117.72088 0.00000 0.00000 0.00000 MINI CONSTR> 408.21933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21097 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 600.55716 0.02085 0.22498 0.00016 MINI INTERN> 28.06838 108.58155 0.00000 37.80373 14.38078 MINI EXTERN> 121.04629 -117.68144 0.00000 0.00000 0.00000 MINI CONSTR> 408.35786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 600.53650 0.02066 0.28725 0.00017 MINI INTERN> 28.00890 108.57118 0.00000 37.77977 14.36547 MINI EXTERN> 120.96287 -117.63499 0.00000 0.00000 0.00000 MINI CONSTR> 408.48329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21097 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 600.51454 0.02195 0.26508 0.00017 MINI INTERN> 28.01102 108.53124 0.00000 37.75667 14.35388 MINI EXTERN> 120.85673 -117.58773 0.00000 0.00000 0.00000 MINI CONSTR> 408.59274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 600.48576 0.02878 0.07853 0.00007 MINI INTERN> 28.14879 108.33145 0.00000 37.73406 14.31710 MINI EXTERN> 120.78713 -117.51174 0.00000 0.00000 0.00000 MINI CONSTR> 408.67898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 600.47656 0.00920 0.28974 0.00019 MINI INTERN> 27.97091 108.48467 0.00000 37.71269 14.33157 MINI EXTERN> 120.66011 -117.49869 0.00000 0.00000 0.00000 MINI CONSTR> 408.81529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 600.44746 0.02910 0.08743 0.00008 MINI INTERN> 28.11853 108.26632 0.00000 37.69185 14.29155 MINI EXTERN> 120.60081 -117.41736 0.00000 0.00000 0.00000 MINI CONSTR> 408.89576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 600.43172 0.01574 0.07261 0.00008 MINI INTERN> 28.07719 108.26765 0.00000 37.67535 14.28480 MINI EXTERN> 120.52301 -117.38365 0.00000 0.00000 0.00000 MINI CONSTR> 408.98737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 600.41583 0.01589 0.07282 0.00009 MINI INTERN> 28.05818 108.24419 0.00000 37.65734 14.27435 MINI EXTERN> 120.44137 -117.34220 0.00000 0.00000 0.00000 MINI CONSTR> 409.08260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 600.40043 0.01541 0.06664 0.00009 MINI INTERN> 28.03423 108.22927 0.00000 37.63933 14.26574 MINI EXTERN> 120.35749 -117.30311 0.00000 0.00000 0.00000 MINI CONSTR> 409.17747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 600.38530 0.01512 0.12639 0.00009 MINI INTERN> 28.07267 108.14276 0.00000 37.61716 14.24585 MINI EXTERN> 120.27058 -117.24337 0.00000 0.00000 0.00000 MINI CONSTR> 409.27965 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 600.37109 0.01422 0.09787 0.00010 MINI INTERN> 28.02761 108.15784 0.00000 37.60135 14.24212 MINI EXTERN> 120.19172 -117.21708 0.00000 0.00000 0.00000 MINI CONSTR> 409.36753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 600.36067 0.01042 0.14205 0.00010 MINI INTERN> 28.04854 108.10067 0.00000 37.58534 14.22800 MINI EXTERN> 120.12708 -117.17364 0.00000 0.00000 0.00000 MINI CONSTR> 409.44468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21099 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 600.35020 0.01047 0.16859 0.00010 MINI INTERN> 28.03109 108.07610 0.00000 37.57096 14.21974 MINI EXTERN> 120.05420 -117.12680 0.00000 0.00000 0.00000 MINI CONSTR> 409.52491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 600.33936 0.01084 0.15059 0.00011 MINI INTERN> 28.01698 108.06478 0.00000 37.55814 14.21171 MINI EXTERN> 120.00016 -117.10590 0.00000 0.00000 0.00000 MINI CONSTR> 409.59349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21100 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 600.33068 0.00868 0.19507 0.00011 MINI INTERN> 28.00229 108.04043 0.00000 37.54377 14.20432 MINI EXTERN> 119.92534 -117.05742 0.00000 0.00000 0.00000 MINI CONSTR> 409.67196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 600.32158 0.00910 0.18404 0.00011 MINI INTERN> 27.96736 108.04470 0.00000 37.53407 14.19945 MINI EXTERN> 119.87559 -117.03341 0.00000 0.00000 0.00000 MINI CONSTR> 409.73381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21101 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 600.31312 0.00846 0.18766 0.00012 MINI INTERN> 27.96229 108.03799 0.00000 37.52210 14.19206 MINI EXTERN> 119.82785 -117.02488 0.00000 0.00000 0.00000 MINI CONSTR> 409.79571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 600.30575 0.00737 0.20521 0.00012 MINI INTERN> 27.93056 108.02207 0.00000 37.51213 14.18607 MINI EXTERN> 119.76807 -116.97436 0.00000 0.00000 0.00000 MINI CONSTR> 409.86121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21101 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 600.29765 0.00810 0.18914 0.00013 MINI INTERN> 27.93446 107.99427 0.00000 37.50224 14.17549 MINI EXTERN> 119.72933 -116.95491 0.00000 0.00000 0.00000 MINI CONSTR> 409.91678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 600.28462 0.01303 0.06066 0.00006 MINI INTERN> 27.81036 108.10783 0.00000 37.49112 14.18934 MINI EXTERN> 119.64538 -116.95277 0.00000 0.00000 0.00000 MINI CONSTR> 409.99334 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21102 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 600.27813 0.00649 0.04459 0.00006 MINI INTERN> 27.81852 108.07727 0.00000 37.48177 14.18139 MINI EXTERN> 119.60238 -116.92513 0.00000 0.00000 0.00000 MINI CONSTR> 410.04193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 600.27137 0.00675 0.08076 0.00006 MINI INTERN> 27.76741 108.10258 0.00000 37.47220 14.17958 MINI EXTERN> 119.54515 -116.90332 0.00000 0.00000 0.00000 MINI CONSTR> 410.10778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21102 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 600.26501 0.00636 0.06416 0.00006 MINI INTERN> 27.77518 108.07557 0.00000 37.46297 14.17171 MINI EXTERN> 119.50354 -116.87983 0.00000 0.00000 0.00000 MINI CONSTR> 410.15588 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 600.25998 0.00503 0.09075 0.00006 MINI INTERN> 27.73991 108.09023 0.00000 37.45523 14.16957 MINI EXTERN> 119.45691 -116.86012 0.00000 0.00000 0.00000 MINI CONSTR> 410.20825 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 600.25405 0.00593 0.07312 0.00007 MINI INTERN> 27.74923 108.05763 0.00000 37.44688 14.16157 MINI EXTERN> 119.41452 -116.83024 0.00000 0.00000 0.00000 MINI CONSTR> 410.25447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 600.25005 0.00400 0.10256 0.00007 MINI INTERN> 27.72743 108.06273 0.00000 37.43986 14.15877 MINI EXTERN> 119.37291 -116.81135 0.00000 0.00000 0.00000 MINI CONSTR> 410.29970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 600.24550 0.00455 0.10603 0.00007 MINI INTERN> 27.71889 108.06075 0.00000 37.43242 14.15421 MINI EXTERN> 119.33779 -116.80022 0.00000 0.00000 0.00000 MINI CONSTR> 410.34165 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 600.24115 0.00435 0.10802 0.00007 MINI INTERN> 27.71305 108.04436 0.00000 37.42573 14.14921 MINI EXTERN> 119.29594 -116.77126 0.00000 0.00000 0.00000 MINI CONSTR> 410.38412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 600.23701 0.00414 0.10731 0.00008 MINI INTERN> 27.70586 108.04286 0.00000 37.41889 14.14515 MINI EXTERN> 119.26151 -116.76065 0.00000 0.00000 0.00000 MINI CONSTR> 410.42339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 600.23172 0.00529 0.03531 0.00003 MINI INTERN> 27.75609 107.97098 0.00000 37.41269 14.13248 MINI EXTERN> 119.23629 -116.72904 0.00000 0.00000 0.00000 MINI CONSTR> 410.45223 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 600.22997 0.00175 0.12421 0.00008 MINI INTERN> 27.69440 108.02846 0.00000 37.40685 14.13644 MINI EXTERN> 119.19282 -116.72710 0.00000 0.00000 0.00000 MINI CONSTR> 410.49810 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 600.22436 0.00560 0.04077 0.00004 MINI INTERN> 27.74769 107.94994 0.00000 37.40144 14.12262 MINI EXTERN> 119.17032 -116.69297 0.00000 0.00000 0.00000 MINI CONSTR> 410.52532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 600.22125 0.00311 0.03089 0.00004 MINI INTERN> 27.73104 107.95407 0.00000 37.39722 14.12011 MINI EXTERN> 119.14162 -116.67967 0.00000 0.00000 0.00000 MINI CONSTR> 410.55687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 600.21808 0.00317 0.03201 0.00004 MINI INTERN> 27.72599 107.94571 0.00000 37.39252 14.11562 MINI EXTERN> 119.11194 -116.66334 0.00000 0.00000 0.00000 MINI CONSTR> 410.58964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 600.21508 0.00300 0.05343 0.00004 MINI INTERN> 27.73473 107.92301 0.00000 37.38747 14.10897 MINI EXTERN> 119.08209 -116.64395 0.00000 0.00000 0.00000 MINI CONSTR> 410.62276 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 600.21234 0.00274 0.02809 0.00004 MINI INTERN> 27.71159 107.93695 0.00000 37.38412 14.10802 MINI EXTERN> 119.05641 -116.63513 0.00000 0.00000 0.00000 MINI CONSTR> 410.65038 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 600.20944 0.00290 0.06132 0.00004 MINI INTERN> 27.73072 107.90362 0.00000 37.37860 14.09994 MINI EXTERN> 119.02343 -116.61194 0.00000 0.00000 0.00000 MINI CONSTR> 410.68507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 600.20656 0.00288 0.04235 0.00004 MINI INTERN> 27.71178 107.91300 0.00000 37.37506 14.09774 MINI EXTERN> 118.99699 -116.60240 0.00000 0.00000 0.00000 MINI CONSTR> 410.71439 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 600.20460 0.00196 0.06623 0.00005 MINI INTERN> 27.72096 107.89392 0.00000 37.37143 14.09224 MINI EXTERN> 118.97324 -116.58702 0.00000 0.00000 0.00000 MINI CONSTR> 410.73982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 600.20255 0.00204 0.07764 0.00005 MINI INTERN> 27.71827 107.88357 0.00000 37.36843 14.08816 MINI EXTERN> 118.94671 -116.56889 0.00000 0.00000 0.00000 MINI CONSTR> 410.76630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 600.20041 0.00214 0.07022 0.00005 MINI INTERN> 27.71186 107.88308 0.00000 37.36583 14.08480 MINI EXTERN> 118.92771 -116.56172 0.00000 0.00000 0.00000 MINI CONSTR> 410.78884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 600.19840 0.00201 0.08000 0.00005 MINI INTERN> 27.70295 107.87923 0.00000 37.36291 14.08155 MINI EXTERN> 118.90059 -116.54420 0.00000 0.00000 0.00000 MINI CONSTR> 410.81538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 600.19584 0.00256 0.02391 0.00002 MINI INTERN> 27.66432 107.91182 0.00000 37.36153 14.08217 MINI EXTERN> 118.88282 -116.54455 0.00000 0.00000 0.00000 MINI CONSTR> 410.83774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 600.19494 0.00091 0.08558 0.00005 MINI INTERN> 27.69782 107.87411 0.00000 37.35824 14.07449 MINI EXTERN> 118.86402 -116.53102 0.00000 0.00000 0.00000 MINI CONSTR> 410.85728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 600.19346 0.00148 0.09646 0.00006 MINI INTERN> 27.68675 107.86913 0.00000 37.35660 14.07145 MINI EXTERN> 118.84048 -116.51066 0.00000 0.00000 0.00000 MINI CONSTR> 410.87971 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 600.19065 0.00281 0.02600 0.00002 MINI INTERN> 27.64992 107.90245 0.00000 37.35507 14.07211 MINI EXTERN> 118.82249 -116.51267 0.00000 0.00000 0.00000 MINI CONSTR> 410.90127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 600.18920 0.00145 0.02199 0.00003 MINI INTERN> 27.65056 107.89580 0.00000 37.35329 14.06872 MINI EXTERN> 118.80587 -116.50351 0.00000 0.00000 0.00000 MINI CONSTR> 410.91846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 600.18773 0.00147 0.02240 0.00003 MINI INTERN> 27.64662 107.89289 0.00000 37.35161 14.06556 MINI EXTERN> 118.78787 -116.49387 0.00000 0.00000 0.00000 MINI CONSTR> 410.93706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 600.18624 0.00150 0.03524 0.00003 MINI INTERN> 27.63466 107.89699 0.00000 37.35001 14.06272 MINI EXTERN> 118.76747 -116.48407 0.00000 0.00000 0.00000 MINI CONSTR> 410.95845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 600.18484 0.00140 0.02885 0.00003 MINI INTERN> 27.63591 107.89036 0.00000 37.34856 14.05912 MINI EXTERN> 118.75174 -116.47572 0.00000 0.00000 0.00000 MINI CONSTR> 410.97486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 600.18362 0.00122 0.03441 0.00003 MINI INTERN> 27.63086 107.88971 0.00000 37.34724 14.05628 MINI EXTERN> 118.73517 -116.46736 0.00000 0.00000 0.00000 MINI CONSTR> 410.99172 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 600.18253 0.00108 0.04448 0.00003 MINI INTERN> 27.62387 107.89001 0.00000 37.34611 14.05364 MINI EXTERN> 118.71841 -116.45782 0.00000 0.00000 0.00000 MINI CONSTR> 411.00831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 600.18142 0.00112 0.05164 0.00003 MINI INTERN> 27.62204 107.88876 0.00000 37.34499 14.05048 MINI EXTERN> 118.70410 -116.45267 0.00000 0.00000 0.00000 MINI CONSTR> 411.02370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 600.18039 0.00103 0.05360 0.00003 MINI INTERN> 27.61990 107.88620 0.00000 37.34394 14.04767 MINI EXTERN> 118.68942 -116.44481 0.00000 0.00000 0.00000 MINI CONSTR> 411.03806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 600.17932 0.00107 0.04876 0.00003 MINI INTERN> 27.61730 107.88180 0.00000 37.34313 14.04482 MINI EXTERN> 118.67460 -116.43431 0.00000 0.00000 0.00000 MINI CONSTR> 411.05197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 600.17832 0.00100 0.05568 0.00004 MINI INTERN> 27.61732 107.87961 0.00000 37.34242 14.04152 MINI EXTERN> 118.66193 -116.43020 0.00000 0.00000 0.00000 MINI CONSTR> 411.06571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 600.17731 0.00100 0.05129 0.00004 MINI INTERN> 27.61294 107.87818 0.00000 37.34169 14.03887 MINI EXTERN> 118.64765 -116.42132 0.00000 0.00000 0.00000 MINI CONSTR> 411.07931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 600.17608 0.00124 0.01713 0.00002 MINI INTERN> 27.62639 107.85817 0.00000 37.34145 14.03435 MINI EXTERN> 118.63739 -116.41087 0.00000 0.00000 0.00000 MINI CONSTR> 411.08919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 600.17563 0.00045 0.05848 0.00004 MINI INTERN> 27.60861 107.87490 0.00000 37.34052 14.03339 MINI EXTERN> 118.62212 -116.40811 0.00000 0.00000 0.00000 MINI CONSTR> 411.10419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 600.17429 0.00134 0.01903 0.00002 MINI INTERN> 27.62340 107.85267 0.00000 37.34057 14.02849 MINI EXTERN> 118.61222 -116.39687 0.00000 0.00000 0.00000 MINI CONSTR> 411.11381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21104 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 600.17401 0.00028 0.06091 0.00004 MINI INTERN> 27.60265 107.87152 0.00000 37.33980 14.02794 MINI EXTERN> 118.59753 -116.39328 0.00000 0.00000 0.00000 MINI CONSTR> 411.12785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 600.17256 0.00145 0.01878 0.00002 MINI INTERN> 27.61971 107.84833 0.00000 37.33990 14.02262 MINI EXTERN> 118.58723 -116.38310 0.00000 0.00000 0.00000 MINI CONSTR> 411.13788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 600.17184 0.00072 0.01459 0.00002 MINI INTERN> 27.61530 107.84956 0.00000 37.33977 14.02043 MINI EXTERN> 118.57691 -116.37798 0.00000 0.00000 0.00000 MINI CONSTR> 411.14785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 600.17104 0.00080 0.02633 0.00002 MINI INTERN> 27.61893 107.84147 0.00000 37.33949 14.01662 MINI EXTERN> 118.56445 -116.36960 0.00000 0.00000 0.00000 MINI CONSTR> 411.15969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 600.17034 0.00070 0.02184 0.00002 MINI INTERN> 27.61675 107.84170 0.00000 37.33946 14.01437 MINI EXTERN> 118.55364 -116.36486 0.00000 0.00000 0.00000 MINI CONSTR> 411.16928 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> 500 600.17034 0.00070 0.02184 0.00002 STPD INTERN> 27.61675 107.84170 0.00000 37.33946 14.01437 STPD EXTERN> 118.55364 -116.36486 0.00000 0.00000 0.00000 STPD CONSTR> 411.16928 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 21103 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21103 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> 0 600.17034 0.00070 0.02184 0.00000 MINI INTERN> 27.61675 107.84170 0.00000 37.33946 14.01437 MINI EXTERN> 118.55364 -116.36486 0.00000 0.00000 0.00000 MINI CONSTR> 411.16928 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 600.15298 0.01736 0.02610 0.00180 MINI INTERN> 27.49142 107.73925 0.00000 37.34611 13.89861 MINI EXTERN> 118.01917 -116.05942 0.00000 0.00000 0.00000 MINI CONSTR> 411.71786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 600.15021 0.00277 0.03928 0.00510 MINI INTERN> 27.54722 107.86619 0.00000 37.34654 13.85179 MINI EXTERN> 118.11273 -116.06595 0.00000 0.00000 0.00000 MINI CONSTR> 411.49168 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 600.14365 0.00656 0.05494 0.01415 MINI INTERN> 27.57568 107.92089 0.00000 37.41827 13.76880 MINI EXTERN> 118.07962 -116.02822 0.00000 0.00000 0.00000 MINI CONSTR> 411.40862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 600.13794 0.00571 0.04384 0.00984 MINI INTERN> 27.51331 107.85774 0.00000 37.47042 13.69675 MINI EXTERN> 117.88734 -115.92420 0.00000 0.00000 0.00000 MINI CONSTR> 411.63659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 600.13354 0.00440 0.04298 0.00846 MINI INTERN> 27.46058 107.90012 0.00000 37.46229 13.68074 MINI EXTERN> 117.81362 -115.82610 0.00000 0.00000 0.00000 MINI CONSTR> 411.64229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 600.12958 0.00396 0.03502 0.00889 MINI INTERN> 27.43520 108.00777 0.00000 37.38801 13.65884 MINI EXTERN> 117.81688 -115.69370 0.00000 0.00000 0.00000 MINI CONSTR> 411.51657 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 600.12739 0.00219 0.02167 0.00390 MINI INTERN> 27.40858 107.97912 0.00000 37.33457 13.65292 MINI EXTERN> 117.81985 -115.61545 0.00000 0.00000 0.00000 MINI CONSTR> 411.54781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 600.12654 0.00085 0.01487 0.00192 MINI INTERN> 27.37681 107.95659 0.00000 37.29589 13.65345 MINI EXTERN> 117.75870 -115.57741 0.00000 0.00000 0.00000 MINI CONSTR> 411.66251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 600.12606 0.00048 0.01224 0.00156 MINI INTERN> 27.37259 107.96497 0.00000 37.25133 13.65172 MINI EXTERN> 117.77679 -115.56376 0.00000 0.00000 0.00000 MINI CONSTR> 411.67242 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> 48 600.12585 0.00021 0.00986 0.02000 CONJ INTERN> 27.38675 107.97552 0.00000 37.22388 13.64894 CONJ EXTERN> 117.79163 -115.56183 0.00000 0.00000 0.00000 CONJ CONSTR> 411.66096 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 ASP 14 N ) 12.256 ( PROT ASP 14 H ) 9.8045 ( PROT ASP 14 CA ) 12.256 ( PROT ASP 14 CB ) 9.8045 ( PROT ASP 14 CG ) 9.8045 ( PROT ASP 14 OD1 ) 9.8045 ( PROT ASP 14 OD2 ) 9.8045 ( PROT ASP 14 C ) 12.256 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64080 7.24699 -13.21277 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00057 0.00037 0.00131 ROTATION MATRIX 1.000000 -0.000090 -0.000293 0.000090 1.000000 0.000254 0.000293 -0.000254 1.000000 AXIS OF ROTATION IS 0.638697 0.735206 -0.227019 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 25.0536 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.290930 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2909" Parameter: A <- "0.2909" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51312 7.24953 -13.41185 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01511 0.00602 -0.02851 ROTATION MATRIX 0.999766 0.014995 0.015566 -0.014741 0.999758 -0.016305 -0.015807 0.016072 0.999746 AXIS OF ROTATION IS -0.599503 -0.580905 0.550586 ANGLE IS 1.55 CENTER OF ROTATION 14.011130 6.927755-13.234740 SHIFT IS -0.028245 TOTAL SQUARE DIFF IS 0.4162 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.115869 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2909" RDCMND substituted energy or value "?RMS" to " 0.1159" Parameter: A <- "0.2909 0.1159" 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 0.2909 0.1159 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 " 411.66" Parameter: H <- "411.66" 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> 0 188.46489 411.66096 5.55297 ENER INTERN> 27.38675 107.97552 0.00000 37.22388 13.64894 ENER EXTERN> 117.79163 -115.56183 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 " 188.46" Parameter: B <- "188.46" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -115.56" Parameter: C <- "-115.56" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 117.79" Parameter: C <- " 2.23" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 2.23" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 27.39" Parameter: D <- "27.39" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 107.98" Parameter: D <- " 135.37" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 37.22" Parameter: D <- " 172.59" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 13.65" Parameter: D <- " 186.24" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 186.24" 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= 188.46 GRMS= 5.55 ELEC= -115.56 VDW= 117.79 RDTITL> *EXTERNAL= 2.23 INTERNAL= 186.24 USER= 0.00 HARM= 411.66 RDTITL> *BOND= 27.39 ANGL= 107.98 DIHE= 37.22 IMPR= 13.65 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21103 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21101 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 CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 492.81184 -304.34695 2.33660 0.02000 MINI INTERN> 27.38675 107.97552 0.00000 37.22388 13.64894 MINI EXTERN> 117.79163 -115.56183 0.00000 0.00000 0.00000 MINI CONSTR> 304.34695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 468.87115 23.94069 1.94920 0.00360 MINI INTERN> 25.56297 106.83921 0.00000 41.02107 14.04909 MINI EXTERN> 64.96195 -112.00718 0.00000 0.00000 0.00000 MINI CONSTR> 328.44403 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21080 ATOM PAIRS WERE FOUND FOR ATOM LIST 741 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 462.18299 6.68816 1.24366 0.00156 MINI INTERN> 22.71602 102.90316 0.00000 41.13862 13.46062 MINI EXTERN> 63.97671 -112.07314 0.00000 0.00000 0.00000 MINI CONSTR> 330.06099 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 458.93507 3.24792 2.76685 0.00161 MINI INTERN> 26.56493 99.22586 0.00000 41.37949 13.46529 MINI EXTERN> 58.41587 -111.08139 0.00000 0.00000 0.00000 MINI CONSTR> 330.96501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 20 456.25738 2.67769 3.05903 0.00167 MINI INTERN> 27.04433 97.87996 0.00000 41.54475 13.42622 MINI EXTERN> 55.78276 -110.77585 0.00000 0.00000 0.00000 MINI CONSTR> 331.35520 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 454.01068 2.24670 2.90603 0.00173 MINI INTERN> 26.24858 97.33989 0.00000 41.69792 13.32836 MINI EXTERN> 54.65297 -110.71677 0.00000 0.00000 0.00000 MINI CONSTR> 331.45974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21077 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 452.01932 1.99136 2.98435 0.00180 MINI INTERN> 26.27748 96.61020 0.00000 41.76378 13.27111 MINI EXTERN> 53.19143 -110.58322 0.00000 0.00000 0.00000 MINI CONSTR> 331.48853 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 449.10325 2.91607 0.91337 0.00078 MINI INTERN> 18.75840 99.91719 0.00000 41.92848 13.18559 MINI EXTERN> 55.60691 -111.82292 0.00000 0.00000 0.00000 MINI CONSTR> 331.52962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21073 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 447.83130 1.27194 0.63392 0.00080 MINI INTERN> 19.39844 99.11019 0.00000 41.91210 13.15713 MINI EXTERN> 54.41247 -111.61420 0.00000 0.00000 0.00000 MINI CONSTR> 331.45518 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 446.60395 1.22735 1.31968 0.00083 MINI INTERN> 17.58767 99.72215 0.00000 42.02124 13.03759 MINI EXTERN> 54.78360 -111.87954 0.00000 0.00000 0.00000 MINI CONSTR> 331.33125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 445.57777 1.02619 1.30974 0.00087 MINI INTERN> 17.56234 99.29783 0.00000 42.05225 12.95697 MINI EXTERN> 54.27273 -111.77630 0.00000 0.00000 0.00000 MINI CONSTR> 331.21193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 444.72851 0.84926 1.41858 0.00090 MINI INTERN> 17.72488 98.75357 0.00000 42.10660 12.85062 MINI EXTERN> 53.82545 -111.61218 0.00000 0.00000 0.00000 MINI CONSTR> 331.07957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 444.01414 0.71436 1.36190 0.00093 MINI INTERN> 17.85801 98.39756 0.00000 42.08614 12.80561 MINI EXTERN> 53.36455 -111.51602 0.00000 0.00000 0.00000 MINI CONSTR> 331.01830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 443.14812 0.86603 0.41596 0.00040 MINI INTERN> 19.64223 97.35611 0.00000 41.79925 12.93702 MINI EXTERN> 51.55851 -111.23880 0.00000 0.00000 0.00000 MINI CONSTR> 331.09378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21069 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 442.94571 0.20241 1.48860 0.00100 MINI INTERN> 17.72070 98.03275 0.00000 42.06362 12.70513 MINI EXTERN> 52.88887 -111.41576 0.00000 0.00000 0.00000 MINI CONSTR> 330.95039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 442.16607 0.77963 0.50764 0.00043 MINI INTERN> 19.86464 96.90153 0.00000 41.69684 12.88657 MINI EXTERN> 50.82945 -111.11477 0.00000 0.00000 0.00000 MINI CONSTR> 331.10180 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21072 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 441.80266 0.36341 0.40113 0.00045 MINI INTERN> 19.66748 96.82566 0.00000 41.68676 12.84165 MINI EXTERN> 50.75795 -111.09017 0.00000 0.00000 0.00000 MINI CONSTR> 331.11333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 441.48274 0.31992 0.42344 0.00046 MINI INTERN> 19.70663 96.67339 0.00000 41.64322 12.81702 MINI EXTERN> 50.52673 -111.04048 0.00000 0.00000 0.00000 MINI CONSTR> 331.15622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 441.28289 0.19985 0.69902 0.00048 MINI INTERN> 20.14423 96.41569 0.00000 41.55434 12.82889 MINI EXTERN> 50.06994 -110.95958 0.00000 0.00000 0.00000 MINI CONSTR> 331.22939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 441.07610 0.20679 0.74256 0.00050 MINI INTERN> 20.18637 96.30086 0.00000 41.51328 12.81065 MINI EXTERN> 49.88977 -110.91673 0.00000 0.00000 0.00000 MINI CONSTR> 331.29190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 440.82220 0.25390 0.21396 0.00022 MINI INTERN> 19.13042 96.55404 0.00000 41.61835 12.69487 MINI EXTERN> 50.50971 -110.97456 0.00000 0.00000 0.00000 MINI CONSTR> 331.28937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 440.76535 0.05685 0.79881 0.00054 MINI INTERN> 20.23407 96.11483 0.00000 41.44139 12.77642 MINI EXTERN> 49.61059 -110.84036 0.00000 0.00000 0.00000 MINI CONSTR> 331.42842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21072 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 440.54586 0.21950 0.28110 0.00023 MINI INTERN> 18.95487 96.44678 0.00000 41.57896 12.63855 MINI EXTERN> 50.42080 -110.91585 0.00000 0.00000 0.00000 MINI CONSTR> 331.42176 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 440.44235 0.10351 0.21556 0.00024 MINI INTERN> 19.02609 96.35631 0.00000 41.53980 12.63215 MINI EXTERN> 50.26908 -110.87743 0.00000 0.00000 0.00000 MINI CONSTR> 331.49634 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21072 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 440.35075 0.09160 0.22878 0.00025 MINI INTERN> 18.99583 96.29770 0.00000 41.51457 12.61299 MINI EXTERN> 50.20358 -110.84563 0.00000 0.00000 0.00000 MINI CONSTR> 331.57170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 440.29241 0.05834 0.37382 0.00026 MINI INTERN> 18.81686 96.30660 0.00000 41.51553 12.57997 MINI EXTERN> 50.27423 -110.83153 0.00000 0.00000 0.00000 MINI CONSTR> 331.63076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 440.23172 0.06069 0.39970 0.00027 MINI INTERN> 18.80342 96.25137 0.00000 41.49234 12.56369 MINI EXTERN> 50.21876 -110.80091 0.00000 0.00000 0.00000 MINI CONSTR> 331.70307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 440.17555 0.05617 0.40290 0.00028 MINI INTERN> 18.83571 96.17405 0.00000 41.46280 12.55069 MINI EXTERN> 50.13543 -110.76334 0.00000 0.00000 0.00000 MINI CONSTR> 331.78021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 440.10921 0.06635 0.12337 0.00012 MINI INTERN> 19.18643 96.05082 0.00000 41.37863 12.59497 MINI EXTERN> 49.73289 -110.71648 0.00000 0.00000 0.00000 MINI CONSTR> 331.88194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 440.07516 0.03405 0.09770 0.00012 MINI INTERN> 19.15587 96.01843 0.00000 41.36414 12.58159 MINI EXTERN> 49.71302 -110.69522 0.00000 0.00000 0.00000 MINI CONSTR> 331.93733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 440.04115 0.03402 0.09333 0.00013 MINI INTERN> 19.15188 95.98269 0.00000 41.34171 12.57310 MINI EXTERN> 49.65649 -110.67004 0.00000 0.00000 0.00000 MINI CONSTR> 332.00530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 440.01458 0.02657 0.19741 0.00013 MINI INTERN> 19.22647 95.94753 0.00000 41.30342 12.58033 MINI EXTERN> 49.51278 -110.64332 0.00000 0.00000 0.00000 MINI CONSTR> 332.08737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21072 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 439.99033 0.02425 0.19782 0.00014 MINI INTERN> 19.20015 95.93014 0.00000 41.28555 12.57265 MINI EXTERN> 49.47455 -110.62222 0.00000 0.00000 0.00000 MINI CONSTR> 332.14951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 439.97048 0.01985 0.22639 0.00014 MINI INTERN> 19.17218 95.92762 0.00000 41.26777 12.56693 MINI EXTERN> 49.43693 -110.61248 0.00000 0.00000 0.00000 MINI CONSTR> 332.21153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21072 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 439.95405 0.01643 0.22233 0.00015 MINI INTERN> 19.16861 95.88874 0.00000 41.25155 12.55944 MINI EXTERN> 49.40022 -110.57728 0.00000 0.00000 0.00000 MINI CONSTR> 332.26277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 439.93347 0.02058 0.06896 0.00006 MINI INTERN> 19.11983 95.82149 0.00000 41.25292 12.52986 MINI EXTERN> 49.47532 -110.55904 0.00000 0.00000 0.00000 MINI CONSTR> 332.29308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21072 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 439.92795 0.00552 0.23275 0.00016 MINI INTERN> 19.21651 95.82633 0.00000 41.21376 12.55220 MINI EXTERN> 49.30376 -110.54650 0.00000 0.00000 0.00000 MINI CONSTR> 332.36190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 439.90723 0.02073 0.07361 0.00007 MINI INTERN> 19.12451 95.76346 0.00000 41.21954 12.51756 MINI EXTERN> 49.40457 -110.51769 0.00000 0.00000 0.00000 MINI CONSTR> 332.39527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21074 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 439.89782 0.00941 0.05611 0.00007 MINI INTERN> 19.11758 95.75902 0.00000 41.20589 12.51637 MINI EXTERN> 49.36914 -110.50665 0.00000 0.00000 0.00000 MINI CONSTR> 332.43648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 439.88876 0.00906 0.10507 0.00007 MINI INTERN> 19.11655 95.71542 0.00000 41.19338 12.50459 MINI EXTERN> 49.36044 -110.48301 0.00000 0.00000 0.00000 MINI CONSTR> 332.48139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21074 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 439.87937 0.00939 0.06432 0.00008 MINI INTERN> 19.12260 95.70749 0.00000 41.17633 12.50560 MINI EXTERN> 49.31015 -110.46914 0.00000 0.00000 0.00000 MINI CONSTR> 332.52633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 439.87247 0.00689 0.11605 0.00008 MINI INTERN> 19.14765 95.65275 0.00000 41.16147 12.49554 MINI EXTERN> 49.29012 -110.44415 0.00000 0.00000 0.00000 MINI CONSTR> 332.56909 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21073 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 439.86556 0.00692 0.12485 0.00008 MINI INTERN> 19.17086 95.61939 0.00000 41.14528 12.49141 MINI EXTERN> 49.25453 -110.42688 0.00000 0.00000 0.00000 MINI CONSTR> 332.61096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 439.85963 0.00592 0.12653 0.00009 MINI INTERN> 19.15859 95.61166 0.00000 41.13339 12.48954 MINI EXTERN> 49.22597 -110.40770 0.00000 0.00000 0.00000 MINI CONSTR> 332.64819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21073 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 439.85246 0.00717 0.04011 0.00004 MINI INTERN> 19.09569 95.67729 0.00000 41.12386 12.49785 MINI EXTERN> 49.18949 -110.41635 0.00000 0.00000 0.00000 MINI CONSTR> 332.68463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 439.85017 0.00229 0.14873 0.00009 MINI INTERN> 19.14296 95.59429 0.00000 41.11184 12.48455 MINI EXTERN> 49.18129 -110.38019 0.00000 0.00000 0.00000 MINI CONSTR> 332.71543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21072 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 439.84569 0.00448 0.14900 0.00010 MINI INTERN> 19.15640 95.57675 0.00000 41.10102 12.48035 MINI EXTERN> 49.16660 -110.38063 0.00000 0.00000 0.00000 MINI CONSTR> 332.74519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 439.83834 0.00734 0.04553 0.00004 MINI INTERN> 19.08742 95.64570 0.00000 41.09019 12.49093 MINI EXTERN> 49.11951 -110.37860 0.00000 0.00000 0.00000 MINI CONSTR> 332.78320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21072 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 439.83462 0.00372 0.03552 0.00004 MINI INTERN> 19.09731 95.62437 0.00000 41.08061 12.48741 MINI EXTERN> 49.10280 -110.36667 0.00000 0.00000 0.00000 MINI CONSTR> 332.80880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 439.83071 0.00390 0.05882 0.00004 MINI INTERN> 19.08115 95.63079 0.00000 41.06922 12.48768 MINI EXTERN> 49.07534 -110.35645 0.00000 0.00000 0.00000 MINI CONSTR> 332.84298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 439.82702 0.00369 0.04741 0.00005 MINI INTERN> 19.09001 95.61045 0.00000 41.05954 12.48402 MINI EXTERN> 49.05965 -110.34559 0.00000 0.00000 0.00000 MINI CONSTR> 332.86894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 439.82399 0.00303 0.06793 0.00005 MINI INTERN> 19.07761 95.61421 0.00000 41.04955 12.48420 MINI EXTERN> 49.03572 -110.33526 0.00000 0.00000 0.00000 MINI CONSTR> 332.89795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 439.82041 0.00358 0.05005 0.00005 MINI INTERN> 19.08764 95.59176 0.00000 41.04029 12.48008 MINI EXTERN> 49.02246 -110.32432 0.00000 0.00000 0.00000 MINI CONSTR> 332.92251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 439.81795 0.00246 0.07534 0.00005 MINI INTERN> 19.08060 95.59448 0.00000 41.03088 12.48025 MINI EXTERN> 49.00082 -110.31737 0.00000 0.00000 0.00000 MINI CONSTR> 332.94830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 439.81526 0.00269 0.08208 0.00005 MINI INTERN> 19.07715 95.58729 0.00000 41.02151 12.47917 MINI EXTERN> 48.98034 -110.30375 0.00000 0.00000 0.00000 MINI CONSTR> 332.97355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 439.81254 0.00273 0.08079 0.00006 MINI INTERN> 19.08444 95.57490 0.00000 41.01281 12.47693 MINI EXTERN> 48.96566 -110.29765 0.00000 0.00000 0.00000 MINI CONSTR> 332.99544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 439.81002 0.00251 0.08632 0.00006 MINI INTERN> 19.08314 95.55988 0.00000 41.00451 12.47445 MINI EXTERN> 48.94998 -110.28004 0.00000 0.00000 0.00000 MINI CONSTR> 333.01812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 439.80755 0.00248 0.08300 0.00006 MINI INTERN> 19.08804 95.55307 0.00000 40.99538 12.47375 MINI EXTERN> 48.93090 -110.27354 0.00000 0.00000 0.00000 MINI CONSTR> 333.03996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 439.80432 0.00322 0.02766 0.00003 MINI INTERN> 19.10869 95.51331 0.00000 40.98936 12.46644 MINI EXTERN> 48.93177 -110.26068 0.00000 0.00000 0.00000 MINI CONSTR> 333.05542 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 439.80316 0.00116 0.09468 0.00006 MINI INTERN> 19.09187 95.53613 0.00000 40.97864 12.47105 MINI EXTERN> 48.89856 -110.25489 0.00000 0.00000 0.00000 MINI CONSTR> 333.08180 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 439.79965 0.00351 0.03082 0.00003 MINI INTERN> 19.11104 95.49510 0.00000 40.97315 12.46300 MINI EXTERN> 48.90277 -110.24220 0.00000 0.00000 0.00000 MINI CONSTR> 333.09679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 439.79890 0.00075 0.09858 0.00007 MINI INTERN> 19.09502 95.52377 0.00000 40.96255 12.46867 MINI EXTERN> 48.86889 -110.24137 0.00000 0.00000 0.00000 MINI CONSTR> 333.12137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 439.79506 0.00384 0.03049 0.00003 MINI INTERN> 19.11390 95.47836 0.00000 40.95648 12.46004 MINI EXTERN> 48.87218 -110.22385 0.00000 0.00000 0.00000 MINI CONSTR> 333.13796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 439.79317 0.00190 0.02528 0.00003 MINI INTERN> 19.10970 95.47774 0.00000 40.94984 12.45946 MINI EXTERN> 48.85965 -110.21817 0.00000 0.00000 0.00000 MINI CONSTR> 333.15493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 439.79113 0.00203 0.04230 0.00003 MINI INTERN> 19.11959 95.45883 0.00000 40.94157 12.45651 MINI EXTERN> 48.84704 -110.20654 0.00000 0.00000 0.00000 MINI CONSTR> 333.17415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 439.78930 0.00183 0.02383 0.00003 MINI INTERN> 19.10905 95.46665 0.00000 40.93556 12.45710 MINI EXTERN> 48.83419 -110.20312 0.00000 0.00000 0.00000 MINI CONSTR> 333.18987 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 439.78743 0.00187 0.04966 0.00003 MINI INTERN> 19.12287 95.44513 0.00000 40.92719 12.45381 MINI EXTERN> 48.82230 -110.19232 0.00000 0.00000 0.00000 MINI CONSTR> 333.20845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 439.78555 0.00188 0.03867 0.00004 MINI INTERN> 19.11556 95.44560 0.00000 40.92089 12.45329 MINI EXTERN> 48.81040 -110.18483 0.00000 0.00000 0.00000 MINI CONSTR> 333.22464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 439.78396 0.00158 0.05390 0.00004 MINI INTERN> 19.12166 95.43483 0.00000 40.91394 12.45135 MINI EXTERN> 48.79989 -110.17813 0.00000 0.00000 0.00000 MINI CONSTR> 333.24043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 439.78233 0.00164 0.06104 0.00004 MINI INTERN> 19.11844 95.42919 0.00000 40.90732 12.45014 MINI EXTERN> 48.78797 -110.16738 0.00000 0.00000 0.00000 MINI CONSTR> 333.25664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 439.78074 0.00159 0.06183 0.00004 MINI INTERN> 19.11746 95.42495 0.00000 40.90130 12.44885 MINI EXTERN> 48.77867 -110.16164 0.00000 0.00000 0.00000 MINI CONSTR> 333.27115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 439.77915 0.00159 0.06342 0.00004 MINI INTERN> 19.11830 95.42128 0.00000 40.89503 12.44769 MINI EXTERN> 48.76899 -110.15774 0.00000 0.00000 0.00000 MINI CONSTR> 333.28559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 439.77754 0.00161 0.06181 0.00004 MINI INTERN> 19.11478 95.41793 0.00000 40.88885 12.44681 MINI EXTERN> 48.75782 -110.14888 0.00000 0.00000 0.00000 MINI CONSTR> 333.30023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 439.77603 0.00151 0.06776 0.00004 MINI INTERN> 19.11770 95.41728 0.00000 40.88209 12.44632 MINI EXTERN> 48.74648 -110.14829 0.00000 0.00000 0.00000 MINI CONSTR> 333.31445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 439.77407 0.00196 0.02136 0.00002 MINI INTERN> 19.10529 95.42667 0.00000 40.87597 12.44754 MINI EXTERN> 48.73184 -110.14185 0.00000 0.00000 0.00000 MINI CONSTR> 333.32860 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 439.77323 0.00084 0.07397 0.00005 MINI INTERN> 19.11002 95.40747 0.00000 40.87094 12.44365 MINI EXTERN> 48.72851 -110.12885 0.00000 0.00000 0.00000 MINI CONSTR> 333.34148 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 439.77189 0.00134 0.08119 0.00005 MINI INTERN> 19.11555 95.40720 0.00000 40.86449 12.44313 MINI EXTERN> 48.71857 -110.13128 0.00000 0.00000 0.00000 MINI CONSTR> 333.35424 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 439.77039 0.00150 0.07516 0.00005 MINI INTERN> 19.11060 95.39986 0.00000 40.85948 12.44110 MINI EXTERN> 48.71208 -110.11982 0.00000 0.00000 0.00000 MINI CONSTR> 333.36709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 439.76890 0.00149 0.07762 0.00005 MINI INTERN> 19.11445 95.39341 0.00000 40.85266 12.43999 MINI EXTERN> 48.70053 -110.11320 0.00000 0.00000 0.00000 MINI CONSTR> 333.38106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 439.76651 0.00239 0.02361 0.00002 MINI INTERN> 19.10487 95.40697 0.00000 40.84448 12.44218 MINI EXTERN> 48.68087 -110.10995 0.00000 0.00000 0.00000 MINI CONSTR> 333.39708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 439.76520 0.00130 0.01996 0.00002 MINI INTERN> 19.10709 95.40135 0.00000 40.83911 12.44093 MINI EXTERN> 48.67285 -110.10438 0.00000 0.00000 0.00000 MINI CONSTR> 333.40826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 439.76384 0.00137 0.02092 0.00002 MINI INTERN> 19.10697 95.39822 0.00000 40.83319 12.43997 MINI EXTERN> 48.66339 -110.09852 0.00000 0.00000 0.00000 MINI CONSTR> 333.42062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 439.76250 0.00133 0.02106 0.00003 MINI INTERN> 19.10708 95.39459 0.00000 40.82745 12.43893 MINI EXTERN> 48.65439 -110.09248 0.00000 0.00000 0.00000 MINI CONSTR> 333.43254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 439.76115 0.00135 0.03539 0.00003 MINI INTERN> 19.10460 95.39555 0.00000 40.82078 12.43840 MINI EXTERN> 48.64316 -110.08755 0.00000 0.00000 0.00000 MINI CONSTR> 333.44621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 439.75984 0.00131 0.02872 0.00003 MINI INTERN> 19.10556 95.38958 0.00000 40.81555 12.43704 MINI EXTERN> 48.63552 -110.08043 0.00000 0.00000 0.00000 MINI CONSTR> 333.45701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 439.75862 0.00122 0.03208 0.00003 MINI INTERN> 19.10611 95.38700 0.00000 40.80989 12.43619 MINI EXTERN> 48.62653 -110.07530 0.00000 0.00000 0.00000 MINI CONSTR> 333.46819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 439.75739 0.00123 0.03395 0.00003 MINI INTERN> 19.10749 95.38418 0.00000 40.80426 12.43527 MINI EXTERN> 48.61786 -110.07083 0.00000 0.00000 0.00000 MINI CONSTR> 333.47917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 439.75627 0.00112 0.04495 0.00003 MINI INTERN> 19.10572 95.38276 0.00000 40.79853 12.43450 MINI EXTERN> 48.60854 -110.06440 0.00000 0.00000 0.00000 MINI CONSTR> 333.49062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 439.75510 0.00117 0.05033 0.00003 MINI INTERN> 19.10859 95.38021 0.00000 40.79294 12.43348 MINI EXTERN> 48.60061 -110.06190 0.00000 0.00000 0.00000 MINI CONSTR> 333.50116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 439.75395 0.00114 0.05091 0.00003 MINI INTERN> 19.10899 95.37730 0.00000 40.78750 12.43263 MINI EXTERN> 48.59189 -110.05592 0.00000 0.00000 0.00000 MINI CONSTR> 333.51155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 439.75281 0.00114 0.05326 0.00003 MINI INTERN> 19.10765 95.37389 0.00000 40.78218 12.43160 MINI EXTERN> 48.58355 -110.04815 0.00000 0.00000 0.00000 MINI CONSTR> 333.52209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 439.75165 0.00116 0.05158 0.00004 MINI INTERN> 19.11085 95.37112 0.00000 40.77704 12.43059 MINI EXTERN> 48.57645 -110.04588 0.00000 0.00000 0.00000 MINI CONSTR> 333.53148 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 439.75055 0.00110 0.05623 0.00004 MINI INTERN> 19.10761 95.36676 0.00000 40.77215 12.42928 MINI EXTERN> 48.56918 -110.03608 0.00000 0.00000 0.00000 MINI CONSTR> 333.54164 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 439.74941 0.00114 0.05344 0.00004 MINI INTERN> 19.11013 95.36505 0.00000 40.76662 12.42859 MINI EXTERN> 48.56053 -110.03290 0.00000 0.00000 0.00000 MINI CONSTR> 333.55138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 439.74796 0.00145 0.01855 0.00002 MINI INTERN> 19.11234 95.35661 0.00000 40.76328 12.42624 MINI EXTERN> 48.55909 -110.02837 0.00000 0.00000 0.00000 MINI CONSTR> 333.55877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 439.74731 0.00065 0.06103 0.00004 MINI INTERN> 19.11041 95.36027 0.00000 40.75629 12.42664 MINI EXTERN> 48.54525 -110.02216 0.00000 0.00000 0.00000 MINI CONSTR> 333.57060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21070 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 439.74575 0.00156 0.01955 0.00002 MINI INTERN> 19.11250 95.35186 0.00000 40.75325 12.42416 MINI EXTERN> 48.54478 -110.01829 0.00000 0.00000 0.00000 MINI CONSTR> 333.57749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 439.74525 0.00050 0.06640 0.00004 MINI INTERN> 19.11586 95.35624 0.00000 40.74604 12.42482 MINI EXTERN> 48.53071 -110.01691 0.00000 0.00000 0.00000 MINI CONSTR> 333.58849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 439.74358 0.00167 0.02131 0.00002 MINI INTERN> 19.11290 95.34730 0.00000 40.74332 12.42204 MINI EXTERN> 48.53079 -110.00852 0.00000 0.00000 0.00000 MINI CONSTR> 333.59574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 439.74318 0.00040 0.06795 0.00005 MINI INTERN> 19.11450 95.35181 0.00000 40.73593 12.42295 MINI EXTERN> 48.51537 -110.00426 0.00000 0.00000 0.00000 MINI CONSTR> 333.60689 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 439.74211 0.00107 0.07574 0.00005 MINI INTERN> 19.11456 95.35173 0.00000 40.73066 12.42164 MINI EXTERN> 48.50939 -110.00237 0.00000 0.00000 0.00000 MINI CONSTR> 333.61650 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> 500 439.74211 0.00107 0.07574 0.00002 STPD INTERN> 19.11456 95.35173 0.00000 40.73066 12.42164 STPD EXTERN> 48.50939 -110.00237 0.00000 0.00000 0.00000 STPD CONSTR> 333.61650 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 21071 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 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> 0 439.74196 0.00015 0.05856 0.00000 MINI INTERN> 19.11336 95.33890 0.00000 40.73457 12.41915 MINI EXTERN> 48.52001 -109.99658 0.00000 0.00000 0.00000 MINI CONSTR> 333.61254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 439.67815 0.06380 0.10641 0.02158 MINI INTERN> 19.00167 94.96639 0.00000 40.28564 12.38965 MINI EXTERN> 47.52170 -109.31263 0.00000 0.00000 0.00000 MINI CONSTR> 334.82573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 439.66213 0.01603 0.06992 0.01355 MINI INTERN> 19.00343 95.05268 0.00000 40.12730 12.31455 MINI EXTERN> 47.47129 -109.16138 0.00000 0.00000 0.00000 MINI CONSTR> 334.85426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 439.65275 0.00938 0.05382 0.01041 MINI INTERN> 19.03163 95.08744 0.00000 40.01678 12.31143 MINI EXTERN> 47.61330 -109.09311 0.00000 0.00000 0.00000 MINI CONSTR> 334.68529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 439.64531 0.00744 0.05030 0.00770 MINI INTERN> 19.04367 95.16327 0.00000 39.95936 12.33255 MINI EXTERN> 47.44999 -109.02146 0.00000 0.00000 0.00000 MINI CONSTR> 334.71792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 439.64052 0.00479 0.03939 0.00508 MINI INTERN> 19.00921 95.17086 0.00000 39.92937 12.30527 MINI EXTERN> 47.49718 -109.02658 0.00000 0.00000 0.00000 MINI CONSTR> 334.75521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 439.63745 0.00307 0.03410 0.00431 MINI INTERN> 19.00509 95.19127 0.00000 39.92674 12.28809 MINI EXTERN> 47.59759 -109.04453 0.00000 0.00000 0.00000 MINI CONSTR> 334.67320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 439.63468 0.00277 0.03071 0.00487 MINI INTERN> 19.00504 95.31130 0.00000 39.89855 12.28750 MINI EXTERN> 47.68407 -109.08883 0.00000 0.00000 0.00000 MINI CONSTR> 334.53706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 439.63212 0.00256 0.02999 0.00409 MINI INTERN> 19.00466 95.40557 0.00000 39.87260 12.28324 MINI EXTERN> 47.79243 -109.15733 0.00000 0.00000 0.00000 MINI CONSTR> 334.43093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 439.63025 0.00187 0.02496 0.00370 MINI INTERN> 19.01948 95.44131 0.00000 39.85575 12.27739 MINI EXTERN> 47.85269 -109.19426 0.00000 0.00000 0.00000 MINI CONSTR> 334.37788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 439.62905 0.00120 0.01892 0.00333 MINI INTERN> 19.00213 95.51324 0.00000 39.83089 12.27561 MINI EXTERN> 47.90925 -109.21818 0.00000 0.00000 0.00000 MINI CONSTR> 334.31612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 439.62820 0.00086 0.01679 0.00238 MINI INTERN> 19.01047 95.54827 0.00000 39.81262 12.28241 MINI EXTERN> 47.94978 -109.25943 0.00000 0.00000 0.00000 MINI CONSTR> 334.28408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 439.62753 0.00066 0.01432 0.00210 MINI INTERN> 19.01221 95.55201 0.00000 39.78683 12.28237 MINI EXTERN> 47.99347 -109.27798 0.00000 0.00000 0.00000 MINI CONSTR> 334.27862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 439.62704 0.00049 0.01386 0.00192 MINI INTERN> 19.00600 95.56355 0.00000 39.75509 12.28642 MINI EXTERN> 48.01998 -109.28553 0.00000 0.00000 0.00000 MINI CONSTR> 334.28153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 439.62658 0.00046 0.01270 0.00233 MINI INTERN> 19.01875 95.58952 0.00000 39.70863 12.28597 MINI EXTERN> 48.03556 -109.29984 0.00000 0.00000 0.00000 MINI CONSTR> 334.28799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 439.62617 0.00041 0.01124 0.00200 MINI INTERN> 19.02925 95.58580 0.00000 39.66489 12.28854 MINI EXTERN> 48.07116 -109.29576 0.00000 0.00000 0.00000 MINI CONSTR> 334.28229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 439.62587 0.00029 0.01039 0.00160 MINI INTERN> 19.02796 95.59620 0.00000 39.62436 12.28521 MINI EXTERN> 48.05872 -109.28360 0.00000 0.00000 0.00000 MINI CONSTR> 334.31702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 439.62559 0.00028 0.00972 0.00174 MINI INTERN> 19.02761 95.60118 0.00000 39.57941 12.28996 MINI EXTERN> 48.04450 -109.27022 0.00000 0.00000 0.00000 MINI CONSTR> 334.35314 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> 85 439.62559 0.00028 0.00972 0.02000 CONJ INTERN> 19.02761 95.60118 0.00000 39.57941 12.28996 CONJ EXTERN> 48.04450 -109.27022 0.00000 0.00000 0.00000 CONJ CONSTR> 334.35314 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 ASP 14 N ) 7.9661 ( PROT ASP 14 H ) 6.3729 ( PROT ASP 14 CA ) 7.9661 ( PROT ASP 14 CB ) 6.3729 ( PROT ASP 14 CG ) 6.3729 ( PROT ASP 14 OD1 ) 6.3729 ( PROT ASP 14 OD2 ) 6.3729 ( PROT ASP 14 C ) 7.9661 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64037 7.24682 -13.21237 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00015 0.00054 0.00091 ROTATION MATRIX 1.000000 -0.000104 -0.000331 0.000104 1.000000 0.000291 0.000331 -0.000291 1.000000 AXIS OF ROTATION IS 0.642229 0.731400 -0.229339 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 31.1328 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.324312 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3243" Parameter: A <- "0.3243" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51575 7.24928 -13.40919 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01248 0.00627 -0.03117 ROTATION MATRIX 0.999748 0.015575 0.016138 -0.015299 0.999737 -0.017072 -0.016400 0.016821 0.999724 AXIS OF ROTATION IS -0.602875 -0.578753 0.549169 ANGLE IS 1.61 CENTER OF ROTATION 14.041071 6.827838-13.302370 SHIFT IS -0.028269 TOTAL SQUARE DIFF IS 0.5923 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.138228 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3243" RDCMND substituted energy or value "?RMS" to " 0.1382" Parameter: A <- "0.3243 0.1382" 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 0.3243 0.1382 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 " 334.35" Parameter: H <- "334.35" 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> 0 105.27245 334.35314 4.04566 ENER INTERN> 19.02761 95.60118 0.00000 39.57941 12.28996 ENER EXTERN> 48.04450 -109.27022 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 " 105.27" Parameter: B <- "105.27" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -109.27" Parameter: C <- "-109.27" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 48.04" Parameter: C <- " -61.23" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -61.23" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 19.03" Parameter: D <- "19.03" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 95.60" Parameter: D <- " 114.63" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 39.58" Parameter: D <- " 154.21" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 12.29" Parameter: D <- " 166.50" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 166.50" 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= 105.27 GRMS= 4.05 ELEC= -109.27 VDW= 48.04 RDTITL> *EXTERNAL= -61.23 INTERNAL= 166.50 USER= 0.00 HARM= 334.35 RDTITL> *BOND= 19.03 ANGL= 95.60 DIHE= 39.58 IMPR= 12.29 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= 105.27 GRMS= 4.05 ELEC= -109.27 VDW= 48.04 RDTITL> *EXTERNAL= -61.23 INTERNAL= 166.50 USER= 0.00 HARM= 334.35 RDTITL> *BOND= 19.03 ANGL= 95.60 DIHE= 39.58 IMPR= 12.29 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= 105.27 GRMS= 4.05 ELEC= -109.27 VDW= 48.04 RDTITL> *EXTERNAL= -61.23 INTERNAL= 166.50 USER= 0.00 HARM= 334.35 RDTITL> *BOND= 19.03 ANGL= 95.60 DIHE= 39.58 IMPR= 12.29 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 4800 0.3243 0.1382 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21071 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21071 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> 0 348.52986 -243.25742 1.66556 0.02000 MINI INTERN> 19.02761 95.60118 0.00000 39.57941 12.28996 MINI EXTERN> 48.04450 -109.27022 0.00000 0.00000 0.00000 MINI CONSTR> 243.25742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 333.79839 14.73147 1.91636 0.00360 MINI INTERN> 17.40217 92.70968 0.00000 42.52456 12.60762 MINI EXTERN> 14.21297 -106.02044 0.00000 0.00000 0.00000 MINI CONSTR> 260.36183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21051 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 330.00230 3.79609 1.40707 0.00156 MINI INTERN> 15.66495 92.44013 0.00000 42.99394 12.02332 MINI EXTERN> 10.15959 -105.37649 0.00000 0.00000 0.00000 MINI CONSTR> 262.09687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 328.12408 1.87822 2.71764 0.00161 MINI INTERN> 19.46030 89.05447 0.00000 43.29072 11.90970 MINI EXTERN> 5.87788 -104.22222 0.00000 0.00000 0.00000 MINI CONSTR> 262.75322 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21050 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 326.35442 1.76966 2.74816 0.00167 MINI INTERN> 19.59930 88.39282 0.00000 43.41195 11.89517 MINI EXTERN> 3.94506 -103.97692 0.00000 0.00000 0.00000 MINI CONSTR> 263.08703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 324.82215 1.53227 2.90734 0.00173 MINI INTERN> 19.80552 87.69297 0.00000 43.49799 11.81029 MINI EXTERN> 2.55749 -103.79742 0.00000 0.00000 0.00000 MINI CONSTR> 263.25531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21044 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 322.36902 2.45313 1.01045 0.00075 MINI INTERN> 14.07588 90.98708 0.00000 43.47798 11.91859 MINI EXTERN> 3.39291 -104.98920 0.00000 0.00000 0.00000 MINI CONSTR> 263.50577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 321.18100 1.18802 0.77730 0.00078 MINI INTERN> 14.31826 90.28036 0.00000 43.49775 11.84643 MINI EXTERN> 2.59536 -104.83596 0.00000 0.00000 0.00000 MINI CONSTR> 263.47880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21044 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 320.08557 1.09543 0.82120 0.00080 MINI INTERN> 14.15150 90.00722 0.00000 43.50019 11.79019 MINI EXTERN> 2.01313 -104.81120 0.00000 0.00000 0.00000 MINI CONSTR> 263.43454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 319.32708 0.75849 1.37558 0.00083 MINI INTERN> 13.49109 90.33287 0.00000 43.47336 11.76705 MINI EXTERN> 1.84710 -104.98380 0.00000 0.00000 0.00000 MINI CONSTR> 263.39941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 50 318.51057 0.81651 1.52776 0.00087 MINI INTERN> 13.30729 90.20821 0.00000 43.45029 11.72176 MINI EXTERN> 1.49257 -104.99533 0.00000 0.00000 0.00000 MINI CONSTR> 263.32580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 317.81189 0.69868 1.47800 0.00090 MINI INTERN> 13.36822 89.89747 0.00000 43.42089 11.67901 MINI EXTERN> 1.13208 -104.93671 0.00000 0.00000 0.00000 MINI CONSTR> 263.25093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21035 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 316.89550 0.91639 0.44909 0.00039 MINI INTERN> 14.95053 88.18550 0.00000 43.42927 11.57388 MINI EXTERN> 0.02495 -104.37010 0.00000 0.00000 0.00000 MINI CONSTR> 263.10146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 316.63555 0.25995 1.61227 0.00096 MINI INTERN> 13.24495 89.60385 0.00000 43.34540 11.60969 MINI EXTERN> 0.62741 -104.91281 0.00000 0.00000 0.00000 MINI CONSTR> 263.11705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21035 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 315.75073 0.88482 0.48779 0.00042 MINI INTERN> 15.03980 87.70552 0.00000 43.35717 11.49945 MINI EXTERN> -0.55067 -104.26406 0.00000 0.00000 0.00000 MINI CONSTR> 262.96353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 315.32745 0.42327 0.37124 0.00043 MINI INTERN> 14.76901 87.75900 0.00000 43.31946 11.48106 MINI EXTERN> -0.62313 -104.30583 0.00000 0.00000 0.00000 MINI CONSTR> 262.92788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21038 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 314.86580 0.46165 0.68000 0.00045 MINI INTERN> 15.29486 87.18991 0.00000 43.28012 11.43293 MINI EXTERN> -1.06275 -104.12612 0.00000 0.00000 0.00000 MINI CONSTR> 262.85686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 314.47061 0.39519 0.46700 0.00046 MINI INTERN> 14.96404 87.28705 0.00000 43.23440 11.41822 MINI EXTERN> -1.08781 -104.18204 0.00000 0.00000 0.00000 MINI CONSTR> 262.83674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21035 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 314.17399 0.29662 0.80860 0.00048 MINI INTERN> 15.40867 86.84485 0.00000 43.19869 11.38198 MINI EXTERN> -1.41864 -104.03600 0.00000 0.00000 0.00000 MINI CONSTR> 262.79444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 313.86942 0.30457 0.85421 0.00050 MINI INTERN> 15.42619 86.71365 0.00000 43.15491 11.36060 MINI EXTERN> -1.55976 -104.00330 0.00000 0.00000 0.00000 MINI CONSTR> 262.77714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21035 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 313.60996 0.25946 0.93774 0.00052 MINI INTERN> 15.48887 86.56502 0.00000 43.11292 11.33968 MINI EXTERN> -1.70171 -103.96101 0.00000 0.00000 0.00000 MINI CONSTR> 262.76618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 313.37646 0.23350 0.88339 0.00054 MINI INTERN> 15.41186 86.51966 0.00000 43.07676 11.32349 MINI EXTERN> -1.76738 -103.95330 0.00000 0.00000 0.00000 MINI CONSTR> 262.76537 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21035 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 313.05328 0.32318 0.25890 0.00023 MINI INTERN> 14.42852 87.13255 0.00000 43.01087 11.33449 MINI EXTERN> -1.46524 -104.19457 0.00000 0.00000 0.00000 MINI CONSTR> 262.80666 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 312.96604 0.08724 0.94672 0.00058 MINI INTERN> 15.39435 86.35919 0.00000 42.99225 11.29404 MINI EXTERN> -1.94209 -103.91145 0.00000 0.00000 0.00000 MINI CONSTR> 262.77974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21035 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 312.66060 0.30544 0.29232 0.00025 MINI INTERN> 14.35284 87.02018 0.00000 42.92326 11.30575 MINI EXTERN> -1.60693 -104.16845 0.00000 0.00000 0.00000 MINI CONSTR> 262.83394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 312.51515 0.14544 0.21518 0.00026 MINI INTERN> 14.43736 86.88378 0.00000 42.88989 11.29357 MINI EXTERN> -1.71194 -104.12372 0.00000 0.00000 0.00000 MINI CONSTR> 262.84622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21035 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 312.35378 0.16137 0.39235 0.00027 MINI INTERN> 14.29198 86.92794 0.00000 42.83937 11.28062 MINI EXTERN> -1.72151 -104.14348 0.00000 0.00000 0.00000 MINI CONSTR> 262.87885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 312.21685 0.13693 0.27270 0.00028 MINI INTERN> 14.36842 86.79516 0.00000 42.80355 11.26928 MINI EXTERN> -1.82085 -104.09872 0.00000 0.00000 0.00000 MINI CONSTR> 262.90001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21035 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 312.11384 0.10301 0.46796 0.00029 MINI INTERN> 14.28533 86.81568 0.00000 42.76191 11.25856 MINI EXTERN> -1.83448 -104.10663 0.00000 0.00000 0.00000 MINI CONSTR> 262.93346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 312.00749 0.10635 0.49342 0.00030 MINI INTERN> 14.29857 86.74846 0.00000 42.72413 11.24759 MINI EXTERN> -1.89307 -104.08275 0.00000 0.00000 0.00000 MINI CONSTR> 262.96456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 311.91690 0.09059 0.54306 0.00031 MINI INTERN> 14.30095 86.69808 0.00000 42.68680 11.23784 MINI EXTERN> -1.94076 -104.06420 0.00000 0.00000 0.00000 MINI CONSTR> 262.99820 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 311.83564 0.08126 0.51141 0.00032 MINI INTERN> 14.31382 86.64436 0.00000 42.65263 11.23257 MINI EXTERN> -1.99051 -104.04594 0.00000 0.00000 0.00000 MINI CONSTR> 263.02870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 311.72323 0.11241 0.14987 0.00014 MINI INTERN> 14.45157 86.45963 0.00000 42.61815 11.22950 MINI EXTERN> -2.11173 -103.98201 0.00000 0.00000 0.00000 MINI CONSTR> 263.05812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 311.69278 0.03045 0.54984 0.00034 MINI INTERN> 14.32841 86.54628 0.00000 42.58424 11.21693 MINI EXTERN> -2.07521 -104.00734 0.00000 0.00000 0.00000 MINI CONSTR> 263.09946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 311.58667 0.10610 0.17091 0.00015 MINI INTERN> 14.46273 86.36830 0.00000 42.54582 11.21837 MINI EXTERN> -2.19539 -103.94670 0.00000 0.00000 0.00000 MINI CONSTR> 263.13355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 311.53627 0.05040 0.12499 0.00015 MINI INTERN> 14.43361 86.35541 0.00000 42.51928 11.21236 MINI EXTERN> -2.20989 -103.93951 0.00000 0.00000 0.00000 MINI CONSTR> 263.16502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 311.48022 0.05605 0.23042 0.00016 MINI INTERN> 14.48814 86.28179 0.00000 42.47578 11.21024 MINI EXTERN> -2.27385 -103.91201 0.00000 0.00000 0.00000 MINI CONSTR> 263.21013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 311.43259 0.04764 0.15932 0.00017 MINI INTERN> 14.45630 86.26988 0.00000 42.44764 11.20439 MINI EXTERN> -2.28673 -103.90428 0.00000 0.00000 0.00000 MINI CONSTR> 263.24538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 311.39690 0.03569 0.27348 0.00017 MINI INTERN> 14.50535 86.21201 0.00000 42.41097 11.20350 MINI EXTERN> -2.33748 -103.88197 0.00000 0.00000 0.00000 MINI CONSTR> 263.28453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 311.35983 0.03707 0.28877 0.00018 MINI INTERN> 14.51800 86.17729 0.00000 42.37759 11.20082 MINI EXTERN> -2.36985 -103.86698 0.00000 0.00000 0.00000 MINI CONSTR> 263.32296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 311.32815 0.03168 0.31740 0.00019 MINI INTERN> 14.53547 86.14219 0.00000 42.34485 11.19871 MINI EXTERN> -2.40209 -103.85172 0.00000 0.00000 0.00000 MINI CONSTR> 263.36074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 311.29961 0.02854 0.29904 0.00019 MINI INTERN> 14.51447 86.13039 0.00000 42.32158 11.19465 MINI EXTERN> -2.41037 -103.84304 0.00000 0.00000 0.00000 MINI CONSTR> 263.39192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 311.26019 0.03942 0.08788 0.00008 MINI INTERN> 14.38422 86.17989 0.00000 42.30639 11.18316 MINI EXTERN> -2.36720 -103.85114 0.00000 0.00000 0.00000 MINI CONSTR> 263.42487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 311.24914 0.01105 0.32125 0.00021 MINI INTERN> 14.53700 86.07510 0.00000 42.26126 11.19115 MINI EXTERN> -2.46144 -103.81703 0.00000 0.00000 0.00000 MINI CONSTR> 263.46309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21033 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 311.21170 0.03744 0.09822 0.00009 MINI INTERN> 14.35941 86.14998 0.00000 42.25249 11.17654 MINI EXTERN> -2.39157 -103.83016 0.00000 0.00000 0.00000 MINI CONSTR> 263.49501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 311.19359 0.01811 0.07401 0.00009 MINI INTERN> 14.38225 86.12034 0.00000 42.22656 11.17658 MINI EXTERN> -2.41873 -103.81737 0.00000 0.00000 0.00000 MINI CONSTR> 263.52395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21032 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 311.17321 0.02038 0.12929 0.00010 MINI INTERN> 14.32062 86.13289 0.00000 42.20312 11.16972 MINI EXTERN> -2.40235 -103.81222 0.00000 0.00000 0.00000 MINI CONSTR> 263.56142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 311.15620 0.01701 0.09342 0.00010 MINI INTERN> 14.34408 86.10310 0.00000 42.17552 11.17003 MINI EXTERN> -2.42960 -103.79891 0.00000 0.00000 0.00000 MINI CONSTR> 263.59198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 311.14067 0.01553 0.10420 0.00010 MINI INTERN> 14.32713 86.09523 0.00000 42.15115 11.16723 MINI EXTERN> -2.43402 -103.79005 0.00000 0.00000 0.00000 MINI CONSTR> 263.62400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 311.12965 0.01102 0.15907 0.00011 MINI INTERN> 14.28099 86.10670 0.00000 42.13319 11.16243 MINI EXTERN> -2.41954 -103.78619 0.00000 0.00000 0.00000 MINI CONSTR> 263.65206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 311.11711 0.01254 0.17463 0.00011 MINI INTERN> 14.25173 86.10594 0.00000 42.11105 11.15889 MINI EXTERN> -2.41420 -103.77891 0.00000 0.00000 0.00000 MINI CONSTR> 263.68261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 311.10618 0.01093 0.16926 0.00011 MINI INTERN> 14.25226 86.09290 0.00000 42.08832 11.15800 MINI EXTERN> -2.42488 -103.76980 0.00000 0.00000 0.00000 MINI CONSTR> 263.70940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 311.09232 0.01386 0.05289 0.00005 MINI INTERN> 14.41063 85.99777 0.00000 42.04430 11.16937 MINI EXTERN> -2.52786 -103.74186 0.00000 0.00000 0.00000 MINI CONSTR> 263.73996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 311.08765 0.00467 0.18657 0.00012 MINI INTERN> 14.22069 86.08465 0.00000 42.04644 11.15385 MINI EXTERN> -2.42490 -103.75537 0.00000 0.00000 0.00000 MINI CONSTR> 263.76229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 311.07922 0.00843 0.19451 0.00013 MINI INTERN> 14.20053 86.08252 0.00000 42.02570 11.15149 MINI EXTERN> -2.42113 -103.74850 0.00000 0.00000 0.00000 MINI CONSTR> 263.78861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 311.06595 0.01328 0.06442 0.00006 MINI INTERN> 14.44311 85.94914 0.00000 41.96926 11.16988 MINI EXTERN> -2.57551 -103.71113 0.00000 0.00000 0.00000 MINI CONSTR> 263.82120 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 311.05959 0.00635 0.04321 0.00006 MINI INTERN> 14.40296 85.96075 0.00000 41.95642 11.16641 MINI EXTERN> -2.55832 -103.70888 0.00000 0.00000 0.00000 MINI CONSTR> 263.84024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 311.05211 0.00749 0.07867 0.00006 MINI INTERN> 14.46878 85.91875 0.00000 41.92030 11.17106 MINI EXTERN> -2.60697 -103.69139 0.00000 0.00000 0.00000 MINI CONSTR> 263.87158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 311.04589 0.00622 0.05679 0.00006 MINI INTERN> 14.43843 85.92546 0.00000 41.90408 11.16846 MINI EXTERN> -2.59551 -103.68742 0.00000 0.00000 0.00000 MINI CONSTR> 263.89239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 311.04108 0.00482 0.09644 0.00006 MINI INTERN> 14.49562 85.89095 0.00000 41.87406 11.17267 MINI EXTERN> -2.63651 -103.67299 0.00000 0.00000 0.00000 MINI CONSTR> 263.91728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 311.03590 0.00517 0.09964 0.00007 MINI INTERN> 14.50158 85.88119 0.00000 41.85169 11.17301 MINI EXTERN> -2.64638 -103.66475 0.00000 0.00000 0.00000 MINI CONSTR> 263.93956 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 311.03128 0.00463 0.10908 0.00007 MINI INTERN> 14.51543 85.86816 0.00000 41.82820 11.17402 MINI EXTERN> -2.66072 -103.65553 0.00000 0.00000 0.00000 MINI CONSTR> 263.96171 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 311.02713 0.00415 0.10425 0.00007 MINI INTERN> 14.50930 85.86559 0.00000 41.81065 11.17353 MINI EXTERN> -2.66158 -103.65007 0.00000 0.00000 0.00000 MINI CONSTR> 263.97971 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 311.02294 0.00418 0.10680 0.00007 MINI INTERN> 14.51343 85.85786 0.00000 41.78908 11.17391 MINI EXTERN> -2.66956 -103.64201 0.00000 0.00000 0.00000 MINI CONSTR> 264.00023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 311.01773 0.00521 0.03393 0.00003 MINI INTERN> 14.36512 85.92194 0.00000 41.79162 11.16236 MINI EXTERN> -2.58339 -103.65297 0.00000 0.00000 0.00000 MINI CONSTR> 264.01306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 311.01626 0.00147 0.11718 0.00008 MINI INTERN> 14.52812 85.84181 0.00000 41.74933 11.17526 MINI EXTERN> -2.68649 -103.62800 0.00000 0.00000 0.00000 MINI CONSTR> 264.03623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 311.01299 0.00328 0.12401 0.00008 MINI INTERN> 14.53744 85.83361 0.00000 41.72757 11.17616 MINI EXTERN> -2.69530 -103.62162 0.00000 0.00000 0.00000 MINI CONSTR> 264.05514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 311.00771 0.00527 0.04297 0.00004 MINI INTERN> 14.34277 85.91909 0.00000 41.73628 11.16110 MINI EXTERN> -2.58115 -103.63638 0.00000 0.00000 0.00000 MINI CONSTR> 264.06601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21031 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 311.00516 0.00255 0.02742 0.00004 MINI INTERN> 14.37486 85.90102 0.00000 41.71647 11.16385 MINI EXTERN> -2.60357 -103.62789 0.00000 0.00000 0.00000 MINI CONSTR> 264.08041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 311.00219 0.00297 0.02779 0.00004 MINI INTERN> 14.37070 85.89943 0.00000 41.69725 11.16382 MINI EXTERN> -2.60413 -103.62229 0.00000 0.00000 0.00000 MINI CONSTR> 264.09741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21033 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 310.99970 0.00249 0.05885 0.00004 MINI INTERN> 14.31724 85.92122 0.00000 41.68447 11.15990 MINI EXTERN> -2.57418 -103.62201 0.00000 0.00000 0.00000 MINI CONSTR> 264.11306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 310.99701 0.00269 0.03469 0.00004 MINI INTERN> 14.35300 85.90169 0.00000 41.66226 11.16308 MINI EXTERN> -2.59887 -103.61250 0.00000 0.00000 0.00000 MINI CONSTR> 264.12835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21033 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 310.99500 0.00202 0.06476 0.00004 MINI INTERN> 14.31063 85.91956 0.00000 41.64940 11.16007 MINI EXTERN> -2.57435 -103.61266 0.00000 0.00000 0.00000 MINI CONSTR> 264.14233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 310.99297 0.00203 0.07179 0.00004 MINI INTERN> 14.30539 85.91902 0.00000 41.63290 11.16006 MINI EXTERN> -2.57484 -103.60569 0.00000 0.00000 0.00000 MINI CONSTR> 264.15614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21033 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 310.99099 0.00198 0.06667 0.00005 MINI INTERN> 14.30560 85.91805 0.00000 41.61749 11.16042 MINI EXTERN> -2.57519 -103.60335 0.00000 0.00000 0.00000 MINI CONSTR> 264.16797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 310.98911 0.00188 0.07956 0.00005 MINI INTERN> 14.29494 85.92044 0.00000 41.60060 11.16006 MINI EXTERN> -2.57201 -103.59688 0.00000 0.00000 0.00000 MINI CONSTR> 264.18196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 310.98728 0.00182 0.07315 0.00005 MINI INTERN> 14.29639 85.91904 0.00000 41.58568 11.16054 MINI EXTERN> -2.57333 -103.59401 0.00000 0.00000 0.00000 MINI CONSTR> 264.19296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 310.98473 0.00255 0.02279 0.00002 MINI INTERN> 14.39491 85.87187 0.00000 41.55559 11.16882 MINI EXTERN> -2.63482 -103.57939 0.00000 0.00000 0.00000 MINI CONSTR> 264.20775 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 310.98385 0.00088 0.08055 0.00005 MINI INTERN> 14.29173 85.91869 0.00000 41.55361 11.16111 MINI EXTERN> -2.57381 -103.58438 0.00000 0.00000 0.00000 MINI CONSTR> 264.21690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 310.98235 0.00150 0.09048 0.00005 MINI INTERN> 14.30780 85.91301 0.00000 41.53565 11.16272 MINI EXTERN> -2.58069 -103.58428 0.00000 0.00000 0.00000 MINI CONSTR> 264.22815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 310.97972 0.00263 0.02577 0.00002 MINI INTERN> 14.40450 85.86512 0.00000 41.50668 11.17099 MINI EXTERN> -2.64383 -103.56572 0.00000 0.00000 0.00000 MINI CONSTR> 264.24198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 310.97829 0.00143 0.02060 0.00002 MINI INTERN> 14.39121 85.87092 0.00000 41.49487 11.17038 MINI EXTERN> -2.63649 -103.56362 0.00000 0.00000 0.00000 MINI CONSTR> 264.25102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 310.97779 0.00050 0.09174 0.00006 MINI INTERN> 14.27276 85.92689 0.00000 41.49412 11.16151 MINI EXTERN> -2.56370 -103.57309 0.00000 0.00000 0.00000 MINI CONSTR> 264.25932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 310.97507 0.00272 0.03395 0.00003 MINI INTERN> 14.41955 85.85744 0.00000 41.45689 11.17374 MINI EXTERN> -2.65503 -103.55222 0.00000 0.00000 0.00000 MINI CONSTR> 264.27469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 310.97376 0.00131 0.01997 0.00003 MINI INTERN> 14.39145 85.87047 0.00000 41.44852 11.17195 MINI EXTERN> -2.63856 -103.55202 0.00000 0.00000 0.00000 MINI CONSTR> 264.28194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 310.97227 0.00149 0.04114 0.00003 MINI INTERN> 14.43061 85.85256 0.00000 41.42494 11.17567 MINI EXTERN> -2.66273 -103.54355 0.00000 0.00000 0.00000 MINI CONSTR> 264.29476 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 310.97078 0.00149 0.02550 0.00003 MINI INTERN> 14.40576 85.86451 0.00000 41.41433 11.17423 MINI EXTERN> -2.64779 -103.54317 0.00000 0.00000 0.00000 MINI CONSTR> 264.30292 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 310.96940 0.00139 0.03189 0.00003 MINI INTERN> 14.41468 85.86065 0.00000 41.39735 11.17550 MINI EXTERN> -2.65394 -103.53791 0.00000 0.00000 0.00000 MINI CONSTR> 264.31307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 310.96831 0.00109 0.04648 0.00003 MINI INTERN> 14.43830 85.85044 0.00000 41.37990 11.17789 MINI EXTERN> -2.66814 -103.53250 0.00000 0.00000 0.00000 MINI CONSTR> 264.32241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 310.96697 0.00133 0.04885 0.00003 MINI INTERN> 14.43804 85.85169 0.00000 41.36482 11.17845 MINI EXTERN> -2.66720 -103.53025 0.00000 0.00000 0.00000 MINI CONSTR> 264.33142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 310.96582 0.00116 0.05532 0.00003 MINI INTERN> 14.44487 85.84873 0.00000 41.34969 11.17952 MINI EXTERN> -2.67280 -103.52449 0.00000 0.00000 0.00000 MINI CONSTR> 264.34030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 310.96462 0.00119 0.05130 0.00004 MINI INTERN> 14.44535 85.84983 0.00000 41.33681 11.18007 MINI EXTERN> -2.67210 -103.52302 0.00000 0.00000 0.00000 MINI CONSTR> 264.34769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 310.96343 0.00120 0.06001 0.00004 MINI INTERN> 14.45118 85.84772 0.00000 41.32069 11.18114 MINI EXTERN> -2.67649 -103.51770 0.00000 0.00000 0.00000 MINI CONSTR> 264.35689 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 310.96227 0.00116 0.05576 0.00004 MINI INTERN> 14.45179 85.84897 0.00000 41.30815 11.18169 MINI EXTERN> -2.67587 -103.51636 0.00000 0.00000 0.00000 MINI CONSTR> 264.36390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 310.96103 0.00124 0.05804 0.00004 MINI INTERN> 14.45435 85.84891 0.00000 41.29302 11.18250 MINI EXTERN> -2.67735 -103.51275 0.00000 0.00000 0.00000 MINI CONSTR> 264.37235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 310.95979 0.00124 0.05956 0.00004 MINI INTERN> 14.45366 85.85148 0.00000 41.27877 11.18297 MINI EXTERN> -2.67554 -103.51178 0.00000 0.00000 0.00000 MINI CONSTR> 264.38022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 310.95825 0.00154 0.01914 0.00002 MINI INTERN> 14.37197 85.88996 0.00000 41.27847 11.17711 MINI EXTERN> -2.62726 -103.51637 0.00000 0.00000 0.00000 MINI CONSTR> 264.38436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 310.95772 0.00053 0.06464 0.00004 MINI INTERN> 14.46374 85.84883 0.00000 41.25196 11.18489 MINI EXTERN> -2.68202 -103.50419 0.00000 0.00000 0.00000 MINI CONSTR> 264.39452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 310.95656 0.00116 0.06682 0.00005 MINI INTERN> 14.46672 85.84937 0.00000 41.23756 11.18569 MINI EXTERN> -2.68294 -103.50194 0.00000 0.00000 0.00000 MINI CONSTR> 264.40209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 310.95547 0.00109 0.07319 0.00005 MINI INTERN> 14.46094 85.85241 0.00000 41.22422 11.18594 MINI EXTERN> -2.68074 -103.49694 0.00000 0.00000 0.00000 MINI CONSTR> 264.40964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 310.95368 0.00179 0.02402 0.00002 MINI INTERN> 14.36116 85.90148 0.00000 41.22662 11.17855 MINI EXTERN> -2.61954 -103.50724 0.00000 0.00000 0.00000 MINI CONSTR> 264.41265 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> 500 310.95368 0.00179 0.02402 0.00002 STPD INTERN> 14.36116 85.90148 0.00000 41.22662 11.17855 STPD EXTERN> -2.61954 -103.50724 0.00000 0.00000 0.00000 STPD CONSTR> 264.41265 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 21034 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 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> 0 310.95368 0.00179 0.02402 0.00000 MINI INTERN> 14.36116 85.90148 0.00000 41.22662 11.17855 MINI EXTERN> -2.61954 -103.50724 0.00000 0.00000 0.00000 MINI CONSTR> 264.41265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 310.90460 0.04908 0.03641 0.02903 MINI INTERN> 14.36545 85.88466 0.00000 40.51730 11.23527 MINI EXTERN> -2.88231 -103.30239 0.00000 0.00000 0.00000 MINI CONSTR> 265.08662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 310.89768 0.00692 0.06425 0.00805 MINI INTERN> 14.36408 85.82880 0.00000 40.56919 11.22394 MINI EXTERN> -2.76947 -103.31104 0.00000 0.00000 0.00000 MINI CONSTR> 264.99218 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 310.89095 0.00673 0.05712 0.00636 MINI INTERN> 14.37296 85.81278 0.00000 40.60557 11.21834 MINI EXTERN> -2.72058 -103.31043 0.00000 0.00000 0.00000 MINI CONSTR> 264.91230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 310.88506 0.00589 0.05426 0.00813 MINI INTERN> 14.36280 85.85121 0.00000 40.68533 11.20095 MINI EXTERN> -2.83545 -103.32467 0.00000 0.00000 0.00000 MINI CONSTR> 264.94489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 310.88119 0.00387 0.03269 0.00416 MINI INTERN> 14.35704 85.89792 0.00000 40.75825 11.20257 MINI EXTERN> -2.94011 -103.32680 0.00000 0.00000 0.00000 MINI CONSTR> 264.93232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 310.87898 0.00221 0.03434 0.00391 MINI INTERN> 14.35317 85.88617 0.00000 40.79966 11.19900 MINI EXTERN> -2.78575 -103.36867 0.00000 0.00000 0.00000 MINI CONSTR> 264.79540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 310.87671 0.00227 0.03245 0.00304 MINI INTERN> 14.35758 85.90347 0.00000 40.88775 11.18344 MINI EXTERN> -2.77760 -103.38779 0.00000 0.00000 0.00000 MINI CONSTR> 264.70987 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 310.87526 0.00145 0.02373 0.00300 MINI INTERN> 14.35750 85.91700 0.00000 40.94235 11.17283 MINI EXTERN> -2.82662 -103.39767 0.00000 0.00000 0.00000 MINI CONSTR> 264.70988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 310.87430 0.00097 0.02105 0.00267 MINI INTERN> 14.34077 85.91567 0.00000 40.97447 11.16895 MINI EXTERN> -2.80989 -103.42949 0.00000 0.00000 0.00000 MINI CONSTR> 264.71381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 310.87353 0.00077 0.01755 0.00165 MINI INTERN> 14.34307 85.92363 0.00000 40.98572 11.16259 MINI EXTERN> -2.80935 -103.44731 0.00000 0.00000 0.00000 MINI CONSTR> 264.71518 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 310.87281 0.00072 0.01645 0.00194 MINI INTERN> 14.33710 85.93448 0.00000 40.97823 11.16363 MINI EXTERN> -2.76539 -103.45714 0.00000 0.00000 0.00000 MINI CONSTR> 264.68189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 310.87227 0.00054 0.01460 0.00191 MINI INTERN> 14.34423 85.92277 0.00000 40.95754 11.17060 MINI EXTERN> -2.72568 -103.46214 0.00000 0.00000 0.00000 MINI CONSTR> 264.66496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 310.87191 0.00036 0.01238 0.00151 MINI INTERN> 14.33823 85.93700 0.00000 40.94318 11.16984 MINI EXTERN> -2.73268 -103.45893 0.00000 0.00000 0.00000 MINI CONSTR> 264.67528 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> 69 310.87165 0.00026 0.00983 0.02000 CONJ INTERN> 14.33460 85.94030 0.00000 40.92083 11.16244 CONJ EXTERN> -2.71390 -103.45425 0.00000 0.00000 0.00000 CONJ CONSTR> 264.68162 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 ASP 14 N ) 5.1780 ( PROT ASP 14 H ) 4.1424 ( PROT ASP 14 CA ) 5.1780 ( PROT ASP 14 CB ) 4.1424 ( PROT ASP 14 CG ) 4.1424 ( PROT ASP 14 OD1 ) 4.1424 ( PROT ASP 14 OD2 ) 4.1424 ( PROT ASP 14 C ) 5.1780 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64010 7.24659 -13.21200 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00013 0.00077 0.00054 ROTATION MATRIX 1.000000 -0.000104 -0.000358 0.000104 1.000000 0.000311 0.000358 -0.000311 1.000000 AXIS OF ROTATION IS 0.640380 0.737400 -0.214837 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 37.8554 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.357617 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3576" Parameter: A <- "0.3576" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51741 7.24944 -13.40863 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.01081 0.00611 -0.03172 ROTATION MATRIX 0.999715 0.016597 0.017140 -0.016282 0.999699 -0.018357 -0.017440 0.018073 0.999685 AXIS OF ROTATION IS -0.606824 -0.576023 0.547687 ANGLE IS 1.72 CENTER OF ROTATION 14.019891 6.808577-13.340634 SHIFT IS -0.027454 TOTAL SQUARE DIFF IS 0.8509 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.165672 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3576" RDCMND substituted energy or value "?RMS" to " 0.1657" Parameter: A <- "0.3576 0.1657" 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 0.3576 0.1657 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 " 264.68" Parameter: H <- "264.68" 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 46.19003 264.68162 2.90488 ENER INTERN> 14.33460 85.94030 0.00000 40.92083 11.16244 ENER EXTERN> -2.71390 -103.45425 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 " 46.19" Parameter: B <- "46.19" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -103.45" Parameter: C <- "-103.45" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -2.71" Parameter: C <- " -106.16" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -106.16" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 14.33" Parameter: D <- "14.33" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 85.94" Parameter: D <- " 100.27" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 40.92" Parameter: D <- " 141.19" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 11.16" Parameter: D <- " 152.35" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 152.35" 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= 46.19 GRMS= 2.90 ELEC= -103.45 VDW= -2.71 RDTITL> *EXTERNAL= -106.16 INTERNAL= 152.35 USER= 0.00 HARM= 264.68 RDTITL> *BOND= 14.33 ANGL= 85.94 DIHE= 40.92 IMPR= 11.16 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21034 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21034 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> 0 237.24383 -191.05380 1.18331 0.02000 MINI INTERN> 14.33460 85.94030 0.00000 40.92083 11.16244 MINI EXTERN> -2.71390 -103.45425 0.00000 0.00000 0.00000 MINI CONSTR> 191.05380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 227.97037 9.27346 1.44233 0.00360 MINI INTERN> 13.35816 82.19045 0.00000 43.47500 11.29269 MINI EXTERN> -24.60112 -100.51756 0.00000 0.00000 0.00000 MINI CONSTR> 202.77275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21024 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 225.72707 2.24329 1.69005 0.00156 MINI INTERN> 12.99134 83.59936 0.00000 44.02329 10.88254 MINI EXTERN> -30.28688 -99.62920 0.00000 0.00000 0.00000 MINI CONSTR> 204.14661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 224.61810 1.10897 2.58868 0.00161 MINI INTERN> 14.88233 82.11647 0.00000 44.13940 10.91732 MINI EXTERN> -32.83611 -99.19108 0.00000 0.00000 0.00000 MINI CONSTR> 204.58977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21023 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 222.59661 2.02150 0.59791 0.00070 MINI INTERN> 12.70450 82.87937 0.00000 44.24459 10.96225 MINI EXTERN> -33.81564 -99.26525 0.00000 0.00000 0.00000 MINI CONSTR> 204.88680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 221.59889 0.99772 0.97029 0.00072 MINI INTERN> 12.99418 82.26562 0.00000 44.32074 10.85943 MINI EXTERN> -34.81778 -99.06856 0.00000 0.00000 0.00000 MINI CONSTR> 205.04524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21021 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 220.73582 0.86306 0.84029 0.00075 MINI INTERN> 12.90593 81.90384 0.00000 44.35073 10.80759 MINI EXTERN> -35.31730 -99.03504 0.00000 0.00000 0.00000 MINI CONSTR> 205.12007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 220.14782 0.58800 1.30184 0.00078 MINI INTERN> 13.27031 81.38491 0.00000 44.37981 10.74762 MINI EXTERN> -35.91926 -98.87034 0.00000 0.00000 0.00000 MINI CONSTR> 205.15478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21021 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 219.46937 0.67845 1.46239 0.00080 MINI INTERN> 13.53904 80.90875 0.00000 44.39333 10.68976 MINI EXTERN> -36.47765 -98.75316 0.00000 0.00000 0.00000 MINI CONSTR> 205.16930 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 218.85677 0.61261 1.40051 0.00083 MINI INTERN> 13.45613 80.73054 0.00000 44.38289 10.65616 MINI EXTERN> -36.80043 -98.74308 0.00000 0.00000 0.00000 MINI CONSTR> 205.17455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21020 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 218.02967 0.82709 0.42502 0.00036 MINI INTERN> 12.14806 81.45937 0.00000 44.31266 10.68003 MINI EXTERN> -36.63534 -99.14455 0.00000 0.00000 0.00000 MINI CONSTR> 205.20944 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 217.74293 0.28674 1.51050 0.00090 MINI INTERN> 13.67435 80.14489 0.00000 44.35307 10.57496 MINI EXTERN> -37.51007 -98.63584 0.00000 0.00000 0.00000 MINI CONSTR> 205.14157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21018 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 217.23144 0.51149 1.56714 0.00093 MINI INTERN> 13.74374 79.90321 0.00000 44.32866 10.53928 MINI EXTERN> -37.80151 -98.59770 0.00000 0.00000 0.00000 MINI CONSTR> 205.11577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 216.42692 0.80453 0.50127 0.00040 MINI INTERN> 11.90823 81.06640 0.00000 44.22142 10.58764 MINI EXTERN> -37.36795 -99.14120 0.00000 0.00000 0.00000 MINI CONSTR> 205.15237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21015 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 216.02985 0.39707 0.36140 0.00042 MINI INTERN> 12.06786 80.76295 0.00000 44.20353 10.55396 MINI EXTERN> -37.62569 -99.05436 0.00000 0.00000 0.00000 MINI CONSTR> 205.12159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 215.58357 0.44628 0.35552 0.00043 MINI INTERN> 12.03181 80.62541 0.00000 44.16474 10.52675 MINI EXTERN> -37.81714 -99.04220 0.00000 0.00000 0.00000 MINI CONSTR> 205.09421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21015 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 215.18972 0.39384 0.72891 0.00045 MINI INTERN> 11.65960 80.84189 0.00000 44.09886 10.51797 MINI EXTERN> -37.83604 -99.17410 0.00000 0.00000 0.00000 MINI CONSTR> 205.08155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 214.79910 0.39063 0.44108 0.00046 MINI INTERN> 11.86856 80.47984 0.00000 44.07564 10.48331 MINI EXTERN> -38.09423 -99.06167 0.00000 0.00000 0.00000 MINI CONSTR> 205.04764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21014 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 214.44856 0.35054 0.52854 0.00048 MINI INTERN> 11.78486 80.43001 0.00000 44.02721 10.46408 MINI EXTERN> -38.20806 -99.07731 0.00000 0.00000 0.00000 MINI CONSTR> 205.02777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 214.20154 0.24702 0.80342 0.00050 MINI INTERN> 11.58543 80.54399 0.00000 43.97536 10.45604 MINI EXTERN> -38.22662 -99.15173 0.00000 0.00000 0.00000 MINI CONSTR> 205.01908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21014 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 213.90759 0.29395 0.88493 0.00052 MINI INTERN> 11.57028 80.46104 0.00000 43.92771 10.43637 MINI EXTERN> -38.34088 -99.14964 0.00000 0.00000 0.00000 MINI CONSTR> 205.00270 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 213.64601 0.26158 0.85862 0.00054 MINI INTERN> 11.57773 80.34928 0.00000 43.89051 10.41881 MINI EXTERN> -38.44954 -99.12963 0.00000 0.00000 0.00000 MINI CONSTR> 204.98885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21013 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 213.38911 0.25690 0.87172 0.00056 MINI INTERN> 11.59852 80.23637 0.00000 43.84818 10.40025 MINI EXTERN> -38.56103 -99.11017 0.00000 0.00000 0.00000 MINI CONSTR> 204.97698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 213.07153 0.31757 0.28038 0.00024 MINI INTERN> 12.06762 79.61278 0.00000 43.85008 10.36198 MINI EXTERN> -38.88982 -98.87604 0.00000 0.00000 0.00000 MINI CONSTR> 204.94493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21013 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 212.98034 0.09120 0.97048 0.00060 MINI INTERN> 11.55552 80.12994 0.00000 43.76750 10.37359 MINI EXTERN> -38.70318 -99.10966 0.00000 0.00000 0.00000 MINI CONSTR> 204.96662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 212.77752 0.20282 1.02092 0.00062 MINI INTERN> 11.61748 80.00935 0.00000 43.72471 10.35597 MINI EXTERN> -38.80850 -99.08386 0.00000 0.00000 0.00000 MINI CONSTR> 204.96237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21014 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 212.44988 0.32764 0.34726 0.00027 MINI INTERN> 12.07414 79.35208 0.00000 43.73371 10.32085 MINI EXTERN> -39.13577 -98.83112 0.00000 0.00000 0.00000 MINI CONSTR> 204.93598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 212.29340 0.15648 0.22351 0.00028 MINI INTERN> 11.98502 79.37171 0.00000 43.69499 10.31407 MINI EXTERN> -39.15678 -98.85710 0.00000 0.00000 0.00000 MINI CONSTR> 204.94149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21013 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 212.10646 0.18693 0.41541 0.00029 MINI INTERN> 12.05787 79.22209 0.00000 43.65811 10.29876 MINI EXTERN> -39.26172 -98.81256 0.00000 0.00000 0.00000 MINI CONSTR> 204.94390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 211.94817 0.15830 0.29473 0.00030 MINI INTERN> 11.99725 79.21026 0.00000 43.61855 10.29047 MINI EXTERN> -39.29583 -98.82533 0.00000 0.00000 0.00000 MINI CONSTR> 204.95280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21011 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 211.80166 0.14651 0.33298 0.00031 MINI INTERN> 11.99491 79.14809 0.00000 43.58240 10.28053 MINI EXTERN> -39.35160 -98.81472 0.00000 0.00000 0.00000 MINI CONSTR> 204.96206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 211.69438 0.10728 0.50441 0.00032 MINI INTERN> 12.03850 79.06223 0.00000 43.55424 10.27139 MINI EXTERN> -39.41311 -98.78959 0.00000 0.00000 0.00000 MINI CONSTR> 204.97073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21012 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 211.56809 0.12629 0.54373 0.00033 MINI INTERN> 12.02123 79.02223 0.00000 43.51803 10.26314 MINI EXTERN> -39.45473 -98.78637 0.00000 0.00000 0.00000 MINI CONSTR> 204.98457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 211.45944 0.10865 0.60775 0.00034 MINI INTERN> 12.02189 78.97464 0.00000 43.48458 10.25526 MINI EXTERN> -39.49767 -98.77843 0.00000 0.00000 0.00000 MINI CONSTR> 204.99918 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21012 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 211.35856 0.10088 0.57030 0.00036 MINI INTERN> 12.01317 78.93625 0.00000 43.45507 10.24890 MINI EXTERN> -39.53314 -98.77469 0.00000 0.00000 0.00000 MINI CONSTR> 205.01300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 211.21598 0.14258 0.16807 0.00015 MINI INTERN> 11.92008 78.96569 0.00000 43.40895 10.24189 MINI EXTERN> -39.54451 -98.80978 0.00000 0.00000 0.00000 MINI CONSTR> 205.03366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21011 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 211.17114 0.04484 0.61670 0.00038 MINI INTERN> 11.99247 78.86855 0.00000 43.39247 10.23544 MINI EXTERN> -39.59839 -98.76733 0.00000 0.00000 0.00000 MINI CONSTR> 205.04794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 211.08769 0.08345 0.64701 0.00040 MINI INTERN> 11.98891 78.83321 0.00000 43.36196 10.22906 MINI EXTERN> -39.63005 -98.76249 0.00000 0.00000 0.00000 MINI CONSTR> 205.06710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 210.95223 0.13546 0.21550 0.00017 MINI INTERN> 11.91044 78.85466 0.00000 43.31561 10.22268 MINI EXTERN> -39.64462 -98.79773 0.00000 0.00000 0.00000 MINI CONSTR> 205.09119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 210.88646 0.06577 0.14361 0.00018 MINI INTERN> 11.90739 78.81698 0.00000 43.29532 10.21804 MINI EXTERN> -39.66994 -98.78810 0.00000 0.00000 0.00000 MINI CONSTR> 205.10678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21011 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 210.81126 0.07520 0.14301 0.00019 MINI INTERN> 11.90490 78.78190 0.00000 43.26601 10.21242 MINI EXTERN> -39.69938 -98.78348 0.00000 0.00000 0.00000 MINI CONSTR> 205.12890 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 210.74767 0.06360 0.30281 0.00019 MINI INTERN> 11.91170 78.75815 0.00000 43.23134 10.20699 MINI EXTERN> -39.72836 -98.78677 0.00000 0.00000 0.00000 MINI CONSTR> 205.15461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 210.68118 0.06649 0.17777 0.00020 MINI INTERN> 11.90225 78.72077 0.00000 43.21031 10.20245 MINI EXTERN> -39.75199 -98.77681 0.00000 0.00000 0.00000 MINI CONSTR> 205.17419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 210.63249 0.04869 0.32873 0.00021 MINI INTERN> 11.91174 78.69875 0.00000 43.18046 10.19809 MINI EXTERN> -39.77719 -98.77834 0.00000 0.00000 0.00000 MINI CONSTR> 205.19899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 210.58091 0.05158 0.35107 0.00021 MINI INTERN> 11.91469 78.66983 0.00000 43.15536 10.19406 MINI EXTERN> -39.80097 -98.77427 0.00000 0.00000 0.00000 MINI CONSTR> 205.22222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 210.53443 0.04648 0.33860 0.00022 MINI INTERN> 11.91186 78.64498 0.00000 43.13418 10.19035 MINI EXTERN> -39.81961 -98.77031 0.00000 0.00000 0.00000 MINI CONSTR> 205.24298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 210.48961 0.04482 0.35287 0.00023 MINI INTERN> 11.91310 78.61934 0.00000 43.11109 10.18678 MINI EXTERN> -39.84041 -98.76649 0.00000 0.00000 0.00000 MINI CONSTR> 205.26621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 210.43268 0.05693 0.11010 0.00010 MINI INTERN> 11.88761 78.58531 0.00000 43.09726 10.18192 MINI EXTERN> -39.85122 -98.75322 0.00000 0.00000 0.00000 MINI CONSTR> 205.28501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 210.41385 0.01883 0.38775 0.00025 MINI INTERN> 11.91516 78.57500 0.00000 43.06890 10.18032 MINI EXTERN> -39.87603 -98.76030 0.00000 0.00000 0.00000 MINI CONSTR> 205.31080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 210.37806 0.03579 0.40411 0.00026 MINI INTERN> 11.91902 78.55134 0.00000 43.04751 10.17748 MINI EXTERN> -39.89512 -98.75652 0.00000 0.00000 0.00000 MINI CONSTR> 205.33434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 210.32156 0.05651 0.13137 0.00011 MINI INTERN> 11.88070 78.52046 0.00000 43.03588 10.17164 MINI EXTERN> -39.89742 -98.74338 0.00000 0.00000 0.00000 MINI CONSTR> 205.35368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 210.29394 0.02761 0.09228 0.00011 MINI INTERN> 11.88267 78.50435 0.00000 43.01875 10.16980 MINI EXTERN> -39.91194 -98.74230 0.00000 0.00000 0.00000 MINI CONSTR> 205.37262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 210.26267 0.03127 0.09121 0.00012 MINI INTERN> 11.88107 78.48475 0.00000 42.99936 10.16683 MINI EXTERN> -39.92577 -98.73953 0.00000 0.00000 0.00000 MINI CONSTR> 205.39596 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 210.23559 0.02708 0.19021 0.00012 MINI INTERN> 11.87488 78.46505 0.00000 42.98148 10.16255 MINI EXTERN> -39.93375 -98.73486 0.00000 0.00000 0.00000 MINI CONSTR> 205.42025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 210.20806 0.02753 0.11289 0.00013 MINI INTERN> 11.87605 78.44898 0.00000 42.96364 10.16100 MINI EXTERN> -39.94882 -98.73407 0.00000 0.00000 0.00000 MINI CONSTR> 205.44129 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 210.18744 0.02062 0.21006 0.00013 MINI INTERN> 11.86982 78.43332 0.00000 42.94812 10.15711 MINI EXTERN> -39.95402 -98.73059 0.00000 0.00000 0.00000 MINI CONSTR> 205.46368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 210.16592 0.02152 0.22202 0.00014 MINI INTERN> 11.86749 78.41829 0.00000 42.93220 10.15452 MINI EXTERN> -39.96319 -98.72856 0.00000 0.00000 0.00000 MINI CONSTR> 205.48517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 210.14677 0.01915 0.24181 0.00014 MINI INTERN> 11.86550 78.40405 0.00000 42.91707 10.15201 MINI EXTERN> -39.97145 -98.72654 0.00000 0.00000 0.00000 MINI CONSTR> 205.50613 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 210.12911 0.01766 0.22766 0.00015 MINI INTERN> 11.86759 78.39031 0.00000 42.90314 10.15069 MINI EXTERN> -39.98206 -98.72484 0.00000 0.00000 0.00000 MINI CONSTR> 205.52428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 210.11071 0.01840 0.23064 0.00015 MINI INTERN> 11.86378 78.37746 0.00000 42.88848 10.14826 MINI EXTERN> -39.98939 -98.72334 0.00000 0.00000 0.00000 MINI CONSTR> 205.54547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 210.08792 0.02280 0.07274 0.00007 MINI INTERN> 11.88313 78.35968 0.00000 42.86888 10.15035 MINI EXTERN> -40.01669 -98.72332 0.00000 0.00000 0.00000 MINI CONSTR> 205.56589 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 210.08207 0.00584 0.25276 0.00016 MINI INTERN> 11.86280 78.35333 0.00000 42.86251 10.14463 MINI EXTERN> -40.00401 -98.72005 0.00000 0.00000 0.00000 MINI CONSTR> 205.58287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 210.05806 0.02401 0.07424 0.00007 MINI INTERN> 11.88488 78.33408 0.00000 42.84129 10.14730 MINI EXTERN> -40.03451 -98.72001 0.00000 0.00000 0.00000 MINI CONSTR> 205.60504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 210.04630 0.01177 0.05996 0.00007 MINI INTERN> 11.88038 78.32514 0.00000 42.83124 10.14542 MINI EXTERN> -40.03815 -98.71871 0.00000 0.00000 0.00000 MINI CONSTR> 205.62098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 210.03305 0.01325 0.10376 0.00008 MINI INTERN> 11.89356 78.30876 0.00000 42.81411 10.14537 MINI EXTERN> -40.05480 -98.71696 0.00000 0.00000 0.00000 MINI CONSTR> 205.64301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 210.02162 0.01143 0.07414 0.00008 MINI INTERN> 11.88693 78.30037 0.00000 42.80445 10.14330 MINI EXTERN> -40.05704 -98.71572 0.00000 0.00000 0.00000 MINI CONSTR> 205.65931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 210.01062 0.01099 0.07675 0.00008 MINI INTERN> 11.88907 78.28895 0.00000 42.79209 10.14220 MINI EXTERN> -40.06501 -98.71429 0.00000 0.00000 0.00000 MINI CONSTR> 205.67762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 210.00231 0.00832 0.13173 0.00009 MINI INTERN> 11.90413 78.27492 0.00000 42.77773 10.14269 MINI EXTERN> -40.08025 -98.71276 0.00000 0.00000 0.00000 MINI CONSTR> 205.69584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 209.99315 0.00915 0.13820 0.00009 MINI INTERN> 11.90909 78.26332 0.00000 42.76580 10.14200 MINI EXTERN> -40.08896 -98.71131 0.00000 0.00000 0.00000 MINI CONSTR> 205.71321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 209.98502 0.00813 0.15206 0.00009 MINI INTERN> 11.91625 78.25149 0.00000 42.75382 10.14162 MINI EXTERN> -40.09858 -98.70986 0.00000 0.00000 0.00000 MINI CONSTR> 205.73028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21011 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 209.97761 0.00740 0.14431 0.00010 MINI INTERN> 11.91176 78.24549 0.00000 42.74582 10.14020 MINI EXTERN> -40.10077 -98.70916 0.00000 0.00000 0.00000 MINI CONSTR> 205.74428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 209.97000 0.00761 0.14676 0.00010 MINI INTERN> 11.91744 78.23423 0.00000 42.73469 10.13973 MINI EXTERN> -40.10904 -98.70775 0.00000 0.00000 0.00000 MINI CONSTR> 205.76070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21011 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 209.96052 0.00948 0.04623 0.00004 MINI INTERN> 11.86720 78.24339 0.00000 42.73621 10.13302 MINI EXTERN> -40.08332 -98.70883 0.00000 0.00000 0.00000 MINI CONSTR> 205.77284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 209.95794 0.00258 0.16093 0.00011 MINI INTERN> 11.92287 78.21753 0.00000 42.71614 10.13851 MINI EXTERN> -40.12092 -98.70580 0.00000 0.00000 0.00000 MINI CONSTR> 205.78961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21011 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 209.95209 0.00585 0.17017 0.00011 MINI INTERN> 11.93374 78.20502 0.00000 42.70493 10.13869 MINI EXTERN> -40.13126 -98.70426 0.00000 0.00000 0.00000 MINI CONSTR> 205.80523 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 209.94256 0.00953 0.05862 0.00005 MINI INTERN> 11.85582 78.22567 0.00000 42.71219 10.12905 MINI EXTERN> -40.08938 -98.70707 0.00000 0.00000 0.00000 MINI CONSTR> 205.81628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 209.93804 0.00452 0.03684 0.00005 MINI INTERN> 11.87047 78.21410 0.00000 42.70263 10.13011 MINI EXTERN> -40.10138 -98.70577 0.00000 0.00000 0.00000 MINI CONSTR> 205.82787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 209.93267 0.00536 0.07074 0.00005 MINI INTERN> 11.84491 78.21696 0.00000 42.69818 10.12628 MINI EXTERN> -40.09070 -98.70638 0.00000 0.00000 0.00000 MINI CONSTR> 205.84342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 209.92805 0.00463 0.04871 0.00005 MINI INTERN> 11.85631 78.20616 0.00000 42.68873 10.12694 MINI EXTERN> -40.10090 -98.70521 0.00000 0.00000 0.00000 MINI CONSTR> 205.85602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 209.92381 0.00424 0.05620 0.00005 MINI INTERN> 11.84961 78.20280 0.00000 42.68242 10.12550 MINI EXTERN> -40.10053 -98.70502 0.00000 0.00000 0.00000 MINI CONSTR> 205.86903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 209.92071 0.00310 0.08379 0.00006 MINI INTERN> 11.83331 78.20441 0.00000 42.67899 10.12302 MINI EXTERN> -40.09379 -98.70549 0.00000 0.00000 0.00000 MINI CONSTR> 205.88027 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 209.91705 0.00366 0.09069 0.00006 MINI INTERN> 11.82399 78.20300 0.00000 42.67343 10.12143 MINI EXTERN> -40.09206 -98.70553 0.00000 0.00000 0.00000 MINI CONSTR> 205.89280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 209.91389 0.00316 0.10085 0.00006 MINI INTERN> 11.81444 78.20203 0.00000 42.66843 10.11983 MINI EXTERN> -40.08978 -98.70564 0.00000 0.00000 0.00000 MINI CONSTR> 205.90458 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 209.91093 0.00295 0.09456 0.00006 MINI INTERN> 11.81967 78.19487 0.00000 42.66189 10.11989 MINI EXTERN> -40.09499 -98.70505 0.00000 0.00000 0.00000 MINI CONSTR> 205.91466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 209.90676 0.00418 0.02790 0.00003 MINI INTERN> 11.88348 78.16082 0.00000 42.64357 10.12628 MINI EXTERN> -40.13369 -98.70103 0.00000 0.00000 0.00000 MINI CONSTR> 205.92732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 209.90543 0.00132 0.10184 0.00007 MINI INTERN> 11.80779 78.19095 0.00000 42.65172 10.11772 MINI EXTERN> -40.09420 -98.70496 0.00000 0.00000 0.00000 MINI CONSTR> 205.93641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 209.90296 0.00247 0.10659 0.00007 MINI INTERN> 11.80120 78.18950 0.00000 42.64691 10.11661 MINI EXTERN> -40.09341 -98.70490 0.00000 0.00000 0.00000 MINI CONSTR> 205.94705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 209.89898 0.00399 0.03532 0.00003 MINI INTERN> 11.89744 78.13971 0.00000 42.62347 10.12621 MINI EXTERN> -40.14816 -98.69946 0.00000 0.00000 0.00000 MINI CONSTR> 205.95976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 209.89703 0.00195 0.02386 0.00003 MINI INTERN> 11.88245 78.14296 0.00000 42.62179 10.12434 MINI EXTERN> -40.14197 -98.70001 0.00000 0.00000 0.00000 MINI CONSTR> 205.96748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 209.89480 0.00223 0.02367 0.00003 MINI INTERN> 11.88413 78.13758 0.00000 42.61597 10.12407 MINI EXTERN> -40.14500 -98.69974 0.00000 0.00000 0.00000 MINI CONSTR> 205.97777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 209.89290 0.00191 0.04984 0.00003 MINI INTERN> 11.91343 78.11924 0.00000 42.60501 10.12655 MINI EXTERN> -40.16238 -98.69822 0.00000 0.00000 0.00000 MINI CONSTR> 205.98927 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 209.89093 0.00197 0.02935 0.00004 MINI INTERN> 11.89430 78.12430 0.00000 42.60388 10.12430 MINI EXTERN> -40.15416 -98.69902 0.00000 0.00000 0.00000 MINI CONSTR> 205.99732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 209.88946 0.00147 0.05477 0.00004 MINI INTERN> 11.91837 78.10897 0.00000 42.59459 10.12631 MINI EXTERN> -40.16840 -98.69788 0.00000 0.00000 0.00000 MINI CONSTR> 206.00749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 209.88793 0.00154 0.05818 0.00004 MINI INTERN> 11.92166 78.10382 0.00000 42.58949 10.12628 MINI EXTERN> -40.17150 -98.69810 0.00000 0.00000 0.00000 MINI CONSTR> 206.01628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 209.88658 0.00135 0.06398 0.00004 MINI INTERN> 11.92413 78.09866 0.00000 42.58456 10.12631 MINI EXTERN> -40.17496 -98.69689 0.00000 0.00000 0.00000 MINI CONSTR> 206.02477 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 209.88530 0.00127 0.05957 0.00004 MINI INTERN> 11.92353 78.09624 0.00000 42.58119 10.12592 MINI EXTERN> -40.17540 -98.69783 0.00000 0.00000 0.00000 MINI CONSTR> 206.03166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 209.88398 0.00132 0.06084 0.00004 MINI INTERN> 11.92212 78.09307 0.00000 42.57705 10.12558 MINI EXTERN> -40.17667 -98.69713 0.00000 0.00000 0.00000 MINI CONSTR> 206.03996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 209.88237 0.00161 0.01960 0.00002 MINI INTERN> 11.87073 78.11418 0.00000 42.58276 10.12023 MINI EXTERN> -40.15129 -98.69958 0.00000 0.00000 0.00000 MINI CONSTR> 206.04534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21010 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 209.88195 0.00042 0.06664 0.00005 MINI INTERN> 11.92945 78.08438 0.00000 42.56891 10.12572 MINI EXTERN> -40.18192 -98.69849 0.00000 0.00000 0.00000 MINI CONSTR> 206.05391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 209.88026 0.00169 0.02211 0.00002 MINI INTERN> 11.86725 78.10970 0.00000 42.57614 10.11945 MINI EXTERN> -40.15204 -98.69976 0.00000 0.00000 0.00000 MINI CONSTR> 206.05951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21009 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 209.87941 0.00085 0.01577 0.00002 MINI INTERN> 11.87583 78.10330 0.00000 42.57172 10.12014 MINI EXTERN> -40.15740 -98.69964 0.00000 0.00000 0.00000 MINI CONSTR> 206.06547 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> 500 209.87941 0.00085 0.01577 0.00002 STPD INTERN> 11.87583 78.10330 0.00000 42.57172 10.12014 STPD EXTERN> -40.15740 -98.69964 0.00000 0.00000 0.00000 STPD CONSTR> 206.06547 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 21009 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21009 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 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> 0 209.87941 0.00085 0.01577 0.00000 MINI INTERN> 11.87583 78.10330 0.00000 42.57172 10.12014 MINI EXTERN> -40.15740 -98.69964 0.00000 0.00000 0.00000 MINI CONSTR> 206.06547 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> 3 209.86522 0.01419 0.00548 0.02000 CONJ INTERN> 11.88229 78.01159 0.00000 42.46963 10.11598 CONJ EXTERN> -40.20124 -98.69923 0.00000 0.00000 0.00000 CONJ CONSTR> 206.28621 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 ASP 14 N ) 3.3657 ( PROT ASP 14 H ) 2.6925 ( PROT ASP 14 CA ) 3.3657 ( PROT ASP 14 CB ) 2.6925 ( PROT ASP 14 CG ) 2.6925 ( PROT ASP 14 OD1 ) 2.6925 ( PROT ASP 14 OD2 ) 2.6925 ( PROT ASP 14 C ) 3.3657 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.63979 7.24633 -13.21169 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00044 0.00103 0.00023 ROTATION MATRIX 1.000000 -0.000092 -0.000367 0.000092 1.000000 0.000319 0.000367 -0.000319 1.000000 AXIS OF ROTATION IS 0.644129 0.741909 -0.186196 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 45.3865 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.391577 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3916" Parameter: A <- "0.3916" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.51923 7.24979 -13.40798 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.00899 0.00576 -0.03237 ROTATION MATRIX 0.999670 0.017922 0.018377 -0.017554 0.999646 -0.019978 -0.018728 0.019649 0.999632 AXIS OF ROTATION IS -0.611055 -0.572161 0.547032 ANGLE IS 1.86 CENTER OF ROTATION 13.997557 6.794523-13.374075 SHIFT IS -0.026501 TOTAL SQUARE DIFF IS 1.2219 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.198535 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3916" RDCMND substituted energy or value "?RMS" to " 0.1985" Parameter: A <- "0.3916 0.1985" 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 0.3916 0.1985 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 " 206.29" Parameter: H <- "206.29" 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 3.57901 206.28621 2.06752 ENER INTERN> 11.88229 78.01159 0.00000 42.46963 10.11598 ENER EXTERN> -40.20124 -98.69923 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 " 3.58" Parameter: B <- "3.58" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -98.70" Parameter: C <- "-98.70" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -40.20" Parameter: C <- " -138.90" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -138.90" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 11.88" Parameter: D <- "11.88" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 78.01" Parameter: D <- " 89.89" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 42.47" Parameter: D <- " 132.36" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 10.12" Parameter: D <- " 142.48" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 142.48" 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= 3.58 GRMS= 2.07 ELEC= -98.70 VDW= -40.20 RDTITL> *EXTERNAL= -138.90 INTERNAL= 142.48 USER= 0.00 HARM= 206.29 RDTITL> *BOND= 11.88 ANGL= 78.01 DIHE= 42.47 IMPR= 10.12 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= 3.58 GRMS= 2.07 ELEC= -98.70 VDW= -40.20 RDTITL> *EXTERNAL= -138.90 INTERNAL= 142.48 USER= 0.00 HARM= 206.29 RDTITL> *BOND= 11.88 ANGL= 78.01 DIHE= 42.47 IMPR= 10.12 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= 3.58 GRMS= 2.07 ELEC= -98.70 VDW= -40.20 RDTITL> *EXTERNAL= -138.90 INTERNAL= 142.48 USER= 0.00 HARM= 206.29 RDTITL> *BOND= 11.88 ANGL= 78.01 DIHE= 42.47 IMPR= 10.12 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 6000 0.3916 0.1985 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 21009 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 21008 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> 0 151.92383 -148.34482 0.83787 0.02000 MINI INTERN> 11.88229 78.01159 0.00000 42.46963 10.11598 MINI EXTERN> -40.20124 -98.69923 0.00000 0.00000 0.00000 MINI CONSTR> 148.34482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 179.86847 -27.94463 15.24403 0.00864 MINI INTERN> 47.43375 70.87947 0.00000 46.24627 8.92423 MINI EXTERN> -57.58777 -92.12926 0.00000 0.00000 0.00000 MINI CONSTR> 156.10177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20995 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 151.43685 28.43161 6.77880 0.00373 MINI INTERN> 14.13354 81.87040 0.00000 44.35933 10.79631 MINI EXTERN> -60.08712 -96.90079 0.00000 0.00000 0.00000 MINI CONSTR> 157.26520 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 144.11670 7.32016 0.47701 0.00067 MINI INTERN> 11.26573 76.71743 0.00000 45.03427 10.14504 MINI EXTERN> -61.05356 -95.22916 0.00000 0.00000 0.00000 MINI CONSTR> 157.23695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20997 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 143.44300 0.67370 1.03924 0.00070 MINI INTERN> 11.59480 76.51913 0.00000 44.98787 10.18505 MINI EXTERN> -62.09967 -95.26133 0.00000 0.00000 0.00000 MINI CONSTR> 157.51714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 142.78246 0.66054 1.04960 0.00072 MINI INTERN> 11.95069 75.92986 0.00000 45.02440 10.13369 MINI EXTERN> -62.83289 -95.11373 0.00000 0.00000 0.00000 MINI CONSTR> 157.69044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20991 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 142.14553 0.63693 1.09914 0.00075 MINI INTERN> 11.79447 75.81969 0.00000 45.03447 10.10887 MINI EXTERN> -63.32179 -95.14141 0.00000 0.00000 0.00000 MINI CONSTR> 157.85124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 141.57991 0.56562 1.21775 0.00078 MINI INTERN> 11.98368 75.46153 0.00000 45.03470 10.07603 MINI EXTERN> -63.89011 -95.05874 0.00000 0.00000 0.00000 MINI CONSTR> 157.97283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20990 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 141.05988 0.52003 1.16202 0.00080 MINI INTERN> 11.93029 75.26251 0.00000 45.02529 10.04355 MINI EXTERN> -64.19365 -95.06683 0.00000 0.00000 0.00000 MINI CONSTR> 158.05872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 140.38424 0.67564 0.37592 0.00035 MINI INTERN> 10.92984 75.21565 0.00000 45.19719 9.85590 MINI EXTERN> -63.86742 -95.05387 0.00000 0.00000 0.00000 MINI CONSTR> 158.10696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20985 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 140.15084 0.23341 1.34336 0.00087 MINI INTERN> 11.92839 74.90744 0.00000 44.99082 9.98478 MINI EXTERN> -64.78366 -95.07082 0.00000 0.00000 0.00000 MINI CONSTR> 158.19388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 139.76600 0.38483 1.47906 0.00090 MINI INTERN> 11.81546 74.77484 0.00000 44.97946 9.94474 MINI EXTERN> -65.02173 -94.97418 0.00000 0.00000 0.00000 MINI CONSTR> 158.24742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20981 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 139.07585 0.69015 0.40916 0.00039 MINI INTERN> 10.76412 74.76463 0.00000 45.14534 9.76215 MINI EXTERN> -64.59795 -95.01878 0.00000 0.00000 0.00000 MINI CONSTR> 158.25634 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 138.71283 0.36302 0.32474 0.00040 MINI INTERN> 10.83175 74.61908 0.00000 45.09329 9.76215 MINI EXTERN> -64.87291 -95.01048 0.00000 0.00000 0.00000 MINI CONSTR> 158.28994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20978 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 138.31433 0.39850 0.32513 0.00042 MINI INTERN> 10.79894 74.47422 0.00000 45.05915 9.73655 MINI EXTERN> -65.07730 -94.99769 0.00000 0.00000 0.00000 MINI CONSTR> 158.32046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 137.95577 0.35857 0.59794 0.00043 MINI INTERN> 10.56995 74.37823 0.00000 45.07737 9.66216 MINI EXTERN> -65.08367 -94.98791 0.00000 0.00000 0.00000 MINI CONSTR> 158.33964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20972 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 137.60473 0.35104 0.40514 0.00045 MINI INTERN> 10.69658 74.21908 0.00000 45.00186 9.67687 MINI EXTERN> -65.36715 -94.98550 0.00000 0.00000 0.00000 MINI CONSTR> 158.36300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 137.29706 0.30767 0.51473 0.00046 MINI INTERN> 10.55656 74.15121 0.00000 44.98946 9.63803 MINI EXTERN> -65.43823 -94.97836 0.00000 0.00000 0.00000 MINI CONSTR> 158.37839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20971 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 137.03799 0.25906 0.70280 0.00048 MINI INTERN> 10.42196 74.09571 0.00000 44.98420 9.59562 MINI EXTERN> -65.46811 -94.98072 0.00000 0.00000 0.00000 MINI CONSTR> 158.38934 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 136.74657 0.29142 0.74460 0.00050 MINI INTERN> 10.42256 73.97134 0.00000 44.93928 9.57783 MINI EXTERN> -65.61163 -94.95776 0.00000 0.00000 0.00000 MINI CONSTR> 158.40494 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20970 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 136.50378 0.24280 0.83863 0.00052 MINI INTERN> 10.39448 73.89651 0.00000 44.91172 9.55643 MINI EXTERN> -65.68740 -94.98237 0.00000 0.00000 0.00000 MINI CONSTR> 158.41441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 136.25744 0.24634 0.77442 0.00054 MINI INTERN> 10.28991 73.86725 0.00000 44.88127 9.54473 MINI EXTERN> -65.78226 -94.97063 0.00000 0.00000 0.00000 MINI CONSTR> 158.42718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20970 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 136.01276 0.24468 0.83259 0.00056 MINI INTERN> 10.37858 73.72550 0.00000 44.82863 9.53541 MINI EXTERN> -65.91359 -94.98035 0.00000 0.00000 0.00000 MINI CONSTR> 158.43858 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 135.71141 0.30135 0.26308 0.00024 MINI INTERN> 10.79581 73.50843 0.00000 44.66969 9.62483 MINI EXTERN> -66.39619 -94.95644 0.00000 0.00000 0.00000 MINI CONSTR> 158.46529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20969 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 135.60274 0.10867 0.87600 0.00060 MINI INTERN> 10.17933 73.67674 0.00000 44.78312 9.49921 MINI EXTERN> -66.01461 -94.98091 0.00000 0.00000 0.00000 MINI CONSTR> 158.45986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 135.40169 0.20105 0.95993 0.00062 MINI INTERN> 10.22842 73.56929 0.00000 44.72749 9.49584 MINI EXTERN> -66.15300 -94.94245 0.00000 0.00000 0.00000 MINI CONSTR> 158.47610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20970 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 135.08743 0.31426 0.30681 0.00027 MINI INTERN> 10.83741 73.25667 0.00000 44.53691 9.60489 MINI EXTERN> -66.70076 -94.95098 0.00000 0.00000 0.00000 MINI CONSTR> 158.50330 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 134.91987 0.16757 0.22107 0.00028 MINI INTERN> 10.72903 73.21801 0.00000 44.52734 9.57820 MINI EXTERN> -66.69352 -94.95030 0.00000 0.00000 0.00000 MINI CONSTR> 158.51110 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20970 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 134.72749 0.19237 0.21563 0.00029 MINI INTERN> 10.71227 73.15100 0.00000 44.48857 9.56869 MINI EXTERN> -66.76819 -94.95010 0.00000 0.00000 0.00000 MINI CONSTR> 158.52524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 134.54758 0.17991 0.23218 0.00030 MINI INTERN> 10.74053 73.07359 0.00000 44.44201 9.56652 MINI EXTERN> -66.86432 -94.95151 0.00000 0.00000 0.00000 MINI CONSTR> 158.54076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20968 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 134.39213 0.15545 0.43934 0.00031 MINI INTERN> 10.90445 72.97771 0.00000 44.36492 9.59051 MINI EXTERN> -67.05535 -94.95198 0.00000 0.00000 0.00000 MINI CONSTR> 158.56187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 134.22944 0.16269 0.29983 0.00032 MINI INTERN> 10.78536 72.93960 0.00000 44.35752 9.56232 MINI EXTERN> -67.02984 -94.95771 0.00000 0.00000 0.00000 MINI CONSTR> 158.57219 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20968 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 134.10808 0.12135 0.48032 0.00033 MINI INTERN> 10.93974 72.84695 0.00000 44.29047 9.58216 MINI EXTERN> -67.19072 -94.95267 0.00000 0.00000 0.00000 MINI CONSTR> 158.59216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 133.96459 0.14350 0.49471 0.00034 MINI INTERN> 10.91268 72.81177 0.00000 44.25950 9.57602 MINI EXTERN> -67.23921 -94.96494 0.00000 0.00000 0.00000 MINI CONSTR> 158.60877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20966 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 133.84870 0.11588 0.60298 0.00036 MINI INTERN> 10.88585 72.77761 0.00000 44.22833 9.57019 MINI EXTERN> -67.29294 -94.94778 0.00000 0.00000 0.00000 MINI CONSTR> 158.62744 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 133.73079 0.11791 0.54382 0.00037 MINI INTERN> 10.94904 72.68505 0.00000 44.19180 9.56794 MINI EXTERN> -67.35572 -94.94944 0.00000 0.00000 0.00000 MINI CONSTR> 158.64212 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 133.58345 0.14734 0.18265 0.00016 MINI INTERN> 10.61263 72.69888 0.00000 44.23958 9.50092 MINI EXTERN> -67.16124 -94.95446 0.00000 0.00000 0.00000 MINI CONSTR> 158.64715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 133.51879 0.06466 0.58449 0.00040 MINI INTERN> 11.02310 72.55429 0.00000 44.12352 9.56460 MINI EXTERN> -67.47256 -94.95086 0.00000 0.00000 0.00000 MINI CONSTR> 158.67671 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 133.36651 0.15229 0.18699 0.00017 MINI INTERN> 10.59032 72.61101 0.00000 44.18689 9.48910 MINI EXTERN> -67.23543 -94.95812 0.00000 0.00000 0.00000 MINI CONSTR> 158.68274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 133.32526 0.04125 0.63910 0.00043 MINI INTERN> 11.07264 72.44188 0.00000 44.06640 9.55702 MINI EXTERN> -67.55618 -94.96830 0.00000 0.00000 0.00000 MINI CONSTR> 158.71180 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 133.17391 0.15135 0.21374 0.00019 MINI INTERN> 10.55334 72.53660 0.00000 44.14259 9.47578 MINI EXTERN> -67.28893 -94.96455 0.00000 0.00000 0.00000 MINI CONSTR> 158.71908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 133.09254 0.08137 0.15892 0.00019 MINI INTERN> 10.59325 72.49389 0.00000 44.10949 9.48314 MINI EXTERN> -67.35794 -94.96667 0.00000 0.00000 0.00000 MINI CONSTR> 158.73738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 133.00662 0.08592 0.16574 0.00020 MINI INTERN> 10.57076 72.46268 0.00000 44.09002 9.47710 MINI EXTERN> -67.37996 -94.97041 0.00000 0.00000 0.00000 MINI CONSTR> 158.75644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 132.92402 0.08260 0.27855 0.00021 MINI INTERN> 10.47881 72.45168 0.00000 44.08695 9.45720 MINI EXTERN> -67.34942 -94.97689 0.00000 0.00000 0.00000 MINI CONSTR> 158.77569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 132.84365 0.08037 0.20759 0.00021 MINI INTERN> 10.52486 72.39951 0.00000 44.05283 9.46462 MINI EXTERN> -67.42015 -94.97496 0.00000 0.00000 0.00000 MINI CONSTR> 158.79694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 132.77254 0.07111 0.25024 0.00022 MINI INTERN> 10.47317 72.38629 0.00000 44.04277 9.45515 MINI EXTERN> -67.41906 -94.98199 0.00000 0.00000 0.00000 MINI CONSTR> 158.81623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 132.71037 0.06217 0.33837 0.00023 MINI INTERN> 10.41263 72.37838 0.00000 44.03752 9.44297 MINI EXTERN> -67.40461 -94.99155 0.00000 0.00000 0.00000 MINI CONSTR> 158.83501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 132.64392 0.06645 0.37339 0.00024 MINI INTERN> 10.40526 72.34518 0.00000 44.01677 9.44118 MINI EXTERN> -67.43801 -94.98409 0.00000 0.00000 0.00000 MINI CONSTR> 158.85762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 132.58403 0.05989 0.38474 0.00025 MINI INTERN> 10.35730 72.33810 0.00000 44.00965 9.43353 MINI EXTERN> -67.43397 -94.99724 0.00000 0.00000 0.00000 MINI CONSTR> 158.87666 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 132.52356 0.06047 0.36686 0.00026 MINI INTERN> 10.36815 72.30352 0.00000 43.99084 9.43392 MINI EXTERN> -67.46474 -95.00496 0.00000 0.00000 0.00000 MINI CONSTR> 158.89685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 132.46549 0.05807 0.40279 0.00027 MINI INTERN> 10.37086 72.26687 0.00000 43.97053 9.43359 MINI EXTERN> -67.50066 -94.99631 0.00000 0.00000 0.00000 MINI CONSTR> 158.92060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 132.39310 0.07239 0.12752 0.00011 MINI INTERN> 10.62482 72.12913 0.00000 43.90215 9.46898 MINI EXTERN> -67.67587 -95.00082 0.00000 0.00000 0.00000 MINI CONSTR> 158.94472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20964 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 132.36411 0.02898 0.42584 0.00029 MINI INTERN> 10.31528 72.23660 0.00000 43.95197 9.42527 MINI EXTERN> -67.51579 -95.01048 0.00000 0.00000 0.00000 MINI CONSTR> 158.96127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 132.31893 0.04518 0.48971 0.00030 MINI INTERN> 10.42657 72.16196 0.00000 43.92292 9.43342 MINI EXTERN> -67.57549 -95.03317 0.00000 0.00000 0.00000 MINI CONSTR> 158.98274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 132.24088 0.07806 0.13545 0.00013 MINI INTERN> 10.64066 72.02883 0.00000 43.85637 9.46748 MINI EXTERN> -67.75138 -95.01135 0.00000 0.00000 0.00000 MINI CONSTR> 159.01026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 132.19818 0.04270 0.11179 0.00013 MINI INTERN> 10.60520 72.01508 0.00000 43.85206 9.46199 MINI EXTERN> -67.75022 -95.01518 0.00000 0.00000 0.00000 MINI CONSTR> 159.02924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 132.15236 0.04582 0.11415 0.00014 MINI INTERN> 10.61356 71.98087 0.00000 43.83842 9.46211 MINI EXTERN> -67.77476 -95.01985 0.00000 0.00000 0.00000 MINI CONSTR> 159.05201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 132.10890 0.04347 0.18822 0.00014 MINI INTERN> 10.68818 71.91962 0.00000 43.81114 9.47128 MINI EXTERN> -67.83906 -95.02056 0.00000 0.00000 0.00000 MINI CONSTR> 159.07831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 132.06802 0.04088 0.13991 0.00015 MINI INTERN> 10.64170 71.90986 0.00000 43.81134 9.46440 MINI EXTERN> -67.82865 -95.02854 0.00000 0.00000 0.00000 MINI CONSTR> 159.09791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 132.03053 0.03749 0.16259 0.00015 MINI INTERN> 10.66905 71.86908 0.00000 43.79633 9.46740 MINI EXTERN> -67.86262 -95.02942 0.00000 0.00000 0.00000 MINI CONSTR> 159.12072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 131.99244 0.03809 0.15545 0.00016 MINI INTERN> 10.66034 71.84367 0.00000 43.78924 9.46610 MINI EXTERN> -67.87594 -95.03409 0.00000 0.00000 0.00000 MINI CONSTR> 159.14312 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 131.96191 0.03053 0.24052 0.00016 MINI INTERN> 10.73088 71.78739 0.00000 43.76802 9.47428 MINI EXTERN> -67.93012 -95.03565 0.00000 0.00000 0.00000 MINI CONSTR> 159.16713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 131.92621 0.03570 0.24377 0.00017 MINI INTERN> 10.72399 71.76282 0.00000 43.76182 9.47380 MINI EXTERN> -67.94458 -95.04223 0.00000 0.00000 0.00000 MINI CONSTR> 159.19059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 131.89361 0.03260 0.27394 0.00018 MINI INTERN> 10.70977 71.73984 0.00000 43.75642 9.47366 MINI EXTERN> -67.95892 -95.04217 0.00000 0.00000 0.00000 MINI CONSTR> 159.21502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 131.86562 0.02799 0.28867 0.00018 MINI INTERN> 10.74945 71.69799 0.00000 43.74560 9.47688 MINI EXTERN> -67.98890 -95.05163 0.00000 0.00000 0.00000 MINI CONSTR> 159.23624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 131.83720 0.02843 0.27553 0.00019 MINI INTERN> 10.73756 71.67339 0.00000 43.74301 9.47566 MINI EXTERN> -67.99769 -95.05129 0.00000 0.00000 0.00000 MINI CONSTR> 159.25656 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 131.79926 0.03793 0.08887 0.00008 MINI INTERN> 10.54952 71.71892 0.00000 43.77655 9.45191 MINI EXTERN> -67.90828 -95.06238 0.00000 0.00000 0.00000 MINI CONSTR> 159.27301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 131.78578 0.01349 0.31456 0.00020 MINI INTERN> 10.72238 71.62481 0.00000 43.73823 9.47504 MINI EXTERN> -68.02004 -95.05458 0.00000 0.00000 0.00000 MINI CONSTR> 159.29994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 131.76394 0.02184 0.35295 0.00021 MINI INTERN> 10.73297 71.60242 0.00000 43.73924 9.47312 MINI EXTERN> -68.02359 -95.07897 0.00000 0.00000 0.00000 MINI CONSTR> 159.31875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 131.72446 0.03948 0.09701 0.00009 MINI INTERN> 10.52964 71.64832 0.00000 43.77345 9.45093 MINI EXTERN> -67.93764 -95.07558 0.00000 0.00000 0.00000 MINI CONSTR> 159.33535 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 131.70317 0.02129 0.07997 0.00010 MINI INTERN> 10.54582 71.61774 0.00000 43.76885 9.45392 MINI EXTERN> -67.95935 -95.07836 0.00000 0.00000 0.00000 MINI CONSTR> 159.35454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 131.68079 0.02238 0.08262 0.00010 MINI INTERN> 10.53748 71.59477 0.00000 43.77021 9.45356 MINI EXTERN> -67.96719 -95.08332 0.00000 0.00000 0.00000 MINI CONSTR> 159.37528 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 131.65938 0.02140 0.07854 0.00010 MINI INTERN> 10.53993 71.56720 0.00000 43.76997 9.45468 MINI EXTERN> -67.98083 -95.08751 0.00000 0.00000 0.00000 MINI CONSTR> 159.39595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 131.63801 0.02138 0.14549 0.00011 MINI INTERN> 10.48706 71.55864 0.00000 43.78249 9.44846 MINI EXTERN> -67.96367 -95.09370 0.00000 0.00000 0.00000 MINI CONSTR> 159.41871 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20962 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 131.61706 0.02094 0.09374 0.00011 MINI INTERN> 10.52236 71.51734 0.00000 43.77661 9.45408 MINI EXTERN> -67.99546 -95.09711 0.00000 0.00000 0.00000 MINI CONSTR> 159.43925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 131.59680 0.02026 0.10302 0.00011 MINI INTERN> 10.51769 71.48845 0.00000 43.77999 9.45457 MINI EXTERN> -68.00551 -95.09990 0.00000 0.00000 0.00000 MINI CONSTR> 159.46151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 131.58147 0.01534 0.17126 0.00012 MINI INTERN> 10.48018 71.47850 0.00000 43.79215 9.44988 MINI EXTERN> -67.99257 -95.10771 0.00000 0.00000 0.00000 MINI CONSTR> 159.48104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 131.56472 0.01675 0.19312 0.00012 MINI INTERN> 10.47747 71.44865 0.00000 43.79562 9.45120 MINI EXTERN> -68.00430 -95.10611 0.00000 0.00000 0.00000 MINI CONSTR> 159.50219 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 131.54966 0.01506 0.19815 0.00013 MINI INTERN> 10.46040 71.43319 0.00000 43.80361 9.45018 MINI EXTERN> -68.00434 -95.11382 0.00000 0.00000 0.00000 MINI CONSTR> 159.52045 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 131.53436 0.01529 0.18949 0.00013 MINI INTERN> 10.46765 71.40790 0.00000 43.80723 9.45204 MINI EXTERN> -68.01690 -95.12212 0.00000 0.00000 0.00000 MINI CONSTR> 159.53856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 131.51992 0.01445 0.20865 0.00014 MINI INTERN> 10.47124 71.37527 0.00000 43.81011 9.45499 MINI EXTERN> -68.03330 -95.11737 0.00000 0.00000 0.00000 MINI CONSTR> 159.55898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 131.50157 0.01834 0.06429 0.00006 MINI INTERN> 10.55380 71.32022 0.00000 43.79803 9.46700 MINI EXTERN> -68.08833 -95.12603 0.00000 0.00000 0.00000 MINI CONSTR> 159.57688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 131.49415 0.00742 0.22063 0.00015 MINI INTERN> 10.45367 71.33976 0.00000 43.82762 9.45431 MINI EXTERN> -68.03743 -95.13756 0.00000 0.00000 0.00000 MINI CONSTR> 159.59380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 131.48279 0.01136 0.25547 0.00015 MINI INTERN> 10.45983 71.30457 0.00000 43.83041 9.45827 MINI EXTERN> -68.05656 -95.12743 0.00000 0.00000 0.00000 MINI CONSTR> 159.61372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 131.46222 0.02057 0.07039 0.00007 MINI INTERN> 10.55819 71.23947 0.00000 43.81734 9.47178 MINI EXTERN> -68.11865 -95.13827 0.00000 0.00000 0.00000 MINI CONSTR> 159.63236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 131.45109 0.01113 0.05904 0.00007 MINI INTERN> 10.54742 71.22044 0.00000 43.82659 9.47163 MINI EXTERN> -68.12038 -95.14283 0.00000 0.00000 0.00000 MINI CONSTR> 159.64822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 131.43959 0.01150 0.06036 0.00007 MINI INTERN> 10.54952 71.19346 0.00000 43.83413 9.47339 MINI EXTERN> -68.13019 -95.14662 0.00000 0.00000 0.00000 MINI CONSTR> 159.66591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 131.42839 0.01120 0.05883 0.00007 MINI INTERN> 10.54652 71.16834 0.00000 43.84313 9.47462 MINI EXTERN> -68.13733 -95.15035 0.00000 0.00000 0.00000 MINI CONSTR> 159.68346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 131.41742 0.01097 0.10393 0.00008 MINI INTERN> 10.57898 71.12573 0.00000 43.84701 9.48021 MINI EXTERN> -68.16351 -95.15492 0.00000 0.00000 0.00000 MINI CONSTR> 159.70390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 131.40647 0.01095 0.07246 0.00008 MINI INTERN> 10.55231 71.11061 0.00000 43.86107 9.47883 MINI EXTERN> -68.15834 -95.15820 0.00000 0.00000 0.00000 MINI CONSTR> 159.72019 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 131.39673 0.00974 0.08983 0.00008 MINI INTERN> 10.56694 71.07784 0.00000 43.86848 9.48209 MINI EXTERN> -68.17370 -95.16290 0.00000 0.00000 0.00000 MINI CONSTR> 159.73799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 131.38821 0.00852 0.12351 0.00008 MINI INTERN> 10.58585 71.04381 0.00000 43.87526 9.48591 MINI EXTERN> -68.19115 -95.16700 0.00000 0.00000 0.00000 MINI CONSTR> 159.75554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 131.37837 0.00984 0.12435 0.00009 MINI INTERN> 10.57662 71.01917 0.00000 43.88798 9.48699 MINI EXTERN> -68.19570 -95.17016 0.00000 0.00000 0.00000 MINI CONSTR> 159.77347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 131.37033 0.00804 0.15302 0.00009 MINI INTERN> 10.58224 70.99359 0.00000 43.89950 9.48861 MINI EXTERN> -68.20342 -95.18027 0.00000 0.00000 0.00000 MINI CONSTR> 159.79009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 131.36209 0.00824 0.13758 0.00009 MINI INTERN> 10.58475 70.96677 0.00000 43.90871 9.49070 MINI EXTERN> -68.21257 -95.18141 0.00000 0.00000 0.00000 MINI CONSTR> 159.80515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 131.35436 0.00773 0.15091 0.00010 MINI INTERN> 10.56385 70.94613 0.00000 43.92294 9.49078 MINI EXTERN> -68.21182 -95.17886 0.00000 0.00000 0.00000 MINI CONSTR> 159.82134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 131.34672 0.00764 0.14441 0.00010 MINI INTERN> 10.57856 70.91546 0.00000 43.93173 9.49386 MINI EXTERN> -68.22532 -95.18426 0.00000 0.00000 0.00000 MINI CONSTR> 159.83668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 131.33704 0.00968 0.04713 0.00004 MINI INTERN> 10.51110 70.92196 0.00000 43.95618 9.48720 MINI EXTERN> -68.19573 -95.19240 0.00000 0.00000 0.00000 MINI CONSTR> 159.84873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 131.33329 0.00376 0.16266 0.00011 MINI INTERN> 10.58852 70.86121 0.00000 43.95332 9.49827 MINI EXTERN> -68.24353 -95.19152 0.00000 0.00000 0.00000 MINI CONSTR> 159.86701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 131.32735 0.00593 0.19127 0.00011 MINI INTERN> 10.58186 70.84471 0.00000 43.96941 9.49787 MINI EXTERN> -68.24153 -95.20611 0.00000 0.00000 0.00000 MINI CONSTR> 159.88114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 131.31623 0.01112 0.05316 0.00005 MINI INTERN> 10.49991 70.85062 0.00000 43.99537 9.49117 MINI EXTERN> -68.21011 -95.20469 0.00000 0.00000 0.00000 MINI CONSTR> 159.89396 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> 500 131.31623 0.01112 0.05316 0.00006 STPD INTERN> 10.49991 70.85062 0.00000 43.99537 9.49117 STPD EXTERN> -68.21011 -95.20469 0.00000 0.00000 0.00000 STPD CONSTR> 159.89396 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 20961 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20961 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 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> 0 131.31623 0.01112 0.05316 0.00000 MINI INTERN> 10.49991 70.85062 0.00000 43.99537 9.49117 MINI EXTERN> -68.21011 -95.20469 0.00000 0.00000 0.00000 MINI CONSTR> 159.89396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 131.16427 0.15196 0.03600 0.00227 MINI INTERN> 10.44296 69.55921 0.00000 44.78503 9.57551 MINI EXTERN> -68.55424 -95.36936 0.00000 0.00000 0.00000 MINI CONSTR> 160.72517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 131.16164 0.00263 0.04898 0.00327 MINI INTERN> 10.42527 69.58588 0.00000 44.76547 9.55694 MINI EXTERN> -68.46096 -95.40412 0.00000 0.00000 0.00000 MINI CONSTR> 160.69315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 131.15480 0.00684 0.07654 0.00617 MINI INTERN> 10.43131 69.59349 0.00000 44.72672 9.54169 MINI EXTERN> -68.26525 -95.47820 0.00000 0.00000 0.00000 MINI CONSTR> 160.60503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 131.14603 0.00877 0.05025 0.01252 MINI INTERN> 10.45200 69.67436 0.00000 44.75567 9.58915 MINI EXTERN> -68.38815 -95.53487 0.00000 0.00000 0.00000 MINI CONSTR> 160.59788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 131.14075 0.00528 0.03815 0.00575 MINI INTERN> 10.47240 69.63158 0.00000 44.80862 9.61069 MINI EXTERN> -68.45137 -95.56840 0.00000 0.00000 0.00000 MINI CONSTR> 160.63722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 131.13662 0.00412 0.03243 0.00629 MINI INTERN> 10.46578 69.52558 0.00000 44.90262 9.63698 MINI EXTERN> -68.48629 -95.59462 0.00000 0.00000 0.00000 MINI CONSTR> 160.68658 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 131.13399 0.00263 0.03427 0.00424 MINI INTERN> 10.44501 69.45120 0.00000 44.96556 9.64796 MINI EXTERN> -68.46802 -95.63015 0.00000 0.00000 0.00000 MINI CONSTR> 160.72243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 131.13184 0.00215 0.03153 0.00449 MINI INTERN> 10.45227 69.36518 0.00000 45.04089 9.65813 MINI EXTERN> -68.47123 -95.69890 0.00000 0.00000 0.00000 MINI CONSTR> 160.78550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 131.13031 0.00152 0.02460 0.00242 MINI INTERN> 10.45336 69.32108 0.00000 45.09055 9.66823 MINI EXTERN> -68.53309 -95.73017 0.00000 0.00000 0.00000 MINI CONSTR> 160.86036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 131.12909 0.00123 0.02876 0.00312 MINI INTERN> 10.44765 69.28255 0.00000 45.12232 9.67344 MINI EXTERN> -68.55237 -95.75392 0.00000 0.00000 0.00000 MINI CONSTR> 160.90941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 131.12700 0.00208 0.03244 0.00678 MINI INTERN> 10.43945 69.28243 0.00000 45.13924 9.67581 MINI EXTERN> -68.60726 -95.77027 0.00000 0.00000 0.00000 MINI CONSTR> 160.96761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 131.12426 0.00275 0.03331 0.00948 MINI INTERN> 10.44136 69.26813 0.00000 45.17671 9.68361 MINI EXTERN> -68.70584 -95.75533 0.00000 0.00000 0.00000 MINI CONSTR> 161.01562 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 131.12159 0.00266 0.03754 0.00819 MINI INTERN> 10.43622 69.26556 0.00000 45.18562 9.69660 MINI EXTERN> -68.67606 -95.80682 0.00000 0.00000 0.00000 MINI CONSTR> 161.02047 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 131.11801 0.00358 0.03833 0.01051 MINI INTERN> 10.45109 69.25975 0.00000 45.24436 9.71975 MINI EXTERN> -68.71600 -95.86752 0.00000 0.00000 0.00000 MINI CONSTR> 161.02657 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 131.11422 0.00379 0.04464 0.01359 MINI INTERN> 10.43990 69.28769 0.00000 45.32396 9.73973 MINI EXTERN> -68.81819 -95.88052 0.00000 0.00000 0.00000 MINI CONSTR> 161.02166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 131.11045 0.00377 0.03405 0.00913 MINI INTERN> 10.46335 69.27414 0.00000 45.38795 9.75318 MINI EXTERN> -68.87883 -95.87445 0.00000 0.00000 0.00000 MINI CONSTR> 160.98512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 131.10746 0.00299 0.03545 0.00987 MINI INTERN> 10.45135 69.23659 0.00000 45.46792 9.74452 MINI EXTERN> -68.82937 -95.88237 0.00000 0.00000 0.00000 MINI CONSTR> 160.91882 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 131.10462 0.00284 0.03206 0.00938 MINI INTERN> 10.44782 69.18657 0.00000 45.53811 9.74681 MINI EXTERN> -68.84439 -95.86675 0.00000 0.00000 0.00000 MINI CONSTR> 160.89644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 131.10251 0.00211 0.03326 0.00678 MINI INTERN> 10.44267 69.17868 0.00000 45.60266 9.74512 MINI EXTERN> -68.93823 -95.84068 0.00000 0.00000 0.00000 MINI CONSTR> 160.91230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 131.10047 0.00205 0.03154 0.00745 MINI INTERN> 10.44498 69.13935 0.00000 45.65337 9.74102 MINI EXTERN> -68.97359 -95.82225 0.00000 0.00000 0.00000 MINI CONSTR> 160.91760 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> 100 131.10047 0.00205 0.03154 0.02000 CONJ INTERN> 10.44498 69.13935 0.00000 45.65337 9.74102 CONJ EXTERN> -68.97359 -95.82225 0.00000 0.00000 0.00000 CONJ CONSTR> 160.91760 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 ASP 14 N ) 2.1877 ( PROT ASP 14 H ) 1.7502 ( PROT ASP 14 CA ) 2.1877 ( PROT ASP 14 CB ) 1.7502 ( PROT ASP 14 CG ) 1.7502 ( PROT ASP 14 OD1 ) 1.7502 ( PROT ASP 14 OD2 ) 1.7502 ( PROT ASP 14 C ) 2.1877 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.63965 7.24595 -13.21153 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00058 0.00141 0.00007 ROTATION MATRIX 1.000000 -0.000140 -0.000432 0.000140 1.000000 0.000395 0.000431 -0.000395 1.000000 AXIS OF ROTATION IS 0.656721 0.717230 -0.233019 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 54.4774 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.429005 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4290" Parameter: A <- "0.4290" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.52102 7.25033 -13.41032 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.00720 0.00522 -0.03003 ROTATION MATRIX 0.999647 0.018607 0.018962 -0.018207 0.999613 -0.021049 -0.019347 0.020696 0.999599 AXIS OF ROTATION IS -0.617820 -0.566960 0.544844 ANGLE IS 1.94 CENTER OF ROTATION 13.944358 6.820028-13.399873 SHIFT IS -0.023769 TOTAL SQUARE DIFF IS 1.8005 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.240998 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4290" RDCMND substituted energy or value "?RMS" to " 0.2410" Parameter: A <- "0.4290 0.2410" 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 0.4290 0.2410 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 " 160.92" Parameter: H <- "160.92" 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 -29.81713 160.91760 1.47193 ENER INTERN> 10.44498 69.13935 0.00000 45.65337 9.74102 ENER EXTERN> -68.97359 -95.82225 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 " -29.82" Parameter: B <- "-29.82" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -95.82" Parameter: C <- "-95.82" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -68.97" Parameter: C <- " -164.79" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -164.79" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 10.44" Parameter: D <- "10.44" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 69.14" Parameter: D <- " 79.58" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 45.65" Parameter: D <- " 125.23" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 9.74" Parameter: D <- " 134.97" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 134.97" 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= -29.82 GRMS= 1.47 ELEC= -95.82 VDW= -68.97 RDTITL> *EXTERNAL= -164.79 INTERNAL= 134.97 USER= 0.00 HARM= 160.92 RDTITL> *BOND= 10.44 ANGL= 69.14 DIHE= 45.65 IMPR= 9.74 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20961 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20963 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 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 84.69555 -114.51268 0.58878 0.02000 MINI INTERN> 10.44498 69.13935 0.00000 45.65337 9.74102 MINI EXTERN> -68.97359 -95.82225 0.00000 0.00000 0.00000 MINI CONSTR> 114.51268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 119.35900 -34.66346 16.26513 0.00864 MINI INTERN> 48.64109 65.23073 0.00000 49.00455 8.91865 MINI EXTERN> -82.78286 -89.79925 0.00000 0.00000 0.00000 MINI CONSTR> 120.14608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20949 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 80.27650 39.08251 0.48914 0.00156 MINI INTERN> 10.15310 68.18623 0.00000 48.04420 9.81467 MINI EXTERN> -83.76051 -92.77278 0.00000 0.00000 0.00000 MINI CONSTR> 120.61157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 79.78231 0.49419 0.99321 0.00067 MINI INTERN> 10.64935 68.10632 0.00000 47.92354 9.83471 MINI EXTERN> -84.72892 -92.89033 0.00000 0.00000 0.00000 MINI CONSTR> 120.88763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20946 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 79.38416 0.39815 0.95084 0.00070 MINI INTERN> 10.76940 67.73048 0.00000 47.95760 9.78368 MINI EXTERN> -85.04512 -92.85176 0.00000 0.00000 0.00000 MINI CONSTR> 121.03988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 79.00469 0.37947 1.00985 0.00072 MINI INTERN> 10.31008 67.91198 0.00000 47.98225 9.75216 MINI EXTERN> -85.14290 -93.01748 0.00000 0.00000 0.00000 MINI CONSTR> 121.20859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20944 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 78.54371 0.46098 0.32353 0.00031 MINI INTERN> 10.08968 67.45103 0.00000 48.07197 9.64813 MINI EXTERN> -85.17216 -92.86378 0.00000 0.00000 0.00000 MINI CONSTR> 121.31886 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 78.42975 0.11396 1.29019 0.00078 MINI INTERN> 10.59283 67.30150 0.00000 48.00398 9.68221 MINI EXTERN> -85.67970 -92.93329 0.00000 0.00000 0.00000 MINI CONSTR> 121.46222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20940 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 77.90876 0.52098 0.34221 0.00034 MINI INTERN> 10.03236 67.13058 0.00000 48.07544 9.58730 MINI EXTERN> -85.64202 -92.84671 0.00000 0.00000 0.00000 MINI CONSTR> 121.57183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 77.63683 0.27193 0.30101 0.00035 MINI INTERN> 10.00958 67.01798 0.00000 48.06629 9.56843 MINI EXTERN> -85.85834 -92.84217 0.00000 0.00000 0.00000 MINI CONSTR> 121.67506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20940 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 77.35766 0.27917 0.30016 0.00036 MINI INTERN> 9.98494 66.88367 0.00000 48.05752 9.54465 MINI EXTERN> -86.05830 -92.83385 0.00000 0.00000 0.00000 MINI CONSTR> 121.77902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 77.07883 0.27883 0.48199 0.00037 MINI INTERN> 9.89803 66.73437 0.00000 48.06323 9.49934 MINI EXTERN> -86.20123 -92.80149 0.00000 0.00000 0.00000 MINI CONSTR> 121.88659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20938 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 76.82586 0.25297 0.41054 0.00039 MINI INTERN> 9.88901 66.62656 0.00000 48.04417 9.48553 MINI EXTERN> -86.38545 -92.80605 0.00000 0.00000 0.00000 MINI CONSTR> 121.97208 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 76.58247 0.24339 0.44302 0.00040 MINI INTERN> 9.83590 66.52762 0.00000 48.03068 9.46234 MINI EXTERN> -86.54003 -92.79123 0.00000 0.00000 0.00000 MINI CONSTR> 122.05718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20941 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 76.37288 0.20959 0.60951 0.00042 MINI INTERN> 9.77775 66.42370 0.00000 48.03008 9.42730 MINI EXTERN> -86.63457 -92.78554 0.00000 0.00000 0.00000 MINI CONSTR> 122.13415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 76.15752 0.21536 0.67163 0.00043 MINI INTERN> 9.71539 66.35223 0.00000 48.01115 9.40793 MINI EXTERN> -86.77480 -92.76363 0.00000 0.00000 0.00000 MINI CONSTR> 122.20925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20941 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 75.95064 0.20688 0.68190 0.00045 MINI INTERN> 9.63860 66.28562 0.00000 48.00408 9.38246 MINI EXTERN> -86.86585 -92.76953 0.00000 0.00000 0.00000 MINI CONSTR> 122.27525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 75.73994 0.21070 0.72978 0.00046 MINI INTERN> 9.64731 66.16781 0.00000 47.97794 9.36462 MINI EXTERN> -86.99513 -92.76617 0.00000 0.00000 0.00000 MINI CONSTR> 122.34357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20941 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 75.54037 0.19957 0.69357 0.00048 MINI INTERN> 9.59938 66.10779 0.00000 47.95078 9.35391 MINI EXTERN> -87.12057 -92.75445 0.00000 0.00000 0.00000 MINI CONSTR> 122.40353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 75.35093 0.18944 0.76388 0.00050 MINI INTERN> 9.72009 65.95987 0.00000 47.90465 9.35289 MINI EXTERN> -87.28047 -92.76925 0.00000 0.00000 0.00000 MINI CONSTR> 122.46316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20941 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 75.10949 0.24144 0.23551 0.00022 MINI INTERN> 9.91963 65.81205 0.00000 47.80547 9.39974 MINI EXTERN> -87.58543 -92.76100 0.00000 0.00000 0.00000 MINI CONSTR> 122.51905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 75.01359 0.09591 0.80554 0.00054 MINI INTERN> 9.48562 65.91929 0.00000 47.88148 9.30812 MINI EXTERN> -87.40609 -92.74303 0.00000 0.00000 0.00000 MINI CONSTR> 122.56821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20938 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 74.86326 0.15033 0.93571 0.00056 MINI INTERN> 9.68370 65.75475 0.00000 47.82608 9.31466 MINI EXTERN> -87.56389 -92.77017 0.00000 0.00000 0.00000 MINI CONSTR> 122.61812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 74.58869 0.27457 0.25863 0.00024 MINI INTERN> 9.93310 65.55191 0.00000 47.70551 9.36976 MINI EXTERN> -87.89939 -92.74464 0.00000 0.00000 0.00000 MINI CONSTR> 122.67243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20938 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 74.44005 0.14863 0.21559 0.00025 MINI INTERN> 9.87375 65.50036 0.00000 47.68795 9.35192 MINI EXTERN> -87.94934 -92.73810 0.00000 0.00000 0.00000 MINI CONSTR> 122.71350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 74.28525 0.15480 0.22076 0.00026 MINI INTERN> 9.88489 65.42025 0.00000 47.65299 9.34390 MINI EXTERN> -88.04105 -92.73401 0.00000 0.00000 0.00000 MINI CONSTR> 122.75828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20934 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 74.13382 0.15144 0.21445 0.00027 MINI INTERN> 9.87332 65.35140 0.00000 47.62259 9.33295 MINI EXTERN> -88.11651 -92.73131 0.00000 0.00000 0.00000 MINI CONSTR> 122.80138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 73.98387 0.14995 0.37871 0.00028 MINI INTERN> 10.02253 65.22173 0.00000 47.55408 9.34421 MINI EXTERN> -88.28592 -92.72431 0.00000 0.00000 0.00000 MINI CONSTR> 122.85154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20931 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 73.83543 0.14844 0.26359 0.00029 MINI INTERN> 9.91136 65.19470 0.00000 47.54487 9.32047 MINI EXTERN> -88.29805 -92.72671 0.00000 0.00000 0.00000 MINI CONSTR> 122.88878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 73.70086 0.13457 0.32291 0.00030 MINI INTERN> 9.96646 65.10772 0.00000 47.49836 9.31994 MINI EXTERN> -88.40261 -92.71949 0.00000 0.00000 0.00000 MINI CONSTR> 122.93047 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20931 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 73.58354 0.11732 0.45339 0.00031 MINI INTERN> 10.07321 65.00746 0.00000 47.44520 9.32492 MINI EXTERN> -88.52081 -92.71710 0.00000 0.00000 0.00000 MINI CONSTR> 122.97065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 73.44989 0.13365 0.46306 0.00032 MINI INTERN> 10.02974 64.96710 0.00000 47.41588 9.31365 MINI EXTERN> -88.57628 -92.71051 0.00000 0.00000 0.00000 MINI CONSTR> 123.01030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20929 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 73.33765 0.11223 0.53795 0.00033 MINI INTERN> 10.09176 64.88424 0.00000 47.37769 9.30960 MINI EXTERN> -88.64920 -92.72230 0.00000 0.00000 0.00000 MINI CONSTR> 123.04587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 73.22181 0.11584 0.49349 0.00034 MINI INTERN> 10.08080 64.83168 0.00000 47.34413 9.30410 MINI EXTERN> -88.71170 -92.70695 0.00000 0.00000 0.00000 MINI CONSTR> 123.07976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20928 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 73.11575 0.10606 0.60959 0.00036 MINI INTERN> 10.11911 64.76829 0.00000 47.30920 9.29748 MINI EXTERN> -88.77183 -92.72263 0.00000 0.00000 0.00000 MINI CONSTR> 123.11614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 73.00809 0.10767 0.55415 0.00037 MINI INTERN> 10.11776 64.71234 0.00000 47.27821 9.29175 MINI EXTERN> -88.82403 -92.71459 0.00000 0.00000 0.00000 MINI CONSTR> 123.14665 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20928 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 72.86742 0.14067 0.18086 0.00016 MINI INTERN> 9.70414 64.82401 0.00000 47.32604 9.23602 MINI EXTERN> -88.67901 -92.71575 0.00000 0.00000 0.00000 MINI CONSTR> 123.17197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 72.81009 0.05733 0.58053 0.00040 MINI INTERN> 10.15598 64.59905 0.00000 47.20600 9.28527 MINI EXTERN> -88.94800 -92.69999 0.00000 0.00000 0.00000 MINI CONSTR> 123.21178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20929 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 72.65839 0.15170 0.18009 0.00017 MINI INTERN> 9.69058 64.73279 0.00000 47.26392 9.22233 MINI EXTERN> -88.77360 -92.71564 0.00000 0.00000 0.00000 MINI CONSTR> 123.23802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 72.61613 0.04226 0.62047 0.00043 MINI INTERN> 10.17101 64.50275 0.00000 47.13975 9.27493 MINI EXTERN> -89.04951 -92.69988 0.00000 0.00000 0.00000 MINI CONSTR> 123.27708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20928 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 72.52274 0.09339 0.68246 0.00044 MINI INTERN> 10.16504 64.46674 0.00000 47.11333 9.26513 MINI EXTERN> -89.07969 -92.71781 0.00000 0.00000 0.00000 MINI CONSTR> 123.30999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 72.36924 0.15350 0.22467 0.00019 MINI INTERN> 9.63751 64.62120 0.00000 47.17952 9.19793 MINI EXTERN> -88.88328 -92.71762 0.00000 0.00000 0.00000 MINI CONSTR> 123.33398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20923 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 72.28933 0.07991 0.15299 0.00020 MINI INTERN> 9.69989 64.55854 0.00000 47.13895 9.20329 MINI EXTERN> -88.95565 -92.71666 0.00000 0.00000 0.00000 MINI CONSTR> 123.36097 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 72.19594 0.09339 0.15678 0.00021 MINI INTERN> 9.69160 64.51831 0.00000 47.10831 9.19642 MINI EXTERN> -88.99377 -92.71850 0.00000 0.00000 0.00000 MINI CONSTR> 123.39358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20923 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 72.11384 0.08210 0.30303 0.00021 MINI INTERN> 9.59141 64.52120 0.00000 47.09911 9.17497 MINI EXTERN> -88.97618 -92.72194 0.00000 0.00000 0.00000 MINI CONSTR> 123.42527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 72.03154 0.08230 0.22321 0.00022 MINI INTERN> 9.63068 64.46831 0.00000 47.05939 9.17870 MINI EXTERN> -89.04197 -92.71772 0.00000 0.00000 0.00000 MINI CONSTR> 123.45415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20924 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 71.96500 0.06654 0.33286 0.00023 MINI INTERN> 9.55916 64.46847 0.00000 47.04902 9.16258 MINI EXTERN> -89.03193 -92.72381 0.00000 0.00000 0.00000 MINI CONSTR> 123.48150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 71.87896 0.08604 0.19821 0.00024 MINI INTERN> 9.63709 64.39385 0.00000 47.00196 9.17022 MINI EXTERN> -89.11225 -92.72313 0.00000 0.00000 0.00000 MINI CONSTR> 123.51123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20922 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 71.81460 0.06436 0.36207 0.00025 MINI INTERN> 9.55419 64.39873 0.00000 46.99116 9.15212 MINI EXTERN> -89.09881 -92.72397 0.00000 0.00000 0.00000 MINI CONSTR> 123.54117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 71.74759 0.06701 0.41302 0.00026 MINI INTERN> 9.57658 64.35148 0.00000 46.96251 9.14772 MINI EXTERN> -89.12973 -92.73072 0.00000 0.00000 0.00000 MINI CONSTR> 123.56975 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20921 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 71.68221 0.06538 0.38012 0.00027 MINI INTERN> 9.54042 64.34419 0.00000 46.94004 9.14270 MINI EXTERN> -89.15403 -92.72702 0.00000 0.00000 0.00000 MINI CONSTR> 123.59590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 71.62440 0.05781 0.47675 0.00028 MINI INTERN> 9.57248 64.29575 0.00000 46.91220 9.13803 MINI EXTERN> -89.18139 -92.73693 0.00000 0.00000 0.00000 MINI CONSTR> 123.62427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20921 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 71.56416 0.06024 0.43787 0.00029 MINI INTERN> 9.55792 64.27827 0.00000 46.88975 9.13515 MINI EXTERN> -89.20635 -92.73886 0.00000 0.00000 0.00000 MINI CONSTR> 123.64829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 71.48286 0.08130 0.13514 0.00012 MINI INTERN> 9.71150 64.17976 0.00000 46.82423 9.15906 MINI EXTERN> -89.33658 -92.73107 0.00000 0.00000 0.00000 MINI CONSTR> 123.67596 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20921 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 71.45179 0.03107 0.45179 0.00031 MINI INTERN> 9.50398 64.25431 0.00000 46.84980 9.12266 MINI EXTERN> -89.23670 -92.74206 0.00000 0.00000 0.00000 MINI CONSTR> 123.69981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 71.40090 0.05089 0.52594 0.00032 MINI INTERN> 9.53303 64.22481 0.00000 46.81119 9.12666 MINI EXTERN> -89.29705 -92.72696 0.00000 0.00000 0.00000 MINI CONSTR> 123.72921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 280 71.31139 0.08951 0.14521 0.00014 MINI INTERN> 9.71787 64.09549 0.00000 46.74683 9.14947 MINI EXTERN> -89.41814 -92.73608 0.00000 0.00000 0.00000 MINI CONSTR> 123.75595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 71.26202 0.04937 0.12069 0.00014 MINI INTERN> 9.69312 64.08180 0.00000 46.73021 9.14298 MINI EXTERN> -89.42665 -92.73849 0.00000 0.00000 0.00000 MINI CONSTR> 123.77904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 290 71.20902 0.05299 0.12442 0.00015 MINI INTERN> 9.69733 64.05473 0.00000 46.70432 9.14040 MINI EXTERN> -89.45378 -92.73971 0.00000 0.00000 0.00000 MINI CONSTR> 123.80574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 71.15888 0.05014 0.12517 0.00015 MINI INTERN> 9.69916 64.02924 0.00000 46.68052 9.13727 MINI EXTERN> -89.47663 -92.74209 0.00000 0.00000 0.00000 MINI CONSTR> 123.83140 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20918 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 71.10973 0.04915 0.21442 0.00016 MINI INTERN> 9.75597 63.98151 0.00000 46.64247 9.14135 MINI EXTERN> -89.53040 -92.74210 0.00000 0.00000 0.00000 MINI CONSTR> 123.86092 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 71.06131 0.04842 0.15819 0.00016 MINI INTERN> 9.71917 63.97267 0.00000 46.62894 9.13322 MINI EXTERN> -89.53005 -92.74695 0.00000 0.00000 0.00000 MINI CONSTR> 123.88431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 310 71.01763 0.04368 0.18823 0.00017 MINI INTERN> 9.74223 63.94081 0.00000 46.60141 9.13318 MINI EXTERN> -89.56249 -92.74740 0.00000 0.00000 0.00000 MINI CONSTR> 123.90989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 70.97859 0.03904 0.26037 0.00018 MINI INTERN> 9.77584 63.90766 0.00000 46.57148 9.13482 MINI EXTERN> -89.60101 -92.74605 0.00000 0.00000 0.00000 MINI CONSTR> 123.93584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 320 70.93735 0.04124 0.28646 0.00018 MINI INTERN> 9.78361 63.88126 0.00000 46.55105 9.13104 MINI EXTERN> -89.61565 -92.75418 0.00000 0.00000 0.00000 MINI CONSTR> 123.96023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 70.89865 0.03870 0.29176 0.00019 MINI INTERN> 9.80269 63.85330 0.00000 46.52519 9.13121 MINI EXTERN> -89.64612 -92.75217 0.00000 0.00000 0.00000 MINI CONSTR> 123.98455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20916 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 70.86020 0.03845 0.31611 0.00020 MINI INTERN> 9.79284 63.84053 0.00000 46.50349 9.12845 MINI EXTERN> -89.66590 -92.74905 0.00000 0.00000 0.00000 MINI CONSTR> 124.00984 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 70.82229 0.03791 0.29366 0.00020 MINI INTERN> 9.80396 63.81330 0.00000 46.48423 9.12584 MINI EXTERN> -89.68107 -92.75581 0.00000 0.00000 0.00000 MINI CONSTR> 124.03184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20916 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 70.78576 0.03653 0.32879 0.00021 MINI INTERN> 9.76233 63.81686 0.00000 46.46801 9.12005 MINI EXTERN> -89.68809 -92.75063 0.00000 0.00000 0.00000 MINI CONSTR> 124.05723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 70.74893 0.03682 0.30339 0.00022 MINI INTERN> 9.80201 63.77728 0.00000 46.44242 9.12098 MINI EXTERN> -89.71733 -92.75690 0.00000 0.00000 0.00000 MINI CONSTR> 124.08048 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 350 70.70214 0.04680 0.10245 0.00010 MINI INTERN> 9.63858 63.82653 0.00000 46.45647 9.09894 MINI EXTERN> -89.65487 -92.76391 0.00000 0.00000 0.00000 MINI CONSTR> 124.10041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 70.68436 0.01778 0.34857 0.00024 MINI INTERN> 9.81277 63.73925 0.00000 46.40056 9.11743 MINI EXTERN> -89.75541 -92.75832 0.00000 0.00000 0.00000 MINI CONSTR> 124.12808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 360 70.65538 0.02898 0.40927 0.00025 MINI INTERN> 9.80075 63.72475 0.00000 46.39052 9.10948 MINI EXTERN> -89.74630 -92.77402 0.00000 0.00000 0.00000 MINI CONSTR> 124.15020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 70.60274 0.05264 0.11328 0.00011 MINI INTERN> 9.62448 63.78028 0.00000 46.40150 9.08982 MINI EXTERN> -89.69386 -92.77021 0.00000 0.00000 0.00000 MINI CONSTR> 124.17072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20914 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 70.57431 0.02843 0.09373 0.00011 MINI INTERN> 9.63759 63.75951 0.00000 46.38156 9.08973 MINI EXTERN> -89.71471 -92.77099 0.00000 0.00000 0.00000 MINI CONSTR> 124.19161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 70.54453 0.02978 0.09678 0.00011 MINI INTERN> 9.63129 63.74622 0.00000 46.36479 9.08664 MINI EXTERN> -89.72536 -92.77323 0.00000 0.00000 0.00000 MINI CONSTR> 124.21418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 380 70.51553 0.02900 0.09535 0.00012 MINI INTERN> 9.63180 63.72995 0.00000 46.34699 9.08438 MINI EXTERN> -89.73868 -92.77555 0.00000 0.00000 0.00000 MINI CONSTR> 124.23664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 70.48686 0.02867 0.16641 0.00012 MINI INTERN> 9.58862 63.73392 0.00000 46.33642 9.07632 MINI EXTERN> -89.73174 -92.77805 0.00000 0.00000 0.00000 MINI CONSTR> 124.26135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 390 70.45824 0.02862 0.11917 0.00013 MINI INTERN> 9.61874 63.70369 0.00000 46.31357 9.07784 MINI EXTERN> -89.75815 -92.78062 0.00000 0.00000 0.00000 MINI CONSTR> 124.28317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 70.43251 0.02573 0.14439 0.00013 MINI INTERN> 9.59862 63.69871 0.00000 46.30027 9.07328 MINI EXTERN> -89.76141 -92.78239 0.00000 0.00000 0.00000 MINI CONSTR> 124.30543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20912 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 70.40959 0.02292 0.19987 0.00014 MINI INTERN> 9.57120 63.69867 0.00000 46.28877 9.06781 MINI EXTERN> -89.76085 -92.78352 0.00000 0.00000 0.00000 MINI CONSTR> 124.32751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 70.38497 0.02462 0.21860 0.00014 MINI INTERN> 9.58755 63.67511 0.00000 46.27061 9.06637 MINI EXTERN> -89.77497 -92.78933 0.00000 0.00000 0.00000 MINI CONSTR> 124.34964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 410 70.36230 0.02267 0.22417 0.00015 MINI INTERN> 9.56332 63.67422 0.00000 46.25869 9.06210 MINI EXTERN> -89.77737 -92.78933 0.00000 0.00000 0.00000 MINI CONSTR> 124.37067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 70.33942 0.02289 0.24246 0.00015 MINI INTERN> 9.55538 63.66589 0.00000 46.24221 9.05992 MINI EXTERN> -89.78933 -92.78782 0.00000 0.00000 0.00000 MINI CONSTR> 124.39315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 420 70.31719 0.02222 0.22642 0.00016 MINI INTERN> 9.56324 63.64770 0.00000 46.22755 9.05813 MINI EXTERN> -89.79869 -92.79343 0.00000 0.00000 0.00000 MINI CONSTR> 124.41269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 70.29585 0.02134 0.25286 0.00016 MINI INTERN> 9.56632 63.63574 0.00000 46.20780 9.05819 MINI EXTERN> -89.81930 -92.78827 0.00000 0.00000 0.00000 MINI CONSTR> 124.43536 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 430 70.27453 0.02132 0.23617 0.00017 MINI INTERN> 9.55200 63.62871 0.00000 46.19726 9.05388 MINI EXTERN> -89.81883 -92.79370 0.00000 0.00000 0.00000 MINI CONSTR> 124.45519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 70.24764 0.02689 0.07948 0.00007 MINI INTERN> 9.65261 63.56601 0.00000 46.16159 9.06503 MINI EXTERN> -89.87880 -92.79438 0.00000 0.00000 0.00000 MINI CONSTR> 124.47556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 440 70.23730 0.01033 0.26677 0.00018 MINI INTERN> 9.53677 63.61276 0.00000 46.17154 9.04825 MINI EXTERN> -89.83017 -92.79736 0.00000 0.00000 0.00000 MINI CONSTR> 124.49552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 70.21992 0.01738 0.31250 0.00019 MINI INTERN> 9.59080 63.57328 0.00000 46.15015 9.05009 MINI EXTERN> -89.85340 -92.80732 0.00000 0.00000 0.00000 MINI CONSTR> 124.51633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 450 70.18886 0.03107 0.08653 0.00008 MINI INTERN> 9.65738 63.52719 0.00000 46.11617 9.06017 MINI EXTERN> -89.91047 -92.79935 0.00000 0.00000 0.00000 MINI CONSTR> 124.53777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 70.17197 0.01689 0.07095 0.00008 MINI INTERN> 9.64371 63.52279 0.00000 46.10607 9.05702 MINI EXTERN> -89.91259 -92.80077 0.00000 0.00000 0.00000 MINI CONSTR> 124.55574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 460 70.15389 0.01807 0.07362 0.00009 MINI INTERN> 9.64784 63.50916 0.00000 46.09103 9.05570 MINI EXTERN> -89.92347 -92.80256 0.00000 0.00000 0.00000 MINI CONSTR> 124.57620 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 70.13648 0.01742 0.07087 0.00009 MINI INTERN> 9.64478 63.49925 0.00000 46.07770 9.05368 MINI EXTERN> -89.93107 -92.80403 0.00000 0.00000 0.00000 MINI CONSTR> 124.59616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 470 70.11888 0.01759 0.12730 0.00009 MINI INTERN> 9.67571 63.47339 0.00000 46.05581 9.05531 MINI EXTERN> -89.95503 -92.80586 0.00000 0.00000 0.00000 MINI CONSTR> 124.61954 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 70.10216 0.01672 0.09462 0.00010 MINI INTERN> 9.65361 63.47265 0.00000 46.04685 9.05149 MINI EXTERN> -89.95431 -92.80620 0.00000 0.00000 0.00000 MINI CONSTR> 124.63807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20910 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 70.08723 0.01493 0.11386 0.00010 MINI INTERN> 9.66594 63.45676 0.00000 46.03139 9.05126 MINI EXTERN> -89.96786 -92.80776 0.00000 0.00000 0.00000 MINI CONSTR> 124.65750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 70.07387 0.01336 0.15411 0.00011 MINI INTERN> 9.68708 63.43740 0.00000 46.01516 9.05164 MINI EXTERN> -89.98329 -92.81081 0.00000 0.00000 0.00000 MINI CONSTR> 124.67669 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20910 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 70.05977 0.01409 0.17154 0.00011 MINI INTERN> 9.67628 63.43310 0.00000 46.00293 9.04969 MINI EXTERN> -89.99011 -92.80825 0.00000 0.00000 0.00000 MINI CONSTR> 124.69613 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 70.04642 0.01336 0.17419 0.00011 MINI INTERN> 9.69054 63.41682 0.00000 45.98866 9.04952 MINI EXTERN> -90.00244 -92.81087 0.00000 0.00000 0.00000 MINI CONSTR> 124.71420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20910 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 70.03324 0.01317 0.18627 0.00012 MINI INTERN> 9.70060 63.40213 0.00000 45.97597 9.04827 MINI EXTERN> -90.01037 -92.81584 0.00000 0.00000 0.00000 MINI CONSTR> 124.73249 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 70.03324 0.01317 0.18627 0.00006 STPD INTERN> 9.70060 63.40213 0.00000 45.97597 9.04827 STPD EXTERN> -90.01037 -92.81584 0.00000 0.00000 0.00000 STPD CONSTR> 124.73249 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 20910 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20910 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 70.03281 0.00043 0.10831 0.00000 MINI INTERN> 9.59971 63.44877 0.00000 45.99853 9.03718 MINI EXTERN> -89.96365 -92.81450 0.00000 0.00000 0.00000 MINI CONSTR> 124.72676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 69.58362 0.44919 0.01913 0.00190 MINI INTERN> 9.60661 62.81653 0.00000 45.22799 8.94569 MINI EXTERN> -90.53783 -92.87699 0.00000 0.00000 0.00000 MINI CONSTR> 126.40161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 69.57716 0.00646 0.06613 0.01004 MINI INTERN> 9.59649 62.78202 0.00000 45.15346 8.89263 MINI EXTERN> -90.02464 -93.00408 0.00000 0.00000 0.00000 MINI CONSTR> 126.18129 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 69.56459 0.01257 0.06275 0.01553 MINI INTERN> 9.59427 62.82408 0.00000 45.10324 8.92231 MINI EXTERN> -89.85754 -92.93848 0.00000 0.00000 0.00000 MINI CONSTR> 125.91670 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 69.55786 0.00673 0.04034 0.00596 MINI INTERN> 9.64762 62.86878 0.00000 45.11841 8.92341 MINI EXTERN> -90.06412 -92.88904 0.00000 0.00000 0.00000 MINI CONSTR> 125.95281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 69.55394 0.00392 0.03644 0.00479 MINI INTERN> 9.64569 62.81160 0.00000 45.15596 8.93001 MINI EXTERN> -90.22966 -92.86120 0.00000 0.00000 0.00000 MINI CONSTR> 126.10154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 69.55048 0.00346 0.03867 0.00708 MINI INTERN> 9.62010 62.78803 0.00000 45.14308 8.92026 MINI EXTERN> -90.30542 -92.89643 0.00000 0.00000 0.00000 MINI CONSTR> 126.28086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 69.54695 0.00352 0.03414 0.00596 MINI INTERN> 9.61643 62.70910 0.00000 45.07536 8.91033 MINI EXTERN> -90.32278 -92.90617 0.00000 0.00000 0.00000 MINI CONSTR> 126.46468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 69.54482 0.00213 0.02337 0.00420 MINI INTERN> 9.62376 62.65718 0.00000 45.05152 8.90008 MINI EXTERN> -90.36667 -92.90331 0.00000 0.00000 0.00000 MINI CONSTR> 126.58227 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 69.54371 0.00111 0.01723 0.00263 MINI INTERN> 9.61473 62.60503 0.00000 45.01355 8.90390 MINI EXTERN> -90.36116 -92.86835 0.00000 0.00000 0.00000 MINI CONSTR> 126.63601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 69.54306 0.00065 0.01421 0.00187 MINI INTERN> 9.61008 62.60022 0.00000 44.98971 8.90390 MINI EXTERN> -90.34187 -92.87036 0.00000 0.00000 0.00000 MINI CONSTR> 126.65137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 69.54264 0.00042 0.01110 0.00159 MINI INTERN> 9.61685 62.60498 0.00000 44.97080 8.89809 MINI EXTERN> -90.30571 -92.89278 0.00000 0.00000 0.00000 MINI CONSTR> 126.65042 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 69.54218 0.00046 0.01217 0.00212 MINI INTERN> 9.62286 62.61985 0.00000 44.94323 8.90643 MINI EXTERN> -90.31626 -92.87919 0.00000 0.00000 0.00000 MINI CONSTR> 126.64525 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> 63 69.54200 0.00018 0.00986 0.02000 CONJ INTERN> 9.62112 62.63565 0.00000 44.94089 8.90403 CONJ EXTERN> -90.32548 -92.87767 0.00000 0.00000 0.00000 CONJ CONSTR> 126.64346 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 ASP 14 N ) 1.4220 ( PROT ASP 14 H ) 1.1376 ( PROT ASP 14 CA ) 1.4220 ( PROT ASP 14 CB ) 1.1376 ( PROT ASP 14 CG ) 1.1376 ( PROT ASP 14 OD1 ) 1.1376 ( PROT ASP 14 OD2 ) 1.1376 ( PROT ASP 14 C ) 1.4220 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.63922 7.24554 -13.21135 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00101 0.00183 -0.00011 ROTATION MATRIX 1.000000 -0.000177 -0.000484 0.000177 1.000000 0.000467 0.000484 -0.000467 1.000000 AXIS OF ROTATION IS 0.671657 0.695841 -0.254326 ANGLE IS 0.04 TOTAL SQUARE DIFF IS 66.0941 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.472537 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4725" Parameter: A <- "0.4725" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.52343 7.25291 -13.41237 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS 0.00480 0.00264 -0.02799 ROTATION MATRIX 0.999636 0.018940 0.019216 -0.018524 0.999595 -0.021598 -0.019617 0.021234 0.999582 AXIS OF ROTATION IS -0.621720 -0.563673 0.543817 ANGLE IS 1.97 CENTER OF ROTATION 13.941959 6.825012-13.395502 SHIFT IS -0.019693 TOTAL SQUARE DIFF IS 2.5861 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.288831 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4725" RDCMND substituted energy or value "?RMS" to " 0.2888" Parameter: A <- "0.4725 0.2888" 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 0.4725 0.2888 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 " 126.64" Parameter: H <- "126.64" 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 -57.10146 126.64346 1.05173 ENER INTERN> 9.62112 62.63565 0.00000 44.94089 8.90403 ENER EXTERN> -90.32548 -92.87767 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 " -57.10" Parameter: B <- "-57.10" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -92.88" Parameter: C <- "-92.88" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -90.33" Parameter: C <- " -183.21" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -183.21" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 9.62" Parameter: D <- "9.62" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 62.64" Parameter: D <- " 72.26" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 44.94" Parameter: D <- " 117.20" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.90" Parameter: D <- " 126.10" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 126.10" 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= -57.10 GRMS= 1.05 ELEC= -92.88 VDW= -90.33 RDTITL> *EXTERNAL= -183.21 INTERNAL= 126.10 USER= 0.00 HARM= 126.64 RDTITL> *BOND= 9.62 ANGL= 62.64 DIHE= 44.94 IMPR= 8.90 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 -> "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= -57.10 GRMS= 1.05 ELEC= -92.88 VDW= -90.33 RDTITL> *EXTERNAL= -183.21 INTERNAL= 126.10 USER= 0.00 HARM= 126.64 RDTITL> *BOND= 9.62 ANGL= 62.64 DIHE= 44.94 IMPR= 8.90 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 -> "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= -57.10 GRMS= 1.05 ELEC= -92.88 VDW= -90.33 RDTITL> *EXTERNAL= -183.21 INTERNAL= 126.10 USER= 0.00 HARM= 126.64 RDTITL> *BOND= 9.62 ANGL= 62.64 DIHE= 44.94 IMPR= 8.90 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 7200 0.4725 0.2888 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20910 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20899 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 31.83953 -88.94099 0.41298 0.02000 MINI INTERN> 9.62112 62.63565 0.00000 44.94089 8.90403 MINI EXTERN> -90.32548 -92.87767 0.00000 0.00000 0.00000 MINI CONSTR> 88.94099 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 68.46236 -36.62283 16.31028 0.00864 MINI INTERN> 49.99309 57.13737 0.00000 48.04627 7.97580 MINI EXTERN> -101.01853 -86.77841 0.00000 0.00000 0.00000 MINI CONSTR> 93.10676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20885 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 28.98597 39.47639 0.50553 0.00156 MINI INTERN> 9.67198 61.70555 0.00000 46.92921 8.96856 MINI EXTERN> -101.53491 -90.17448 0.00000 0.00000 0.00000 MINI CONSTR> 93.42006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 28.67634 0.30964 0.38369 0.00067 MINI INTERN> 9.62572 61.96471 0.00000 46.79132 8.98305 MINI EXTERN> -101.91869 -90.33501 0.00000 0.00000 0.00000 MINI CONSTR> 93.56525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20881 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 28.43459 0.24175 0.29996 0.00029 MINI INTERN> 9.56022 61.67061 0.00000 46.81571 8.90073 MINI EXTERN> -101.80513 -90.38842 0.00000 0.00000 0.00000 MINI CONSTR> 93.68087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 28.24623 0.18836 0.23226 0.00030 MINI INTERN> 9.55714 61.58414 0.00000 46.78360 8.88731 MINI EXTERN> -101.92056 -90.43284 0.00000 0.00000 0.00000 MINI CONSTR> 93.78744 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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 28.03532 0.21091 0.22975 0.00031 MINI INTERN> 9.54162 61.45933 0.00000 46.75557 8.86324 MINI EXTERN> -102.03489 -90.46626 0.00000 0.00000 0.00000 MINI CONSTR> 93.91670 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 27.82320 0.21211 0.38813 0.00032 MINI INTERN> 9.64752 61.16853 0.00000 46.73247 8.81824 MINI EXTERN> -102.16053 -90.44365 0.00000 0.00000 0.00000 MINI CONSTR> 94.06062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 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> 40 27.64038 0.18282 0.32850 0.00034 MINI INTERN> 9.54501 61.17095 0.00000 46.70114 8.81193 MINI EXTERN> -102.27862 -90.48768 0.00000 0.00000 0.00000 MINI CONSTR> 94.17766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 27.47353 0.16685 0.37702 0.00035 MINI INTERN> 9.56208 61.02756 0.00000 46.68158 8.78589 MINI EXTERN> -102.39677 -90.47842 0.00000 0.00000 0.00000 MINI CONSTR> 94.29161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20877 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 27.32372 0.14981 0.51601 0.00036 MINI INTERN> 9.68078 60.80524 0.00000 46.65911 8.75671 MINI EXTERN> -102.54835 -90.43277 0.00000 0.00000 0.00000 MINI CONSTR> 94.40301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 27.17337 0.15035 0.54116 0.00037 MINI INTERN> 9.66309 60.70555 0.00000 46.63992 8.73527 MINI EXTERN> -102.64547 -90.43226 0.00000 0.00000 0.00000 MINI CONSTR> 94.50725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20876 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 27.03004 0.14333 0.59744 0.00039 MINI INTERN> 9.60086 60.68082 0.00000 46.61307 8.72358 MINI EXTERN> -102.75550 -90.44280 0.00000 0.00000 0.00000 MINI CONSTR> 94.61001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 26.89031 0.13973 0.61343 0.00040 MINI INTERN> 9.57879 60.61634 0.00000 46.59127 8.71523 MINI EXTERN> -102.86752 -90.44761 0.00000 0.00000 0.00000 MINI CONSTR> 94.70381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20876 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 26.74595 0.14437 0.56919 0.00042 MINI INTERN> 9.52814 60.53755 0.00000 46.57608 8.68988 MINI EXTERN> -102.94517 -90.43771 0.00000 0.00000 0.00000 MINI CONSTR> 94.79717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 26.56938 0.17657 0.20369 0.00018 MINI INTERN> 9.37934 60.70491 0.00000 46.52278 8.73940 MINI EXTERN> -103.16711 -90.49744 0.00000 0.00000 0.00000 MINI CONSTR> 94.88751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20873 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 26.48914 0.08024 0.66228 0.00045 MINI INTERN> 9.53029 60.37497 0.00000 46.52062 8.66487 MINI EXTERN> -103.15517 -90.42500 0.00000 0.00000 0.00000 MINI CONSTR> 94.97856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 26.38407 0.10507 0.80503 0.00046 MINI INTERN> 9.47288 60.45301 0.00000 46.47536 8.68307 MINI EXTERN> -103.31628 -90.44801 0.00000 0.00000 0.00000 MINI CONSTR> 95.06404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20871 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 26.18416 0.19992 0.22073 0.00020 MINI INTERN> 9.35966 60.49994 0.00000 46.43250 8.71271 MINI EXTERN> -103.47746 -90.48661 0.00000 0.00000 0.00000 MINI CONSTR> 95.14341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 26.14077 0.04338 0.75897 0.00050 MINI INTERN> 9.35334 60.31149 0.00000 46.45389 8.62966 MINI EXTERN> -103.39833 -90.43008 0.00000 0.00000 0.00000 MINI CONSTR> 95.22081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20868 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 25.94390 0.19687 0.24305 0.00022 MINI INTERN> 9.35681 60.37108 0.00000 46.36712 8.69790 MINI EXTERN> -103.67144 -90.47977 0.00000 0.00000 0.00000 MINI CONSTR> 95.30221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 25.91488 0.02902 0.76535 0.00054 MINI INTERN> 9.25654 60.20579 0.00000 46.41992 8.59280 MINI EXTERN> -103.50636 -90.42576 0.00000 0.00000 0.00000 MINI CONSTR> 95.37194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20866 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 25.70213 0.21275 0.26645 0.00023 MINI INTERN> 9.32145 60.26461 0.00000 46.30173 8.68132 MINI EXTERN> -103.85058 -90.47747 0.00000 0.00000 0.00000 MINI CONSTR> 95.46106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 25.59794 0.10419 0.18024 0.00024 MINI INTERN> 9.32981 60.15869 0.00000 46.27994 8.65956 MINI EXTERN> -103.89313 -90.45998 0.00000 0.00000 0.00000 MINI CONSTR> 95.52305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20863 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 25.48746 0.11048 0.34138 0.00025 MINI INTERN> 9.31122 60.16785 0.00000 46.23301 8.67135 MINI EXTERN> -104.02220 -90.47910 0.00000 0.00000 0.00000 MINI CONSTR> 95.60532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 25.38094 0.10652 0.27487 0.00026 MINI INTERN> 9.31909 60.08262 0.00000 46.20245 8.65716 MINI EXTERN> -104.08349 -90.46591 0.00000 0.00000 0.00000 MINI CONSTR> 95.66902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20861 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 25.28121 0.09973 0.30450 0.00027 MINI INTERN> 9.33898 60.02052 0.00000 46.16457 8.65365 MINI EXTERN> -104.16757 -90.46441 0.00000 0.00000 0.00000 MINI CONSTR> 95.73548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 25.18942 0.09178 0.40200 0.00028 MINI INTERN> 9.33777 59.99731 0.00000 46.12470 8.65518 MINI EXTERN> -104.25863 -90.46952 0.00000 0.00000 0.00000 MINI CONSTR> 95.80261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20858 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 25.09692 0.09251 0.45071 0.00029 MINI INTERN> 9.35824 59.92355 0.00000 46.09179 8.64666 MINI EXTERN> -104.32257 -90.46633 0.00000 0.00000 0.00000 MINI CONSTR> 95.86558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 25.00716 0.08976 0.45755 0.00030 MINI INTERN> 9.40243 59.85341 0.00000 46.04934 8.64541 MINI EXTERN> -104.40736 -90.46115 0.00000 0.00000 0.00000 MINI CONSTR> 95.92507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20856 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 24.91834 0.08882 0.47915 0.00031 MINI INTERN> 9.42045 59.80055 0.00000 46.00998 8.64152 MINI EXTERN> -104.48248 -90.45641 0.00000 0.00000 0.00000 MINI CONSTR> 95.98472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 24.82882 0.08951 0.46505 0.00032 MINI INTERN> 9.43382 59.72518 0.00000 45.98038 8.63088 MINI EXTERN> -104.53077 -90.45098 0.00000 0.00000 0.00000 MINI CONSTR> 96.04031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20854 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 24.74404 0.08478 0.50161 0.00033 MINI INTERN> 9.40372 59.69820 0.00000 45.95048 8.61998 MINI EXTERN> -104.57889 -90.44650 0.00000 0.00000 0.00000 MINI CONSTR> 96.09706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 24.63449 0.10955 0.15778 0.00014 MINI INTERN> 9.27317 59.63044 0.00000 45.96160 8.57540 MINI EXTERN> -104.51822 -90.43063 0.00000 0.00000 0.00000 MINI CONSTR> 96.14272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20853 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 24.58744 0.04705 0.54726 0.00036 MINI INTERN> 9.50319 59.54342 0.00000 45.87361 8.61425 MINI EXTERN> -104.71252 -90.43910 0.00000 0.00000 0.00000 MINI CONSTR> 96.20459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 24.51430 0.07314 0.61022 0.00037 MINI INTERN> 9.45609 59.54098 0.00000 45.84570 8.60367 MINI EXTERN> -104.75279 -90.43665 0.00000 0.00000 0.00000 MINI CONSTR> 96.25730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20853 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 24.43261 0.08169 0.57027 0.00038 MINI INTERN> 9.56925 59.43614 0.00000 45.79112 8.61191 MINI EXTERN> -104.85428 -90.43213 0.00000 0.00000 0.00000 MINI CONSTR> 96.31060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 24.30464 0.12797 0.17560 0.00017 MINI INTERN> 9.23652 59.46946 0.00000 45.83525 8.54693 MINI EXTERN> -104.71350 -90.42838 0.00000 0.00000 0.00000 MINI CONSTR> 96.35835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20853 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 24.23404 0.07060 0.15019 0.00017 MINI INTERN> 9.24268 59.43778 0.00000 45.80183 8.54633 MINI EXTERN> -104.76884 -90.43003 0.00000 0.00000 0.00000 MINI CONSTR> 96.40430 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 24.16019 0.07385 0.15346 0.00018 MINI INTERN> 9.23025 59.40462 0.00000 45.77251 8.53964 MINI EXTERN> -104.80962 -90.43045 0.00000 0.00000 0.00000 MINI CONSTR> 96.45324 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20854 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 24.08626 0.07393 0.14681 0.00019 MINI INTERN> 9.23234 59.36590 0.00000 45.73929 8.53540 MINI EXTERN> -104.85832 -90.43068 0.00000 0.00000 0.00000 MINI CONSTR> 96.50232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 24.00942 0.07684 0.25270 0.00019 MINI INTERN> 9.17150 59.34290 0.00000 45.71877 8.51628 MINI EXTERN> -104.86849 -90.42915 0.00000 0.00000 0.00000 MINI CONSTR> 96.55761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20853 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 23.93812 0.07130 0.19804 0.00020 MINI INTERN> 9.19907 59.29712 0.00000 45.68070 8.51793 MINI EXTERN> -104.92939 -90.43058 0.00000 0.00000 0.00000 MINI CONSTR> 96.60328 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 23.87198 0.06614 0.22464 0.00021 MINI INTERN> 9.16703 59.27859 0.00000 45.65616 8.50904 MINI EXTERN> -104.95591 -90.43217 0.00000 0.00000 0.00000 MINI CONSTR> 96.64923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20848 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 23.80472 0.06726 0.23249 0.00021 MINI INTERN> 9.15567 59.25258 0.00000 45.62551 8.50397 MINI EXTERN> -104.99561 -90.43295 0.00000 0.00000 0.00000 MINI CONSTR> 96.69556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 23.74746 0.05726 0.32173 0.00022 MINI INTERN> 9.10757 59.23927 0.00000 45.60842 8.49022 MINI EXTERN> -105.00297 -90.43504 0.00000 0.00000 0.00000 MINI CONSTR> 96.73999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20847 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 23.68287 0.06459 0.35176 0.00023 MINI INTERN> 9.11122 59.21079 0.00000 45.57289 8.48748 MINI EXTERN> -105.05153 -90.43464 0.00000 0.00000 0.00000 MINI CONSTR> 96.78667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 23.62368 0.05920 0.36400 0.00024 MINI INTERN> 9.07337 59.19446 0.00000 45.55299 8.47738 MINI EXTERN> -105.06614 -90.43767 0.00000 0.00000 0.00000 MINI CONSTR> 96.82929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20845 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 23.56167 0.06201 0.38588 0.00025 MINI INTERN> 9.07544 59.15744 0.00000 45.52249 8.47170 MINI EXTERN> -105.10168 -90.43837 0.00000 0.00000 0.00000 MINI CONSTR> 96.87465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 23.50248 0.05920 0.36797 0.00026 MINI INTERN> 9.06686 59.13889 0.00000 45.49229 8.46950 MINI EXTERN> -105.14083 -90.43950 0.00000 0.00000 0.00000 MINI CONSTR> 96.91527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20845 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 23.44564 0.05684 0.40807 0.00027 MINI INTERN> 9.11052 59.08005 0.00000 45.45661 8.46847 MINI EXTERN> -105.18859 -90.43991 0.00000 0.00000 0.00000 MINI CONSTR> 96.95849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 23.38830 0.05734 0.38337 0.00028 MINI INTERN> 9.05432 59.08345 0.00000 45.43730 8.45927 MINI EXTERN> -105.20151 -90.44320 0.00000 0.00000 0.00000 MINI CONSTR> 96.99865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20845 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 23.31512 0.07318 0.13050 0.00012 MINI INTERN> 9.23729 58.97196 0.00000 45.36224 8.48659 MINI EXTERN> -105.34358 -90.43805 0.00000 0.00000 0.00000 MINI CONSTR> 97.03867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 23.28553 0.02959 0.43456 0.00030 MINI INTERN> 9.02201 59.04659 0.00000 45.38779 8.44725 MINI EXTERN> -105.24988 -90.44691 0.00000 0.00000 0.00000 MINI CONSTR> 97.07868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20845 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 23.23613 0.04940 0.50012 0.00031 MINI INTERN> 9.06207 59.01795 0.00000 45.34388 8.45215 MINI EXTERN> -105.31608 -90.44462 0.00000 0.00000 0.00000 MINI CONSTR> 97.12078 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 23.18315 0.05298 0.47329 0.00032 MINI INTERN> 8.98967 59.01150 0.00000 45.33634 8.43559 MINI EXTERN> -105.29980 -90.44969 0.00000 0.00000 0.00000 MINI CONSTR> 97.15955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20846 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 23.09742 0.08573 0.14692 0.00014 MINI INTERN> 9.24392 58.85649 0.00000 45.24294 8.47209 MINI EXTERN> -105.47862 -90.44134 0.00000 0.00000 0.00000 MINI CONSTR> 97.20194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 23.05085 0.04658 0.11746 0.00014 MINI INTERN> 9.21465 58.84349 0.00000 45.22461 8.46432 MINI EXTERN> -105.48999 -90.44250 0.00000 0.00000 0.00000 MINI CONSTR> 97.23627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20844 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 22.99928 0.05157 0.12241 0.00015 MINI INTERN> 9.21939 58.81536 0.00000 45.19425 8.46139 MINI EXTERN> -105.52408 -90.44342 0.00000 0.00000 0.00000 MINI CONSTR> 97.27639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 22.94891 0.05037 0.19867 0.00015 MINI INTERN> 9.27008 58.76632 0.00000 45.15273 8.46429 MINI EXTERN> -105.58084 -90.44320 0.00000 0.00000 0.00000 MINI CONSTR> 97.31953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20844 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 22.90165 0.04725 0.15842 0.00016 MINI INTERN> 9.23761 58.75820 0.00000 45.13316 8.45695 MINI EXTERN> -105.59374 -90.44518 0.00000 0.00000 0.00000 MINI CONSTR> 97.35466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 22.85699 0.04467 0.17437 0.00016 MINI INTERN> 9.25565 58.72446 0.00000 45.10335 8.45539 MINI EXTERN> -105.62818 -90.44495 0.00000 0.00000 0.00000 MINI CONSTR> 97.39128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20843 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 22.81070 0.04628 0.17313 0.00017 MINI INTERN> 9.25076 58.69962 0.00000 45.07806 8.45077 MINI EXTERN> -105.65147 -90.44555 0.00000 0.00000 0.00000 MINI CONSTR> 97.42852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 22.77166 0.03904 0.25884 0.00018 MINI INTERN> 9.29916 58.66103 0.00000 45.04041 8.45398 MINI EXTERN> -105.70321 -90.44568 0.00000 0.00000 0.00000 MINI CONSTR> 97.46597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20843 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 22.72934 0.04232 0.28346 0.00018 MINI INTERN> 9.29664 58.63151 0.00000 45.01721 8.44859 MINI EXTERN> -105.72157 -90.44525 0.00000 0.00000 0.00000 MINI CONSTR> 97.50221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 22.68921 0.04013 0.28862 0.00019 MINI INTERN> 9.32157 58.60115 0.00000 44.98614 8.44878 MINI EXTERN> -105.75994 -90.44540 0.00000 0.00000 0.00000 MINI CONSTR> 97.53692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20842 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 22.64863 0.04058 0.31327 0.00020 MINI INTERN> 9.31603 58.58896 0.00000 44.95960 8.44579 MINI EXTERN> -105.78705 -90.44773 0.00000 0.00000 0.00000 MINI CONSTR> 97.57303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 22.60884 0.03979 0.29426 0.00020 MINI INTERN> 9.32074 58.55604 0.00000 44.93729 8.44166 MINI EXTERN> -105.80602 -90.44646 0.00000 0.00000 0.00000 MINI CONSTR> 97.60559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20841 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 22.57094 0.03790 0.33033 0.00021 MINI INTERN> 9.29010 58.56221 0.00000 44.91571 8.43656 MINI EXTERN> -105.82330 -90.45071 0.00000 0.00000 0.00000 MINI CONSTR> 97.64037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 22.53180 0.03914 0.30797 0.00022 MINI INTERN> 9.32639 58.51652 0.00000 44.88559 8.43665 MINI EXTERN> -105.85883 -90.44852 0.00000 0.00000 0.00000 MINI CONSTR> 97.67400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20839 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 22.48261 0.04919 0.10589 0.00010 MINI INTERN> 9.15688 58.56602 0.00000 44.89871 8.41273 MINI EXTERN> -105.80069 -90.45477 0.00000 0.00000 0.00000 MINI CONSTR> 97.70372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 22.46146 0.02116 0.35294 0.00024 MINI INTERN> 9.33845 58.47450 0.00000 44.83517 8.43190 MINI EXTERN> -105.90943 -90.44995 0.00000 0.00000 0.00000 MINI CONSTR> 97.74082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 22.42908 0.03238 0.40649 0.00025 MINI INTERN> 9.30924 58.45256 0.00000 44.82369 8.42157 MINI EXTERN> -105.90261 -90.44882 0.00000 0.00000 0.00000 MINI CONSTR> 97.77346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 22.39304 0.03604 0.38339 0.00025 MINI INTERN> 9.36813 58.41080 0.00000 44.78559 8.42687 MINI EXTERN> -105.95709 -90.44809 0.00000 0.00000 0.00000 MINI CONSTR> 97.80684 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20838 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 22.33744 0.05560 0.12056 0.00011 MINI INTERN> 9.13473 58.49680 0.00000 44.80838 8.39788 MINI EXTERN> -105.87821 -90.45858 0.00000 0.00000 0.00000 MINI CONSTR> 97.83644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 22.32770 0.00974 0.41045 0.00027 MINI INTERN> 9.37118 58.36968 0.00000 44.74086 8.42046 MINI EXTERN> -105.99645 -90.44865 0.00000 0.00000 0.00000 MINI CONSTR> 97.87063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20839 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 22.27091 0.05679 0.14379 0.00012 MINI INTERN> 9.11719 58.46675 0.00000 44.76729 8.38964 MINI EXTERN> -105.90967 -90.46044 0.00000 0.00000 0.00000 MINI CONSTR> 97.90017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 22.24148 0.02943 0.09995 0.00012 MINI INTERN> 9.14448 58.43879 0.00000 44.74165 8.39119 MINI EXTERN> -105.94164 -90.46010 0.00000 0.00000 0.00000 MINI CONSTR> 97.92710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20839 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 22.20808 0.03340 0.16822 0.00013 MINI INTERN> 9.09743 58.44128 0.00000 44.72767 8.38163 MINI EXTERN> -105.93942 -90.46266 0.00000 0.00000 0.00000 MINI CONSTR> 97.96214 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 22.17845 0.02963 0.09506 0.00013 MINI INTERN> 9.14612 58.40207 0.00000 44.69780 8.38587 MINI EXTERN> -105.98099 -90.46112 0.00000 0.00000 0.00000 MINI CONSTR> 97.98870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20839 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 22.14658 0.03188 0.19570 0.00014 MINI INTERN> 9.08198 58.41524 0.00000 44.68667 8.37427 MINI EXTERN> -105.97156 -90.46475 0.00000 0.00000 0.00000 MINI CONSTR> 98.02473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 22.11459 0.03199 0.14604 0.00014 MINI INTERN> 9.11314 58.37825 0.00000 44.65973 8.37515 MINI EXTERN> -106.00301 -90.46315 0.00000 0.00000 0.00000 MINI CONSTR> 98.05448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20839 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 22.08888 0.02571 0.21141 0.00015 MINI INTERN> 9.07010 58.38550 0.00000 44.64813 8.36705 MINI EXTERN> -106.00042 -90.46596 0.00000 0.00000 0.00000 MINI CONSTR> 98.08448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 22.05563 0.03325 0.14502 0.00015 MINI INTERN> 9.10783 58.35073 0.00000 44.61723 8.36988 MINI EXTERN> -106.04023 -90.46503 0.00000 0.00000 0.00000 MINI CONSTR> 98.11522 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 22.03215 0.02347 0.22670 0.00016 MINI INTERN> 9.06237 58.35899 0.00000 44.60714 8.36122 MINI EXTERN> -106.03461 -90.46767 0.00000 0.00000 0.00000 MINI CONSTR> 98.14473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 22.00625 0.02590 0.27038 0.00016 MINI INTERN> 9.06903 58.33187 0.00000 44.58739 8.35746 MINI EXTERN> -106.04856 -90.46636 0.00000 0.00000 0.00000 MINI CONSTR> 98.17543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 21.97918 0.02707 0.24218 0.00017 MINI INTERN> 9.05167 58.32899 0.00000 44.57062 8.35400 MINI EXTERN> -106.06037 -90.46834 0.00000 0.00000 0.00000 MINI CONSTR> 98.20262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 21.95436 0.02483 0.29977 0.00018 MINI INTERN> 9.04889 58.32330 0.00000 44.54770 8.35188 MINI EXTERN> -106.08176 -90.47015 0.00000 0.00000 0.00000 MINI CONSTR> 98.23449 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20836 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 21.92859 0.02576 0.27276 0.00018 MINI INTERN> 9.04372 58.30872 0.00000 44.53100 8.34891 MINI EXTERN> -106.09390 -90.47042 0.00000 0.00000 0.00000 MINI CONSTR> 98.26055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 21.89464 0.03395 0.08864 0.00008 MINI INTERN> 9.16489 58.22476 0.00000 44.48646 8.36137 MINI EXTERN> -106.16641 -90.46421 0.00000 0.00000 0.00000 MINI CONSTR> 98.28777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20837 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 21.88011 0.01453 0.28352 0.00020 MINI INTERN> 9.02278 58.28551 0.00000 44.49856 8.34060 MINI EXTERN> -106.11240 -90.47138 0.00000 0.00000 0.00000 MINI CONSTR> 98.31644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 21.84257 0.03754 0.08692 0.00008 MINI INTERN> 9.16120 58.19443 0.00000 44.44694 8.35566 MINI EXTERN> -106.19781 -90.46482 0.00000 0.00000 0.00000 MINI CONSTR> 98.34696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20835 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 21.83125 0.01132 0.31197 0.00021 MINI INTERN> 9.02500 58.25734 0.00000 44.45740 8.33597 MINI EXTERN> -106.14788 -90.47220 0.00000 0.00000 0.00000 MINI CONSTR> 98.37561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 21.79366 0.03759 0.10198 0.00009 MINI INTERN> 9.17127 58.15920 0.00000 44.40574 8.35176 MINI EXTERN> -106.23428 -90.46481 0.00000 0.00000 0.00000 MINI CONSTR> 98.40476 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20834 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 21.78636 0.00729 0.32637 0.00023 MINI INTERN> 9.01350 58.22817 0.00000 44.42478 8.32835 MINI EXTERN> -106.16741 -90.47178 0.00000 0.00000 0.00000 MINI CONSTR> 98.43077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 21.74569 0.04068 0.10911 0.00010 MINI INTERN> 9.17173 58.12888 0.00000 44.36673 8.34674 MINI EXTERN> -106.26590 -90.46509 0.00000 0.00000 0.00000 MINI CONSTR> 98.46260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20833 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 21.72511 0.02057 0.07954 0.00010 MINI INTERN> 9.15006 58.12539 0.00000 44.35546 8.34192 MINI EXTERN> -106.26832 -90.46576 0.00000 0.00000 0.00000 MINI CONSTR> 98.48636 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 21.70150 0.02361 0.13859 0.00011 MINI INTERN> 9.18404 58.09452 0.00000 44.32693 8.34320 MINI EXTERN> -106.30101 -90.46479 0.00000 0.00000 0.00000 MINI CONSTR> 98.51861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20832 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 21.68129 0.02021 0.07761 0.00011 MINI INTERN> 9.14721 58.09847 0.00000 44.31978 8.33678 MINI EXTERN> -106.29585 -90.46588 0.00000 0.00000 0.00000 MINI CONSTR> 98.54078 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 21.65896 0.02233 0.16033 0.00011 MINI INTERN> 9.19049 58.06304 0.00000 44.28931 8.33893 MINI EXTERN> -106.33210 -90.46447 0.00000 0.00000 0.00000 MINI CONSTR> 98.57377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20832 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 21.63606 0.02290 0.10193 0.00012 MINI INTERN> 9.15811 58.06503 0.00000 44.27823 8.33317 MINI EXTERN> -106.33236 -90.46573 0.00000 0.00000 0.00000 MINI CONSTR> 98.59961 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 21.63606 0.02290 0.10193 0.00014 STPD INTERN> 9.15811 58.06503 0.00000 44.27823 8.33317 STPD EXTERN> -106.33236 -90.46573 0.00000 0.00000 0.00000 STPD CONSTR> 98.59961 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 20832 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20832 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 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 21.63606 0.02290 0.10193 0.00000 MINI INTERN> 9.15811 58.06503 0.00000 44.27823 8.33317 MINI EXTERN> -106.33236 -90.46573 0.00000 0.00000 0.00000 MINI CONSTR> 98.59961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 20.60809 1.02797 0.04984 0.00895 MINI INTERN> 9.07624 56.78586 0.00000 42.65288 8.10743 MINI EXTERN> -107.97384 -90.32994 0.00000 0.00000 0.00000 MINI CONSTR> 102.28945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 20.59502 0.01307 0.09451 0.00915 MINI INTERN> 9.02323 56.77166 0.00000 42.55005 8.03299 MINI EXTERN> -107.46597 -90.45175 0.00000 0.00000 0.00000 MINI CONSTR> 102.13481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 20.54522 0.04980 0.18871 0.03809 MINI INTERN> 8.96287 56.60220 0.00000 42.24182 7.97042 MINI EXTERN> -106.48249 -90.28006 0.00000 0.00000 0.00000 MINI CONSTR> 101.53046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 20.34137 0.20385 0.34093 0.13103 MINI INTERN> 9.06003 56.58603 0.00000 41.77344 7.72570 MINI EXTERN> -106.63767 -88.59271 0.00000 0.00000 0.00000 MINI CONSTR> 100.42655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 20.18911 0.15226 0.34476 0.08064 MINI INTERN> 8.97669 56.04344 0.00000 41.66955 7.73183 MINI EXTERN> -108.25626 -86.39290 0.00000 0.00000 0.00000 MINI CONSTR> 100.41677 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 20.08856 0.10055 0.32791 0.05864 MINI INTERN> 8.95125 55.62441 0.00000 41.67824 7.86364 MINI EXTERN> -109.58911 -85.18734 0.00000 0.00000 0.00000 MINI CONSTR> 100.74747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 20.00141 0.08715 0.34012 0.05752 MINI INTERN> 9.00705 55.47704 0.00000 41.56658 7.83235 MINI EXTERN> -110.35918 -84.70443 0.00000 0.00000 0.00000 MINI CONSTR> 101.18200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 19.91144 0.08996 0.36040 0.05736 MINI INTERN> 8.88120 55.23771 0.00000 41.33832 7.66602 MINI EXTERN> -110.61270 -84.35081 0.00000 0.00000 0.00000 MINI CONSTR> 101.75171 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 19.81805 0.09340 0.36496 0.06121 MINI INTERN> 8.76926 54.92495 0.00000 41.18836 7.47957 MINI EXTERN> -111.02295 -84.03358 0.00000 0.00000 0.00000 MINI CONSTR> 102.51243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 19.71065 0.10739 0.40884 0.07284 MINI INTERN> 8.76925 54.55172 0.00000 41.01368 7.29870 MINI EXTERN> -112.09474 -83.45673 0.00000 0.00000 0.00000 MINI CONSTR> 103.62878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 19.60190 0.10875 0.41604 0.06856 MINI INTERN> 8.67390 54.30437 0.00000 41.24953 7.21056 MINI EXTERN> -113.86722 -82.94393 0.00000 0.00000 0.00000 MINI CONSTR> 104.97471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 19.50895 0.09295 0.41723 0.05724 MINI INTERN> 8.61712 53.83536 0.00000 41.70936 7.15644 MINI EXTERN> -115.25181 -82.73573 0.00000 0.00000 0.00000 MINI CONSTR> 106.17821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 19.42704 0.08191 0.42946 0.05305 MINI INTERN> 8.62895 53.18063 0.00000 42.01449 7.08850 MINI EXTERN> -116.07564 -82.54037 0.00000 0.00000 0.00000 MINI CONSTR> 107.13046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 19.34839 0.07866 0.44829 0.05243 MINI INTERN> 8.49285 52.60700 0.00000 42.25412 7.06090 MINI EXTERN> -116.65586 -82.26654 0.00000 0.00000 0.00000 MINI CONSTR> 107.85591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 19.26803 0.08036 0.47036 0.05358 MINI INTERN> 8.44362 52.12195 0.00000 42.36650 7.13767 MINI EXTERN> -117.16024 -82.02826 0.00000 0.00000 0.00000 MINI CONSTR> 108.38678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 19.18661 0.08142 0.47780 0.05478 MINI INTERN> 8.23561 51.81104 0.00000 42.40504 7.21678 MINI EXTERN> -117.20053 -82.00027 0.00000 0.00000 0.00000 MINI CONSTR> 108.71895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 19.10478 0.08183 0.47546 0.05441 MINI INTERN> 8.19979 51.62679 0.00000 42.31318 7.22167 MINI EXTERN> -116.77567 -82.34333 0.00000 0.00000 0.00000 MINI CONSTR> 108.86237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 19.02342 0.08137 0.48563 0.05602 MINI INTERN> 8.18286 51.68134 0.00000 42.08241 7.24330 MINI EXTERN> -115.99367 -83.01417 0.00000 0.00000 0.00000 MINI CONSTR> 108.84134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 18.94360 0.07981 0.48465 0.05477 MINI INTERN> 8.28591 51.82506 0.00000 41.85166 7.24632 MINI EXTERN> -115.13317 -83.83917 0.00000 0.00000 0.00000 MINI CONSTR> 108.70699 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 18.85922 0.08439 0.48805 0.05915 MINI INTERN> 8.39755 52.06115 0.00000 41.55956 7.24177 MINI EXTERN> -114.34079 -84.55928 0.00000 0.00000 0.00000 MINI CONSTR> 108.49926 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 18.85922 0.08439 0.48805 0.02000 CONJ INTERN> 8.39755 52.06115 0.00000 41.55956 7.24177 CONJ EXTERN> -114.34079 -84.55928 0.00000 0.00000 0.00000 CONJ CONSTR> 108.49926 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 ASP 14 N ) 0.92430 ( PROT ASP 14 H ) 0.73944 ( PROT ASP 14 CA ) 0.92430 ( PROT ASP 14 CB ) 0.73944 ( PROT ASP 14 CG ) 0.73944 ( PROT ASP 14 OD1 ) 0.73944 ( PROT ASP 14 OD2 ) 0.73944 ( PROT ASP 14 C ) 0.92430 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.63708 7.24265 -13.21250 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00315 0.00471 0.00104 ROTATION MATRIX 0.999995 0.002445 0.002055 -0.002440 0.999995 -0.002149 -0.002060 0.002144 0.999996 AXIS OF ROTATION IS -0.557884 -0.534638 0.634766 ANGLE IS 0.22 TOTAL SQUARE DIFF IS 87.5867 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.543968 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.5440" Parameter: A <- "0.5440" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.53322 7.25820 -13.41168 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.00500 -0.00266 -0.02867 ROTATION MATRIX 0.999713 0.016987 0.016892 -0.016652 0.999666 -0.019758 -0.017222 0.019471 0.999662 AXIS OF ROTATION IS -0.633529 -0.550916 0.543261 ANGLE IS 1.77 CENTER OF ROTATION 14.087372 6.582660-13.460597 SHIFT IS -0.010947 TOTAL SQUARE DIFF IS 3.7679 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.348634 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.5440" RDCMND substituted energy or value "?RMS" to " 0.3486" Parameter: A <- "0.5440 0.3486" 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 0.5440 0.3486 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 " 108.50" Parameter: H <- "108.50" 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 -89.64004 108.49926 0.85094 ENER INTERN> 8.39755 52.06115 0.00000 41.55956 7.24177 ENER EXTERN> -114.34079 -84.55928 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 " -89.64" Parameter: B <- "-89.64" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -84.56" Parameter: C <- "-84.56" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -114.34" Parameter: C <- " -198.90" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -198.90" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 8.40" Parameter: D <- "8.40" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 52.06" Parameter: D <- " 60.46" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 41.56" Parameter: D <- " 102.02" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.24" Parameter: D <- " 109.26" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 109.26" 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= -89.64 GRMS= 0.85 ELEC= -84.56 VDW= -114.34 RDTITL> *EXTERNAL= -198.90 INTERNAL= 109.26 USER= 0.00 HARM= 108.50 RDTITL> *BOND= 8.40 ANGL= 52.06 DIHE= 41.56 IMPR= 7.24 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20832 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20854 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 -15.68212 -73.95792 0.53121 0.02000 MINI INTERN> 8.39755 52.06115 0.00000 41.55956 7.24177 MINI EXTERN> -114.34079 -84.55928 0.00000 0.00000 0.00000 MINI CONSTR> 73.95792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -8.65310 -7.02902 8.05945 0.00360 MINI INTERN> 16.99021 53.03080 0.00000 42.21026 7.12953 MINI EXTERN> -121.69116 -81.76442 0.00000 0.00000 0.00000 MINI CONSTR> 75.44169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20843 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -18.97356 10.32046 0.49642 0.00065 MINI INTERN> 8.48568 51.45807 0.00000 42.38422 7.04446 MINI EXTERN> -121.63560 -82.18457 0.00000 0.00000 0.00000 MINI CONSTR> 75.47419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -19.22931 0.25575 0.87046 0.00067 MINI INTERN> 8.53257 51.27209 0.00000 42.40198 7.03563 MINI EXTERN> -121.76742 -82.24440 0.00000 0.00000 0.00000 MINI CONSTR> 75.54023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20843 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -19.58612 0.35681 0.29120 0.00029 MINI INTERN> 8.37092 51.29547 0.00000 42.43241 7.01998 MINI EXTERN> -121.98001 -82.31820 0.00000 0.00000 0.00000 MINI CONSTR> 75.59330 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -19.68739 0.10127 1.09849 0.00072 MINI INTERN> 8.57211 51.05888 0.00000 42.42721 7.01817 MINI EXTERN> -122.17057 -82.25159 0.00000 0.00000 0.00000 MINI CONSTR> 75.65840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20838 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -20.07819 0.39079 0.33041 0.00031 MINI INTERN> 8.34535 51.13095 0.00000 42.45684 6.99556 MINI EXTERN> -122.39473 -82.32492 0.00000 0.00000 0.00000 MINI CONSTR> 75.71276 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -20.29192 0.21373 0.31524 0.00032 MINI INTERN> 8.31793 51.06258 0.00000 42.46265 6.98442 MINI EXTERN> -122.57217 -82.31330 0.00000 0.00000 0.00000 MINI CONSTR> 75.76598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20831 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -20.49007 0.19815 0.25794 0.00034 MINI INTERN> 8.32328 50.96914 0.00000 42.46165 6.97654 MINI EXTERN> -122.74133 -82.29391 0.00000 0.00000 0.00000 MINI CONSTR> 75.81455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -20.68373 0.19366 0.46045 0.00035 MINI INTERN> 8.28642 50.95285 0.00000 42.46791 6.96072 MINI EXTERN> -122.92603 -82.29661 0.00000 0.00000 0.00000 MINI CONSTR> 75.87101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20827 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -20.88133 0.19760 0.37880 0.00036 MINI INTERN> 8.27392 50.86343 0.00000 42.45972 6.95347 MINI EXTERN> -123.08109 -82.26916 0.00000 0.00000 0.00000 MINI CONSTR> 75.91839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -21.03169 0.15036 0.53440 0.00037 MINI INTERN> 8.24785 50.83767 0.00000 42.45962 6.94114 MINI EXTERN> -123.21701 -82.26435 0.00000 0.00000 0.00000 MINI CONSTR> 75.96339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20825 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -21.19168 0.16000 0.57847 0.00039 MINI INTERN> 8.26672 50.76727 0.00000 42.45286 6.93229 MINI EXTERN> -123.36225 -82.25505 0.00000 0.00000 0.00000 MINI CONSTR> 76.00647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -21.34665 0.15497 0.61139 0.00040 MINI INTERN> 8.21931 50.73179 0.00000 42.44622 6.92209 MINI EXTERN> -123.47516 -82.23913 0.00000 0.00000 0.00000 MINI CONSTR> 76.04823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20825 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -21.49832 0.15167 0.62023 0.00042 MINI INTERN> 8.27680 50.63477 0.00000 42.43067 6.91689 MINI EXTERN> -123.61617 -82.22766 0.00000 0.00000 0.00000 MINI CONSTR> 76.08637 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -21.64892 0.15060 0.59541 0.00043 MINI INTERN> 8.20074 50.61827 0.00000 42.42366 6.90610 MINI EXTERN> -123.70753 -82.21520 0.00000 0.00000 0.00000 MINI CONSTR> 76.12503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20825 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -21.83550 0.18658 0.20949 0.00019 MINI INTERN> 8.28823 50.46077 0.00000 42.38893 6.90979 MINI EXTERN> -123.85894 -82.18360 0.00000 0.00000 0.00000 MINI CONSTR> 76.15932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -21.91823 0.08274 0.67368 0.00046 MINI INTERN> 8.18303 50.52815 0.00000 42.39661 6.89011 MINI EXTERN> -123.91661 -82.19779 0.00000 0.00000 0.00000 MINI CONSTR> 76.19827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20822 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -22.11118 0.19294 0.21817 0.00020 MINI INTERN> 8.27926 50.36418 0.00000 42.35682 6.89555 MINI EXTERN> -124.06755 -82.16975 0.00000 0.00000 0.00000 MINI CONSTR> 76.23033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -22.16016 0.04899 0.78630 0.00050 MINI INTERN> 8.27700 50.38112 0.00000 42.35978 6.87858 MINI EXTERN> -124.13164 -82.18959 0.00000 0.00000 0.00000 MINI CONSTR> 76.26457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20821 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -22.36993 0.20977 0.23114 0.00022 MINI INTERN> 8.27336 50.27316 0.00000 42.32106 6.88235 MINI EXTERN> -124.25655 -82.16054 0.00000 0.00000 0.00000 MINI CONSTR> 76.29723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -22.48469 0.11475 0.19573 0.00022 MINI INTERN> 8.26098 50.23945 0.00000 42.30605 6.87566 MINI EXTERN> -124.33239 -82.16057 0.00000 0.00000 0.00000 MINI CONSTR> 76.32614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20818 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -22.60482 0.12014 0.19837 0.00023 MINI INTERN> 8.25667 50.19845 0.00000 42.28673 6.86964 MINI EXTERN> -124.41561 -82.15805 0.00000 0.00000 0.00000 MINI CONSTR> 76.35736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -22.72610 0.12128 0.18547 0.00024 MINI INTERN> 8.24583 50.16046 0.00000 42.26808 6.86280 MINI EXTERN> -124.49400 -82.15794 0.00000 0.00000 0.00000 MINI CONSTR> 76.38868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20813 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -22.85359 0.12749 0.32419 0.00025 MINI INTERN> 8.27295 50.09942 0.00000 42.23854 6.85832 MINI EXTERN> -124.59668 -82.15148 0.00000 0.00000 0.00000 MINI CONSTR> 76.42533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -22.96566 0.11206 0.27509 0.00026 MINI INTERN> 8.27092 50.05979 0.00000 42.22000 6.85211 MINI EXTERN> -124.66549 -82.15633 0.00000 0.00000 0.00000 MINI CONSTR> 76.45334 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20810 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -23.07341 0.10776 0.29713 0.00027 MINI INTERN> 8.26486 50.02607 0.00000 42.19782 6.84719 MINI EXTERN> -124.73683 -82.15520 0.00000 0.00000 0.00000 MINI CONSTR> 76.48267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -23.18210 0.10869 0.30937 0.00028 MINI INTERN> 8.27519 49.98107 0.00000 42.17603 6.84151 MINI EXTERN> -124.80733 -82.16034 0.00000 0.00000 0.00000 MINI CONSTR> 76.51176 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20806 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -23.27503 0.09293 0.40862 0.00029 MINI INTERN> 8.28678 49.94544 0.00000 42.15038 6.83839 MINI EXTERN> -124.87930 -82.15711 0.00000 0.00000 0.00000 MINI CONSTR> 76.54039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -23.37234 0.09731 0.48389 0.00030 MINI INTERN> 8.32052 49.89195 0.00000 42.12910 6.83211 MINI EXTERN> -124.94496 -82.16961 0.00000 0.00000 0.00000 MINI CONSTR> 76.56855 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20805 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -23.46359 0.09125 0.51263 0.00031 MINI INTERN> 8.33291 49.85487 0.00000 42.10619 6.82821 MINI EXTERN> -125.00697 -82.17354 0.00000 0.00000 0.00000 MINI CONSTR> 76.59473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -23.56307 0.09947 0.44998 0.00032 MINI INTERN> 8.31638 49.82939 0.00000 42.08262 6.82512 MINI EXTERN> -125.06543 -82.17186 0.00000 0.00000 0.00000 MINI CONSTR> 76.62071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20803 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -23.64853 0.08546 0.57325 0.00033 MINI INTERN> 8.26773 49.83370 0.00000 42.06178 6.81940 MINI EXTERN> -125.11248 -82.16857 0.00000 0.00000 0.00000 MINI CONSTR> 76.64991 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -23.74068 0.09215 0.53103 0.00034 MINI INTERN> 8.26739 49.80048 0.00000 42.04052 6.81554 MINI EXTERN> -125.16397 -82.17459 0.00000 0.00000 0.00000 MINI CONSTR> 76.67394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20802 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -23.83807 0.09739 0.48484 0.00036 MINI INTERN> 8.32509 49.73086 0.00000 42.01325 6.81264 MINI EXTERN> -125.23243 -82.18743 0.00000 0.00000 0.00000 MINI CONSTR> 76.69995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -23.95971 0.12164 0.16831 0.00015 MINI INTERN> 8.16467 49.76722 0.00000 42.01377 6.79795 MINI EXTERN> -125.22782 -82.20025 0.00000 0.00000 0.00000 MINI CONSTR> 76.72474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20800 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -24.00727 0.04756 0.56813 0.00038 MINI INTERN> 8.34872 49.66096 0.00000 41.96709 6.80386 MINI EXTERN> -125.33616 -82.20429 0.00000 0.00000 0.00000 MINI CONSTR> 76.75254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -24.07831 0.07104 0.69110 0.00040 MINI INTERN> 8.22926 49.71157 0.00000 41.95403 6.79630 MINI EXTERN> -125.35357 -82.19527 0.00000 0.00000 0.00000 MINI CONSTR> 76.77937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20799 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -24.21964 0.14134 0.19227 0.00017 MINI INTERN> 8.14527 49.68682 0.00000 41.94879 6.78399 MINI EXTERN> -125.36435 -82.22200 0.00000 0.00000 0.00000 MINI CONSTR> 76.80183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -24.24817 0.02853 0.62181 0.00043 MINI INTERN> 8.32981 49.59588 0.00000 41.89520 6.79477 MINI EXTERN> -125.47949 -82.21310 0.00000 0.00000 0.00000 MINI CONSTR> 76.82876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20796 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -24.38699 0.13881 0.22382 0.00019 MINI INTERN> 8.12720 49.63914 0.00000 41.90454 6.77505 MINI EXTERN> -125.44953 -82.23692 0.00000 0.00000 0.00000 MINI CONSTR> 76.85352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -24.45943 0.07245 0.15950 0.00019 MINI INTERN> 8.14211 49.60460 0.00000 41.88259 6.77317 MINI EXTERN> -125.49296 -82.24362 0.00000 0.00000 0.00000 MINI CONSTR> 76.87468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20796 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -24.54321 0.08378 0.15295 0.00020 MINI INTERN> 8.14166 49.57576 0.00000 41.85843 6.76947 MINI EXTERN> -125.53758 -82.25186 0.00000 0.00000 0.00000 MINI CONSTR> 76.90092 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -24.63156 0.08835 0.26454 0.00021 MINI INTERN> 8.12206 49.55663 0.00000 41.83618 6.76205 MINI EXTERN> -125.57404 -82.26590 0.00000 0.00000 0.00000 MINI CONSTR> 76.93146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20795 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -24.70918 0.07762 0.22853 0.00021 MINI INTERN> 8.11399 49.53420 0.00000 41.81301 6.75937 MINI EXTERN> -125.61480 -82.27074 0.00000 0.00000 0.00000 MINI CONSTR> 76.95580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -24.78282 0.07364 0.24591 0.00022 MINI INTERN> 8.10662 49.51241 0.00000 41.79272 6.75475 MINI EXTERN> -125.64813 -82.28158 0.00000 0.00000 0.00000 MINI CONSTR> 76.98038 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20793 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -24.86074 0.07792 0.24270 0.00023 MINI INTERN> 8.11735 49.47888 0.00000 41.76855 6.75131 MINI EXTERN> -125.68936 -82.29350 0.00000 0.00000 0.00000 MINI CONSTR> 77.00603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -24.92601 0.06528 0.33695 0.00024 MINI INTERN> 8.08696 49.47501 0.00000 41.75060 6.74555 MINI EXTERN> -125.71422 -82.30131 0.00000 0.00000 0.00000 MINI CONSTR> 77.03139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20791 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -24.99716 0.07115 0.39349 0.00025 MINI INTERN> 8.12420 49.42997 0.00000 41.72505 6.74242 MINI EXTERN> -125.75738 -82.31849 0.00000 0.00000 0.00000 MINI CONSTR> 77.05706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -25.06272 0.06556 0.41775 0.00026 MINI INTERN> 8.11323 49.41353 0.00000 41.70594 6.73798 MINI EXTERN> -125.78554 -82.32882 0.00000 0.00000 0.00000 MINI CONSTR> 77.08095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20791 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -25.13388 0.07115 0.36833 0.00027 MINI INTERN> 8.07317 49.41043 0.00000 41.68737 6.73393 MINI EXTERN> -125.81112 -82.33247 0.00000 0.00000 0.00000 MINI CONSTR> 77.10483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -25.20962 0.07575 0.40765 0.00028 MINI INTERN> 8.09713 49.37240 0.00000 41.65884 6.73102 MINI EXTERN> -125.85523 -82.34724 0.00000 0.00000 0.00000 MINI CONSTR> 77.13347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20792 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -25.27337 0.06374 0.45343 0.00029 MINI INTERN> 8.07437 49.36396 0.00000 41.63727 6.72740 MINI EXTERN> -125.88628 -82.34930 0.00000 0.00000 0.00000 MINI CONSTR> 77.15922 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -25.34094 0.06757 0.42463 0.00030 MINI INTERN> 8.08819 49.33195 0.00000 41.61687 6.72384 MINI EXTERN> -125.91531 -82.36877 0.00000 0.00000 0.00000 MINI CONSTR> 77.18229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20790 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -25.42833 0.08740 0.14553 0.00013 MINI INTERN> 8.12457 49.27802 0.00000 41.58365 6.72782 MINI EXTERN> -125.97645 -82.37138 0.00000 0.00000 0.00000 MINI CONSTR> 77.20544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -25.46332 0.03498 0.48090 0.00032 MINI INTERN> 8.06251 49.30470 0.00000 41.57450 6.71754 MINI EXTERN> -125.97479 -82.37931 0.00000 0.00000 0.00000 MINI CONSTR> 77.23154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20791 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -25.51737 0.05405 0.56153 0.00033 MINI INTERN> 8.13380 49.25041 0.00000 41.54954 6.71594 MINI EXTERN> -126.01272 -82.40899 0.00000 0.00000 0.00000 MINI CONSTR> 77.25465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -25.57692 0.05955 0.56657 0.00034 MINI INTERN> 8.11329 49.24052 0.00000 41.53212 6.71114 MINI EXTERN> -126.03295 -82.41981 0.00000 0.00000 0.00000 MINI CONSTR> 77.27876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20792 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -25.64164 0.06472 0.52288 0.00035 MINI INTERN> 8.05775 49.24595 0.00000 41.51754 6.70487 MINI EXTERN> -126.04589 -82.42559 0.00000 0.00000 0.00000 MINI CONSTR> 77.30374 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -25.74350 0.10187 0.17117 0.00015 MINI INTERN> 8.12033 49.17099 0.00000 41.47505 6.71282 MINI EXTERN> -126.12486 -82.42670 0.00000 0.00000 0.00000 MINI CONSTR> 77.32885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20792 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -25.80012 0.05662 0.13229 0.00016 MINI INTERN> 8.10645 49.15772 0.00000 41.45832 6.70886 MINI EXTERN> -126.14381 -82.43862 0.00000 0.00000 0.00000 MINI CONSTR> 77.35096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -25.85957 0.05945 0.13857 0.00016 MINI INTERN> 8.10755 49.13647 0.00000 41.43686 6.70611 MINI EXTERN> -126.17174 -82.45040 0.00000 0.00000 0.00000 MINI CONSTR> 77.37557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20789 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -25.91929 0.05972 0.22063 0.00017 MINI INTERN> 8.12940 49.10569 0.00000 41.41018 6.70482 MINI EXTERN> -126.20982 -82.46229 0.00000 0.00000 0.00000 MINI CONSTR> 77.40274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -25.97415 0.05486 0.13419 0.00018 MINI INTERN> 8.09815 49.10120 0.00000 41.39658 6.70019 MINI EXTERN> -126.22171 -82.47233 0.00000 0.00000 0.00000 MINI CONSTR> 77.42377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20789 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -26.03108 0.05693 0.25886 0.00018 MINI INTERN> 8.12609 49.06916 0.00000 41.36817 6.69955 MINI EXTERN> -126.26264 -82.48335 0.00000 0.00000 0.00000 MINI CONSTR> 77.45195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -26.08866 0.05757 0.20052 0.00019 MINI INTERN> 8.11983 49.05083 0.00000 41.35019 6.69601 MINI EXTERN> -126.28250 -82.49800 0.00000 0.00000 0.00000 MINI CONSTR> 77.47498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20789 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -26.14633 0.05767 0.21025 0.00020 MINI INTERN> 8.11051 49.03561 0.00000 41.32937 6.69291 MINI EXTERN> -126.30699 -82.50858 0.00000 0.00000 0.00000 MINI CONSTR> 77.50086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -26.19522 0.04889 0.28932 0.00020 MINI INTERN> 8.14082 49.00431 0.00000 41.30528 6.69180 MINI EXTERN> -126.33959 -82.52359 0.00000 0.00000 0.00000 MINI CONSTR> 77.52575 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20789 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -26.25458 0.05936 0.23861 0.00021 MINI INTERN> 8.10808 48.99910 0.00000 41.28834 6.68744 MINI EXTERN> -126.35548 -82.53276 0.00000 0.00000 0.00000 MINI CONSTR> 77.55071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -26.29917 0.04459 0.31620 0.00022 MINI INTERN> 8.13133 48.97309 0.00000 41.26529 6.68663 MINI EXTERN> -126.38639 -82.54382 0.00000 0.00000 0.00000 MINI CONSTR> 77.57470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20783 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -26.34864 0.04948 0.35358 0.00023 MINI INTERN> 8.15821 48.94261 0.00000 41.24325 6.68462 MINI EXTERN> -126.41334 -82.56340 0.00000 0.00000 0.00000 MINI CONSTR> 77.59941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -26.40008 0.05144 0.34596 0.00024 MINI INTERN> 8.13235 48.93739 0.00000 41.22531 6.68164 MINI EXTERN> -126.43247 -82.56795 0.00000 0.00000 0.00000 MINI CONSTR> 77.62364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20781 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -26.44988 0.04980 0.36135 0.00025 MINI INTERN> 8.15470 48.90860 0.00000 41.20551 6.67889 MINI EXTERN> -126.45415 -82.59107 0.00000 0.00000 0.00000 MINI CONSTR> 77.64763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -26.50078 0.05090 0.34829 0.00025 MINI INTERN> 8.15028 48.89253 0.00000 41.18363 6.67756 MINI EXTERN> -126.48139 -82.59614 0.00000 0.00000 0.00000 MINI CONSTR> 77.67275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20781 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -26.56630 0.06552 0.12310 0.00011 MINI INTERN> 8.05901 48.91179 0.00000 41.18032 6.66745 MINI EXTERN> -126.46578 -82.61488 0.00000 0.00000 0.00000 MINI CONSTR> 77.69580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -26.59493 0.02863 0.41279 0.00027 MINI INTERN> 8.14199 48.86447 0.00000 41.14536 6.67198 MINI EXTERN> -126.52215 -82.61964 0.00000 0.00000 0.00000 MINI CONSTR> 77.72307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20781 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -26.63701 0.04208 0.47838 0.00028 MINI INTERN> 8.15859 48.84376 0.00000 41.13008 6.66749 MINI EXTERN> -126.53233 -82.65099 0.00000 0.00000 0.00000 MINI CONSTR> 77.74640 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -26.68431 0.04730 0.47126 0.00029 MINI INTERN> 8.17794 48.81688 0.00000 41.10663 6.66718 MINI EXTERN> -126.56273 -82.66145 0.00000 0.00000 0.00000 MINI CONSTR> 77.77123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20781 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -26.73268 0.04837 0.45238 0.00030 MINI INTERN> 8.17456 48.80011 0.00000 41.08317 6.66689 MINI EXTERN> -126.59357 -82.66099 0.00000 0.00000 0.00000 MINI CONSTR> 77.79715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -26.80937 0.07669 0.14593 0.00013 MINI INTERN> 8.03996 48.83524 0.00000 41.08703 6.65327 MINI EXTERN> -126.56003 -82.68571 0.00000 0.00000 0.00000 MINI CONSTR> 77.82087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20779 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -26.82222 0.01285 0.48748 0.00033 MINI INTERN> 8.17002 48.77108 0.00000 41.04619 6.66166 MINI EXTERN> -126.63065 -82.68753 0.00000 0.00000 0.00000 MINI CONSTR> 77.84702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -26.90151 0.07929 0.16913 0.00014 MINI INTERN> 8.02834 48.80844 0.00000 41.05127 6.64748 MINI EXTERN> -126.59372 -82.71429 0.00000 0.00000 0.00000 MINI CONSTR> 77.87096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20778 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -26.94311 0.04160 0.12059 0.00015 MINI INTERN> 8.04040 48.78734 0.00000 41.03286 6.64672 MINI EXTERN> -126.61532 -82.72746 0.00000 0.00000 0.00000 MINI CONSTR> 77.89235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -26.99081 0.04770 0.19619 0.00015 MINI INTERN> 8.01706 48.78265 0.00000 41.01632 6.64170 MINI EXTERN> -126.62535 -82.74417 0.00000 0.00000 0.00000 MINI CONSTR> 77.92096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20777 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -27.03555 0.04473 0.16592 0.00016 MINI INTERN> 8.02607 48.76231 0.00000 40.99729 6.64020 MINI EXTERN> -126.64541 -82.76082 0.00000 0.00000 0.00000 MINI CONSTR> 77.94482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -27.07884 0.04329 0.17514 0.00016 MINI INTERN> 8.01561 48.75221 0.00000 40.98085 6.63708 MINI EXTERN> -126.65896 -82.77537 0.00000 0.00000 0.00000 MINI CONSTR> 77.96973 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20775 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -27.12599 0.04716 0.15709 0.00017 MINI INTERN> 8.02008 48.73287 0.00000 40.96009 6.63544 MINI EXTERN> -126.68061 -82.79013 0.00000 0.00000 0.00000 MINI CONSTR> 77.99626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -27.16954 0.04354 0.19789 0.00018 MINI INTERN> 8.01326 48.72156 0.00000 40.94322 6.63185 MINI EXTERN> -126.69271 -82.80952 0.00000 0.00000 0.00000 MINI CONSTR> 78.02280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20773 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -27.20839 0.03885 0.26548 0.00018 MINI INTERN> 7.99584 48.71719 0.00000 40.92766 6.62813 MINI EXTERN> -126.70311 -82.82290 0.00000 0.00000 0.00000 MINI CONSTR> 78.04881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -27.24935 0.04096 0.28559 0.00019 MINI INTERN> 8.00123 48.70114 0.00000 40.91060 6.62540 MINI EXTERN> -126.71647 -82.84511 0.00000 0.00000 0.00000 MINI CONSTR> 78.07386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20773 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -27.29039 0.04104 0.29080 0.00020 MINI INTERN> 7.98273 48.69574 0.00000 40.89508 6.62214 MINI EXTERN> -126.72765 -82.85775 0.00000 0.00000 0.00000 MINI CONSTR> 78.09930 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -27.33158 0.04119 0.32393 0.00020 MINI INTERN> 7.99797 48.67511 0.00000 40.87535 6.62031 MINI EXTERN> -126.74532 -82.88066 0.00000 0.00000 0.00000 MINI CONSTR> 78.12565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20770 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -27.37333 0.04175 0.29763 0.00021 MINI INTERN> 7.97857 48.66876 0.00000 40.85971 6.61760 MINI EXTERN> -126.75780 -82.89058 0.00000 0.00000 0.00000 MINI CONSTR> 78.15040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -27.41004 0.03671 0.36544 0.00022 MINI INTERN> 7.99543 48.65059 0.00000 40.84105 6.61546 MINI EXTERN> -126.77235 -82.91685 0.00000 0.00000 0.00000 MINI CONSTR> 78.17661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20770 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -27.45160 0.04155 0.32536 0.00023 MINI INTERN> 7.97614 48.64472 0.00000 40.82682 6.61239 MINI EXTERN> -126.78145 -82.93093 0.00000 0.00000 0.00000 MINI CONSTR> 78.20070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -27.50441 0.05281 0.11239 0.00010 MINI INTERN> 8.03537 48.59292 0.00000 40.79524 6.61804 MINI EXTERN> -126.83021 -82.94057 0.00000 0.00000 0.00000 MINI CONSTR> 78.22481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20768 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -27.52906 0.02465 0.35182 0.00024 MINI INTERN> 7.95717 48.62734 0.00000 40.79371 6.60721 MINI EXTERN> -126.80561 -82.96121 0.00000 0.00000 0.00000 MINI CONSTR> 78.25233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -27.58461 0.05555 0.11741 0.00011 MINI INTERN> 8.03386 48.56639 0.00000 40.75968 6.61398 MINI EXTERN> -126.85833 -82.97674 0.00000 0.00000 0.00000 MINI CONSTR> 78.27656 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20767 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -27.60182 0.01721 0.41392 0.00026 MINI INTERN> 7.98664 48.59110 0.00000 40.75713 6.60411 MINI EXTERN> -126.83505 -83.00833 0.00000 0.00000 0.00000 MINI CONSTR> 78.30258 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -27.63980 0.03798 0.42344 0.00027 MINI INTERN> 7.94445 48.59768 0.00000 40.74334 6.60013 MINI EXTERN> -126.84113 -83.01409 0.00000 0.00000 0.00000 MINI CONSTR> 78.32981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20765 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -27.67628 0.03648 0.44819 0.00028 MINI INTERN> 7.96613 48.57845 0.00000 40.72573 6.59810 MINI EXTERN> -126.85150 -83.04832 0.00000 0.00000 0.00000 MINI CONSTR> 78.35514 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 -27.67628 0.03648 0.44819 0.00014 STPD INTERN> 7.96613 48.57845 0.00000 40.72573 6.59810 STPD EXTERN> -126.85150 -83.04832 0.00000 0.00000 0.00000 STPD CONSTR> 78.35514 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 20765 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20765 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 -27.68213 0.00585 0.33294 0.00000 MINI INTERN> 8.09550 48.50489 0.00000 40.69791 6.61363 MINI EXTERN> -126.92149 -83.02399 0.00000 0.00000 0.00000 MINI CONSTR> 78.35142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -29.80994 2.12781 1.60526 0.31540 MINI INTERN> 8.45613 47.57600 0.00000 38.86750 6.48754 MINI EXTERN> -128.58937 -84.20704 0.00000 0.00000 0.00000 MINI CONSTR> 81.59931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -30.80002 0.99008 0.50192 0.04312 MINI INTERN> 7.81572 47.39004 0.00000 37.93714 6.58162 MINI EXTERN> -130.37880 -84.45230 0.00000 0.00000 0.00000 MINI CONSTR> 84.30657 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -31.10368 0.30366 0.33251 0.04331 MINI INTERN> 7.99127 46.84376 0.00000 37.76256 6.38005 MINI EXTERN> -129.43071 -85.57882 0.00000 0.00000 0.00000 MINI CONSTR> 84.92822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -31.32098 0.21730 0.36776 0.04008 MINI INTERN> 7.93690 46.91148 0.00000 37.57143 6.40475 MINI EXTERN> -129.12401 -86.23286 0.00000 0.00000 0.00000 MINI CONSTR> 85.21133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -31.51978 0.19880 0.28258 0.04263 MINI INTERN> 7.82111 47.19892 0.00000 37.39237 6.35759 MINI EXTERN> -129.33915 -86.40532 0.00000 0.00000 0.00000 MINI CONSTR> 85.45471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -31.70159 0.18181 0.25103 0.04200 MINI INTERN> 7.87783 47.18816 0.00000 37.13190 6.29652 MINI EXTERN> -129.20077 -86.64052 0.00000 0.00000 0.00000 MINI CONSTR> 85.64530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -31.80148 0.09989 0.21242 0.02251 MINI INTERN> 7.91130 47.13301 0.00000 37.01214 6.32664 MINI EXTERN> -129.25872 -86.60788 0.00000 0.00000 0.00000 MINI CONSTR> 85.68203 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -31.90518 0.10370 0.22798 0.02577 MINI INTERN> 7.81604 47.05322 0.00000 37.09908 6.24412 MINI EXTERN> -129.15536 -86.54300 0.00000 0.00000 0.00000 MINI CONSTR> 85.58072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -32.00906 0.10387 0.24344 0.03023 MINI INTERN> 7.89583 47.08722 0.00000 37.25632 6.24254 MINI EXTERN> -128.96090 -86.88533 0.00000 0.00000 0.00000 MINI CONSTR> 85.35526 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -32.10008 0.09103 0.20996 0.02618 MINI INTERN> 7.92256 46.96592 0.00000 37.52793 6.31293 MINI EXTERN> -128.80689 -87.13018 0.00000 0.00000 0.00000 MINI CONSTR> 85.10763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -32.17430 0.07422 0.18662 0.02887 MINI INTERN> 7.95188 47.18374 0.00000 37.81304 6.27706 MINI EXTERN> -129.14026 -87.13049 0.00000 0.00000 0.00000 MINI CONSTR> 84.87073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -32.25402 0.07971 0.21608 0.03475 MINI INTERN> 7.92317 47.17617 0.00000 38.16817 6.29685 MINI EXTERN> -129.05749 -87.28802 0.00000 0.00000 0.00000 MINI CONSTR> 84.52713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -32.35894 0.10492 0.24734 0.05288 MINI INTERN> 7.95186 47.05295 0.00000 38.63025 6.27357 MINI EXTERN> -128.70869 -87.55635 0.00000 0.00000 0.00000 MINI CONSTR> 83.99748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -32.53831 0.17937 0.45436 0.08298 MINI INTERN> 7.99329 47.08904 0.00000 39.16652 6.31819 MINI EXTERN> -128.08833 -88.17699 0.00000 0.00000 0.00000 MINI CONSTR> 83.15997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -32.71662 0.17831 0.52262 0.06972 MINI INTERN> 8.05507 47.74613 0.00000 39.09984 6.42198 MINI EXTERN> -127.70213 -88.81585 0.00000 0.00000 0.00000 MINI CONSTR> 82.47834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -32.79728 0.08066 0.31064 0.02966 MINI INTERN> 7.94004 47.90121 0.00000 38.92921 6.47787 MINI EXTERN> -127.45174 -88.77679 0.00000 0.00000 0.00000 MINI CONSTR> 82.18291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -32.84959 0.05231 0.30531 0.02027 MINI INTERN> 7.93545 47.76193 0.00000 38.90404 6.49507 MINI EXTERN> -127.41426 -88.56050 0.00000 0.00000 0.00000 MINI CONSTR> 82.02869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -32.89002 0.04043 0.23766 0.01785 MINI INTERN> 7.93364 47.82218 0.00000 38.93885 6.42732 MINI EXTERN> -127.62332 -88.29817 0.00000 0.00000 0.00000 MINI CONSTR> 81.90949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -32.92011 0.03009 0.24552 0.01531 MINI INTERN> 7.95479 47.92502 0.00000 38.93670 6.32795 MINI EXTERN> -127.74989 -88.14653 0.00000 0.00000 0.00000 MINI CONSTR> 81.83186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -32.95276 0.03265 0.26076 0.01600 MINI INTERN> 8.03143 47.84537 0.00000 38.89968 6.34052 MINI EXTERN> -127.89225 -87.91074 0.00000 0.00000 0.00000 MINI CONSTR> 81.73323 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 -32.95276 0.03265 0.26076 0.02000 CONJ INTERN> 8.03143 47.84537 0.00000 38.89968 6.34052 CONJ EXTERN> -127.89225 -87.91074 0.00000 0.00000 0.00000 CONJ CONSTR> 81.73323 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 ASP 14 N ) 0.60080 ( PROT ASP 14 H ) 0.48064 ( PROT ASP 14 CA ) 0.60080 ( PROT ASP 14 CB ) 0.48064 ( PROT ASP 14 CG ) 0.48064 ( PROT ASP 14 OD1 ) 0.48064 ( PROT ASP 14 OD2 ) 0.48064 ( PROT ASP 14 C ) 0.60080 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.63602 7.24166 -13.21130 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00421 0.00570 -0.00016 ROTATION MATRIX 1.000000 -0.000195 -0.000652 0.000195 1.000000 0.000816 0.000651 -0.000816 0.999999 AXIS OF ROTATION IS 0.768162 0.613391 -0.183515 ANGLE IS 0.06 TOTAL SQUARE DIFF IS 101.4599 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.585466 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 296 CENTER OF ATOMS BEFORE TRANSLATION 13.54477 7.26660 -13.42333 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.01655 -0.01105 -0.01702 ROTATION MATRIX 0.999632 0.018667 0.019676 -0.018226 0.999583 -0.022396 -0.020086 0.022029 0.999556 AXIS OF ROTATION IS -0.633633 -0.567121 0.526197 ANGLE IS 2.01 CENTER OF ROTATION 13.977661 6.705150-13.499769 SHIFT IS 0.007796 TOTAL SQUARE DIFF IS 4.8947 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.397358 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 " 0.3974" Parameter: A <- "0.5855 0.3974" 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 0.3974 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 " 81.73" Parameter: H <- "81.73" 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 -114.68599 81.73323 0.60801 ENER INTERN> 8.03143 47.84537 0.00000 38.89968 6.34052 ENER EXTERN> -127.89225 -87.91074 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 " -114.69" Parameter: B <- "-114.69" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -87.91" Parameter: C <- "-87.91" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -127.89" Parameter: C <- " -215.80" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -215.80" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 8.03" Parameter: D <- "8.03" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 47.85" Parameter: D <- " 55.88" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 38.90" Parameter: D <- " 94.78" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.34" Parameter: D <- " 101.12" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 101.12" 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= -114.69 GRMS= 0.61 ELEC= -87.91 VDW= -127.89 RDTITL> *EXTERNAL= -215.80 INTERNAL= 101.12 USER= 0.00 HARM= 81.73 RDTITL> *BOND= 8.03 ANGL= 47.85 DIHE= 38.90 IMPR= 6.34 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= -114.69 GRMS= 0.61 ELEC= -87.91 VDW= -127.89 RDTITL> *EXTERNAL= -215.80 INTERNAL= 101.12 USER= 0.00 HARM= 81.73 RDTITL> *BOND= 8.03 ANGL= 47.85 DIHE= 38.90 IMPR= 6.34 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= -114.69 GRMS= 0.61 ELEC= -87.91 VDW= -127.89 RDTITL> *EXTERNAL= -215.80 INTERNAL= 101.12 USER= 0.00 HARM= 81.73 RDTITL> *BOND= 8.03 ANGL= 47.85 DIHE= 38.90 IMPR= 6.34 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 8400 0.5855 0.3974 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20765 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20754 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 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 -58.73946 -55.94653 0.33456 0.02000 MINI INTERN> 8.03143 47.84537 0.00000 38.89968 6.34052 MINI EXTERN> -127.89225 -87.91074 0.00000 0.00000 0.00000 MINI CONSTR> 55.94653 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -53.95165 -4.78781 6.16171 0.00360 MINI INTERN> 13.00098 48.54387 0.00000 39.64098 6.55789 MINI EXTERN> -133.66473 -85.59917 0.00000 0.00000 0.00000 MINI CONSTR> 57.56853 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20738 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -60.04509 6.09344 0.31320 0.00065 MINI INTERN> 8.13013 47.59983 0.00000 39.55000 6.51782 MINI EXTERN> -133.34214 -86.11597 0.00000 0.00000 0.00000 MINI CONSTR> 57.61522 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -60.22593 0.18084 0.21962 0.00028 MINI INTERN> 8.09173 47.43802 0.00000 39.53461 6.46520 MINI EXTERN> -133.12733 -86.34421 0.00000 0.00000 0.00000 MINI CONSTR> 57.71604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20737 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -60.33562 0.10969 0.43261 0.00029 MINI INTERN> 8.10189 47.35791 0.00000 39.50635 6.44787 MINI EXTERN> -133.10741 -86.46376 0.00000 0.00000 0.00000 MINI CONSTR> 57.82153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -60.42723 0.09160 0.44272 0.00030 MINI INTERN> 8.08078 47.32082 0.00000 39.48036 6.44136 MINI EXTERN> -133.14418 -86.51287 0.00000 0.00000 0.00000 MINI CONSTR> 57.90650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20735 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -60.51403 0.08680 0.46974 0.00031 MINI INTERN> 8.05586 47.29330 0.00000 39.45397 6.43741 MINI EXTERN> -133.20346 -86.54519 0.00000 0.00000 0.00000 MINI CONSTR> 57.99409 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -60.60426 0.09024 0.45530 0.00032 MINI INTERN> 8.05327 47.25280 0.00000 39.42827 6.43374 MINI EXTERN> -133.27009 -86.58190 0.00000 0.00000 0.00000 MINI CONSTR> 58.07964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20732 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -60.71362 0.10936 0.16040 0.00014 MINI INTERN> 8.04803 47.18877 0.00000 39.40346 6.42984 MINI EXTERN> -133.35032 -86.59223 0.00000 0.00000 0.00000 MINI CONSTR> 58.15881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -60.76729 0.05367 0.49135 0.00035 MINI INTERN> 8.05217 47.17592 0.00000 39.37668 6.42769 MINI EXTERN> -133.43328 -86.61773 0.00000 0.00000 0.00000 MINI CONSTR> 58.25125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20730 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -60.88608 0.11879 0.16167 0.00015 MINI INTERN> 8.03996 47.11385 0.00000 39.34988 6.42442 MINI EXTERN> -133.52447 -86.62605 0.00000 0.00000 0.00000 MINI CONSTR> 58.33632 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -60.92877 0.04269 0.52680 0.00037 MINI INTERN> 8.03218 47.11648 0.00000 39.32327 6.42410 MINI EXTERN> -133.60344 -86.64759 0.00000 0.00000 0.00000 MINI CONSTR> 58.42624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20729 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -61.05308 0.12431 0.16606 0.00016 MINI INTERN> 8.03179 47.04160 0.00000 39.29482 6.42004 MINI EXTERN> -133.70381 -86.64992 0.00000 0.00000 0.00000 MINI CONSTR> 58.51240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -61.08406 0.03099 0.56775 0.00040 MINI INTERN> 8.05744 47.02438 0.00000 39.26910 6.41728 MINI EXTERN> -133.78783 -86.66279 0.00000 0.00000 0.00000 MINI CONSTR> 58.59836 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20729 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -61.21330 0.12924 0.18956 0.00017 MINI INTERN> 8.03022 46.96685 0.00000 39.23834 6.41563 MINI EXTERN> -133.88229 -86.66719 0.00000 0.00000 0.00000 MINI CONSTR> 58.68514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -61.28141 0.06811 0.14790 0.00018 MINI INTERN> 8.01841 46.94392 0.00000 39.21491 6.41422 MINI EXTERN> -133.95152 -86.67727 0.00000 0.00000 0.00000 MINI CONSTR> 58.75592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20725 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -61.35647 0.07506 0.23721 0.00019 MINI INTERN> 8.02779 46.90250 0.00000 39.18410 6.41196 MINI EXTERN> -134.04223 -86.68422 0.00000 0.00000 0.00000 MINI CONSTR> 58.84362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -61.42363 0.06716 0.13959 0.00019 MINI INTERN> 8.00921 46.88309 0.00000 39.16151 6.41048 MINI EXTERN> -134.10595 -86.69175 0.00000 0.00000 0.00000 MINI CONSTR> 58.90978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20723 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -61.50198 0.07835 0.26903 0.00020 MINI INTERN> 8.03341 46.82944 0.00000 39.12654 6.40755 MINI EXTERN> -134.20395 -86.70000 0.00000 0.00000 0.00000 MINI CONSTR> 59.00504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -61.57089 0.06891 0.22447 0.00021 MINI INTERN> 8.00877 46.81461 0.00000 39.10037 6.40646 MINI EXTERN> -134.27126 -86.70640 0.00000 0.00000 0.00000 MINI CONSTR> 59.07657 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20722 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -61.63064 0.05975 0.30927 0.00022 MINI INTERN> 8.03121 46.77274 0.00000 39.07245 6.40396 MINI EXTERN> -134.34444 -86.71710 0.00000 0.00000 0.00000 MINI CONSTR> 59.15055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -61.69316 0.06252 0.34227 0.00022 MINI INTERN> 8.00708 46.76105 0.00000 39.04461 6.40312 MINI EXTERN> -134.41240 -86.71961 0.00000 0.00000 0.00000 MINI CONSTR> 59.22300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20722 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -61.75489 0.06173 0.34243 0.00023 MINI INTERN> 8.01183 46.72969 0.00000 39.01774 6.40115 MINI EXTERN> -134.47798 -86.72963 0.00000 0.00000 0.00000 MINI CONSTR> 59.29231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -61.81509 0.06021 0.37628 0.00024 MINI INTERN> 8.03236 46.68850 0.00000 38.99023 6.39844 MINI EXTERN> -134.54331 -86.74398 0.00000 0.00000 0.00000 MINI CONSTR> 59.36266 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20722 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -61.87483 0.05974 0.37377 0.00025 MINI INTERN> 8.02148 46.66889 0.00000 38.96307 6.39712 MINI EXTERN> -134.60522 -86.75035 0.00000 0.00000 0.00000 MINI CONSTR> 59.43016 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -61.93348 0.05864 0.41229 0.00026 MINI INTERN> 7.99960 46.65784 0.00000 38.93409 6.39620 MINI EXTERN> -134.66837 -86.75355 0.00000 0.00000 0.00000 MINI CONSTR> 59.50072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20723 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -61.99401 0.06053 0.37838 0.00027 MINI INTERN> 8.01549 46.61810 0.00000 38.90809 6.39354 MINI EXTERN> -134.72536 -86.76826 0.00000 0.00000 0.00000 MINI CONSTR> 59.56440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -62.07028 0.07628 0.13273 0.00012 MINI INTERN> 7.97136 46.60560 0.00000 38.88279 6.39189 MINI EXTERN> -134.77315 -86.77549 0.00000 0.00000 0.00000 MINI CONSTR> 59.62673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20720 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -62.10795 0.03766 0.40519 0.00029 MINI INTERN> 8.00647 46.57277 0.00000 38.85169 6.39029 MINI EXTERN> -134.84262 -86.78432 0.00000 0.00000 0.00000 MINI CONSTR> 59.69777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -62.17320 0.06526 0.41454 0.00030 MINI INTERN> 8.00630 46.54281 0.00000 38.81876 6.38817 MINI EXTERN> -134.90853 -86.79420 0.00000 0.00000 0.00000 MINI CONSTR> 59.77348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20722 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -62.25807 0.08487 0.12964 0.00013 MINI INTERN> 7.96241 46.52424 0.00000 38.79116 6.38582 MINI EXTERN> -134.95640 -86.80541 0.00000 0.00000 0.00000 MINI CONSTR> 59.84010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -62.28643 0.02836 0.45892 0.00032 MINI INTERN> 7.99382 46.50346 0.00000 38.75808 6.38504 MINI EXTERN> -135.02365 -86.81333 0.00000 0.00000 0.00000 MINI CONSTR> 59.91015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20722 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -62.37350 0.08707 0.15105 0.00014 MINI INTERN> 7.95662 46.47455 0.00000 38.73216 6.38182 MINI EXTERN> -135.06693 -86.82560 0.00000 0.00000 0.00000 MINI CONSTR> 59.97389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -62.38910 0.01560 0.51658 0.00034 MINI INTERN> 7.97324 46.47634 0.00000 38.70061 6.38291 MINI EXTERN> -135.12688 -86.83235 0.00000 0.00000 0.00000 MINI CONSTR> 60.03702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20722 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -62.47820 0.08910 0.17566 0.00015 MINI INTERN> 7.94819 46.43250 0.00000 38.67666 6.37831 MINI EXTERN> -135.16614 -86.84447 0.00000 0.00000 0.00000 MINI CONSTR> 60.09676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -62.52566 0.04746 0.12741 0.00015 MINI INTERN> 7.95298 46.40580 0.00000 38.65268 6.37643 MINI EXTERN> -135.21006 -86.85261 0.00000 0.00000 0.00000 MINI CONSTR> 60.14913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20719 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -62.57866 0.05300 0.20601 0.00016 MINI INTERN> 7.94548 46.38759 0.00000 38.62191 6.37449 MINI EXTERN> -135.26090 -86.86365 0.00000 0.00000 0.00000 MINI CONSTR> 60.21642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -62.62656 0.04790 0.12329 0.00017 MINI INTERN> 7.94919 46.36143 0.00000 38.59820 6.37278 MINI EXTERN> -135.30361 -86.87174 0.00000 0.00000 0.00000 MINI CONSTR> 60.26720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20718 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -62.67600 0.04943 0.24628 0.00017 MINI INTERN> 7.95639 46.33223 0.00000 38.56776 6.36991 MINI EXTERN> -135.35336 -86.88328 0.00000 0.00000 0.00000 MINI CONSTR> 60.33436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -62.72582 0.04983 0.18560 0.00018 MINI INTERN> 7.94311 46.31967 0.00000 38.54168 6.36888 MINI EXTERN> -135.39557 -86.89210 0.00000 0.00000 0.00000 MINI CONSTR> 60.38851 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20713 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -62.77721 0.05139 0.18356 0.00019 MINI INTERN> 7.93329 46.30422 0.00000 38.51254 6.36744 MINI EXTERN> -135.44188 -86.90232 0.00000 0.00000 0.00000 MINI CONSTR> 60.44949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -62.81956 0.04235 0.27550 0.00019 MINI INTERN> 7.95095 46.26967 0.00000 38.48550 6.36432 MINI EXTERN> -135.48555 -86.91299 0.00000 0.00000 0.00000 MINI CONSTR> 60.50854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20712 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -62.86393 0.04437 0.31216 0.00020 MINI INTERN> 7.92064 46.27729 0.00000 38.45691 6.36445 MINI EXTERN> -135.52654 -86.92218 0.00000 0.00000 0.00000 MINI CONSTR> 60.56550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -62.90794 0.04400 0.31507 0.00021 MINI INTERN> 7.92567 46.25160 0.00000 38.43128 6.36217 MINI EXTERN> -135.56659 -86.93169 0.00000 0.00000 0.00000 MINI CONSTR> 60.61962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20712 ATOM PAIRS WERE FOUND FOR ATOM LIST 729 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -62.95216 0.04422 0.32076 0.00021 MINI INTERN> 7.94664 46.21167 0.00000 38.40593 6.35890 MINI EXTERN> -135.60778 -86.94187 0.00000 0.00000 0.00000 MINI CONSTR> 60.67436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -62.99561 0.04345 0.35545 0.00022 MINI INTERN> 7.91866 46.21799 0.00000 38.37709 6.35889 MINI EXTERN> -135.64775 -86.95167 0.00000 0.00000 0.00000 MINI CONSTR> 60.73117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20713 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -63.04052 0.04491 0.32394 0.00023 MINI INTERN> 7.94489 46.17129 0.00000 38.35349 6.35522 MINI EXTERN> -135.68672 -86.96131 0.00000 0.00000 0.00000 MINI CONSTR> 60.78264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -63.08288 0.04236 0.37397 0.00024 MINI INTERN> 7.90221 46.19347 0.00000 38.32382 6.35659 MINI EXTERN> -135.72611 -86.97158 0.00000 0.00000 0.00000 MINI CONSTR> 60.83872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20710 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -63.13841 0.05553 0.11677 0.00010 MINI INTERN> 7.92687 46.14043 0.00000 38.30258 6.35342 MINI EXTERN> -135.76552 -86.98053 0.00000 0.00000 0.00000 MINI CONSTR> 60.88434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -63.16218 0.02377 0.38210 0.00026 MINI INTERN> 7.91216 46.14577 0.00000 38.27476 6.35201 MINI EXTERN> -135.79724 -86.99001 0.00000 0.00000 0.00000 MINI CONSTR> 60.94037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20707 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -63.19715 0.03496 0.45570 0.00027 MINI INTERN> 7.98765 46.06440 0.00000 38.25274 6.34628 MINI EXTERN> -135.83944 -87.00046 0.00000 0.00000 0.00000 MINI CONSTR> 60.99166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -63.23495 0.03781 0.47056 0.00028 MINI INTERN> 7.98786 46.04673 0.00000 38.22793 6.34448 MINI EXTERN> -135.87406 -87.00991 0.00000 0.00000 0.00000 MINI CONSTR> 61.04201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20705 ATOM PAIRS WERE FOUND FOR ATOM LIST 728 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -63.30246 0.06751 0.12917 0.00012 MINI INTERN> 7.92155 46.06765 0.00000 38.20122 6.34656 MINI EXTERN> -135.91018 -87.01936 0.00000 0.00000 0.00000 MINI CONSTR> 61.09010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -63.33973 0.03727 0.11093 0.00012 MINI INTERN> 7.91505 46.05484 0.00000 38.17820 6.34510 MINI EXTERN> -135.94115 -87.02809 0.00000 0.00000 0.00000 MINI CONSTR> 61.13632 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20704 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -63.37877 0.03904 0.11217 0.00013 MINI INTERN> 7.91485 46.03640 0.00000 38.15356 6.34335 MINI EXTERN> -135.97531 -87.03764 0.00000 0.00000 0.00000 MINI CONSTR> 61.18602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -63.41917 0.04040 0.10644 0.00013 MINI INTERN> 7.91434 46.01713 0.00000 38.12809 6.34144 MINI EXTERN> -136.01002 -87.04751 0.00000 0.00000 0.00000 MINI CONSTR> 61.23736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20703 ATOM PAIRS WERE FOUND FOR ATOM LIST 727 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -63.45962 0.04045 0.11413 0.00014 MINI INTERN> 7.91186 46.00043 0.00000 38.10187 6.33979 MINI EXTERN> -136.04559 -87.05768 0.00000 0.00000 0.00000 MINI CONSTR> 61.28971 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -63.49914 0.03952 0.10650 0.00014 MINI INTERN> 7.90950 45.98309 0.00000 38.07656 6.33799 MINI EXTERN> -136.07923 -87.06744 0.00000 0.00000 0.00000 MINI CONSTR> 61.34037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20701 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -63.54116 0.04202 0.19388 0.00015 MINI INTERN> 7.91468 45.96247 0.00000 38.04605 6.33629 MINI EXTERN> -136.12167 -87.07974 0.00000 0.00000 0.00000 MINI CONSTR> 61.40077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -63.58208 0.04091 0.13407 0.00015 MINI INTERN> 7.90451 45.94825 0.00000 38.02156 6.33448 MINI EXTERN> -136.15244 -87.08826 0.00000 0.00000 0.00000 MINI CONSTR> 61.44983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20700 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -63.61941 0.03733 0.17089 0.00016 MINI INTERN> 7.91084 45.92715 0.00000 37.99562 6.33261 MINI EXTERN> -136.18737 -87.09961 0.00000 0.00000 0.00000 MINI CONSTR> 61.50135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -63.65649 0.03708 0.18363 0.00016 MINI INTERN> 7.90210 45.91618 0.00000 37.97037 6.33124 MINI EXTERN> -136.21973 -87.10793 0.00000 0.00000 0.00000 MINI CONSTR> 61.55129 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20700 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -63.68826 0.03177 0.24126 0.00017 MINI INTERN> 7.91596 45.89291 0.00000 37.94636 6.32931 MINI EXTERN> -136.25222 -87.11953 0.00000 0.00000 0.00000 MINI CONSTR> 61.59896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -63.72206 0.03381 0.28814 0.00018 MINI INTERN> 7.89377 45.89398 0.00000 37.92104 6.32861 MINI EXTERN> -136.28303 -87.12498 0.00000 0.00000 0.00000 MINI CONSTR> 61.64854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20699 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -63.75373 0.03167 0.30660 0.00018 MINI INTERN> 7.89165 45.88088 0.00000 37.89849 6.32714 MINI EXTERN> -136.31161 -87.13346 0.00000 0.00000 0.00000 MINI CONSTR> 61.69319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -63.78842 0.03469 0.27189 0.00019 MINI INTERN> 7.89894 45.85830 0.00000 37.87664 6.32516 MINI EXTERN> -136.34012 -87.14406 0.00000 0.00000 0.00000 MINI CONSTR> 61.73672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20696 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -63.82035 0.03193 0.30902 0.00020 MINI INTERN> 7.93090 45.81879 0.00000 37.85410 6.32174 MINI EXTERN> -136.36922 -87.15916 0.00000 0.00000 0.00000 MINI CONSTR> 61.78250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -63.85287 0.03252 0.30669 0.00020 MINI INTERN> 7.92725 45.80622 0.00000 37.83147 6.32036 MINI EXTERN> -136.39760 -87.16765 0.00000 0.00000 0.00000 MINI CONSTR> 61.82707 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20696 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -63.88568 0.03281 0.29554 0.00021 MINI INTERN> 7.91776 45.79802 0.00000 37.80857 6.31932 MINI EXTERN> -136.42612 -87.17514 0.00000 0.00000 0.00000 MINI CONSTR> 61.87190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -63.92819 0.04251 0.09984 0.00009 MINI INTERN> 7.88869 45.79063 0.00000 37.78824 6.31726 MINI EXTERN> -136.44600 -87.18000 0.00000 0.00000 0.00000 MINI CONSTR> 61.91298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20692 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -63.94544 0.01725 0.34922 0.00023 MINI INTERN> 7.92867 45.76198 0.00000 37.76367 6.31563 MINI EXTERN> -136.48179 -87.19455 0.00000 0.00000 0.00000 MINI CONSTR> 61.96095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -63.97338 0.02794 0.39381 0.00024 MINI INTERN> 7.87757 45.78701 0.00000 37.74034 6.31636 MINI EXTERN> -136.50668 -87.19360 0.00000 0.00000 0.00000 MINI CONSTR> 62.00563 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20692 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -64.00571 0.03233 0.37029 0.00025 MINI INTERN> 7.89117 45.76197 0.00000 37.71807 6.31436 MINI EXTERN> -136.53586 -87.20520 0.00000 0.00000 0.00000 MINI CONSTR> 62.04977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -64.05583 0.05012 0.11625 0.00011 MINI INTERN> 7.88460 45.73053 0.00000 37.69779 6.31045 MINI EXTERN> -136.55530 -87.21569 0.00000 0.00000 0.00000 MINI CONSTR> 62.09179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20692 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -64.08461 0.02878 0.09572 0.00011 MINI INTERN> 7.88074 45.71960 0.00000 37.67758 6.30925 MINI EXTERN> -136.57999 -87.22323 0.00000 0.00000 0.00000 MINI CONSTR> 62.13143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -64.11443 0.02982 0.09797 0.00011 MINI INTERN> 7.87936 45.70573 0.00000 37.65609 6.30763 MINI EXTERN> -136.60550 -87.23163 0.00000 0.00000 0.00000 MINI CONSTR> 62.17389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20690 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -64.14370 0.02928 0.10016 0.00012 MINI INTERN> 7.87824 45.69189 0.00000 37.63488 6.30602 MINI EXTERN> -136.63059 -87.23995 0.00000 0.00000 0.00000 MINI CONSTR> 62.21580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -64.17455 0.03085 0.15659 0.00012 MINI INTERN> 7.88281 45.67244 0.00000 37.61094 6.30367 MINI EXTERN> -136.65792 -87.25003 0.00000 0.00000 0.00000 MINI CONSTR> 62.26353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20689 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -64.20376 0.02921 0.13314 0.00013 MINI INTERN> 7.87371 45.66485 0.00000 37.59020 6.30262 MINI EXTERN> -136.68236 -87.25689 0.00000 0.00000 0.00000 MINI CONSTR> 62.30411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -64.23232 0.02856 0.14023 0.00013 MINI INTERN> 7.87727 45.64758 0.00000 37.56907 6.30072 MINI EXTERN> -136.70710 -87.26593 0.00000 0.00000 0.00000 MINI CONSTR> 62.34606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20689 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -64.26280 0.03048 0.13183 0.00014 MINI INTERN> 7.87040 45.63765 0.00000 37.54671 6.29938 MINI EXTERN> -136.73310 -87.27379 0.00000 0.00000 0.00000 MINI CONSTR> 62.38995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -64.29039 0.02759 0.16056 0.00014 MINI INTERN> 7.87220 45.62190 0.00000 37.52526 6.29746 MINI EXTERN> -136.75746 -87.28233 0.00000 0.00000 0.00000 MINI CONSTR> 62.43260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20688 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -64.31940 0.02901 0.16186 0.00015 MINI INTERN> 7.87831 45.60243 0.00000 37.50379 6.29545 MINI EXTERN> -136.78278 -87.29191 0.00000 0.00000 0.00000 MINI CONSTR> 62.47532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -64.34381 0.02441 0.21329 0.00015 MINI INTERN> 7.87048 45.59588 0.00000 37.48282 6.29407 MINI EXTERN> -136.80537 -87.29831 0.00000 0.00000 0.00000 MINI CONSTR> 62.51663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20686 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -64.37081 0.02699 0.25356 0.00016 MINI INTERN> 7.89167 45.56616 0.00000 37.46127 6.29132 MINI EXTERN> -136.83149 -87.30995 0.00000 0.00000 0.00000 MINI CONSTR> 62.56021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -64.39544 0.02463 0.27002 0.00016 MINI INTERN> 7.89250 45.55298 0.00000 37.44161 6.28970 MINI EXTERN> -136.85380 -87.31762 0.00000 0.00000 0.00000 MINI CONSTR> 62.59919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20684 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -64.42258 0.02714 0.23702 0.00017 MINI INTERN> 7.87631 45.55073 0.00000 37.42203 6.28882 MINI EXTERN> -136.87488 -87.32294 0.00000 0.00000 0.00000 MINI CONSTR> 62.63735 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -64.44609 0.02351 0.30378 0.00018 MINI INTERN> 7.85316 45.55783 0.00000 37.39968 6.28852 MINI EXTERN> -136.89882 -87.32703 0.00000 0.00000 0.00000 MINI CONSTR> 62.68057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20683 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -64.47142 0.02533 0.28329 0.00018 MINI INTERN> 7.85236 45.54495 0.00000 37.38162 6.28708 MINI EXTERN> -136.91958 -87.33420 0.00000 0.00000 0.00000 MINI CONSTR> 62.71635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -64.49884 0.02742 0.25377 0.00019 MINI INTERN> 7.86883 45.51661 0.00000 37.36214 6.28430 MINI EXTERN> -136.94188 -87.34477 0.00000 0.00000 0.00000 MINI CONSTR> 62.75593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20682 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -64.53391 0.03507 0.08551 0.00008 MINI INTERN> 7.86243 45.50498 0.00000 37.34196 6.28379 MINI EXTERN> -136.96864 -87.35336 0.00000 0.00000 0.00000 MINI CONSTR> 62.79493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -64.54902 0.01511 0.29126 0.00020 MINI INTERN> 7.86835 45.48936 0.00000 37.32084 6.28079 MINI EXTERN> -136.98800 -87.35904 0.00000 0.00000 0.00000 MINI CONSTR> 62.83867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20681 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -64.57128 0.02227 0.34995 0.00021 MINI INTERN> 7.87235 45.48472 0.00000 37.29902 6.28005 MINI EXTERN> -137.01138 -87.37472 0.00000 0.00000 0.00000 MINI CONSTR> 62.87868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -64.59644 0.02515 0.33048 0.00022 MINI INTERN> 7.87090 45.46778 0.00000 37.28004 6.27781 MINI EXTERN> -137.03183 -87.37908 0.00000 0.00000 0.00000 MINI CONSTR> 62.91794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20681 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -64.63575 0.03932 0.10353 0.00009 MINI INTERN> 7.85859 45.45442 0.00000 37.26138 6.27751 MINI EXTERN> -137.05888 -87.38372 0.00000 0.00000 0.00000 MINI CONSTR> 62.95495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -64.65806 0.02230 0.08467 0.00010 MINI INTERN> 7.85650 45.44380 0.00000 37.24411 6.27601 MINI EXTERN> -137.07719 -87.39056 0.00000 0.00000 0.00000 MINI CONSTR> 62.98927 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20680 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -64.68118 0.02312 0.08692 0.00010 MINI INTERN> 7.85554 45.43224 0.00000 37.22556 6.27454 MINI EXTERN> -137.09769 -87.39756 0.00000 0.00000 0.00000 MINI CONSTR> 63.02619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -64.70546 0.02428 0.13112 0.00011 MINI INTERN> 7.85685 45.41902 0.00000 37.20471 6.27307 MINI EXTERN> -137.12185 -87.40498 0.00000 0.00000 0.00000 MINI CONSTR> 63.06772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20677 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -64.72703 0.02157 0.08536 0.00011 MINI INTERN> 7.85306 45.40935 0.00000 37.18870 6.27154 MINI EXTERN> -137.13798 -87.41136 0.00000 0.00000 0.00000 MINI CONSTR> 63.09966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -64.75014 0.02311 0.15350 0.00011 MINI INTERN> 7.85562 45.39737 0.00000 37.16748 6.27023 MINI EXTERN> -137.16257 -87.41979 0.00000 0.00000 0.00000 MINI CONSTR> 63.14153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20676 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -64.77343 0.02329 0.12385 0.00012 MINI INTERN> 7.85325 45.38363 0.00000 37.15009 6.26845 MINI EXTERN> -137.18133 -87.42465 0.00000 0.00000 0.00000 MINI CONSTR> 63.17712 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 -64.77343 0.02329 0.12385 0.00014 STPD INTERN> 7.85325 45.38363 0.00000 37.15009 6.26845 STPD EXTERN> -137.18133 -87.42465 0.00000 0.00000 0.00000 STPD CONSTR> 63.17712 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 20676 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20676 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 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 -64.77343 0.02329 0.12385 0.00000 MINI INTERN> 7.85325 45.38363 0.00000 37.15009 6.26845 MINI EXTERN> -137.18133 -87.42465 0.00000 0.00000 0.00000 MINI CONSTR> 63.17712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -66.68484 1.91141 0.13199 0.05484 MINI INTERN> 7.76823 43.68745 0.00000 34.37860 6.07710 MINI EXTERN> -140.79230 -88.28161 0.00000 0.00000 0.00000 MINI CONSTR> 70.47769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -66.70862 0.02378 0.10020 0.00800 MINI INTERN> 7.69925 43.74106 0.00000 34.31821 6.03627 MINI EXTERN> -140.53177 -88.47654 0.00000 0.00000 0.00000 MINI CONSTR> 70.50490 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -66.75983 0.05121 0.14626 0.02426 MINI INTERN> 7.52155 43.49453 0.00000 34.11855 5.99382 MINI EXTERN> -139.61490 -88.60881 0.00000 0.00000 0.00000 MINI CONSTR> 70.33543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -66.82910 0.06927 0.14204 0.03438 MINI INTERN> 7.64405 43.52631 0.00000 34.07001 5.97372 MINI EXTERN> -139.52044 -88.63173 0.00000 0.00000 0.00000 MINI CONSTR> 70.10898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -66.87771 0.04861 0.11535 0.01790 MINI INTERN> 7.67129 43.50500 0.00000 34.07548 5.93611 MINI EXTERN> -139.60871 -88.44986 0.00000 0.00000 0.00000 MINI CONSTR> 69.99298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -66.90101 0.02329 0.07840 0.01432 MINI INTERN> 7.67096 43.43077 0.00000 34.12619 5.94344 MINI EXTERN> -139.74342 -88.29656 0.00000 0.00000 0.00000 MINI CONSTR> 69.96760 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -66.91711 0.01611 0.07472 0.01097 MINI INTERN> 7.69256 43.47384 0.00000 34.12979 5.93801 MINI EXTERN> -139.85692 -88.26824 0.00000 0.00000 0.00000 MINI CONSTR> 69.97385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -66.93011 0.01300 0.07306 0.00903 MINI INTERN> 7.67360 43.48527 0.00000 34.11325 5.95657 MINI EXTERN> -139.98588 -88.16944 0.00000 0.00000 0.00000 MINI CONSTR> 69.99652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -66.94126 0.01115 0.05668 0.01088 MINI INTERN> 7.68862 43.44777 0.00000 34.10609 5.94039 MINI EXTERN> -140.00840 -88.14097 0.00000 0.00000 0.00000 MINI CONSTR> 70.02523 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -66.94900 0.00774 0.05156 0.00797 MINI INTERN> 7.66659 43.42280 0.00000 34.08898 5.95088 MINI EXTERN> -140.07267 -88.04456 0.00000 0.00000 0.00000 MINI CONSTR> 70.03897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -66.95552 0.00653 0.04254 0.00723 MINI INTERN> 7.66862 43.35796 0.00000 34.11892 5.94363 MINI EXTERN> -139.99006 -88.08929 0.00000 0.00000 0.00000 MINI CONSTR> 70.03469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -66.95955 0.00403 0.03957 0.00612 MINI INTERN> 7.66931 43.35205 0.00000 34.12013 5.94332 MINI EXTERN> -139.94810 -88.12045 0.00000 0.00000 0.00000 MINI CONSTR> 70.02419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -66.96329 0.00374 0.03533 0.00637 MINI INTERN> 7.66446 43.40602 0.00000 34.10033 5.95277 MINI EXTERN> -140.03418 -88.05679 0.00000 0.00000 0.00000 MINI CONSTR> 70.00409 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -66.96621 0.00291 0.03115 0.00522 MINI INTERN> 7.67121 43.38505 0.00000 34.09345 5.95802 MINI EXTERN> -139.97464 -88.06874 0.00000 0.00000 0.00000 MINI CONSTR> 69.96945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -66.96814 0.00193 0.02492 0.00390 MINI INTERN> 7.68222 43.37804 0.00000 34.08781 5.96061 MINI EXTERN> -139.90652 -88.10512 0.00000 0.00000 0.00000 MINI CONSTR> 69.93481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -66.96999 0.00185 0.02523 0.00441 MINI INTERN> 7.68270 43.36818 0.00000 34.09762 5.96225 MINI EXTERN> -139.87006 -88.11090 0.00000 0.00000 0.00000 MINI CONSTR> 69.90023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -66.97166 0.00167 0.02316 0.00425 MINI INTERN> 7.67774 43.37561 0.00000 34.09829 5.97405 MINI EXTERN> -139.85248 -88.12269 0.00000 0.00000 0.00000 MINI CONSTR> 69.87781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -66.97290 0.00124 0.01971 0.00429 MINI INTERN> 7.68291 43.39372 0.00000 34.11334 5.97102 MINI EXTERN> -139.87580 -88.12710 0.00000 0.00000 0.00000 MINI CONSTR> 69.86902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -66.97402 0.00112 0.01835 0.00314 MINI INTERN> 7.67995 43.38958 0.00000 34.12852 5.97261 MINI EXTERN> -139.89694 -88.10967 0.00000 0.00000 0.00000 MINI CONSTR> 69.86192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -66.97478 0.00077 0.01591 0.00252 MINI INTERN> 7.68471 43.38963 0.00000 34.12594 5.97322 MINI EXTERN> -139.89289 -88.11138 0.00000 0.00000 0.00000 MINI CONSTR> 69.85598 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 -66.97478 0.00077 0.01591 0.02000 CONJ INTERN> 7.68471 43.38963 0.00000 34.12594 5.97322 CONJ EXTERN> -139.89289 -88.11138 0.00000 0.00000 0.00000 CONJ CONSTR> 69.85598 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 ASP 14 N ) 0.39052 ( PROT ASP 14 H ) 0.31241 ( PROT ASP 14 CA ) 0.39052 ( PROT ASP 14 CB ) 0.31241 ( PROT ASP 14 CG ) 0.31241 ( PROT ASP 14 OD1 ) 0.31241 ( PROT ASP 14 OD2 ) 0.31241 ( PROT ASP 14 C ) 0.39052 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.63554 7.24155 -13.20913 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00469 0.00582 -0.00233 ROTATION MATRIX 1.000000 0.000142 -0.000187 -0.000142 1.000000 0.000293 0.000187 -0.000293 1.000000 AXIS OF ROTATION IS 0.780900 0.496616 0.378903 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 133.5249 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.671638 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.6716" Parameter: A <- "0.6716" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.55454 7.27936 -13.43418 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.02632 -0.02382 -0.00618 ROTATION MATRIX 0.999677 0.017347 0.018573 -0.016946 0.999625 -0.021532 -0.018939 0.021211 0.999596 AXIS OF ROTATION IS -0.643636 -0.564868 0.516388 ANGLE IS 1.90 CENTER OF ROTATION 14.016730 6.738573-13.423323 SHIFT IS 0.027202 TOTAL SQUARE DIFF IS 7.7186 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.498986 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.6716" RDCMND substituted energy or value "?RMS" to " 0.4990" Parameter: A <- "0.6716 0.4990" 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 0.6716 0.4990 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 " 69.86" Parameter: H <- "69.86" 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 -136.83076 69.85598 0.40853 ENER INTERN> 7.68471 43.38963 0.00000 34.12594 5.97322 ENER EXTERN> -139.89289 -88.11138 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 " -136.83" Parameter: B <- "-136.83" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -88.11" Parameter: C <- "-88.11" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -139.89" Parameter: C <- " -228.00" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -228.00" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.68" Parameter: D <- "7.68" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 43.39" Parameter: D <- " 51.07" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 34.13" Parameter: D <- " 85.20" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.97" Parameter: D <- " 91.17" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 91.17" 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= 9000 ENER= -136.83 GRMS= 0.41 ELEC= -88.11 VDW= -139.89 RDTITL> *EXTERNAL= -228.00 INTERNAL= 91.17 USER= 0.00 HARM= 69.86 RDTITL> *BOND= 7.68 ANGL= 43.39 DIHE= 34.13 IMPR= 5.97 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20676 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20617 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 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 -89.73461 -47.09615 0.15240 0.02000 MINI INTERN> 7.68471 43.38963 0.00000 34.12594 5.97322 MINI EXTERN> -139.89289 -88.11138 0.00000 0.00000 0.00000 MINI CONSTR> 47.09615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -90.26558 0.53098 0.96301 0.00150 MINI INTERN> 8.10903 44.01415 0.00000 35.17100 6.08341 MINI EXTERN> -147.52885 -85.22402 0.00000 0.00000 0.00000 MINI CONSTR> 49.10970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20612 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -90.45753 0.19194 0.87526 0.00065 MINI INTERN> 8.00711 43.30656 0.00000 34.95084 6.03421 MINI EXTERN> -146.00313 -85.82784 0.00000 0.00000 0.00000 MINI CONSTR> 49.07472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -90.65710 0.19957 0.47555 0.00028 MINI INTERN> 8.02999 43.05018 0.00000 34.88103 6.01563 MINI EXTERN> -145.53458 -86.19522 0.00000 0.00000 0.00000 MINI CONSTR> 49.09587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20610 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -90.70640 0.04930 0.48025 0.00029 MINI INTERN> 7.99660 42.99205 0.00000 34.81421 6.00292 MINI EXTERN> -145.25741 -86.37058 0.00000 0.00000 0.00000 MINI CONSTR> 49.11581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -90.78166 0.07525 0.15436 0.00013 MINI INTERN> 7.79629 43.13213 0.00000 34.74683 6.01122 MINI EXTERN> -144.98817 -86.62568 0.00000 0.00000 0.00000 MINI CONSTR> 49.14571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20609 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -90.81670 0.03504 0.10696 0.00013 MINI INTERN> 7.80036 43.08599 0.00000 34.70639 6.00533 MINI EXTERN> -144.87675 -86.71046 0.00000 0.00000 0.00000 MINI CONSTR> 49.17244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -90.85784 0.04114 0.19978 0.00013 MINI INTERN> 7.76138 43.08843 0.00000 34.65116 6.00352 MINI EXTERN> -144.73839 -86.83980 0.00000 0.00000 0.00000 MINI CONSTR> 49.21585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20609 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -90.89433 0.03649 0.13843 0.00014 MINI INTERN> 7.76609 43.04699 0.00000 34.61474 5.99906 MINI EXTERN> -144.67903 -86.89407 0.00000 0.00000 0.00000 MINI CONSTR> 49.25188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -90.93007 0.03573 0.14659 0.00014 MINI INTERN> 7.75872 43.02350 0.00000 34.57703 5.99633 MINI EXTERN> -144.62721 -86.95278 0.00000 0.00000 0.00000 MINI CONSTR> 49.29435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20608 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -90.95915 0.02908 0.24278 0.00015 MINI INTERN> 7.74274 43.01898 0.00000 34.54245 5.99555 MINI EXTERN> -144.58729 -87.00979 0.00000 0.00000 0.00000 MINI CONSTR> 49.33821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -90.99308 0.03393 0.24081 0.00016 MINI INTERN> 7.74558 42.98796 0.00000 34.51169 5.99279 MINI EXTERN> -144.57173 -87.04229 0.00000 0.00000 0.00000 MINI CONSTR> 49.38293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20608 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -91.02981 0.03673 0.16329 0.00016 MINI INTERN> 7.74925 42.95431 0.00000 34.48394 5.98954 MINI EXTERN> -144.56969 -87.06398 0.00000 0.00000 0.00000 MINI CONSTR> 49.42682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -91.05478 0.02497 0.25902 0.00017 MINI INTERN> 7.74314 42.94463 0.00000 34.45780 5.98887 MINI EXTERN> -144.56528 -87.09500 0.00000 0.00000 0.00000 MINI CONSTR> 49.47107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20609 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -91.08707 0.03229 0.28351 0.00017 MINI INTERN> 7.75158 42.91168 0.00000 34.43111 5.98639 MINI EXTERN> -144.57612 -87.11276 0.00000 0.00000 0.00000 MINI CONSTR> 49.52106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -91.11759 0.03053 0.27542 0.00018 MINI INTERN> 7.75056 42.89178 0.00000 34.40808 5.98460 MINI EXTERN> -144.58853 -87.12952 0.00000 0.00000 0.00000 MINI CONSTR> 49.56545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20609 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -91.14820 0.03060 0.28896 0.00019 MINI INTERN> 7.75238 42.86930 0.00000 34.38466 5.98274 MINI EXTERN> -144.60605 -87.14480 0.00000 0.00000 0.00000 MINI CONSTR> 49.61358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -91.17950 0.03131 0.29699 0.00019 MINI INTERN> 7.75324 42.84799 0.00000 34.36167 5.98091 MINI EXTERN> -144.62718 -87.15902 0.00000 0.00000 0.00000 MINI CONSTR> 49.66289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20606 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -91.22033 0.04083 0.09407 0.00008 MINI INTERN> 7.73266 42.84643 0.00000 34.33786 5.97861 MINI EXTERN> -144.64882 -87.17437 0.00000 0.00000 0.00000 MINI CONSTR> 49.70731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -91.23634 0.01601 0.32642 0.00021 MINI INTERN> 7.75316 42.81329 0.00000 34.31987 5.97791 MINI EXTERN> -144.67280 -87.18423 0.00000 0.00000 0.00000 MINI CONSTR> 49.75645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20604 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -91.26623 0.02989 0.33228 0.00022 MINI INTERN> 7.75256 42.79620 0.00000 34.29896 5.97637 MINI EXTERN> -144.69933 -87.19603 0.00000 0.00000 0.00000 MINI CONSTR> 49.80504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -91.31016 0.04392 0.10304 0.00009 MINI INTERN> 7.72556 42.80100 0.00000 34.27451 5.97433 MINI EXTERN> -144.72557 -87.21058 0.00000 0.00000 0.00000 MINI CONSTR> 49.85059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20603 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -91.32050 0.01034 0.35750 0.00023 MINI INTERN> 7.75190 42.76570 0.00000 34.26037 5.97367 MINI EXTERN> -144.75230 -87.21675 0.00000 0.00000 0.00000 MINI CONSTR> 49.89691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -91.34923 0.02873 0.37843 0.00024 MINI INTERN> 7.75308 42.74888 0.00000 34.23979 5.97220 MINI EXTERN> -144.78344 -87.22752 0.00000 0.00000 0.00000 MINI CONSTR> 49.94777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20602 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -91.39742 0.04819 0.12694 0.00010 MINI INTERN> 7.71960 42.75861 0.00000 34.21389 5.97020 MINI EXTERN> -144.81249 -87.24147 0.00000 0.00000 0.00000 MINI CONSTR> 49.99423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -91.42202 0.02459 0.08789 0.00011 MINI INTERN> 7.71952 42.74278 0.00000 34.19918 5.96922 MINI EXTERN> -144.83692 -87.24849 0.00000 0.00000 0.00000 MINI CONSTR> 50.03270 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20600 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -91.45165 0.02964 0.08782 0.00011 MINI INTERN> 7.71795 42.72802 0.00000 34.17914 5.96785 MINI EXTERN> -144.86843 -87.25807 0.00000 0.00000 0.00000 MINI CONSTR> 50.08188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -91.48105 0.02939 0.08972 0.00012 MINI INTERN> 7.71634 42.71373 0.00000 34.15914 5.96648 MINI EXTERN> -144.90027 -87.26749 0.00000 0.00000 0.00000 MINI CONSTR> 50.13103 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20599 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -91.50881 0.02776 0.17801 0.00012 MINI INTERN> 7.71462 42.70472 0.00000 34.13593 5.96486 MINI EXTERN> -144.93440 -87.27832 0.00000 0.00000 0.00000 MINI CONSTR> 50.18378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -91.53705 0.02824 0.11101 0.00012 MINI INTERN> 7.71316 42.68772 0.00000 34.12018 5.96379 MINI EXTERN> -144.96263 -87.28558 0.00000 0.00000 0.00000 MINI CONSTR> 50.22633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20597 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -91.56559 0.02855 0.11178 0.00013 MINI INTERN> 7.71196 42.67350 0.00000 34.10079 5.96244 MINI EXTERN> -144.99454 -87.29448 0.00000 0.00000 0.00000 MINI CONSTR> 50.27475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -91.59398 0.02839 0.12090 0.00013 MINI INTERN> 7.71079 42.65973 0.00000 34.08106 5.96107 MINI EXTERN> -145.02679 -87.30348 0.00000 0.00000 0.00000 MINI CONSTR> 50.32364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20596 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -91.61677 0.02279 0.21440 0.00014 MINI INTERN> 7.71146 42.65084 0.00000 34.06054 5.95959 MINI EXTERN> -145.05736 -87.31284 0.00000 0.00000 0.00000 MINI CONSTR> 50.37100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -91.64339 0.02661 0.21617 0.00014 MINI INTERN> 7.71082 42.63719 0.00000 34.04222 5.95830 MINI EXTERN> -145.08772 -87.32112 0.00000 0.00000 0.00000 MINI CONSTR> 50.41691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20596 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -91.67012 0.02673 0.22416 0.00015 MINI INTERN> 7.71050 42.62338 0.00000 34.02339 5.95697 MINI EXTERN> -145.11868 -87.32964 0.00000 0.00000 0.00000 MINI CONSTR> 50.46396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -91.69614 0.02602 0.24099 0.00015 MINI INTERN> 7.71077 42.60975 0.00000 34.00439 5.95560 MINI EXTERN> -145.14959 -87.33822 0.00000 0.00000 0.00000 MINI CONSTR> 50.51116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20595 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -91.72050 0.02435 0.26478 0.00016 MINI INTERN> 7.71119 42.59738 0.00000 33.98586 5.95427 MINI EXTERN> -145.17941 -87.34658 0.00000 0.00000 0.00000 MINI CONSTR> 50.55679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -91.74406 0.02357 0.25013 0.00017 MINI INTERN> 7.70960 42.58602 0.00000 33.97039 5.95322 MINI EXTERN> -145.20559 -87.35351 0.00000 0.00000 0.00000 MINI CONSTR> 50.59581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20592 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -91.76915 0.02508 0.26182 0.00017 MINI INTERN> 7.70965 42.57289 0.00000 33.95212 5.95187 MINI EXTERN> -145.23527 -87.36177 0.00000 0.00000 0.00000 MINI CONSTR> 50.64137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -91.79478 0.02563 0.26923 0.00018 MINI INTERN> 7.70917 42.55966 0.00000 33.93370 5.95051 MINI EXTERN> -145.26523 -87.37010 0.00000 0.00000 0.00000 MINI CONSTR> 50.68751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20590 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -91.82865 0.03388 0.08230 0.00008 MINI INTERN> 7.70236 42.54269 0.00000 33.92029 5.94993 MINI EXTERN> -145.29721 -87.37574 0.00000 0.00000 0.00000 MINI CONSTR> 50.72903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -91.84132 0.01266 0.29276 0.00019 MINI INTERN> 7.70888 42.53596 0.00000 33.89908 5.94795 MINI EXTERN> -145.32091 -87.38569 0.00000 0.00000 0.00000 MINI CONSTR> 50.77342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20588 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -91.86511 0.02379 0.29993 0.00020 MINI INTERN> 7.70975 42.52253 0.00000 33.88168 5.94658 MINI EXTERN> -145.34909 -87.39342 0.00000 0.00000 0.00000 MINI CONSTR> 50.81687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -91.88904 0.02393 0.31055 0.00021 MINI INTERN> 7.70652 42.51296 0.00000 33.86372 5.94534 MINI EXTERN> -145.37736 -87.40157 0.00000 0.00000 0.00000 MINI CONSTR> 50.86135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20587 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -91.91218 0.02314 0.32844 0.00021 MINI INTERN> 7.71668 42.49102 0.00000 33.84628 5.94350 MINI EXTERN> -145.40661 -87.40891 0.00000 0.00000 0.00000 MINI CONSTR> 50.90587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -91.95033 0.03815 0.10766 0.00009 MINI INTERN> 7.69904 42.48308 0.00000 33.83234 5.94378 MINI EXTERN> -145.44084 -87.41484 0.00000 0.00000 0.00000 MINI CONSTR> 50.94713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20585 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -91.97037 0.02005 0.07831 0.00010 MINI INTERN> 7.69677 42.47397 0.00000 33.81795 5.94258 MINI EXTERN> -145.46194 -87.42126 0.00000 0.00000 0.00000 MINI CONSTR> 50.98156 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -91.99432 0.02395 0.07775 0.00010 MINI INTERN> 7.69641 42.46175 0.00000 33.80035 5.94128 MINI EXTERN> -145.48982 -87.42904 0.00000 0.00000 0.00000 MINI CONSTR> 51.02474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20581 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -92.01827 0.02395 0.08019 0.00010 MINI INTERN> 7.69439 42.45123 0.00000 33.78258 5.94007 MINI EXTERN> -145.51781 -87.43694 0.00000 0.00000 0.00000 MINI CONSTR> 51.06821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -92.04073 0.02246 0.15197 0.00011 MINI INTERN> 7.69730 42.43904 0.00000 33.76431 5.93912 MINI EXTERN> -145.54943 -87.44502 0.00000 0.00000 0.00000 MINI CONSTR> 51.11397 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20579 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -92.06333 0.02261 0.09902 0.00011 MINI INTERN> 7.69643 42.42621 0.00000 33.74884 5.93760 MINI EXTERN> -145.57187 -87.45175 0.00000 0.00000 0.00000 MINI CONSTR> 51.15121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -92.08562 0.02229 0.11190 0.00011 MINI INTERN> 7.69064 42.42043 0.00000 33.73159 5.93664 MINI EXTERN> -145.59805 -87.45958 0.00000 0.00000 0.00000 MINI CONSTR> 51.19272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20580 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -92.10594 0.02032 0.13651 0.00012 MINI INTERN> 7.69350 42.40780 0.00000 33.71574 5.93550 MINI EXTERN> -145.62390 -87.46644 0.00000 0.00000 0.00000 MINI CONSTR> 51.23187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -92.12412 0.01818 0.18448 0.00012 MINI INTERN> 7.69846 42.39519 0.00000 33.70036 5.93444 MINI EXTERN> -145.64944 -87.47307 0.00000 0.00000 0.00000 MINI CONSTR> 51.26995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20580 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -92.14623 0.02211 0.18140 0.00013 MINI INTERN> 7.69386 42.38795 0.00000 33.68336 5.93336 MINI EXTERN> -145.67439 -87.48076 0.00000 0.00000 0.00000 MINI CONSTR> 51.31039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -92.16877 0.02254 0.14167 0.00013 MINI INTERN> 7.69731 42.37090 0.00000 33.66791 5.93166 MINI EXTERN> -145.69756 -87.48723 0.00000 0.00000 0.00000 MINI CONSTR> 51.34823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20581 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -92.18505 0.01628 0.20074 0.00014 MINI INTERN> 7.70006 42.36197 0.00000 33.65305 5.93084 MINI EXTERN> -145.72188 -87.49370 0.00000 0.00000 0.00000 MINI CONSTR> 51.38461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -92.20483 0.01978 0.23302 0.00014 MINI INTERN> 7.68661 42.36579 0.00000 33.63541 5.93032 MINI EXTERN> -145.74614 -87.50207 0.00000 0.00000 0.00000 MINI CONSTR> 51.42524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20581 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -92.22433 0.01949 0.21636 0.00015 MINI INTERN> 7.69686 42.34493 0.00000 33.62163 5.92872 MINI EXTERN> -145.76882 -87.50755 0.00000 0.00000 0.00000 MINI CONSTR> 51.45991 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -92.24468 0.02036 0.22994 0.00015 MINI INTERN> 7.69721 42.33464 0.00000 33.60483 5.92754 MINI EXTERN> -145.79372 -87.51511 0.00000 0.00000 0.00000 MINI CONSTR> 51.49993 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20579 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -92.26358 0.01890 0.26493 0.00016 MINI INTERN> 7.70117 42.32246 0.00000 33.58786 5.92633 MINI EXTERN> -145.81950 -87.52269 0.00000 0.00000 0.00000 MINI CONSTR> 51.54080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -92.28270 0.01912 0.24532 0.00016 MINI INTERN> 7.69794 42.31415 0.00000 33.57410 5.92521 MINI EXTERN> -145.83947 -87.52842 0.00000 0.00000 0.00000 MINI CONSTR> 51.57378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20577 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -92.30420 0.02150 0.24537 0.00017 MINI INTERN> 7.69597 42.30498 0.00000 33.55676 5.92399 MINI EXTERN> -145.86400 -87.53639 0.00000 0.00000 0.00000 MINI CONSTR> 51.61448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -92.33143 0.02723 0.07897 0.00007 MINI INTERN> 7.68232 42.29362 0.00000 33.54244 5.92148 MINI EXTERN> -145.87949 -87.54115 0.00000 0.00000 0.00000 MINI CONSTR> 51.64936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20576 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -92.34000 0.00857 0.27045 0.00018 MINI INTERN> 7.69792 42.28473 0.00000 33.52675 5.92166 MINI EXTERN> -145.90827 -87.54938 0.00000 0.00000 0.00000 MINI CONSTR> 51.68659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -92.35975 0.01975 0.28024 0.00019 MINI INTERN> 7.69991 42.27287 0.00000 33.51005 5.92035 MINI EXTERN> -145.93201 -87.55696 0.00000 0.00000 0.00000 MINI CONSTR> 51.72603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20574 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -92.37885 0.01910 0.29618 0.00020 MINI INTERN> 7.69433 42.26786 0.00000 33.49343 5.91920 MINI EXTERN> -145.95431 -87.56481 0.00000 0.00000 0.00000 MINI CONSTR> 51.76544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -92.41042 0.03157 0.09802 0.00009 MINI INTERN> 7.67901 42.25270 0.00000 33.47884 5.91630 MINI EXTERN> -145.97117 -87.56767 0.00000 0.00000 0.00000 MINI CONSTR> 51.80156 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20574 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -92.42694 0.01653 0.07038 0.00009 MINI INTERN> 7.67875 42.24451 0.00000 33.46595 5.91550 MINI EXTERN> -145.98998 -87.57365 0.00000 0.00000 0.00000 MINI CONSTR> 51.83197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -92.44667 0.01973 0.07086 0.00009 MINI INTERN> 7.67909 42.23315 0.00000 33.44996 5.91416 MINI EXTERN> -146.01290 -87.58028 0.00000 0.00000 0.00000 MINI CONSTR> 51.87015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20574 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -92.46642 0.01975 0.12565 0.00010 MINI INTERN> 7.67488 42.22508 0.00000 33.43251 5.91256 MINI EXTERN> -146.03685 -87.58650 0.00000 0.00000 0.00000 MINI CONSTR> 51.91190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -92.48439 0.01797 0.09542 0.00010 MINI INTERN> 7.67939 42.21108 0.00000 33.41878 5.91138 MINI EXTERN> -146.05714 -87.59262 0.00000 0.00000 0.00000 MINI CONSTR> 51.94473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20573 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -92.50161 0.01722 0.10783 0.00010 MINI INTERN> 7.67489 42.20536 0.00000 33.40415 5.91026 MINI EXTERN> -146.07695 -87.59852 0.00000 0.00000 0.00000 MINI CONSTR> 51.97920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -92.51967 0.01806 0.10207 0.00011 MINI INTERN> 7.67596 42.19415 0.00000 33.38946 5.90901 MINI EXTERN> -146.09784 -87.60460 0.00000 0.00000 0.00000 MINI CONSTR> 52.01420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20573 ATOM PAIRS WERE FOUND FOR ATOM LIST 719 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -92.53727 0.01760 0.11646 0.00011 MINI INTERN> 7.67108 42.18884 0.00000 33.37427 5.90792 MINI EXTERN> -146.11838 -87.61077 0.00000 0.00000 0.00000 MINI CONSTR> 52.04978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -92.55199 0.01473 0.16579 0.00011 MINI INTERN> 7.67537 42.17592 0.00000 33.36045 5.90634 MINI EXTERN> -146.13805 -87.61540 0.00000 0.00000 0.00000 MINI CONSTR> 52.08337 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20573 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -92.57161 0.01961 0.10951 0.00012 MINI INTERN> 7.66912 42.17124 0.00000 33.34576 5.90564 MINI EXTERN> -146.15782 -87.62261 0.00000 0.00000 0.00000 MINI CONSTR> 52.11705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -92.58541 0.01380 0.17570 0.00012 MINI INTERN> 7.67022 42.16189 0.00000 33.33182 5.90415 MINI EXTERN> -146.17710 -87.62703 0.00000 0.00000 0.00000 MINI CONSTR> 52.15064 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20573 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -92.60190 0.01650 0.20348 0.00013 MINI INTERN> 7.68466 42.13884 0.00000 33.31742 5.90227 MINI EXTERN> -146.19930 -87.63220 0.00000 0.00000 0.00000 MINI CONSTR> 52.18640 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -92.61809 0.01619 0.18975 0.00013 MINI INTERN> 7.66720 42.14621 0.00000 33.30345 5.90188 MINI EXTERN> -146.21587 -87.63837 0.00000 0.00000 0.00000 MINI CONSTR> 52.21740 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20572 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -92.63391 0.01581 0.21123 0.00014 MINI INTERN> 7.68701 42.11832 0.00000 33.29013 5.89987 MINI EXTERN> -146.23704 -87.64328 0.00000 0.00000 0.00000 MINI CONSTR> 52.25108 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -92.65027 0.01637 0.19800 0.00014 MINI INTERN> 7.66919 42.12556 0.00000 33.27577 5.89935 MINI EXTERN> -146.25405 -87.64918 0.00000 0.00000 0.00000 MINI CONSTR> 52.28309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20572 ATOM PAIRS WERE FOUND FOR ATOM LIST 720 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -92.66664 0.01637 0.20773 0.00015 MINI INTERN> 7.67705 42.10856 0.00000 33.26171 5.89776 MINI EXTERN> -146.27457 -87.65439 0.00000 0.00000 0.00000 MINI CONSTR> 52.31724 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -92.68751 0.02087 0.06997 0.00006 MINI INTERN> 7.66983 42.10481 0.00000 33.24814 5.89753 MINI EXTERN> -146.29047 -87.66412 0.00000 0.00000 0.00000 MINI CONSTR> 52.34677 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20570 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -92.69608 0.00857 0.23066 0.00016 MINI INTERN> 7.67492 42.09355 0.00000 33.23488 5.89547 MINI EXTERN> -146.31049 -87.66470 0.00000 0.00000 0.00000 MINI CONSTR> 52.38028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -92.71937 0.02329 0.07388 0.00007 MINI INTERN> 7.66932 42.08670 0.00000 33.22054 5.89514 MINI EXTERN> -146.32730 -87.67539 0.00000 0.00000 0.00000 MINI CONSTR> 52.41162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20568 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -92.72588 0.00651 0.25133 0.00017 MINI INTERN> 7.65988 42.09137 0.00000 33.20707 5.89384 MINI EXTERN> -146.34577 -87.67617 0.00000 0.00000 0.00000 MINI CONSTR> 52.44390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -92.75023 0.02435 0.08258 0.00007 MINI INTERN> 7.66793 42.07009 0.00000 33.19341 5.89285 MINI EXTERN> -146.36302 -87.68658 0.00000 0.00000 0.00000 MINI CONSTR> 52.47510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20566 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -92.75480 0.00457 0.26669 0.00018 MINI INTERN> 7.67769 42.05686 0.00000 33.18154 5.89065 MINI EXTERN> -146.38260 -87.68506 0.00000 0.00000 0.00000 MINI CONSTR> 52.50612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -92.78074 0.02594 0.09372 0.00008 MINI INTERN> 7.66844 42.05171 0.00000 33.16639 5.89045 MINI EXTERN> -146.39855 -87.69763 0.00000 0.00000 0.00000 MINI CONSTR> 52.53845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20565 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -92.79433 0.01359 0.06533 0.00008 MINI INTERN> 7.66429 42.04666 0.00000 33.15516 5.88944 MINI EXTERN> -146.41365 -87.70118 0.00000 0.00000 0.00000 MINI CONSTR> 52.56495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -92.81028 0.01595 0.10975 0.00008 MINI INTERN> 7.66799 42.03489 0.00000 33.13975 5.88814 MINI EXTERN> -146.43307 -87.70861 0.00000 0.00000 0.00000 MINI CONSTR> 52.60064 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20564 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -92.82395 0.01367 0.06423 0.00009 MINI INTERN> 7.66326 42.02982 0.00000 33.12897 5.88711 MINI EXTERN> -146.44790 -87.71150 0.00000 0.00000 0.00000 MINI CONSTR> 52.62630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -92.83970 0.01575 0.12641 0.00009 MINI INTERN> 7.66746 42.01807 0.00000 33.11291 5.88580 MINI EXTERN> -146.46753 -87.71961 0.00000 0.00000 0.00000 MINI CONSTR> 52.66321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20564 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -92.85546 0.01576 0.07951 0.00009 MINI INTERN> 7.66332 42.01116 0.00000 33.10043 5.88460 MINI EXTERN> -146.48444 -87.72333 0.00000 0.00000 0.00000 MINI CONSTR> 52.69279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -92.86944 0.01398 0.06679 0.00010 MINI INTERN> 7.66348 42.00210 0.00000 33.08835 5.88339 MINI EXTERN> -146.50069 -87.72751 0.00000 0.00000 0.00000 MINI CONSTR> 52.72144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20564 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -92.88313 0.01369 0.14847 0.00010 MINI INTERN> 7.66992 41.98969 0.00000 33.07309 5.88211 MINI EXTERN> -146.51877 -87.73549 0.00000 0.00000 0.00000 MINI CONSTR> 52.75633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -92.89718 0.01406 0.16039 0.00011 MINI INTERN> 7.65739 41.99344 0.00000 33.05941 5.88148 MINI EXTERN> -146.53469 -87.74109 0.00000 0.00000 0.00000 MINI CONSTR> 52.78688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20561 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -92.91049 0.01331 0.16373 0.00011 MINI INTERN> 7.66539 41.97786 0.00000 33.04730 5.88003 MINI EXTERN> -146.55083 -87.74609 0.00000 0.00000 0.00000 MINI CONSTR> 52.81584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -92.92470 0.01421 0.17290 0.00011 MINI INTERN> 7.67279 41.96192 0.00000 33.03432 5.87847 MINI EXTERN> -146.56835 -87.75078 0.00000 0.00000 0.00000 MINI CONSTR> 52.84694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20561 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -92.93772 0.01302 0.18473 0.00012 MINI INTERN> 7.66045 41.96640 0.00000 33.02115 5.87793 MINI EXTERN> -146.58314 -87.75662 0.00000 0.00000 0.00000 MINI CONSTR> 52.87611 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 -92.93772 0.01302 0.18473 0.00006 STPD INTERN> 7.66045 41.96640 0.00000 33.02115 5.87793 STPD EXTERN> -146.58314 -87.75662 0.00000 0.00000 0.00000 STPD CONSTR> 52.87611 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 20561 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20561 ATOM PAIRS WERE FOUND FOR ATOM LIST 721 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 -92.93806 0.00034 0.10901 0.00000 MINI INTERN> 7.66005 41.96258 0.00000 33.02565 5.87745 MINI EXTERN> -146.58353 -87.74949 0.00000 0.00000 0.00000 MINI CONSTR> 52.86923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -94.51717 1.57910 0.18432 0.12374 MINI INTERN> 7.65030 40.43825 0.00000 30.57290 5.67808 MINI EXTERN> -150.34189 -88.51026 0.00000 0.00000 0.00000 MINI CONSTR> 59.99546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -94.54759 0.03042 0.08739 0.00674 MINI INTERN> 7.57544 40.49704 0.00000 30.50718 5.63409 MINI EXTERN> -150.23066 -88.64624 0.00000 0.00000 0.00000 MINI CONSTR> 60.11556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -94.59343 0.04585 0.15377 0.03127 MINI INTERN> 7.41982 40.17813 0.00000 30.27877 5.58868 MINI EXTERN> -149.44858 -88.69017 0.00000 0.00000 0.00000 MINI CONSTR> 60.07992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -94.66429 0.07086 0.15276 0.04043 MINI INTERN> 7.43864 40.19747 0.00000 30.14389 5.55564 MINI EXTERN> -149.25389 -88.73005 0.00000 0.00000 0.00000 MINI CONSTR> 59.98402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -94.72144 0.05714 0.15228 0.02169 MINI INTERN> 7.46655 40.19473 0.00000 30.06282 5.51854 MINI EXTERN> -149.21337 -88.67226 0.00000 0.00000 0.00000 MINI CONSTR> 59.92157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -94.76214 0.04070 0.09781 0.02427 MINI INTERN> 7.53535 40.10390 0.00000 30.05680 5.51417 MINI EXTERN> -149.33212 -88.53987 0.00000 0.00000 0.00000 MINI CONSTR> 59.89963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -94.78580 0.02366 0.09730 0.01336 MINI INTERN> 7.55590 40.13652 0.00000 30.00944 5.50664 MINI EXTERN> -149.37888 -88.51973 0.00000 0.00000 0.00000 MINI CONSTR> 59.90431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -94.80591 0.02011 0.09264 0.01092 MINI INTERN> 7.51380 40.18445 0.00000 29.97758 5.51485 MINI EXTERN> -149.41819 -88.50221 0.00000 0.00000 0.00000 MINI CONSTR> 59.92382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -94.82663 0.02071 0.08801 0.02008 MINI INTERN> 7.54118 40.15803 0.00000 29.95478 5.49110 MINI EXTERN> -149.43735 -88.49772 0.00000 0.00000 0.00000 MINI CONSTR> 59.96336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -94.84519 0.01856 0.08060 0.01642 MINI INTERN> 7.53720 40.09828 0.00000 29.92034 5.49245 MINI EXTERN> -149.53386 -88.36500 0.00000 0.00000 0.00000 MINI CONSTR> 60.00542 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -94.86184 0.01665 0.08189 0.01444 MINI INTERN> 7.52165 40.05099 0.00000 29.91837 5.49856 MINI EXTERN> -149.47968 -88.40455 0.00000 0.00000 0.00000 MINI CONSTR> 60.03283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -94.87419 0.01236 0.05935 0.01219 MINI INTERN> 7.53352 40.02522 0.00000 29.92223 5.49861 MINI EXTERN> -149.41009 -88.48575 0.00000 0.00000 0.00000 MINI CONSTR> 60.04207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -94.88712 0.01292 0.06848 0.01276 MINI INTERN> 7.54736 40.05813 0.00000 29.87400 5.50025 MINI EXTERN> -149.46363 -88.44405 0.00000 0.00000 0.00000 MINI CONSTR> 60.04082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -94.89785 0.01074 0.06541 0.01239 MINI INTERN> 7.54364 40.06231 0.00000 29.86526 5.50023 MINI EXTERN> -149.46199 -88.43427 0.00000 0.00000 0.00000 MINI CONSTR> 60.02698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -94.90754 0.00969 0.06456 0.01307 MINI INTERN> 7.55764 40.05852 0.00000 29.84070 5.51965 MINI EXTERN> -149.39217 -88.48780 0.00000 0.00000 0.00000 MINI CONSTR> 59.99593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -94.91825 0.01071 0.06424 0.01329 MINI INTERN> 7.57285 39.98759 0.00000 29.82434 5.51445 MINI EXTERN> -149.26155 -88.50839 0.00000 0.00000 0.00000 MINI CONSTR> 59.95245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -94.93166 0.01341 0.07449 0.01982 MINI INTERN> 7.56182 39.93405 0.00000 29.76750 5.52921 MINI EXTERN> -149.17937 -88.45406 0.00000 0.00000 0.00000 MINI CONSTR> 59.90919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -94.94303 0.01137 0.06746 0.01957 MINI INTERN> 7.55799 39.94282 0.00000 29.78441 5.53312 MINI EXTERN> -149.21279 -88.44183 0.00000 0.00000 0.00000 MINI CONSTR> 59.89325 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -94.95300 0.00997 0.05776 0.01479 MINI INTERN> 7.55172 39.94480 0.00000 29.80324 5.54260 MINI EXTERN> -149.34707 -88.34170 0.00000 0.00000 0.00000 MINI CONSTR> 59.89341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -94.96217 0.00917 0.05751 0.01664 MINI INTERN> 7.54486 39.90743 0.00000 29.80982 5.56995 MINI EXTERN> -149.38312 -88.30885 0.00000 0.00000 0.00000 MINI CONSTR> 59.89774 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 -94.96217 0.00917 0.05751 0.02000 CONJ INTERN> 7.54486 39.90743 0.00000 29.80982 5.56995 CONJ EXTERN> -149.38312 -88.30885 0.00000 0.00000 0.00000 CONJ CONSTR> 59.89774 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 ASP 14 N ) 0.25384 ( PROT ASP 14 H ) 0.20307 ( PROT ASP 14 CA ) 0.25384 ( PROT ASP 14 CB ) 0.20307 ( PROT ASP 14 CG ) 0.20307 ( PROT ASP 14 OD1 ) 0.20307 ( PROT ASP 14 OD2 ) 0.20307 ( PROT ASP 14 C ) 0.25384 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.63644 7.24081 -13.20736 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00379 0.00655 -0.00410 ROTATION MATRIX 0.999998 0.001329 0.001131 -0.001328 0.999999 -0.001102 -0.001132 0.001100 0.999999 AXIS OF ROTATION IS -0.533652 -0.548334 0.643852 ANGLE IS 0.12 TOTAL SQUARE DIFF IS 176.3686 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.771907 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.7719" Parameter: A <- "0.7719" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.56073 7.29090 -13.44118 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.03250 -0.03535 0.00082 ROTATION MATRIX 0.999714 0.016390 0.017394 -0.016024 0.999652 -0.020976 -0.017732 0.020691 0.999629 AXIS OF ROTATION IS -0.657118 -0.553959 0.511199 ANGLE IS 1.82 CENTER OF ROTATION 14.099996 6.766276-13.276030 SHIFT IS 0.041361 TOTAL SQUARE DIFF IS 11.4239 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.607052 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.7719" RDCMND substituted energy or value "?RMS" to " 0.6071" Parameter: A <- "0.7719 0.6071" 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 0.7719 0.6071 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 " 59.90" Parameter: H <- "59.90" 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 -154.85991 59.89774 0.30997 ENER INTERN> 7.54486 39.90743 0.00000 29.80982 5.56995 ENER EXTERN> -149.38312 -88.30885 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 " -154.86" Parameter: B <- "-154.86" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -88.31" Parameter: C <- "-88.31" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -149.38" Parameter: C <- " -237.69" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -237.69" 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 " 39.91" Parameter: D <- " 47.45" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 29.81" Parameter: D <- " 77.26" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.57" Parameter: D <- " 82.83" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 82.83" 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= -154.86 GRMS= 0.31 ELEC= -88.31 VDW= -149.38 RDTITL> *EXTERNAL= -237.69 INTERNAL= 82.83 USER= 0.00 HARM= 59.90 RDTITL> *BOND= 7.54 ANGL= 39.91 DIHE= 29.81 IMPR= 5.57 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= -154.86 GRMS= 0.31 ELEC= -88.31 VDW= -149.38 RDTITL> *EXTERNAL= -237.69 INTERNAL= 82.83 USER= 0.00 HARM= 59.90 RDTITL> *BOND= 7.54 ANGL= 39.91 DIHE= 29.81 IMPR= 5.57 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= -154.86 GRMS= 0.31 ELEC= -88.31 VDW= -149.38 RDTITL> *EXTERNAL= -237.69 INTERNAL= 82.83 USER= 0.00 HARM= 59.90 RDTITL> *BOND= 7.54 ANGL= 39.91 DIHE= 29.81 IMPR= 5.57 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 9600 0.7719 0.6071 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20561 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20483 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 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 -114.87458 -39.98532 0.12548 0.02000 MINI INTERN> 7.54486 39.90743 0.00000 29.80982 5.56995 MINI EXTERN> -149.38312 -88.30885 0.00000 0.00000 0.00000 MINI CONSTR> 39.98532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -108.44066 -6.43392 6.99324 0.00360 MINI INTERN> 13.77418 41.45140 0.00000 30.45801 5.69479 MINI EXTERN> -155.18474 -86.01022 0.00000 0.00000 0.00000 MINI CONSTR> 41.37591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20473 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -115.44568 7.00502 0.20838 0.00065 MINI INTERN> 7.89723 40.07188 0.00000 30.39594 5.62482 MINI EXTERN> -154.32699 -86.48475 0.00000 0.00000 0.00000 MINI CONSTR> 41.37618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -115.51024 0.06456 0.45885 0.00028 MINI INTERN> 7.66587 39.95100 0.00000 30.28588 5.60012 MINI EXTERN> -153.45410 -86.95278 0.00000 0.00000 0.00000 MINI CONSTR> 41.39377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20474 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -115.57565 0.06541 0.12273 0.00012 MINI INTERN> 7.73400 39.78759 0.00000 30.23073 5.60134 MINI EXTERN> -153.24816 -87.09485 0.00000 0.00000 0.00000 MINI CONSTR> 41.41369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -115.60530 0.02965 0.09274 0.00013 MINI INTERN> 7.70102 39.76590 0.00000 30.19360 5.59594 MINI EXTERN> -153.09012 -87.20806 0.00000 0.00000 0.00000 MINI CONSTR> 41.43642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20473 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -115.63563 0.03033 0.18352 0.00013 MINI INTERN> 7.71987 39.70420 0.00000 30.14576 5.59340 MINI EXTERN> -152.94755 -87.32195 0.00000 0.00000 0.00000 MINI CONSTR> 41.47065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -115.66460 0.02897 0.11671 0.00013 MINI INTERN> 7.68453 39.70195 0.00000 30.11595 5.58903 MINI EXTERN> -152.86447 -87.39221 0.00000 0.00000 0.00000 MINI CONSTR> 41.50062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20472 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -115.69114 0.02654 0.13797 0.00014 MINI INTERN> 7.68316 39.67636 0.00000 30.08313 5.58674 MINI EXTERN> -152.80427 -87.45239 0.00000 0.00000 0.00000 MINI CONSTR> 41.53613 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -115.71126 0.02012 0.20796 0.00014 MINI INTERN> 7.70375 39.64168 0.00000 30.05433 5.58599 MINI EXTERN> -152.77250 -87.49431 0.00000 0.00000 0.00000 MINI CONSTR> 41.56981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20470 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -115.73593 0.02467 0.21950 0.00015 MINI INTERN> 7.70073 39.62457 0.00000 30.02740 5.58426 MINI EXTERN> -152.75024 -87.53012 0.00000 0.00000 0.00000 MINI CONSTR> 41.60747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -115.75908 0.02315 0.23990 0.00016 MINI INTERN> 7.70388 39.60476 0.00000 30.00293 5.58270 MINI EXTERN> -152.74105 -87.55789 0.00000 0.00000 0.00000 MINI CONSTR> 41.64559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20468 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -115.78120 0.02212 0.23019 0.00016 MINI INTERN> 7.69261 39.60023 0.00000 29.98317 5.58103 MINI EXTERN> -152.73857 -87.57915 0.00000 0.00000 0.00000 MINI CONSTR> 41.67948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -115.80330 0.02210 0.24884 0.00017 MINI INTERN> 7.70027 39.57622 0.00000 29.96461 5.57831 MINI EXTERN> -152.74323 -87.59674 0.00000 0.00000 0.00000 MINI CONSTR> 41.71727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20467 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -115.83117 0.02788 0.07954 0.00007 MINI INTERN> 7.61095 39.63017 0.00000 29.95617 5.57195 MINI EXTERN> -152.73225 -87.61706 0.00000 0.00000 0.00000 MINI CONSTR> 41.74889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -115.84275 0.01158 0.27082 0.00018 MINI INTERN> 7.70898 39.54731 0.00000 29.92856 5.57594 MINI EXTERN> -152.76755 -87.62264 0.00000 0.00000 0.00000 MINI CONSTR> 41.78665 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20465 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -115.86111 0.01836 0.30975 0.00019 MINI INTERN> 7.65244 39.59015 0.00000 29.91218 5.57510 MINI EXTERN> -152.77641 -87.63672 0.00000 0.00000 0.00000 MINI CONSTR> 41.82216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -115.88160 0.02049 0.29377 0.00019 MINI INTERN> 7.69673 39.54156 0.00000 29.89360 5.57473 MINI EXTERN> -152.80268 -87.64302 0.00000 0.00000 0.00000 MINI CONSTR> 41.85748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20466 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -115.91390 0.03230 0.09155 0.00008 MINI INTERN> 7.59515 39.59280 0.00000 29.89344 5.56536 MINI EXTERN> -152.79448 -87.65810 0.00000 0.00000 0.00000 MINI CONSTR> 41.89193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -115.93221 0.01831 0.07513 0.00009 MINI INTERN> 7.60118 39.57864 0.00000 29.87904 5.56503 MINI EXTERN> -152.81590 -87.66372 0.00000 0.00000 0.00000 MINI CONSTR> 41.92352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20465 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -115.95208 0.01986 0.07740 0.00009 MINI INTERN> 7.59787 39.57013 0.00000 29.86524 5.56347 MINI EXTERN> -152.83734 -87.67047 0.00000 0.00000 0.00000 MINI CONSTR> 41.95904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -115.97198 0.01991 0.07459 0.00009 MINI INTERN> 7.59849 39.55917 0.00000 29.85096 5.56231 MINI EXTERN> -152.86122 -87.67638 0.00000 0.00000 0.00000 MINI CONSTR> 41.99469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20464 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -115.99268 0.02069 0.07442 0.00010 MINI INTERN> 7.59720 39.54945 0.00000 29.83652 5.56095 MINI EXTERN> -152.88662 -87.68232 0.00000 0.00000 0.00000 MINI CONSTR> 42.03213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -116.01415 0.02148 0.12872 0.00010 MINI INTERN> 7.57550 39.55379 0.00000 29.82401 5.55745 MINI EXTERN> -152.90868 -87.69083 0.00000 0.00000 0.00000 MINI CONSTR> 42.07460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20462 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -116.03397 0.01982 0.09330 0.00010 MINI INTERN> 7.58603 39.53705 0.00000 29.80897 5.55756 MINI EXTERN> -152.93780 -87.69435 0.00000 0.00000 0.00000 MINI CONSTR> 42.10857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -116.05330 0.01932 0.11032 0.00011 MINI INTERN> 7.58358 39.52724 0.00000 29.79687 5.55555 MINI EXTERN> -152.96224 -87.69951 0.00000 0.00000 0.00000 MINI CONSTR> 42.14521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20461 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -116.07097 0.01767 0.12839 0.00011 MINI INTERN> 7.57339 39.52629 0.00000 29.78569 5.55388 MINI EXTERN> -152.98473 -87.70483 0.00000 0.00000 0.00000 MINI CONSTR> 42.17934 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -116.08738 0.01641 0.16968 0.00012 MINI INTERN> 7.55810 39.53143 0.00000 29.77468 5.55211 MINI EXTERN> -153.00660 -87.71079 0.00000 0.00000 0.00000 MINI CONSTR> 42.21369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20461 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -116.10552 0.01814 0.18325 0.00012 MINI INTERN> 7.56770 39.51141 0.00000 29.76315 5.55029 MINI EXTERN> -153.03245 -87.71436 0.00000 0.00000 0.00000 MINI CONSTR> 42.24875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -116.12275 0.01723 0.18791 0.00012 MINI INTERN> 7.55133 39.51782 0.00000 29.75195 5.54912 MINI EXTERN> -153.05521 -87.71986 0.00000 0.00000 0.00000 MINI CONSTR> 42.28210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20461 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -116.14132 0.01858 0.19520 0.00013 MINI INTERN> 7.55253 39.50908 0.00000 29.73871 5.54811 MINI EXTERN> -153.08330 -87.72443 0.00000 0.00000 0.00000 MINI CONSTR> 42.31799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -116.15860 0.01727 0.21388 0.00013 MINI INTERN> 7.54828 39.50138 0.00000 29.72809 5.54624 MINI EXTERN> -153.10662 -87.72882 0.00000 0.00000 0.00000 MINI CONSTR> 42.35286 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20459 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -116.17597 0.01737 0.19811 0.00014 MINI INTERN> 7.54844 39.49554 0.00000 29.71591 5.54586 MINI EXTERN> -153.13310 -87.73278 0.00000 0.00000 0.00000 MINI CONSTR> 42.38416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -116.19275 0.01679 0.23896 0.00014 MINI INTERN> 7.54663 39.48562 0.00000 29.70486 5.54361 MINI EXTERN> -153.15726 -87.73746 0.00000 0.00000 0.00000 MINI CONSTR> 42.42124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20458 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -116.20989 0.01714 0.21694 0.00015 MINI INTERN> 7.54297 39.48188 0.00000 29.69386 5.54303 MINI EXTERN> -153.18161 -87.74148 0.00000 0.00000 0.00000 MINI CONSTR> 42.45146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -116.23327 0.02338 0.07110 0.00006 MINI INTERN> 7.59876 39.43445 0.00000 29.67184 5.54710 MINI EXTERN> -153.23011 -87.73849 0.00000 0.00000 0.00000 MINI CONSTR> 42.48318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20456 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -116.24310 0.00983 0.23426 0.00016 MINI INTERN> 7.54021 39.46817 0.00000 29.67142 5.54058 MINI EXTERN> -153.23119 -87.75018 0.00000 0.00000 0.00000 MINI CONSTR> 42.51790 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -116.26757 0.02448 0.07577 0.00007 MINI INTERN> 7.59981 39.41827 0.00000 29.64830 5.54512 MINI EXTERN> -153.28241 -87.74638 0.00000 0.00000 0.00000 MINI CONSTR> 42.54970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20456 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -116.27480 0.00723 0.25954 0.00017 MINI INTERN> 7.54377 39.45666 0.00000 29.64670 5.53975 MINI EXTERN> -153.28561 -87.75868 0.00000 0.00000 0.00000 MINI CONSTR> 42.58262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -116.30043 0.02563 0.08248 0.00007 MINI INTERN> 7.60192 39.40237 0.00000 29.62540 5.54332 MINI EXTERN> -153.33340 -87.75402 0.00000 0.00000 0.00000 MINI CONSTR> 42.61397 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20453 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -116.30621 0.00577 0.26636 0.00019 MINI INTERN> 7.52813 39.45002 0.00000 29.62822 5.53623 MINI EXTERN> -153.32683 -87.76796 0.00000 0.00000 0.00000 MINI CONSTR> 42.64598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -116.33491 0.02870 0.08012 0.00008 MINI INTERN> 7.59904 39.38860 0.00000 29.60250 5.54098 MINI EXTERN> -153.38461 -87.76275 0.00000 0.00000 0.00000 MINI CONSTR> 42.68133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20453 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -116.34976 0.01486 0.07004 0.00008 MINI INTERN> 7.59272 39.38650 0.00000 29.59318 5.53979 MINI EXTERN> -153.40495 -87.76704 0.00000 0.00000 0.00000 MINI CONSTR> 42.71004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -116.36546 0.01569 0.07264 0.00009 MINI INTERN> 7.59488 39.37783 0.00000 29.58218 5.53889 MINI EXTERN> -153.42956 -87.77078 0.00000 0.00000 0.00000 MINI CONSTR> 42.74111 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20452 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -116.38130 0.01585 0.06842 0.00009 MINI INTERN> 7.59233 39.37221 0.00000 29.57184 5.53769 MINI EXTERN> -153.45252 -87.77511 0.00000 0.00000 0.00000 MINI CONSTR> 42.77225 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -116.39813 0.01683 0.12402 0.00009 MINI INTERN> 7.60844 39.35584 0.00000 29.55603 5.53794 MINI EXTERN> -153.48779 -87.77782 0.00000 0.00000 0.00000 MINI CONSTR> 42.80923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20452 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -116.41460 0.01647 0.08651 0.00010 MINI INTERN> 7.59858 39.35289 0.00000 29.54793 5.53586 MINI EXTERN> -153.50601 -87.78316 0.00000 0.00000 0.00000 MINI CONSTR> 42.83931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -116.43002 0.01543 0.10559 0.00010 MINI INTERN> 7.60049 39.34668 0.00000 29.53559 5.53552 MINI EXTERN> -153.53278 -87.78686 0.00000 0.00000 0.00000 MINI CONSTR> 42.87135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20450 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -116.44534 0.01532 0.11310 0.00010 MINI INTERN> 7.60619 39.33449 0.00000 29.52493 5.53435 MINI EXTERN> -153.55717 -87.79066 0.00000 0.00000 0.00000 MINI CONSTR> 42.90252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -116.45861 0.01326 0.15450 0.00011 MINI INTERN> 7.61143 39.32824 0.00000 29.51229 5.53448 MINI EXTERN> -153.58422 -87.79370 0.00000 0.00000 0.00000 MINI CONSTR> 42.93288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20449 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -116.47357 0.01497 0.17124 0.00011 MINI INTERN> 7.62163 39.31042 0.00000 29.50273 5.53262 MINI EXTERN> -153.60760 -87.79772 0.00000 0.00000 0.00000 MINI CONSTR> 42.96435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -116.48766 0.01409 0.17529 0.00011 MINI INTERN> 7.62268 39.30583 0.00000 29.49107 5.53244 MINI EXTERN> -153.63225 -87.80115 0.00000 0.00000 0.00000 MINI CONSTR> 42.99371 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20448 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -116.50192 0.01425 0.18920 0.00012 MINI INTERN> 7.61009 39.31241 0.00000 29.47993 5.53210 MINI EXTERN> -153.65441 -87.80602 0.00000 0.00000 0.00000 MINI CONSTR> 43.02398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -116.51634 0.01443 0.17701 0.00012 MINI INTERN> 7.62339 39.29219 0.00000 29.47106 5.53051 MINI EXTERN> -153.67619 -87.80924 0.00000 0.00000 0.00000 MINI CONSTR> 43.05195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20444 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -116.52927 0.01293 0.21771 0.00013 MINI INTERN> 7.60535 39.30563 0.00000 29.45936 5.53048 MINI EXTERN> -153.69832 -87.81457 0.00000 0.00000 0.00000 MINI CONSTR> 43.08281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -116.54342 0.01415 0.19757 0.00013 MINI INTERN> 7.61092 39.29363 0.00000 29.45017 5.52949 MINI EXTERN> -153.71908 -87.81791 0.00000 0.00000 0.00000 MINI CONSTR> 43.10935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20443 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -116.56188 0.01846 0.06543 0.00006 MINI INTERN> 7.57483 39.30191 0.00000 29.44925 5.52500 MINI EXTERN> -153.72138 -87.82705 0.00000 0.00000 0.00000 MINI CONSTR> 43.13556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -116.57047 0.00860 0.20768 0.00014 MINI INTERN> 7.62193 39.27308 0.00000 29.42973 5.52786 MINI EXTERN> -153.76439 -87.82512 0.00000 0.00000 0.00000 MINI CONSTR> 43.16645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20442 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -116.59043 0.01995 0.06833 0.00006 MINI INTERN> 7.57198 39.29092 0.00000 29.42947 5.52299 MINI EXTERN> -153.76404 -87.83598 0.00000 0.00000 0.00000 MINI CONSTR> 43.19423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -116.59710 0.00667 0.23057 0.00015 MINI INTERN> 7.63919 39.24420 0.00000 29.41109 5.52514 MINI EXTERN> -153.80790 -87.83281 0.00000 0.00000 0.00000 MINI CONSTR> 43.22400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20442 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -116.60874 0.01165 0.27088 0.00016 MINI INTERN> 7.58966 39.28414 0.00000 29.40173 5.52500 MINI EXTERN> -153.82094 -87.84085 0.00000 0.00000 0.00000 MINI CONSTR> 43.25252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -116.63122 0.02248 0.07533 0.00007 MINI INTERN> 7.56730 39.27535 0.00000 29.40129 5.51997 MINI EXTERN> -153.82457 -87.84929 0.00000 0.00000 0.00000 MINI CONSTR> 43.27873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20442 ATOM PAIRS WERE FOUND FOR ATOM LIST 722 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -116.63526 0.00404 0.25827 0.00017 MINI INTERN> 7.64879 39.22033 0.00000 29.38176 5.52270 MINI EXTERN> -153.87159 -87.84451 0.00000 0.00000 0.00000 MINI CONSTR> 43.30725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -116.65788 0.02262 0.08816 0.00007 MINI INTERN> 7.56433 39.26434 0.00000 29.38312 5.51772 MINI EXTERN> -153.86366 -87.85851 0.00000 0.00000 0.00000 MINI CONSTR> 43.33478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20442 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -116.67002 0.01213 0.06344 0.00008 MINI INTERN> 7.56948 39.25656 0.00000 29.37331 5.51766 MINI EXTERN> -153.88463 -87.86117 0.00000 0.00000 0.00000 MINI CONSTR> 43.35877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -116.68399 0.01397 0.10218 0.00008 MINI INTERN> 7.55872 39.25616 0.00000 29.36512 5.51558 MINI EXTERN> -153.90176 -87.86796 0.00000 0.00000 0.00000 MINI CONSTR> 43.39015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20442 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -116.69636 0.01237 0.06065 0.00008 MINI INTERN> 7.57024 39.24386 0.00000 29.35451 5.51590 MINI EXTERN> -153.92483 -87.86974 0.00000 0.00000 0.00000 MINI CONSTR> 43.41370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -116.71117 0.01482 0.11520 0.00009 MINI INTERN> 7.55917 39.24249 0.00000 29.34591 5.51344 MINI EXTERN> -153.94282 -87.87744 0.00000 0.00000 0.00000 MINI CONSTR> 43.44807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20440 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -116.72442 0.01324 0.09244 0.00009 MINI INTERN> 7.55774 39.23954 0.00000 29.33572 5.51326 MINI EXTERN> -153.96373 -87.88119 0.00000 0.00000 0.00000 MINI CONSTR> 43.47425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -116.73683 0.01241 0.10343 0.00009 MINI INTERN> 7.55518 39.23466 0.00000 29.32755 5.51194 MINI EXTERN> -153.98115 -87.88620 0.00000 0.00000 0.00000 MINI CONSTR> 43.50119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20439 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -116.74994 0.01311 0.10232 0.00010 MINI INTERN> 7.56020 39.22386 0.00000 29.31829 5.51090 MINI EXTERN> -154.00155 -87.89042 0.00000 0.00000 0.00000 MINI CONSTR> 43.52878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -116.76112 0.01118 0.14218 0.00010 MINI INTERN> 7.54577 39.22960 0.00000 29.31082 5.50945 MINI EXTERN> -154.01582 -87.89682 0.00000 0.00000 0.00000 MINI CONSTR> 43.55588 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20439 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -116.77533 0.01422 0.10700 0.00010 MINI INTERN> 7.56230 39.21001 0.00000 29.30014 5.50903 MINI EXTERN> -154.04026 -87.89941 0.00000 0.00000 0.00000 MINI CONSTR> 43.58285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -116.78544 0.01011 0.15507 0.00011 MINI INTERN> 7.55432 39.20963 0.00000 29.29370 5.50722 MINI EXTERN> -154.05352 -87.90546 0.00000 0.00000 0.00000 MINI CONSTR> 43.60867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20439 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -116.79709 0.01164 0.17261 0.00011 MINI INTERN> 7.53543 39.22102 0.00000 29.28509 5.50648 MINI EXTERN> -154.06895 -87.91172 0.00000 0.00000 0.00000 MINI CONSTR> 43.63555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -116.80933 0.01225 0.16410 0.00011 MINI INTERN> 7.54822 39.20284 0.00000 29.27705 5.50519 MINI EXTERN> -154.08807 -87.91530 0.00000 0.00000 0.00000 MINI CONSTR> 43.66074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20439 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -116.82106 0.01173 0.18353 0.00012 MINI INTERN> 7.53306 39.21448 0.00000 29.26629 5.50553 MINI EXTERN> -154.10740 -87.92040 0.00000 0.00000 0.00000 MINI CONSTR> 43.68738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -116.83329 0.01223 0.17305 0.00012 MINI INTERN> 7.53284 39.20569 0.00000 29.25957 5.50372 MINI EXTERN> -154.12244 -87.92576 0.00000 0.00000 0.00000 MINI CONSTR> 43.71309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20439 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -116.84869 0.01540 0.05995 0.00005 MINI INTERN> 7.57246 39.17202 0.00000 29.24493 5.50546 MINI EXTERN> -154.15651 -87.92407 0.00000 0.00000 0.00000 MINI CONSTR> 43.73702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -116.85587 0.00718 0.19700 0.00013 MINI INTERN> 7.52602 39.20078 0.00000 29.24305 5.50184 MINI EXTERN> -154.15616 -87.93593 0.00000 0.00000 0.00000 MINI CONSTR> 43.76453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20438 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -116.87244 0.01657 0.06298 0.00006 MINI INTERN> 7.57264 39.16108 0.00000 29.22765 5.50384 MINI EXTERN> -154.19261 -87.93336 0.00000 0.00000 0.00000 MINI CONSTR> 43.78832 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -116.87842 0.00599 0.20760 0.00014 MINI INTERN> 7.53771 39.17670 0.00000 29.22824 5.49897 MINI EXTERN> -154.18975 -87.94525 0.00000 0.00000 0.00000 MINI CONSTR> 43.81496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20437 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -116.88875 0.01032 0.24735 0.00015 MINI INTERN> 7.52139 39.19414 0.00000 29.21550 5.50047 MINI EXTERN> -154.21173 -87.94987 0.00000 0.00000 0.00000 MINI CONSTR> 43.84137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -116.90796 0.01921 0.06877 0.00006 MINI INTERN> 7.57286 39.14462 0.00000 29.20186 5.50136 MINI EXTERN> -154.24640 -87.94777 0.00000 0.00000 0.00000 MINI CONSTR> 43.86550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20436 ATOM PAIRS WERE FOUND FOR ATOM LIST 726 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -116.91869 0.01073 0.05834 0.00007 MINI INTERN> 7.56953 39.14085 0.00000 29.19528 5.50018 MINI EXTERN> -154.26007 -87.95280 0.00000 0.00000 0.00000 MINI CONSTR> 43.88834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -116.93011 0.01141 0.05967 0.00007 MINI INTERN> 7.56964 39.13570 0.00000 29.18690 5.49943 MINI EXTERN> -154.27744 -87.95757 0.00000 0.00000 0.00000 MINI CONSTR> 43.91324 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20433 ATOM PAIRS WERE FOUND FOR ATOM LIST 725 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -116.94177 0.01166 0.05840 0.00007 MINI INTERN> 7.56719 39.13211 0.00000 29.17875 5.49854 MINI EXTERN> -154.29414 -87.96282 0.00000 0.00000 0.00000 MINI CONSTR> 43.93861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -116.95331 0.01154 0.06166 0.00007 MINI INTERN> 7.56928 39.12527 0.00000 29.17017 5.49778 MINI EXTERN> -154.31217 -87.96763 0.00000 0.00000 0.00000 MINI CONSTR> 43.96399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20433 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -116.96480 0.01149 0.05851 0.00008 MINI INTERN> 7.56768 39.12062 0.00000 29.16239 5.49677 MINI EXTERN> -154.32831 -87.97295 0.00000 0.00000 0.00000 MINI CONSTR> 43.98900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -116.97687 0.01207 0.10643 0.00008 MINI INTERN> 7.58002 39.10879 0.00000 29.15027 5.49686 MINI EXTERN> -154.35417 -87.97702 0.00000 0.00000 0.00000 MINI CONSTR> 44.01838 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20433 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -116.98872 0.01185 0.07718 0.00008 MINI INTERN> 7.57423 39.10478 0.00000 29.14437 5.49519 MINI EXTERN> -154.36649 -87.98319 0.00000 0.00000 0.00000 MINI CONSTR> 44.04239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -116.99967 0.01095 0.09167 0.00008 MINI INTERN> 7.57755 39.09846 0.00000 29.13530 5.49477 MINI EXTERN> -154.38536 -87.98782 0.00000 0.00000 0.00000 MINI CONSTR> 44.06742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20433 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -117.01094 0.01128 0.09482 0.00009 MINI INTERN> 7.57293 39.09760 0.00000 29.12709 5.49409 MINI EXTERN> -154.40167 -87.99343 0.00000 0.00000 0.00000 MINI CONSTR> 44.09246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -117.02066 0.00972 0.13149 0.00009 MINI INTERN> 7.58777 39.08264 0.00000 29.11780 5.49370 MINI EXTERN> -154.42247 -87.99710 0.00000 0.00000 0.00000 MINI CONSTR> 44.11701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20431 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -117.03285 0.01219 0.10023 0.00009 MINI INTERN> 7.56944 39.09033 0.00000 29.11154 5.49246 MINI EXTERN> -154.43346 -88.00431 0.00000 0.00000 0.00000 MINI CONSTR> 44.14114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -117.04170 0.00885 0.14276 0.00010 MINI INTERN> 7.57905 39.08151 0.00000 29.10216 5.49248 MINI EXTERN> -154.45338 -88.00804 0.00000 0.00000 0.00000 MINI CONSTR> 44.16451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20431 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -117.05183 0.01013 0.15982 0.00010 MINI INTERN> 7.59669 39.06135 0.00000 29.09429 5.49140 MINI EXTERN> -154.47222 -88.01220 0.00000 0.00000 0.00000 MINI CONSTR> 44.18886 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -117.06247 0.01064 0.15151 0.00011 MINI INTERN> 7.58275 39.06940 0.00000 29.08668 5.49108 MINI EXTERN> -154.48575 -88.01821 0.00000 0.00000 0.00000 MINI CONSTR> 44.21158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20431 ATOM PAIRS WERE FOUND FOR ATOM LIST 723 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -117.07265 0.01018 0.16995 0.00011 MINI INTERN> 7.59703 39.04894 0.00000 29.08084 5.48913 MINI EXTERN> -154.50074 -88.02349 0.00000 0.00000 0.00000 MINI CONSTR> 44.23564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -117.08336 0.01071 0.15956 0.00011 MINI INTERN> 7.59549 39.04809 0.00000 29.07175 5.48920 MINI EXTERN> -154.51859 -88.02832 0.00000 0.00000 0.00000 MINI CONSTR> 44.25901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20431 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -117.09369 0.01033 0.17382 0.00012 MINI INTERN> 7.57430 39.06262 0.00000 29.06417 5.48880 MINI EXTERN> -154.53110 -88.03562 0.00000 0.00000 0.00000 MINI CONSTR> 44.28314 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 -117.09369 0.01033 0.17382 0.00014 STPD INTERN> 7.57430 39.06262 0.00000 29.06417 5.48880 STPD EXTERN> -154.53110 -88.03562 0.00000 0.00000 0.00000 STPD CONSTR> 44.28314 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 20431 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20431 ATOM PAIRS WERE FOUND FOR ATOM LIST 724 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 -117.09369 0.01033 0.17382 0.00000 MINI INTERN> 7.57430 39.06262 0.00000 29.06417 5.48880 MINI EXTERN> -154.53110 -88.03562 0.00000 0.00000 0.00000 MINI CONSTR> 44.28314 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -118.84434 1.75065 0.60008 0.60679 MINI INTERN> 7.59782 37.99660 0.00000 26.55404 5.30224 MINI EXTERN> -159.37942 -89.08586 0.00000 0.00000 0.00000 MINI CONSTR> 52.17024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -119.12536 0.28102 0.24525 0.04767 MINI INTERN> 7.51676 38.08474 0.00000 25.98729 5.26740 MINI EXTERN> -160.17558 -89.55106 0.00000 0.00000 0.00000 MINI CONSTR> 53.74508 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -119.38908 0.26372 0.36366 0.09610 MINI INTERN> 7.40905 37.72504 0.00000 25.12568 5.17606 MINI EXTERN> -159.71053 -90.08632 0.00000 0.00000 0.00000 MINI CONSTR> 54.97195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -119.61847 0.22940 0.21010 0.05901 MINI INTERN> 7.39212 37.73544 0.00000 24.63178 5.15335 MINI EXTERN> -160.50210 -90.00046 0.00000 0.00000 0.00000 MINI CONSTR> 55.97141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -119.76383 0.14536 0.24894 0.05385 MINI INTERN> 7.47478 37.57854 0.00000 24.58789 5.06507 MINI EXTERN> -161.17471 -89.69322 0.00000 0.00000 0.00000 MINI CONSTR> 56.39783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -119.92038 0.15654 0.22760 0.05403 MINI INTERN> 7.54253 37.45759 0.00000 24.45586 5.10688 MINI EXTERN> -161.81996 -89.31311 0.00000 0.00000 0.00000 MINI CONSTR> 56.64983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -120.02754 0.10717 0.18323 0.04209 MINI INTERN> 7.45356 37.54639 0.00000 24.34534 5.06123 MINI EXTERN> -161.53407 -89.50022 0.00000 0.00000 0.00000 MINI CONSTR> 56.60023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -120.11487 0.08733 0.18007 0.03299 MINI INTERN> 7.33765 37.25030 0.00000 24.36680 5.04440 MINI EXTERN> -160.79671 -89.67077 0.00000 0.00000 0.00000 MINI CONSTR> 56.35346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -120.21597 0.10110 0.18297 0.05175 MINI INTERN> 7.35611 37.34096 0.00000 24.53148 4.97872 MINI EXTERN> -160.41379 -89.88150 0.00000 0.00000 0.00000 MINI CONSTR> 55.87205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -120.30756 0.09159 0.18235 0.04257 MINI INTERN> 7.34573 37.26064 0.00000 24.68662 5.00743 MINI EXTERN> -160.06253 -89.85029 0.00000 0.00000 0.00000 MINI CONSTR> 55.30483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -120.41383 0.10627 0.23539 0.05614 MINI INTERN> 7.35209 37.19429 0.00000 24.99326 5.01457 MINI EXTERN> -159.19428 -90.29805 0.00000 0.00000 0.00000 MINI CONSTR> 54.52428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -120.53530 0.12147 0.18462 0.06258 MINI INTERN> 7.38485 37.45871 0.00000 25.29364 5.00888 MINI EXTERN> -158.74682 -90.54155 0.00000 0.00000 0.00000 MINI CONSTR> 53.60699 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -120.62130 0.08600 0.18168 0.04431 MINI INTERN> 7.35276 37.65675 0.00000 25.42188 5.03206 MINI EXTERN> -158.56748 -90.47851 0.00000 0.00000 0.00000 MINI CONSTR> 52.96125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -120.70551 0.08421 0.19662 0.04654 MINI INTERN> 7.46250 37.59902 0.00000 25.73547 5.03141 MINI EXTERN> -158.45272 -90.41469 0.00000 0.00000 0.00000 MINI CONSTR> 52.33351 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -120.88164 0.17613 0.32723 0.12376 MINI INTERN> 7.48559 37.96080 0.00000 26.24201 5.11435 MINI EXTERN> -158.15501 -90.62385 0.00000 0.00000 0.00000 MINI CONSTR> 51.09447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -121.02588 0.14424 0.19830 0.05528 MINI INTERN> 7.53094 38.06891 0.00000 26.42935 5.17768 MINI EXTERN> -157.42088 -90.92436 0.00000 0.00000 0.00000 MINI CONSTR> 50.11249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -121.08544 0.05956 0.17770 0.03301 MINI INTERN> 7.52244 38.13996 0.00000 26.27750 5.23063 MINI EXTERN> -156.86250 -91.10411 0.00000 0.00000 0.00000 MINI CONSTR> 49.71063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -121.13714 0.05169 0.18521 0.03234 MINI INTERN> 7.51140 38.21766 0.00000 26.20010 5.27231 MINI EXTERN> -156.21606 -91.49059 0.00000 0.00000 0.00000 MINI CONSTR> 49.36804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -121.19038 0.05324 0.16890 0.03397 MINI INTERN> 7.48967 38.17211 0.00000 26.13200 5.22717 MINI EXTERN> -155.85799 -91.40834 0.00000 0.00000 0.00000 MINI CONSTR> 49.05500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -121.23328 0.04290 0.14986 0.02942 MINI INTERN> 7.46990 38.16318 0.00000 26.12264 5.22645 MINI EXTERN> -155.93659 -91.15083 0.00000 0.00000 0.00000 MINI CONSTR> 48.87197 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 -121.23328 0.04290 0.14986 0.02000 CONJ INTERN> 7.46990 38.16318 0.00000 26.12264 5.22645 CONJ EXTERN> -155.93659 -91.15083 0.00000 0.00000 0.00000 CONJ CONSTR> 48.87197 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 ASP 14 N ) 0.16499 ( PROT ASP 14 H ) 0.13199 ( PROT ASP 14 CA ) 0.16499 ( PROT ASP 14 CB ) 0.13199 ( PROT ASP 14 CG ) 0.13199 ( PROT ASP 14 OD1 ) 0.13199 ( PROT ASP 14 OD2 ) 0.13199 ( PROT ASP 14 C ) 0.16499 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.64215 7.24418 -13.20589 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS -0.00192 0.00318 -0.00557 ROTATION MATRIX 0.999975 0.004969 0.005048 -0.004941 0.999972 -0.005640 -0.005076 0.005615 0.999971 AXIS OF ROTATION IS -0.622015 -0.559554 0.547720 ANGLE IS 0.52 TOTAL SQUARE DIFF IS 221.6291 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 0.865302 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.8653" Parameter: A <- "0.8653" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.57196 7.30333 -13.44047 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.04373 -0.04778 0.00011 ROTATION MATRIX 0.999765 0.014914 0.015720 -0.014598 0.999693 -0.020017 -0.016014 0.019782 0.999676 AXIS OF ROTATION IS -0.676411 -0.539330 0.501589 ANGLE IS 1.69 CENTER OF ROTATION 14.362520 6.536599-13.143556 SHIFT IS 0.055408 TOTAL SQUARE DIFF IS 14.8424 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.691943 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.8653" RDCMND substituted energy or value "?RMS" to " 0.6919" Parameter: A <- "0.8653 0.6919" 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 0.8653 0.6919 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 " 48.87" Parameter: H <- "48.87" 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 -170.10525 48.87197 0.28481 ENER INTERN> 7.46990 38.16318 0.00000 26.12264 5.22645 ENER EXTERN> -155.93659 -91.15083 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 " -170.11" Parameter: B <- "-170.11" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -91.15" Parameter: C <- "-91.15" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -155.94" Parameter: C <- " -247.09" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -247.09" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.47" Parameter: D <- "7.47" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 38.16" Parameter: D <- " 45.63" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 26.12" Parameter: D <- " 71.75" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.23" Parameter: D <- " 76.98" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 76.98" 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= 10200 ENER= -170.11 GRMS= 0.28 ELEC= -91.15 VDW= -155.94 RDTITL> *EXTERNAL= -247.09 INTERNAL= 76.98 USER= 0.00 HARM= 48.87 RDTITL> *BOND= 7.47 ANGL= 38.16 DIHE= 26.12 IMPR= 5.23 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 "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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20431 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20384 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 -137.72696 -32.37829 0.17971 0.02000 MINI INTERN> 7.46990 38.16318 0.00000 26.12264 5.22645 MINI EXTERN> -155.93659 -91.15083 0.00000 0.00000 0.00000 MINI CONSTR> 32.37829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -128.54753 -9.17944 8.15627 0.00360 MINI INTERN> 15.43904 41.04283 0.00000 26.09451 5.37450 MINI EXTERN> -159.22634 -90.33285 0.00000 0.00000 0.00000 MINI CONSTR> 33.06077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20376 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -138.11449 9.56697 0.94465 0.00065 MINI INTERN> 7.91198 38.52710 0.00000 26.17110 5.24736 MINI EXTERN> -158.71401 -90.33401 0.00000 0.00000 0.00000 MINI CONSTR> 33.07599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -138.36161 0.24712 0.31960 0.00028 MINI INTERN> 7.59903 38.35565 0.00000 26.19581 5.22097 MINI EXTERN> -158.37859 -90.45701 0.00000 0.00000 0.00000 MINI CONSTR> 33.10252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20375 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -138.41418 0.05257 0.40910 0.00029 MINI INTERN> 7.54635 38.30295 0.00000 26.19095 5.21385 MINI EXTERN> -158.24795 -90.55047 0.00000 0.00000 0.00000 MINI CONSTR> 33.13013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -138.48401 0.06983 0.12321 0.00013 MINI INTERN> 7.61965 38.20969 0.00000 26.16104 5.21194 MINI EXTERN> -158.23230 -90.61270 0.00000 0.00000 0.00000 MINI CONSTR> 33.15868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20374 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -138.52171 0.03770 0.10206 0.00013 MINI INTERN> 7.59898 38.19180 0.00000 26.15249 5.20933 MINI EXTERN> -158.19100 -90.67118 0.00000 0.00000 0.00000 MINI CONSTR> 33.18787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -138.56000 0.03829 0.09921 0.00013 MINI INTERN> 7.58978 38.17423 0.00000 26.14040 5.20725 MINI EXTERN> -158.17216 -90.72192 0.00000 0.00000 0.00000 MINI CONSTR> 33.22241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20374 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -138.59535 0.03535 0.18982 0.00014 MINI INTERN> 7.62158 38.13860 0.00000 26.12112 5.20544 MINI EXTERN> -158.18652 -90.75762 0.00000 0.00000 0.00000 MINI CONSTR> 33.26205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -138.62888 0.03353 0.14036 0.00014 MINI INTERN> 7.58831 38.14685 0.00000 26.11310 5.20425 MINI EXTERN> -158.18779 -90.78804 0.00000 0.00000 0.00000 MINI CONSTR> 33.29444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20372 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -138.65540 0.02652 0.21316 0.00015 MINI INTERN> 7.62276 38.11458 0.00000 26.09732 5.20293 MINI EXTERN> -158.21788 -90.80358 0.00000 0.00000 0.00000 MINI CONSTR> 33.32846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -138.68968 0.03427 0.14192 0.00016 MINI INTERN> 7.58460 38.12707 0.00000 26.09052 5.20153 MINI EXTERN> -158.22935 -90.82626 0.00000 0.00000 0.00000 MINI CONSTR> 33.36221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20372 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -138.71393 0.02425 0.22624 0.00016 MINI INTERN> 7.61813 38.09895 0.00000 26.07461 5.20046 MINI EXTERN> -158.26850 -90.83395 0.00000 0.00000 0.00000 MINI CONSTR> 33.39636 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -138.74440 0.03047 0.24446 0.00017 MINI INTERN> 7.62189 38.08390 0.00000 26.06409 5.19815 MINI EXTERN> -158.29977 -90.84632 0.00000 0.00000 0.00000 MINI CONSTR> 33.43366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20372 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -138.76987 0.02547 0.27870 0.00017 MINI INTERN> 7.60327 38.09737 0.00000 26.05151 5.19799 MINI EXTERN> -158.33113 -90.85607 0.00000 0.00000 0.00000 MINI CONSTR> 33.46719 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -138.79722 0.02735 0.25573 0.00018 MINI INTERN> 7.62561 38.06736 0.00000 26.04172 5.19626 MINI EXTERN> -158.36443 -90.86193 0.00000 0.00000 0.00000 MINI CONSTR> 33.49819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20372 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -138.82365 0.02643 0.28992 0.00019 MINI INTERN> 7.57850 38.10119 0.00000 26.03255 5.19581 MINI EXTERN> -158.38953 -90.87462 0.00000 0.00000 0.00000 MINI CONSTR> 33.53245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -138.85806 0.03442 0.08970 0.00008 MINI INTERN> 7.55108 38.09640 0.00000 26.03240 5.19341 MINI EXTERN> -158.40221 -90.88983 0.00000 0.00000 0.00000 MINI CONSTR> 33.56070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20369 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -138.87291 0.01485 0.29813 0.00020 MINI INTERN> 7.64053 38.03576 0.00000 26.00965 5.19260 MINI EXTERN> -158.46752 -90.87927 0.00000 0.00000 0.00000 MINI CONSTR> 33.59535 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -138.89498 0.02207 0.35323 0.00021 MINI INTERN> 7.57106 38.09311 0.00000 26.00128 5.19296 MINI EXTERN> -158.48844 -90.89226 0.00000 0.00000 0.00000 MINI CONSTR> 33.62731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20367 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -138.91920 0.02423 0.35465 0.00022 MINI INTERN> 7.59218 38.07251 0.00000 25.98804 5.19211 MINI EXTERN> -158.52958 -90.89327 0.00000 0.00000 0.00000 MINI CONSTR> 33.65881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -138.94525 0.02604 0.32856 0.00022 MINI INTERN> 7.64325 38.02441 0.00000 25.97365 5.19065 MINI EXTERN> -158.57712 -90.89079 0.00000 0.00000 0.00000 MINI CONSTR> 33.69071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20365 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -138.98723 0.04198 0.10291 0.00010 MINI INTERN> 7.54478 38.06729 0.00000 25.98037 5.18691 MINI EXTERN> -158.57349 -90.91618 0.00000 0.00000 0.00000 MINI CONSTR> 33.72310 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -139.01016 0.02293 0.08594 0.00010 MINI INTERN> 7.54764 38.06039 0.00000 25.96949 5.18602 MINI EXTERN> -158.60693 -90.91845 0.00000 0.00000 0.00000 MINI CONSTR> 33.75167 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20364 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -139.03416 0.02400 0.08892 0.00010 MINI INTERN> 7.54534 38.05591 0.00000 25.95955 5.18477 MINI EXTERN> -158.63939 -90.92292 0.00000 0.00000 0.00000 MINI CONSTR> 33.78257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -139.05787 0.02372 0.09036 0.00011 MINI INTERN> 7.54485 38.05000 0.00000 25.94952 5.18351 MINI EXTERN> -158.67195 -90.92702 0.00000 0.00000 0.00000 MINI CONSTR> 33.81321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20361 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -139.08219 0.02432 0.08453 0.00011 MINI INTERN> 7.54691 38.04298 0.00000 25.93823 5.18245 MINI EXTERN> -158.70707 -90.93019 0.00000 0.00000 0.00000 MINI CONSTR> 33.84451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -139.10792 0.02573 0.15474 0.00012 MINI INTERN> 7.53160 38.04722 0.00000 25.92936 5.18052 MINI EXTERN> -158.73881 -90.93952 0.00000 0.00000 0.00000 MINI CONSTR> 33.88171 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -139.13289 0.02497 0.11407 0.00012 MINI INTERN> 7.53592 38.04004 0.00000 25.91610 5.17999 MINI EXTERN> -158.77654 -90.94035 0.00000 0.00000 0.00000 MINI CONSTR> 33.91195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -139.15540 0.02251 0.13846 0.00012 MINI INTERN> 7.52907 38.03926 0.00000 25.90691 5.17857 MINI EXTERN> -158.80625 -90.94592 0.00000 0.00000 0.00000 MINI CONSTR> 33.94296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -139.17599 0.02059 0.18798 0.00013 MINI INTERN> 7.53143 38.03030 0.00000 25.89865 5.17673 MINI EXTERN> -158.83525 -90.95156 0.00000 0.00000 0.00000 MINI CONSTR> 33.97371 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -139.19785 0.02185 0.20533 0.00013 MINI INTERN> 7.51305 38.04365 0.00000 25.88730 5.17629 MINI EXTERN> -158.86597 -90.95615 0.00000 0.00000 0.00000 MINI CONSTR> 34.00397 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20360 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -139.21955 0.02170 0.20571 0.00014 MINI INTERN> 7.51455 38.03429 0.00000 25.87881 5.17454 MINI EXTERN> -158.89427 -90.96086 0.00000 0.00000 0.00000 MINI CONSTR> 34.03339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -139.24246 0.02291 0.22065 0.00014 MINI INTERN> 7.53104 38.01476 0.00000 25.86729 5.17307 MINI EXTERN> -158.93062 -90.96324 0.00000 0.00000 0.00000 MINI CONSTR> 34.06525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20359 ATOM PAIRS WERE FOUND FOR ATOM LIST 731 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -139.26366 0.02120 0.22651 0.00015 MINI INTERN> 7.51077 38.02757 0.00000 25.85752 5.17225 MINI EXTERN> -158.95751 -90.96892 0.00000 0.00000 0.00000 MINI CONSTR> 34.09467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -139.28573 0.02208 0.21925 0.00015 MINI INTERN> 7.52446 38.00973 0.00000 25.84680 5.17088 MINI EXTERN> -158.99047 -90.97083 0.00000 0.00000 0.00000 MINI CONSTR> 34.12368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20359 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -139.30636 0.02062 0.24876 0.00016 MINI INTERN> 7.50599 38.02743 0.00000 25.83299 5.17121 MINI EXTERN> -159.02399 -90.97362 0.00000 0.00000 0.00000 MINI CONSTR> 34.15363 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -139.32741 0.02106 0.24053 0.00017 MINI INTERN> 7.50237 38.02240 0.00000 25.82471 5.16956 MINI EXTERN> -159.04985 -90.97873 0.00000 0.00000 0.00000 MINI CONSTR> 34.18213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20357 ATOM PAIRS WERE FOUND FOR ATOM LIST 730 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -139.34832 0.02091 0.23612 0.00017 MINI INTERN> 7.51429 38.00276 0.00000 25.81664 5.16741 MINI EXTERN> -159.07749 -90.98286 0.00000 0.00000 0.00000 MINI CONSTR> 34.21093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -139.37644 0.02812 0.08103 0.00007 MINI INTERN> 7.55596 37.96902 0.00000 25.79538 5.16848 MINI EXTERN> -159.13070 -90.97298 0.00000 0.00000 0.00000 MINI CONSTR> 34.23840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20355 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -139.38759 0.01116 0.27196 0.00019 MINI INTERN> 7.51800 37.99037 0.00000 25.79649 5.16490 MINI EXTERN> -159.13601 -90.99033 0.00000 0.00000 0.00000 MINI CONSTR> 34.26898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -139.40513 0.01754 0.32744 0.00019 MINI INTERN> 7.49588 38.01814 0.00000 25.77985 5.16635 MINI EXTERN> -159.17222 -90.99117 0.00000 0.00000 0.00000 MINI CONSTR> 34.29804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20354 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -139.43835 0.03321 0.09092 0.00008 MINI INTERN> 7.55888 37.95359 0.00000 25.76258 5.16554 MINI EXTERN> -159.22173 -90.98194 0.00000 0.00000 0.00000 MINI CONSTR> 34.32474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -139.44458 0.00624 0.31543 0.00021 MINI INTERN> 7.52716 37.96953 0.00000 25.76616 5.16133 MINI EXTERN> -159.22199 -91.00007 0.00000 0.00000 0.00000 MINI CONSTR> 34.35330 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20353 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -139.47802 0.03344 0.10326 0.00009 MINI INTERN> 7.56463 37.94087 0.00000 25.74070 5.16364 MINI EXTERN> -159.28161 -90.98724 0.00000 0.00000 0.00000 MINI CONSTR> 34.38098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -139.49647 0.01845 0.07456 0.00009 MINI INTERN> 7.55117 37.94521 0.00000 25.73353 5.16243 MINI EXTERN> -159.30175 -90.99285 0.00000 0.00000 0.00000 MINI CONSTR> 34.40578 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20353 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -139.51699 0.02052 0.07927 0.00010 MINI INTERN> 7.55448 37.93848 0.00000 25.72192 5.16147 MINI EXTERN> -159.33294 -90.99545 0.00000 0.00000 0.00000 MINI CONSTR> 34.43504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -139.53688 0.01989 0.07928 0.00010 MINI INTERN> 7.55574 37.93269 0.00000 25.71131 5.16039 MINI EXTERN> -159.36173 -90.99862 0.00000 0.00000 0.00000 MINI CONSTR> 34.46334 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20351 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -139.55676 0.01989 0.13884 0.00010 MINI INTERN> 7.57063 37.92116 0.00000 25.69592 5.15995 MINI EXTERN> -159.40099 -90.99835 0.00000 0.00000 0.00000 MINI CONSTR> 34.49493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -139.57685 0.02009 0.10503 0.00011 MINI INTERN> 7.56510 37.91705 0.00000 25.68816 5.15835 MINI EXTERN> -159.42352 -91.00369 0.00000 0.00000 0.00000 MINI CONSTR> 34.52169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20349 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -139.59512 0.01827 0.12351 0.00011 MINI INTERN> 7.57173 37.90934 0.00000 25.67645 5.15762 MINI EXTERN> -159.45402 -91.00532 0.00000 0.00000 0.00000 MINI CONSTR> 34.54907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -139.61198 0.01686 0.16577 0.00011 MINI INTERN> 7.57537 37.90765 0.00000 25.66338 5.15740 MINI EXTERN> -159.48602 -91.00624 0.00000 0.00000 0.00000 MINI CONSTR> 34.57648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20349 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -139.63192 0.01995 0.13116 0.00012 MINI INTERN> 7.57463 37.89926 0.00000 25.65550 5.15575 MINI EXTERN> -159.50897 -91.01097 0.00000 0.00000 0.00000 MINI CONSTR> 34.60289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -139.64783 0.01591 0.17483 0.00012 MINI INTERN> 7.58657 37.89104 0.00000 25.64229 5.15549 MINI EXTERN> -159.54190 -91.01084 0.00000 0.00000 0.00000 MINI CONSTR> 34.62951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20348 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -139.66730 0.01947 0.18951 0.00013 MINI INTERN> 7.56956 37.90169 0.00000 25.63152 5.15465 MINI EXTERN> -159.56772 -91.01601 0.00000 0.00000 0.00000 MINI CONSTR> 34.65900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -139.68452 0.01721 0.20218 0.00013 MINI INTERN> 7.59239 37.87948 0.00000 25.61999 5.15350 MINI EXTERN> -159.59945 -91.01632 0.00000 0.00000 0.00000 MINI CONSTR> 34.68590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20347 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -139.70231 0.01779 0.21898 0.00014 MINI INTERN> 7.57873 37.88936 0.00000 25.60886 5.15299 MINI EXTERN> -159.62552 -91.02037 0.00000 0.00000 0.00000 MINI CONSTR> 34.71363 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -139.72014 0.01784 0.20360 0.00014 MINI INTERN> 7.59418 37.86987 0.00000 25.59967 5.15153 MINI EXTERN> -159.65180 -91.02230 0.00000 0.00000 0.00000 MINI CONSTR> 34.73870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20346 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -139.73732 0.01718 0.23054 0.00015 MINI INTERN> 7.55852 37.89779 0.00000 25.59024 5.15114 MINI EXTERN> -159.67158 -91.02937 0.00000 0.00000 0.00000 MINI CONSTR> 34.76594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -139.75979 0.02246 0.07215 0.00006 MINI INTERN> 7.53979 37.89401 0.00000 25.58864 5.14837 MINI EXTERN> -159.68032 -91.03904 0.00000 0.00000 0.00000 MINI CONSTR> 34.78877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20344 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -139.76998 0.01019 0.24095 0.00016 MINI INTERN> 7.60736 37.84901 0.00000 25.56905 5.14858 MINI EXTERN> -159.73070 -91.03002 0.00000 0.00000 0.00000 MINI CONSTR> 34.81675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -139.78519 0.01521 0.27408 0.00016 MINI INTERN> 7.55718 37.89217 0.00000 25.55961 5.14885 MINI EXTERN> -159.74756 -91.03775 0.00000 0.00000 0.00000 MINI CONSTR> 34.84230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20342 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -139.80268 0.01749 0.25630 0.00017 MINI INTERN> 7.58982 37.86334 0.00000 25.54618 5.14814 MINI EXTERN> -159.78306 -91.03537 0.00000 0.00000 0.00000 MINI CONSTR> 34.86828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -139.81740 0.01472 0.29666 0.00018 MINI INTERN> 7.61839 37.82929 0.00000 25.54006 5.14525 MINI EXTERN> -159.80545 -91.03916 0.00000 0.00000 0.00000 MINI CONSTR> 34.89421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20339 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -139.83417 0.01677 0.28365 0.00018 MINI INTERN> 7.62491 37.82586 0.00000 25.52616 5.14546 MINI EXTERN> -159.83769 -91.03847 0.00000 0.00000 0.00000 MINI CONSTR> 34.91959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -139.86187 0.02770 0.08728 0.00008 MINI INTERN> 7.53174 37.87708 0.00000 25.52933 5.14254 MINI EXTERN> -159.82809 -91.05854 0.00000 0.00000 0.00000 MINI CONSTR> 34.94407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20337 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -139.87714 0.01527 0.06960 0.00008 MINI INTERN> 7.54004 37.86782 0.00000 25.51908 5.14191 MINI EXTERN> -159.85350 -91.05930 0.00000 0.00000 0.00000 MINI CONSTR> 34.96682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -139.89340 0.01626 0.07267 0.00009 MINI INTERN> 7.53770 37.86577 0.00000 25.50961 5.14092 MINI EXTERN> -159.87669 -91.06271 0.00000 0.00000 0.00000 MINI CONSTR> 34.99200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20335 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -139.91025 0.01686 0.11302 0.00009 MINI INTERN> 7.52291 37.87283 0.00000 25.50097 5.13955 MINI EXTERN> -159.89735 -91.06917 0.00000 0.00000 0.00000 MINI CONSTR> 35.02001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -139.92496 0.01470 0.07164 0.00009 MINI INTERN> 7.53723 37.85925 0.00000 25.49037 5.13915 MINI EXTERN> -159.92358 -91.06828 0.00000 0.00000 0.00000 MINI CONSTR> 35.04090 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20334 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -139.94123 0.01628 0.13062 0.00010 MINI INTERN> 7.51869 37.86829 0.00000 25.48284 5.13744 MINI EXTERN> -159.94169 -91.07620 0.00000 0.00000 0.00000 MINI CONSTR> 35.06939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -139.95667 0.01543 0.06742 0.00010 MINI INTERN> 7.53858 37.85175 0.00000 25.47043 5.13748 MINI EXTERN> -159.97182 -91.07338 0.00000 0.00000 0.00000 MINI CONSTR> 35.09030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20334 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -139.97325 0.01659 0.14618 0.00010 MINI INTERN> 7.51810 37.86159 0.00000 25.46306 5.13545 MINI EXTERN> -159.98967 -91.08258 0.00000 0.00000 0.00000 MINI CONSTR> 35.12079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -139.99117 0.01792 0.09076 0.00011 MINI INTERN> 7.52844 37.85204 0.00000 25.44983 5.13537 MINI EXTERN> -160.02086 -91.08160 0.00000 0.00000 0.00000 MINI CONSTR> 35.14561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20334 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -140.00649 0.01532 0.12747 0.00011 MINI INTERN> 7.52297 37.85126 0.00000 25.44155 5.13388 MINI EXTERN> -160.04127 -91.08692 0.00000 0.00000 0.00000 MINI CONSTR> 35.17204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -140.02039 0.01390 0.16349 0.00011 MINI INTERN> 7.51433 37.85517 0.00000 25.43312 5.13278 MINI EXTERN> -160.06095 -91.09179 0.00000 0.00000 0.00000 MINI CONSTR> 35.19695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20333 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -140.03631 0.01592 0.17833 0.00012 MINI INTERN> 7.52895 37.83926 0.00000 25.42236 5.13159 MINI EXTERN> -160.08851 -91.09345 0.00000 0.00000 0.00000 MINI CONSTR> 35.22349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -140.05063 0.01432 0.18693 0.00012 MINI INTERN> 7.51156 37.85130 0.00000 25.41359 5.13090 MINI EXTERN> -160.10725 -91.09834 0.00000 0.00000 0.00000 MINI CONSTR> 35.24760 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20332 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -140.06573 0.01509 0.17947 0.00013 MINI INTERN> 7.52033 37.83986 0.00000 25.40410 5.12986 MINI EXTERN> -160.13094 -91.10006 0.00000 0.00000 0.00000 MINI CONSTR> 35.27112 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -140.08004 0.01431 0.20541 0.00013 MINI INTERN> 7.50588 37.85419 0.00000 25.39207 5.13007 MINI EXTERN> -160.15585 -91.10243 0.00000 0.00000 0.00000 MINI CONSTR> 35.29602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20332 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -140.09501 0.01497 0.19061 0.00014 MINI INTERN> 7.50799 37.84549 0.00000 25.38469 5.12848 MINI EXTERN> -160.17478 -91.10650 0.00000 0.00000 0.00000 MINI CONSTR> 35.31962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -140.11372 0.01871 0.06630 0.00006 MINI INTERN> 7.54447 37.81488 0.00000 25.36907 5.12880 MINI EXTERN> -160.21290 -91.09961 0.00000 0.00000 0.00000 MINI CONSTR> 35.34158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20333 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -140.12217 0.00845 0.21768 0.00015 MINI INTERN> 7.50141 37.84593 0.00000 25.36651 5.12679 MINI EXTERN> -160.21664 -91.11289 0.00000 0.00000 0.00000 MINI CONSTR> 35.36672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -140.14224 0.02007 0.06973 0.00006 MINI INTERN> 7.54503 37.80876 0.00000 25.35008 5.12721 MINI EXTERN> -160.25726 -91.10451 0.00000 0.00000 0.00000 MINI CONSTR> 35.38845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20333 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -140.14896 0.00672 0.23441 0.00016 MINI INTERN> 7.52089 37.82022 0.00000 25.34991 5.12407 MINI EXTERN> -160.25903 -91.11776 0.00000 0.00000 0.00000 MINI CONSTR> 35.41274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -140.17058 0.02162 0.07554 0.00007 MINI INTERN> 7.54699 37.80144 0.00000 25.33100 5.12557 MINI EXTERN> -160.30181 -91.10924 0.00000 0.00000 0.00000 MINI CONSTR> 35.43548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20332 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -140.17602 0.00544 0.24181 0.00017 MINI INTERN> 7.50122 37.83166 0.00000 25.33224 5.12263 MINI EXTERN> -160.29759 -91.12529 0.00000 0.00000 0.00000 MINI CONSTR> 35.45911 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -140.19062 0.01460 0.26041 0.00018 MINI INTERN> 7.51982 37.81370 0.00000 25.32095 5.12153 MINI EXTERN> -160.32597 -91.12634 0.00000 0.00000 0.00000 MINI CONSTR> 35.48569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20330 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -140.21430 0.02368 0.08969 0.00008 MINI INTERN> 7.54890 37.79084 0.00000 25.30133 5.12294 MINI EXTERN> -160.37056 -91.11678 0.00000 0.00000 0.00000 MINI CONSTR> 35.50903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -140.22697 0.01267 0.06198 0.00008 MINI INTERN> 7.53983 37.79381 0.00000 25.29471 5.12201 MINI EXTERN> -160.38552 -91.12090 0.00000 0.00000 0.00000 MINI CONSTR> 35.52910 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20331 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -140.24105 0.01408 0.06694 0.00008 MINI INTERN> 7.54162 37.78975 0.00000 25.28476 5.12122 MINI EXTERN> -160.40843 -91.12300 0.00000 0.00000 0.00000 MINI CONSTR> 35.55304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -140.25485 0.01381 0.11241 0.00008 MINI INTERN> 7.55401 37.77875 0.00000 25.27289 5.12047 MINI EXTERN> -160.43636 -91.12336 0.00000 0.00000 0.00000 MINI CONSTR> 35.57875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20331 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -140.26846 0.01360 0.09010 0.00009 MINI INTERN> 7.54243 37.78473 0.00000 25.26493 5.11974 MINI EXTERN> -160.45349 -91.12730 0.00000 0.00000 0.00000 MINI CONSTR> 35.60051 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -140.28114 0.01269 0.10060 0.00009 MINI INTERN> 7.54648 37.77943 0.00000 25.25545 5.11903 MINI EXTERN> -160.47543 -91.12886 0.00000 0.00000 0.00000 MINI CONSTR> 35.62276 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20329 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -140.29391 0.01276 0.10702 0.00009 MINI INTERN> 7.55272 37.77156 0.00000 25.24626 5.11817 MINI EXTERN> -160.49717 -91.13048 0.00000 0.00000 0.00000 MINI CONSTR> 35.64504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -140.30754 0.01364 0.10160 0.00010 MINI INTERN> 7.54663 37.77361 0.00000 25.23728 5.11740 MINI EXTERN> -160.51693 -91.13365 0.00000 0.00000 0.00000 MINI CONSTR> 35.66811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20327 ATOM PAIRS WERE FOUND FOR ATOM LIST 735 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -140.31886 0.01132 0.14512 0.00010 MINI INTERN> 7.56140 37.76101 0.00000 25.22685 5.11667 MINI EXTERN> -160.54185 -91.13373 0.00000 0.00000 0.00000 MINI CONSTR> 35.69078 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -140.33156 0.01270 0.16598 0.00011 MINI INTERN> 7.54533 37.77353 0.00000 25.21747 5.11625 MINI EXTERN> -160.56073 -91.13760 0.00000 0.00000 0.00000 MINI CONSTR> 35.71417 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20325 ATOM PAIRS WERE FOUND FOR ATOM LIST 736 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -140.34347 0.01191 0.17136 0.00011 MINI INTERN> 7.55291 37.76560 0.00000 25.20810 5.11555 MINI EXTERN> -160.58266 -91.13861 0.00000 0.00000 0.00000 MINI CONSTR> 35.73564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -140.35589 0.01242 0.16356 0.00011 MINI INTERN> 7.56790 37.74782 0.00000 25.20039 5.11419 MINI EXTERN> -160.60271 -91.14008 0.00000 0.00000 0.00000 MINI CONSTR> 35.75660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20326 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -140.36770 0.01180 0.18099 0.00012 MINI INTERN> 7.54359 37.76837 0.00000 25.19144 5.11412 MINI EXTERN> -160.61928 -91.14434 0.00000 0.00000 0.00000 MINI CONSTR> 35.77840 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 -140.36770 0.01180 0.18099 0.00014 STPD INTERN> 7.54359 37.76837 0.00000 25.19144 5.11412 STPD EXTERN> -160.61928 -91.14434 0.00000 0.00000 0.00000 STPD CONSTR> 35.77840 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 20326 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20326 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 -140.36770 0.01180 0.18099 0.00000 MINI INTERN> 7.54359 37.76837 0.00000 25.19144 5.11412 MINI EXTERN> -160.61928 -91.14434 0.00000 0.00000 0.00000 MINI CONSTR> 35.77840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -141.88478 1.51708 0.17305 0.18551 MINI INTERN> 7.59445 37.49402 0.00000 23.43324 4.98603 MINI EXTERN> -165.06296 -91.38015 0.00000 0.00000 0.00000 MINI CONSTR> 41.05059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -141.91311 0.02834 0.09105 0.00702 MINI INTERN> 7.55270 37.55138 0.00000 23.39840 4.96477 MINI EXTERN> -165.08365 -91.45173 0.00000 0.00000 0.00000 MINI CONSTR> 41.15503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -141.98040 0.06729 0.18524 0.04357 MINI INTERN> 7.33180 37.24103 0.00000 23.30122 4.91753 MINI EXTERN> -164.65235 -91.47043 0.00000 0.00000 0.00000 MINI CONSTR> 41.35080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -142.09564 0.11523 0.21124 0.06140 MINI INTERN> 7.41602 37.20782 0.00000 23.22719 4.91609 MINI EXTERN> -164.95685 -91.59846 0.00000 0.00000 0.00000 MINI CONSTR> 41.69256 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -142.21570 0.12006 0.19804 0.04351 MINI INTERN> 7.48772 37.12454 0.00000 23.05303 4.90104 MINI EXTERN> -165.18627 -91.66801 0.00000 0.00000 0.00000 MINI CONSTR> 42.07226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -142.28988 0.07418 0.14915 0.04577 MINI INTERN> 7.47391 37.10443 0.00000 22.85647 4.87999 MINI EXTERN> -165.24536 -91.68383 0.00000 0.00000 0.00000 MINI CONSTR> 42.32451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -142.33621 0.04633 0.11981 0.02373 MINI INTERN> 7.51017 37.25250 0.00000 22.66277 4.86037 MINI EXTERN> -165.35065 -91.76390 0.00000 0.00000 0.00000 MINI CONSTR> 42.49253 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -142.37118 0.03497 0.11642 0.01826 MINI INTERN> 7.47385 37.29322 0.00000 22.57772 4.86300 MINI EXTERN> -165.43311 -91.77528 0.00000 0.00000 0.00000 MINI CONSTR> 42.62942 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -142.41509 0.04391 0.11363 0.03320 MINI INTERN> 7.46665 37.19601 0.00000 22.49017 4.82643 MINI EXTERN> -165.47139 -91.73229 0.00000 0.00000 0.00000 MINI CONSTR> 42.80934 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -142.45461 0.03952 0.12519 0.02792 MINI INTERN> 7.44420 37.17635 0.00000 22.43524 4.81407 MINI EXTERN> -165.59904 -91.69676 0.00000 0.00000 0.00000 MINI CONSTR> 42.97132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -142.49331 0.03870 0.12031 0.02889 MINI INTERN> 7.47663 37.10230 0.00000 22.40525 4.83081 MINI EXTERN> -165.56932 -91.85911 0.00000 0.00000 0.00000 MINI CONSTR> 43.12013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -142.52716 0.03385 0.11934 0.02765 MINI INTERN> 7.49704 37.12386 0.00000 22.36440 4.80337 MINI EXTERN> -165.59896 -91.95617 0.00000 0.00000 0.00000 MINI CONSTR> 43.23931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -142.56029 0.03313 0.11300 0.02899 MINI INTERN> 7.47763 37.13582 0.00000 22.37483 4.81320 MINI EXTERN> -165.71997 -91.98689 0.00000 0.00000 0.00000 MINI CONSTR> 43.34510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -142.59165 0.03136 0.10749 0.03027 MINI INTERN> 7.49645 37.10518 0.00000 22.37022 4.82169 MINI EXTERN> -165.84262 -91.96641 0.00000 0.00000 0.00000 MINI CONSTR> 43.42384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -142.62249 0.03084 0.09812 0.03001 MINI INTERN> 7.52003 37.05860 0.00000 22.35982 4.82318 MINI EXTERN> -165.84199 -92.01890 0.00000 0.00000 0.00000 MINI CONSTR> 43.47676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -142.65099 0.02850 0.10325 0.02613 MINI INTERN> 7.50106 37.04354 0.00000 22.27903 4.79260 MINI EXTERN> -165.67349 -92.09740 0.00000 0.00000 0.00000 MINI CONSTR> 43.50368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -142.67893 0.02794 0.11095 0.02988 MINI INTERN> 7.51811 37.04297 0.00000 22.15813 4.81181 MINI EXTERN> -165.53430 -92.19249 0.00000 0.00000 0.00000 MINI CONSTR> 43.51685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -142.71368 0.03475 0.10425 0.04593 MINI INTERN> 7.51995 37.11543 0.00000 22.10745 4.77732 MINI EXTERN> -165.47403 -92.29142 0.00000 0.00000 0.00000 MINI CONSTR> 43.53162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -142.74151 0.02783 0.09488 0.02518 MINI INTERN> 7.46370 37.15105 0.00000 22.10094 4.76943 MINI EXTERN> -165.58840 -92.18363 0.00000 0.00000 0.00000 MINI CONSTR> 43.54541 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -142.77074 0.02924 0.10595 0.03049 MINI INTERN> 7.47023 37.13811 0.00000 22.12808 4.79317 MINI EXTERN> -165.61808 -92.23818 0.00000 0.00000 0.00000 MINI CONSTR> 43.55593 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 -142.77074 0.02924 0.10595 0.02000 CONJ INTERN> 7.47023 37.13811 0.00000 22.12808 4.79317 CONJ EXTERN> -165.61808 -92.23818 0.00000 0.00000 0.00000 CONJ CONSTR> 43.55593 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 ASP 14 N ) 0.10725 ( PROT ASP 14 H ) 0.85797E-01 ( PROT ASP 14 CA ) 0.10725 ( PROT ASP 14 CB ) 0.85797E-01 ( PROT ASP 14 CG ) 0.85797E-01 ( PROT ASP 14 OD1 ) 0.85797E-01 ( PROT ASP 14 OD2 ) 0.85797E-01 ( PROT ASP 14 C ) 0.10725 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.63576 7.24106 -13.20565 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.00447 0.00630 -0.00581 ROTATION MATRIX 0.999999 0.000866 0.000739 -0.000865 0.999999 -0.000574 -0.000739 0.000573 1.000000 AXIS OF ROTATION IS -0.450169 -0.579900 0.679017 ANGLE IS 0.07 TOTAL SQUARE DIFF IS 304.3989 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 1.014088 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.0141" Parameter: A <- "1.0141" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.58845 7.31283 -13.45605 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.06022 -0.05728 0.01569 ROTATION MATRIX 0.999858 0.011543 0.012314 -0.011331 0.999788 -0.017212 -0.012510 0.017070 0.999776 AXIS OF ROTATION IS -0.712555 -0.515959 0.475449 ANGLE IS 1.38 CENTER OF ROTATION 14.353740 6.558915-13.043199 SHIFT IS 0.079926 TOTAL SQUARE DIFF IS 22.0714 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.843789 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.0141" RDCMND substituted energy or value "?RMS" to " 0.8438" Parameter: A <- "1.0141 0.8438" 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 1.0141 0.8438 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 " 43.56" Parameter: H <- "43.56" 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 -186.32667 43.55593 0.19704 ENER INTERN> 7.47023 37.13811 0.00000 22.12808 4.79317 ENER EXTERN> -165.61808 -92.23818 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 " -186.33" Parameter: B <- "-186.33" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -92.24" Parameter: C <- "-92.24" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -165.62" Parameter: C <- " -257.86" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -257.86" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.47" Parameter: D <- "7.47" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 37.14" Parameter: D <- " 44.61" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 22.13" Parameter: D <- " 66.74" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.79" Parameter: D <- " 71.53" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 71.53" 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= 10800 ENER= -186.33 GRMS= 0.20 ELEC= -92.24 VDW= -165.62 RDTITL> *EXTERNAL= -257.86 INTERNAL= 71.53 USER= 0.00 HARM= 43.56 RDTITL> *BOND= 7.47 ANGL= 37.14 DIHE= 22.13 IMPR= 4.79 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= -186.33 GRMS= 0.20 ELEC= -92.24 VDW= -165.62 RDTITL> *EXTERNAL= -257.86 INTERNAL= 71.53 USER= 0.00 HARM= 43.56 RDTITL> *BOND= 7.47 ANGL= 37.14 DIHE= 22.13 IMPR= 4.79 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= -186.33 GRMS= 0.20 ELEC= -92.24 VDW= -165.62 RDTITL> *EXTERNAL= -257.86 INTERNAL= 71.53 USER= 0.00 HARM= 43.56 RDTITL> *BOND= 7.47 ANGL= 37.14 DIHE= 22.13 IMPR= 4.79 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 10800 1.0141 0.8438 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20326 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20216 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 -157.61562 -28.71106 0.12074 0.02000 MINI INTERN> 7.47023 37.13811 0.00000 22.12808 4.79317 MINI EXTERN> -165.61808 -92.23818 0.00000 0.00000 0.00000 MINI CONSTR> 28.71106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -156.59564 -1.01998 2.28335 0.00360 MINI INTERN> 9.31892 37.25922 0.00000 22.27251 4.81393 MINI EXTERN> -167.96650 -91.44578 0.00000 0.00000 0.00000 MINI CONSTR> 29.15206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20208 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -156.45885 -0.13679 2.54691 0.00156 MINI INTERN> 8.74531 37.23306 0.00000 22.27521 4.84038 MINI EXTERN> -167.24524 -91.47345 0.00000 0.00000 0.00000 MINI CONSTR> 29.16588 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -157.64840 1.18956 1.03711 0.00067 MINI INTERN> 7.87657 37.21835 0.00000 22.28381 4.80344 MINI EXTERN> -167.13212 -91.88223 0.00000 0.00000 0.00000 MINI CONSTR> 29.18377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20207 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -157.89830 0.24990 0.07343 0.00012 MINI INTERN> 7.56397 37.18923 0.00000 22.27849 4.79261 MINI EXTERN> -167.06047 -91.86270 0.00000 0.00000 0.00000 MINI CONSTR> 29.20057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -157.90906 0.01076 0.20229 0.00013 MINI INTERN> 7.58588 37.17072 0.00000 22.26465 4.79646 MINI EXTERN> -167.04237 -91.90580 0.00000 0.00000 0.00000 MINI CONSTR> 29.22140 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20207 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -157.91945 0.01039 0.19889 0.00013 MINI INTERN> 7.58918 37.15847 0.00000 22.25664 4.79628 MINI EXTERN> -167.03291 -91.92325 0.00000 0.00000 0.00000 MINI CONSTR> 29.23615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -157.92962 0.01017 0.19999 0.00013 MINI INTERN> 7.60658 37.13811 0.00000 22.24654 4.79558 MINI EXTERN> -167.03481 -91.93397 0.00000 0.00000 0.00000 MINI CONSTR> 29.25235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20206 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -157.93906 0.00944 0.20982 0.00014 MINI INTERN> 7.61684 37.12114 0.00000 22.23815 4.79503 MINI EXTERN> -167.03670 -91.94228 0.00000 0.00000 0.00000 MINI CONSTR> 29.26876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -157.95452 0.01546 0.06520 0.00006 MINI INTERN> 7.52582 37.17033 0.00000 22.24751 4.79990 MINI EXTERN> -167.00686 -91.97497 0.00000 0.00000 0.00000 MINI CONSTR> 29.28376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20206 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -157.96281 0.00829 0.05208 0.00006 MINI INTERN> 7.53221 37.16246 0.00000 22.24153 4.79939 MINI EXTERN> -167.01509 -91.98065 0.00000 0.00000 0.00000 MINI CONSTR> 29.29734 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -157.97147 0.00866 0.05406 0.00006 MINI INTERN> 7.52896 37.16117 0.00000 22.23706 4.79949 MINI EXTERN> -167.02193 -91.98852 0.00000 0.00000 0.00000 MINI CONSTR> 29.31230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20206 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -157.98034 0.00887 0.08777 0.00007 MINI INTERN> 7.50974 37.17114 0.00000 22.23512 4.80030 MINI EXTERN> -167.02518 -92.00061 0.00000 0.00000 0.00000 MINI CONSTR> 29.32915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -157.98901 0.00867 0.06998 0.00007 MINI INTERN> 7.51643 37.16477 0.00000 22.22876 4.79980 MINI EXTERN> -167.03959 -92.00272 0.00000 0.00000 0.00000 MINI CONSTR> 29.34354 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20206 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -157.99719 0.00818 0.07867 0.00007 MINI INTERN> 7.51257 37.16419 0.00000 22.22547 4.79952 MINI EXTERN> -167.04907 -92.00833 0.00000 0.00000 0.00000 MINI CONSTR> 29.35846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -158.00576 0.00857 0.07698 0.00007 MINI INTERN> 7.51550 37.15949 0.00000 22.22074 4.79925 MINI EXTERN> -167.06300 -92.01141 0.00000 0.00000 0.00000 MINI CONSTR> 29.37368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20206 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -158.01305 0.00729 0.11415 0.00008 MINI INTERN> 7.49650 37.17167 0.00000 22.21949 4.79917 MINI EXTERN> -167.06909 -92.01968 0.00000 0.00000 0.00000 MINI CONSTR> 29.38890 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -158.02140 0.00835 0.12072 0.00008 MINI INTERN> 7.50446 37.16283 0.00000 22.21495 4.79881 MINI EXTERN> -167.08515 -92.02162 0.00000 0.00000 0.00000 MINI CONSTR> 29.40433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20207 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -158.02910 0.00770 0.12818 0.00008 MINI INTERN> 7.49143 37.17204 0.00000 22.21197 4.79847 MINI EXTERN> -167.09555 -92.02644 0.00000 0.00000 0.00000 MINI CONSTR> 29.41900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -158.03701 0.00791 0.13762 0.00009 MINI INTERN> 7.49805 37.16409 0.00000 22.20819 4.79790 MINI EXTERN> -167.11080 -92.02856 0.00000 0.00000 0.00000 MINI CONSTR> 29.43411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20207 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -158.04482 0.00781 0.13013 0.00009 MINI INTERN> 7.49236 37.16883 0.00000 22.20368 4.79771 MINI EXTERN> -167.12495 -92.03034 0.00000 0.00000 0.00000 MINI CONSTR> 29.44789 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -158.05202 0.00720 0.15892 0.00009 MINI INTERN> 7.50303 37.15736 0.00000 22.20042 4.79697 MINI EXTERN> -167.14065 -92.03248 0.00000 0.00000 0.00000 MINI CONSTR> 29.46333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20207 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -158.05963 0.00762 0.14505 0.00010 MINI INTERN> 7.50299 37.15637 0.00000 22.19636 4.79655 MINI EXTERN> -167.15471 -92.03352 0.00000 0.00000 0.00000 MINI CONSTR> 29.47633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -158.06968 0.01005 0.04783 0.00004 MINI INTERN> 7.54578 37.12998 0.00000 22.18103 4.79760 MINI EXTERN> -167.19307 -92.02039 0.00000 0.00000 0.00000 MINI CONSTR> 29.48939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20207 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -158.07435 0.00467 0.15354 0.00010 MINI INTERN> 7.49609 37.15993 0.00000 22.18958 4.79578 MINI EXTERN> -167.18177 -92.03852 0.00000 0.00000 0.00000 MINI CONSTR> 29.50456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -158.08528 0.01093 0.04908 0.00004 MINI INTERN> 7.54750 37.12759 0.00000 22.17237 4.79724 MINI EXTERN> -167.22514 -92.02329 0.00000 0.00000 0.00000 MINI CONSTR> 29.51847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -158.08920 0.00392 0.16388 0.00011 MINI INTERN> 7.48699 37.16654 0.00000 22.18231 4.79520 MINI EXTERN> -167.21024 -92.04335 0.00000 0.00000 0.00000 MINI CONSTR> 29.53333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -158.09702 0.00782 0.17287 0.00012 MINI INTERN> 7.49708 37.15697 0.00000 22.17809 4.79469 MINI EXTERN> -167.22821 -92.04433 0.00000 0.00000 0.00000 MINI CONSTR> 29.54868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -158.10869 0.01167 0.05587 0.00005 MINI INTERN> 7.55361 37.12228 0.00000 22.15848 4.79671 MINI EXTERN> -167.27583 -92.02654 0.00000 0.00000 0.00000 MINI CONSTR> 29.56260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -158.11110 0.00241 0.18404 0.00012 MINI INTERN> 7.47737 37.17368 0.00000 22.17122 4.79430 MINI EXTERN> -167.25411 -92.05013 0.00000 0.00000 0.00000 MINI CONSTR> 29.57656 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -158.12355 0.01245 0.06332 0.00005 MINI INTERN> 7.55737 37.11977 0.00000 22.14925 4.79646 MINI EXTERN> -167.30894 -92.02842 0.00000 0.00000 0.00000 MINI CONSTR> 29.59096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -158.13017 0.00662 0.04553 0.00006 MINI INTERN> 7.54585 37.12612 0.00000 22.14854 4.79590 MINI EXTERN> -167.31628 -92.03320 0.00000 0.00000 0.00000 MINI CONSTR> 29.60290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -158.13759 0.00742 0.04829 0.00006 MINI INTERN> 7.54860 37.12441 0.00000 22.14369 4.79580 MINI EXTERN> -167.33328 -92.03389 0.00000 0.00000 0.00000 MINI CONSTR> 29.61707 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -158.14509 0.00750 0.07851 0.00006 MINI INTERN> 7.56481 37.11507 0.00000 22.13538 4.79614 MINI EXTERN> -167.35816 -92.03089 0.00000 0.00000 0.00000 MINI CONSTR> 29.63255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -158.15172 0.00663 0.04553 0.00006 MINI INTERN> 7.54666 37.12510 0.00000 22.13638 4.79527 MINI EXTERN> -167.36153 -92.03753 0.00000 0.00000 0.00000 MINI CONSTR> 29.64393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -158.15901 0.00729 0.09336 0.00006 MINI INTERN> 7.57393 37.10860 0.00000 22.12599 4.79588 MINI EXTERN> -167.39132 -92.03204 0.00000 0.00000 0.00000 MINI CONSTR> 29.65994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 737 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -158.16641 0.00740 0.06800 0.00007 MINI INTERN> 7.55643 37.12049 0.00000 22.12483 4.79538 MINI EXTERN> -167.39901 -92.03734 0.00000 0.00000 0.00000 MINI CONSTR> 29.67282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -158.17259 0.00618 0.10137 0.00007 MINI INTERN> 7.57647 37.10787 0.00000 22.11709 4.79571 MINI EXTERN> -167.42221 -92.03401 0.00000 0.00000 0.00000 MINI CONSTR> 29.68651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -158.18062 0.00803 0.06121 0.00007 MINI INTERN> 7.55657 37.11964 0.00000 22.11712 4.79483 MINI EXTERN> -167.42797 -92.04071 0.00000 0.00000 0.00000 MINI CONSTR> 29.69990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -158.18687 0.00625 0.11156 0.00007 MINI INTERN> 7.58418 37.10196 0.00000 22.10792 4.79525 MINI EXTERN> -167.45485 -92.03600 0.00000 0.00000 0.00000 MINI CONSTR> 29.71467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -158.19348 0.00660 0.12228 0.00008 MINI INTERN> 7.57645 37.11048 0.00000 22.10315 4.79546 MINI EXTERN> -167.46956 -92.03760 0.00000 0.00000 0.00000 MINI CONSTR> 29.72814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -158.19999 0.00652 0.12416 0.00008 MINI INTERN> 7.58756 37.10175 0.00000 22.09827 4.79525 MINI EXTERN> -167.48649 -92.03739 0.00000 0.00000 0.00000 MINI CONSTR> 29.74105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20205 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -158.20690 0.00691 0.13029 0.00008 MINI INTERN> 7.59078 37.09998 0.00000 22.09337 4.79514 MINI EXTERN> -167.50290 -92.03822 0.00000 0.00000 0.00000 MINI CONSTR> 29.75494 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -158.21359 0.00670 0.12347 0.00009 MINI INTERN> 7.58800 37.10150 0.00000 22.09021 4.79482 MINI EXTERN> -167.51501 -92.04051 0.00000 0.00000 0.00000 MINI CONSTR> 29.76740 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20204 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -158.22053 0.00694 0.13251 0.00009 MINI INTERN> 7.59276 37.09893 0.00000 22.08480 4.79475 MINI EXTERN> -167.53248 -92.04095 0.00000 0.00000 0.00000 MINI CONSTR> 29.78166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -158.22706 0.00652 0.15180 0.00009 MINI INTERN> 7.60521 37.09063 0.00000 22.07861 4.79471 MINI EXTERN> -167.55215 -92.04020 0.00000 0.00000 0.00000 MINI CONSTR> 29.79612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20203 ATOM PAIRS WERE FOUND FOR ATOM LIST 740 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -158.23365 0.00659 0.14045 0.00010 MINI INTERN> 7.59785 37.09589 0.00000 22.07586 4.79443 MINI EXTERN> -167.56257 -92.04308 0.00000 0.00000 0.00000 MINI CONSTR> 29.80796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -158.24100 0.00735 0.14240 0.00010 MINI INTERN> 7.59912 37.09543 0.00000 22.07094 4.79425 MINI EXTERN> -167.57880 -92.04446 0.00000 0.00000 0.00000 MINI CONSTR> 29.82252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20203 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -158.25048 0.00948 0.04544 0.00004 MINI INTERN> 7.53400 37.13353 0.00000 22.08140 4.79140 MINI EXTERN> -167.56207 -92.06397 0.00000 0.00000 0.00000 MINI CONSTR> 29.83524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -158.25364 0.00316 0.15610 0.00011 MINI INTERN> 7.60486 37.09287 0.00000 22.06144 4.79407 MINI EXTERN> -167.60939 -92.04612 0.00000 0.00000 0.00000 MINI CONSTR> 29.84864 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20202 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -158.26016 0.00652 0.16965 0.00011 MINI INTERN> 7.61508 37.08238 0.00000 22.05823 4.79325 MINI EXTERN> -167.62353 -92.04806 0.00000 0.00000 0.00000 MINI CONSTR> 29.86249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -158.27043 0.01027 0.05467 0.00005 MINI INTERN> 7.52759 37.13809 0.00000 22.07055 4.79037 MINI EXTERN> -167.60084 -92.07097 0.00000 0.00000 0.00000 MINI CONSTR> 29.87479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20199 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -158.27226 0.00182 0.17365 0.00012 MINI INTERN> 7.61392 37.08829 0.00000 22.04751 4.79371 MINI EXTERN> -167.65397 -92.04890 0.00000 0.00000 0.00000 MINI CONSTR> 29.88719 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -158.28354 0.01129 0.05847 0.00005 MINI INTERN> 7.52558 37.13972 0.00000 22.06286 4.78977 MINI EXTERN> -167.62724 -92.07505 0.00000 0.00000 0.00000 MINI CONSTR> 29.90082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20199 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -158.28932 0.00578 0.04169 0.00005 MINI INTERN> 7.53806 37.13196 0.00000 22.05650 4.79009 MINI EXTERN> -167.64474 -92.07288 0.00000 0.00000 0.00000 MINI CONSTR> 29.91170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -158.29605 0.00673 0.04441 0.00006 MINI INTERN> 7.53587 37.13327 0.00000 22.05296 4.78967 MINI EXTERN> -167.65742 -92.07552 0.00000 0.00000 0.00000 MINI CONSTR> 29.92512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20199 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -158.30243 0.00638 0.07823 0.00006 MINI INTERN> 7.51496 37.14758 0.00000 22.05295 4.78862 MINI EXTERN> -167.66252 -92.08317 0.00000 0.00000 0.00000 MINI CONSTR> 29.93915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -158.30826 0.00583 0.04236 0.00006 MINI INTERN> 7.53849 37.13187 0.00000 22.04475 4.78927 MINI EXTERN> -167.68377 -92.07818 0.00000 0.00000 0.00000 MINI CONSTR> 29.94932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20198 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -158.31452 0.00626 0.08981 0.00006 MINI INTERN> 7.51315 37.14839 0.00000 22.04623 4.78782 MINI EXTERN> -167.68616 -92.08779 0.00000 0.00000 0.00000 MINI CONSTR> 29.96384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -158.32101 0.00649 0.06572 0.00006 MINI INTERN> 7.52163 37.14442 0.00000 22.03930 4.78830 MINI EXTERN> -167.70430 -92.08588 0.00000 0.00000 0.00000 MINI CONSTR> 29.97552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20198 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -158.32625 0.00525 0.09631 0.00007 MINI INTERN> 7.50688 37.15388 0.00000 22.03927 4.78728 MINI EXTERN> -167.70894 -92.09230 0.00000 0.00000 0.00000 MINI CONSTR> 29.98767 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -158.33315 0.00689 0.06481 0.00007 MINI INTERN> 7.52738 37.13930 0.00000 22.03163 4.78762 MINI EXTERN> -167.72988 -92.08896 0.00000 0.00000 0.00000 MINI CONSTR> 29.99975 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20198 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -158.33816 0.00501 0.10278 0.00007 MINI INTERN> 7.50792 37.15269 0.00000 22.03209 4.78656 MINI EXTERN> -167.73309 -92.09625 0.00000 0.00000 0.00000 MINI CONSTR> 30.01192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -158.34400 0.00584 0.11890 0.00007 MINI INTERN> 7.49887 37.16234 0.00000 22.02761 4.78664 MINI EXTERN> -167.74552 -92.09855 0.00000 0.00000 0.00000 MINI CONSTR> 30.02460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20198 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -158.34955 0.00555 0.12157 0.00008 MINI INTERN> 7.49548 37.16380 0.00000 22.02539 4.78602 MINI EXTERN> -167.75452 -92.10184 0.00000 0.00000 0.00000 MINI CONSTR> 30.03611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -158.35536 0.00581 0.11455 0.00008 MINI INTERN> 7.50452 37.15546 0.00000 22.02166 4.78557 MINI EXTERN> -167.76728 -92.10262 0.00000 0.00000 0.00000 MINI CONSTR> 30.04733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20198 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -158.36109 0.00573 0.12750 0.00008 MINI INTERN> 7.49736 37.16471 0.00000 22.01620 4.78593 MINI EXTERN> -167.78114 -92.10375 0.00000 0.00000 0.00000 MINI CONSTR> 30.05960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -158.36702 0.00593 0.11946 0.00009 MINI INTERN> 7.50006 37.15944 0.00000 22.01448 4.78497 MINI EXTERN> -167.79016 -92.10707 0.00000 0.00000 0.00000 MINI CONSTR> 30.07127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20198 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -158.37292 0.00591 0.12564 0.00009 MINI INTERN> 7.49378 37.16594 0.00000 22.01028 4.78491 MINI EXTERN> -167.80220 -92.10928 0.00000 0.00000 0.00000 MINI CONSTR> 30.08365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -158.38046 0.00754 0.04213 0.00004 MINI INTERN> 7.55379 37.12488 0.00000 21.99439 4.78684 MINI EXTERN> -167.83988 -92.09481 0.00000 0.00000 0.00000 MINI CONSTR> 30.09432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20197 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -158.38358 0.00312 0.13946 0.00010 MINI INTERN> 7.48806 37.16991 0.00000 22.00454 4.78402 MINI EXTERN> -167.82190 -92.11477 0.00000 0.00000 0.00000 MINI CONSTR> 30.10656 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -158.39207 0.00849 0.04476 0.00004 MINI INTERN> 7.55627 37.12392 0.00000 21.98598 4.78645 MINI EXTERN> -167.86511 -92.09758 0.00000 0.00000 0.00000 MINI CONSTR> 30.11800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20197 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -158.39443 0.00236 0.15293 0.00010 MINI INTERN> 7.49830 37.16072 0.00000 21.99741 4.78308 MINI EXTERN> -167.84579 -92.11792 0.00000 0.00000 0.00000 MINI CONSTR> 30.12977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -158.40332 0.00889 0.05004 0.00004 MINI INTERN> 7.56115 37.12118 0.00000 21.97743 4.78609 MINI EXTERN> -167.89042 -92.09985 0.00000 0.00000 0.00000 MINI CONSTR> 30.14111 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -158.40502 0.00169 0.16197 0.00011 MINI INTERN> 7.47845 37.17870 0.00000 21.99097 4.78277 MINI EXTERN> -167.86443 -92.12392 0.00000 0.00000 0.00000 MINI CONSTR> 30.15244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -158.41449 0.00948 0.05701 0.00005 MINI INTERN> 7.56478 37.11975 0.00000 21.96877 4.78578 MINI EXTERN> -167.91562 -92.10215 0.00000 0.00000 0.00000 MINI CONSTR> 30.16420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20197 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -158.41948 0.00499 0.04027 0.00005 MINI INTERN> 7.55360 37.12645 0.00000 21.96829 4.78501 MINI EXTERN> -167.91973 -92.10696 0.00000 0.00000 0.00000 MINI CONSTR> 30.17387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -158.42530 0.00582 0.06645 0.00005 MINI INTERN> 7.57133 37.11597 0.00000 21.96003 4.78548 MINI EXTERN> -167.94090 -92.10397 0.00000 0.00000 0.00000 MINI CONSTR> 30.18677 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 739 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -158.43038 0.00509 0.03876 0.00005 MINI INTERN> 7.55201 37.12810 0.00000 21.96106 4.78447 MINI EXTERN> -167.94156 -92.11069 0.00000 0.00000 0.00000 MINI CONSTR> 30.19623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -158.43651 0.00613 0.04085 0.00005 MINI INTERN> 7.55398 37.12735 0.00000 21.95624 4.78431 MINI EXTERN> -167.95532 -92.11196 0.00000 0.00000 0.00000 MINI CONSTR> 30.20890 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -158.44196 0.00545 0.08137 0.00006 MINI INTERN> 7.57944 37.11180 0.00000 21.94660 4.78500 MINI EXTERN> -167.97945 -92.10720 0.00000 0.00000 0.00000 MINI CONSTR> 30.22184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -158.44792 0.00596 0.05006 0.00006 MINI INTERN> 7.56292 37.12173 0.00000 21.94672 4.78399 MINI EXTERN> -167.98248 -92.11356 0.00000 0.00000 0.00000 MINI CONSTR> 30.23275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -158.45354 0.00562 0.06391 0.00006 MINI INTERN> 7.56558 37.12166 0.00000 21.94121 4.78409 MINI EXTERN> -167.99702 -92.11395 0.00000 0.00000 0.00000 MINI CONSTR> 30.24488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -158.45808 0.00454 0.09178 0.00006 MINI INTERN> 7.58371 37.11030 0.00000 21.93410 4.78444 MINI EXTERN> -168.01528 -92.11115 0.00000 0.00000 0.00000 MINI CONSTR> 30.25580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -158.46405 0.00597 0.06638 0.00007 MINI INTERN> 7.57277 37.11562 0.00000 21.93377 4.78341 MINI EXTERN> -168.01967 -92.11673 0.00000 0.00000 0.00000 MINI CONSTR> 30.26679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -158.46830 0.00425 0.09927 0.00007 MINI INTERN> 7.59092 37.10455 0.00000 21.92661 4.78380 MINI EXTERN> -168.03784 -92.11380 0.00000 0.00000 0.00000 MINI CONSTR> 30.27747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20195 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -158.47314 0.00485 0.11490 0.00007 MINI INTERN> 7.58463 37.11260 0.00000 21.92172 4.78407 MINI EXTERN> -168.04970 -92.11506 0.00000 0.00000 0.00000 MINI CONSTR> 30.28859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -158.47828 0.00514 0.10472 0.00007 MINI INTERN> 7.59335 37.10467 0.00000 21.91815 4.78364 MINI EXTERN> -168.06099 -92.11581 0.00000 0.00000 0.00000 MINI CONSTR> 30.29870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -158.48369 0.00541 0.11853 0.00008 MINI INTERN> 7.59350 37.10658 0.00000 21.91297 4.78367 MINI EXTERN> -168.07456 -92.11684 0.00000 0.00000 0.00000 MINI CONSTR> 30.31100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -158.48879 0.00510 0.11477 0.00008 MINI INTERN> 7.59949 37.10020 0.00000 21.91015 4.78305 MINI EXTERN> -168.08440 -92.11861 0.00000 0.00000 0.00000 MINI CONSTR> 30.32134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -158.49541 0.00662 0.03887 0.00003 MINI INTERN> 7.54198 37.13760 0.00000 21.91776 4.78088 MINI EXTERN> -168.07028 -92.13458 0.00000 0.00000 0.00000 MINI CONSTR> 30.33123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -158.49852 0.00311 0.12450 0.00008 MINI INTERN> 7.60486 37.09769 0.00000 21.90172 4.78278 MINI EXTERN> -168.10764 -92.12048 0.00000 0.00000 0.00000 MINI CONSTR> 30.34255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -158.50565 0.00713 0.04067 0.00004 MINI INTERN> 7.54059 37.13889 0.00000 21.91084 4.78027 MINI EXTERN> -168.09050 -92.13850 0.00000 0.00000 0.00000 MINI CONSTR> 30.35276 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -158.50814 0.00249 0.13628 0.00009 MINI INTERN> 7.59669 37.10708 0.00000 21.89383 4.78271 MINI EXTERN> -168.12823 -92.12391 0.00000 0.00000 0.00000 MINI CONSTR> 30.36369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20196 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -158.51250 0.00436 0.15856 0.00009 MINI INTERN> 7.60619 37.09450 0.00000 21.89370 4.78113 MINI EXTERN> -168.13432 -92.12807 0.00000 0.00000 0.00000 MINI CONSTR> 30.37437 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -158.51735 0.00485 0.15458 0.00010 MINI INTERN> 7.61728 37.08929 0.00000 21.88655 4.78171 MINI EXTERN> -168.15130 -92.12558 0.00000 0.00000 0.00000 MINI CONSTR> 30.38471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20193 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -158.52547 0.00812 0.04585 0.00004 MINI INTERN> 7.53619 37.14288 0.00000 21.89739 4.77910 MINI EXTERN> -168.12931 -92.14638 0.00000 0.00000 0.00000 MINI CONSTR> 30.39466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -158.53001 0.00454 0.03738 0.00004 MINI INTERN> 7.54461 37.13729 0.00000 21.89258 4.77914 MINI EXTERN> -168.14188 -92.14575 0.00000 0.00000 0.00000 MINI CONSTR> 30.40400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20192 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -158.53498 0.00497 0.03885 0.00005 MINI INTERN> 7.54209 37.13932 0.00000 21.88939 4.77881 MINI EXTERN> -168.15111 -92.14806 0.00000 0.00000 0.00000 MINI CONSTR> 30.41457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -158.53996 0.00498 0.03750 0.00005 MINI INTERN> 7.54366 37.13851 0.00000 21.88546 4.77861 MINI EXTERN> -168.16193 -92.14935 0.00000 0.00000 0.00000 MINI CONSTR> 30.42507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20191 ATOM PAIRS WERE FOUND FOR ATOM LIST 738 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -158.54515 0.00519 0.03760 0.00005 MINI INTERN> 7.54347 37.13892 0.00000 21.88170 4.77833 MINI EXTERN> -168.17248 -92.15118 0.00000 0.00000 0.00000 MINI CONSTR> 30.43609 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 -158.54515 0.00519 0.03760 0.00006 STPD INTERN> 7.54347 37.13892 0.00000 21.88170 4.77833 STPD EXTERN> -168.17248 -92.15118 0.00000 0.00000 0.00000 STPD CONSTR> 30.43609 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 20191 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20191 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 -158.54515 0.00519 0.03760 0.00000 MINI INTERN> 7.54347 37.13892 0.00000 21.88170 4.77833 MINI EXTERN> -168.17248 -92.15118 0.00000 0.00000 0.00000 MINI CONSTR> 30.43609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -159.22851 0.68336 0.33325 0.20102 MINI INTERN> 7.54634 37.15669 0.00000 21.05079 4.72831 MINI EXTERN> -170.60443 -92.17970 0.00000 0.00000 0.00000 MINI CONSTR> 33.07349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -159.41921 0.19070 0.09339 0.01873 MINI INTERN> 7.60894 37.37411 0.00000 20.80753 4.71243 MINI EXTERN> -171.31451 -92.55746 0.00000 0.00000 0.00000 MINI CONSTR> 33.94976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -159.44382 0.02461 0.16019 0.01871 MINI INTERN> 7.56406 37.33200 0.00000 20.74509 4.69225 MINI EXTERN> -171.23162 -92.56475 0.00000 0.00000 0.00000 MINI CONSTR> 34.01915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -159.54681 0.10298 0.17025 0.06527 MINI INTERN> 7.44638 37.18857 0.00000 20.61639 4.64659 MINI EXTERN> -171.28420 -92.43182 0.00000 0.00000 0.00000 MINI CONSTR> 34.27127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -159.63240 0.08559 0.18062 0.05959 MINI INTERN> 7.56779 37.10852 0.00000 20.51104 4.64430 MINI EXTERN> -171.41694 -92.52044 0.00000 0.00000 0.00000 MINI CONSTR> 34.47332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -159.69044 0.05804 0.12706 0.02502 MINI INTERN> 7.57373 37.08349 0.00000 20.39089 4.61017 MINI EXTERN> -171.41379 -92.54422 0.00000 0.00000 0.00000 MINI CONSTR> 34.60929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -159.72536 0.03492 0.11468 0.02649 MINI INTERN> 7.60630 37.10140 0.00000 20.30230 4.63162 MINI EXTERN> -171.40069 -92.65311 0.00000 0.00000 0.00000 MINI CONSTR> 34.68681 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -159.76174 0.03638 0.11551 0.03008 MINI INTERN> 7.58014 37.05062 0.00000 20.25135 4.61289 MINI EXTERN> -171.31373 -92.70812 0.00000 0.00000 0.00000 MINI CONSTR> 34.76510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -159.79106 0.02932 0.12175 0.01678 MINI INTERN> 7.55315 37.02532 0.00000 20.24037 4.59219 MINI EXTERN> -171.32836 -92.69977 0.00000 0.00000 0.00000 MINI CONSTR> 34.82603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -159.83012 0.03906 0.11544 0.03006 MINI INTERN> 7.60138 36.86208 0.00000 20.25739 4.57235 MINI EXTERN> -171.43832 -92.58754 0.00000 0.00000 0.00000 MINI CONSTR> 34.90255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -159.86626 0.03614 0.10664 0.03101 MINI INTERN> 7.57504 36.79195 0.00000 20.23622 4.57462 MINI EXTERN> -171.42684 -92.57937 0.00000 0.00000 0.00000 MINI CONSTR> 34.96211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -159.88886 0.02260 0.09072 0.01802 MINI INTERN> 7.57124 36.76314 0.00000 20.22773 4.56054 MINI EXTERN> -171.30825 -92.68942 0.00000 0.00000 0.00000 MINI CONSTR> 34.98616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -159.90805 0.01920 0.07778 0.01611 MINI INTERN> 7.55068 36.64781 0.00000 20.19064 4.55742 MINI EXTERN> -171.16620 -92.68454 0.00000 0.00000 0.00000 MINI CONSTR> 34.99614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -159.92207 0.01402 0.07269 0.01778 MINI INTERN> 7.55637 36.68212 0.00000 20.20974 4.59887 MINI EXTERN> -171.20246 -92.76028 0.00000 0.00000 0.00000 MINI CONSTR> 34.99357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -159.93382 0.01175 0.06498 0.01088 MINI INTERN> 7.57498 36.67986 0.00000 20.26393 4.58416 MINI EXTERN> -171.27633 -92.74432 0.00000 0.00000 0.00000 MINI CONSTR> 34.98390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -159.94488 0.01106 0.06353 0.01255 MINI INTERN> 7.59019 36.62827 0.00000 20.29663 4.58968 MINI EXTERN> -171.33120 -92.67891 0.00000 0.00000 0.00000 MINI CONSTR> 34.96046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -159.95613 0.01125 0.07122 0.01520 MINI INTERN> 7.58972 36.61877 0.00000 20.33106 4.57024 MINI EXTERN> -171.22644 -92.75891 0.00000 0.00000 0.00000 MINI CONSTR> 34.91942 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -159.96619 0.01006 0.06320 0.01436 MINI INTERN> 7.54241 36.59677 0.00000 20.33062 4.57282 MINI EXTERN> -171.06152 -92.82076 0.00000 0.00000 0.00000 MINI CONSTR> 34.87346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -159.97498 0.00879 0.05690 0.01067 MINI INTERN> 7.56182 36.62606 0.00000 20.31128 4.56715 MINI EXTERN> -170.95586 -92.91116 0.00000 0.00000 0.00000 MINI CONSTR> 34.82572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -159.98174 0.00675 0.04960 0.01002 MINI INTERN> 7.57930 36.65372 0.00000 20.32039 4.57367 MINI EXTERN> -171.01945 -92.87664 0.00000 0.00000 0.00000 MINI CONSTR> 34.78727 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 -159.98174 0.00675 0.04960 0.02000 CONJ INTERN> 7.57930 36.65372 0.00000 20.32039 4.57367 CONJ EXTERN> -171.01945 -92.87664 0.00000 0.00000 0.00000 CONJ CONSTR> 34.78727 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 ASP 14 N ) 0.69710E-01 ( PROT ASP 14 H ) 0.55768E-01 ( PROT ASP 14 CA ) 0.69710E-01 ( PROT ASP 14 CB ) 0.55768E-01 ( PROT ASP 14 CG ) 0.55768E-01 ( PROT ASP 14 OD1 ) 0.55768E-01 ( PROT ASP 14 OD2 ) 0.55768E-01 ( PROT ASP 14 C ) 0.69710E-01 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.62311 7.23129 -13.20332 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.01712 0.01608 -0.00814 ROTATION MATRIX 0.999994 -0.002282 -0.002643 0.002293 0.999990 0.003925 0.002634 -0.003931 0.999989 AXIS OF ROTATION IS 0.747406 0.501972 -0.435211 ANGLE IS 0.30 TOTAL SQUARE DIFF IS 374.5529 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 1.124892 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.1249" Parameter: A <- "1.1249" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.59239 7.31403 -13.46670 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.06416 -0.05848 0.02634 ROTATION MATRIX 0.999940 0.007247 0.008199 -0.007141 0.999891 -0.012941 -0.008292 0.012882 0.999883 AXIS OF ROTATION IS -0.762881 -0.487165 0.425068 ANGLE IS 0.97 TOTAL SQUARE DIFF IS 27.5197 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 0.942195 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.1249" RDCMND substituted energy or value "?RMS" to " 0.9422" Parameter: A <- "1.1249 0.9422" 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 1.1249 0.9422 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 " 34.79" Parameter: H <- "34.79" 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 -194.76901 34.78727 0.12862 ENER INTERN> 7.57930 36.65372 0.00000 20.32039 4.57367 ENER EXTERN> -171.01945 -92.87664 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 " -194.77" Parameter: B <- "-194.77" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -92.88" Parameter: C <- "-92.88" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -171.02" Parameter: C <- " -263.90" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -263.90" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.58" Parameter: D <- "7.58" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 36.65" Parameter: D <- " 44.23" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 20.32" Parameter: D <- " 64.55" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.57" Parameter: D <- " 69.12" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 69.12" 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= -194.77 GRMS= 0.13 ELEC= -92.88 VDW= -171.02 RDTITL> *EXTERNAL= -263.90 INTERNAL= 69.12 USER= 0.00 HARM= 34.79 RDTITL> *BOND= 7.58 ANGL= 36.65 DIHE= 20.32 IMPR= 4.57 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: 3/17/14 17:25:10 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 296 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 20191 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20106 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 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 -171.96130 -22.80771 0.06404 0.02000 MINI INTERN> 7.57930 36.65372 0.00000 20.32039 4.57367 MINI EXTERN> -171.01945 -92.87664 0.00000 0.00000 0.00000 MINI CONSTR> 22.80771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -165.01019 -6.95111 6.18922 0.00360 MINI INTERN> 13.07743 38.23392 0.00000 20.59648 4.69409 MINI EXTERN> -173.38372 -91.45429 0.00000 0.00000 0.00000 MINI CONSTR> 23.22590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20103 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -171.98593 6.97574 0.67973 0.00065 MINI INTERN> 7.76918 36.79349 0.00000 20.50583 4.58827 MINI EXTERN> -173.11392 -91.75119 0.00000 0.00000 0.00000 MINI CONSTR> 23.22241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -172.11142 0.12549 0.28350 0.00028 MINI INTERN> 7.68102 36.78687 0.00000 20.45159 4.57369 MINI EXTERN> -172.87787 -91.95211 0.00000 0.00000 0.00000 MINI CONSTR> 23.22539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20103 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -172.13425 0.02283 0.21981 0.00012 MINI INTERN> 7.67100 36.74834 0.00000 20.43834 4.58072 MINI EXTERN> -172.73291 -92.06962 0.00000 0.00000 0.00000 MINI CONSTR> 23.22989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -172.14735 0.01309 0.06401 0.00005 MINI INTERN> 7.66975 36.73263 0.00000 20.42182 4.58258 MINI EXTERN> -172.65760 -92.13029 0.00000 0.00000 0.00000 MINI CONSTR> 23.23377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20103 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -172.15346 0.00611 0.05390 0.00005 MINI INTERN> 7.66278 36.72533 0.00000 20.40902 4.58423 MINI EXTERN> -172.59136 -92.18160 0.00000 0.00000 0.00000 MINI CONSTR> 23.23814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -172.15895 0.00549 0.05659 0.00006 MINI INTERN> 7.65710 36.71808 0.00000 20.39668 4.58554 MINI EXTERN> -172.53281 -92.22675 0.00000 0.00000 0.00000 MINI CONSTR> 23.24321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20101 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -172.16277 0.00382 0.09769 0.00006 MINI INTERN> 7.65403 36.71286 0.00000 20.38579 4.58658 MINI EXTERN> -172.48725 -92.26318 0.00000 0.00000 0.00000 MINI CONSTR> 23.24839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -172.16688 0.00411 0.10660 0.00006 MINI INTERN> 7.65017 36.70795 0.00000 20.37632 4.58726 MINI EXTERN> -172.44925 -92.29321 0.00000 0.00000 0.00000 MINI CONSTR> 23.25388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20100 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -172.17064 0.00375 0.10238 0.00006 MINI INTERN> 7.64681 36.70352 0.00000 20.36892 4.58763 MINI EXTERN> -172.42173 -92.31471 0.00000 0.00000 0.00000 MINI CONSTR> 23.25892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -172.17438 0.00374 0.10402 0.00006 MINI INTERN> 7.64404 36.69935 0.00000 20.36153 4.58787 MINI EXTERN> -172.39677 -92.33506 0.00000 0.00000 0.00000 MINI CONSTR> 23.26466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20100 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -172.17913 0.00475 0.03310 0.00003 MINI INTERN> 7.63864 36.69212 0.00000 20.35646 4.58751 MINI EXTERN> -172.37802 -92.34577 0.00000 0.00000 0.00000 MINI CONSTR> 23.26994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -172.18099 0.00186 0.11331 0.00007 MINI INTERN> 7.64061 36.69192 0.00000 20.34922 4.58796 MINI EXTERN> -172.36213 -92.36466 0.00000 0.00000 0.00000 MINI CONSTR> 23.27610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20100 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -172.18442 0.00343 0.11498 0.00007 MINI INTERN> 7.63967 36.68729 0.00000 20.34374 4.58775 MINI EXTERN> -172.34969 -92.37548 0.00000 0.00000 0.00000 MINI CONSTR> 23.28230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -172.18946 0.00504 0.03541 0.00003 MINI INTERN> 7.63299 36.68292 0.00000 20.33944 4.58724 MINI EXTERN> -172.33943 -92.38082 0.00000 0.00000 0.00000 MINI CONSTR> 23.28819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20099 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -172.19057 0.00111 0.12327 0.00008 MINI INTERN> 7.63857 36.68060 0.00000 20.33411 4.58736 MINI EXTERN> -172.33398 -92.39154 0.00000 0.00000 0.00000 MINI CONSTR> 23.29432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -172.19608 0.00551 0.03667 0.00003 MINI INTERN> 7.63062 36.67852 0.00000 20.32996 4.58682 MINI EXTERN> -172.32731 -92.39556 0.00000 0.00000 0.00000 MINI CONSTR> 23.30087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20098 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -172.19892 0.00285 0.03023 0.00003 MINI INTERN> 7.63035 36.67674 0.00000 20.32625 4.58658 MINI EXTERN> -172.32479 -92.40042 0.00000 0.00000 0.00000 MINI CONSTR> 23.30638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -172.20217 0.00325 0.03003 0.00004 MINI INTERN> 7.62970 36.67502 0.00000 20.32209 4.58631 MINI EXTERN> -172.32311 -92.40509 0.00000 0.00000 0.00000 MINI CONSTR> 23.31291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20098 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -172.20542 0.00325 0.03037 0.00004 MINI INTERN> 7.62915 36.67352 0.00000 20.31807 4.58603 MINI EXTERN> -172.32281 -92.40895 0.00000 0.00000 0.00000 MINI CONSTR> 23.31957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -172.20864 0.00322 0.05669 0.00004 MINI INTERN> 7.62776 36.67263 0.00000 20.31377 4.58585 MINI EXTERN> -172.32350 -92.41210 0.00000 0.00000 0.00000 MINI CONSTR> 23.32696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20098 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -172.21176 0.00312 0.03742 0.00004 MINI INTERN> 7.62817 36.67120 0.00000 20.31052 4.58551 MINI EXTERN> -172.32563 -92.41448 0.00000 0.00000 0.00000 MINI CONSTR> 23.33294 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -172.21458 0.00281 0.03000 0.00004 MINI INTERN> 7.62836 36.67021 0.00000 20.30748 4.58521 MINI EXTERN> -172.32823 -92.41635 0.00000 0.00000 0.00000 MINI CONSTR> 23.33874 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20097 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -172.21753 0.00296 0.06804 0.00004 MINI INTERN> 7.62727 36.66980 0.00000 20.30342 4.58516 MINI EXTERN> -172.33179 -92.41768 0.00000 0.00000 0.00000 MINI CONSTR> 23.34630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -172.22086 0.00333 0.03963 0.00004 MINI INTERN> 7.62798 36.66860 0.00000 20.30043 4.58475 MINI EXTERN> -172.33602 -92.41908 0.00000 0.00000 0.00000 MINI CONSTR> 23.35248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20097 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -172.22397 0.00311 0.04834 0.00005 MINI INTERN> 7.62804 36.66781 0.00000 20.29694 4.58455 MINI EXTERN> -172.34093 -92.41988 0.00000 0.00000 0.00000 MINI CONSTR> 23.35950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -172.22636 0.00239 0.07373 0.00005 MINI INTERN> 7.62778 36.66758 0.00000 20.29382 4.58450 MINI EXTERN> -172.34565 -92.42017 0.00000 0.00000 0.00000 MINI CONSTR> 23.36578 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20097 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -172.22941 0.00305 0.07651 0.00005 MINI INTERN> 7.62860 36.66638 0.00000 20.29053 4.58430 MINI EXTERN> -172.35145 -92.42045 0.00000 0.00000 0.00000 MINI CONSTR> 23.37267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -172.23239 0.00298 0.08215 0.00005 MINI INTERN> 7.62964 36.66507 0.00000 20.28727 4.58413 MINI EXTERN> -172.35761 -92.42049 0.00000 0.00000 0.00000 MINI CONSTR> 23.37960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20097 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -172.23520 0.00281 0.08996 0.00005 MINI INTERN> 7.63056 36.66402 0.00000 20.28414 4.58398 MINI EXTERN> -172.36388 -92.42037 0.00000 0.00000 0.00000 MINI CONSTR> 23.38635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -172.23793 0.00273 0.08511 0.00006 MINI INTERN> 7.63022 36.66443 0.00000 20.28155 4.58374 MINI EXTERN> -172.36961 -92.42044 0.00000 0.00000 0.00000 MINI CONSTR> 23.39217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20096 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -172.24082 0.00290 0.08920 0.00006 MINI INTERN> 7.63149 36.66312 0.00000 20.27849 4.58358 MINI EXTERN> -172.37637 -92.42010 0.00000 0.00000 0.00000 MINI CONSTR> 23.39897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -172.24380 0.00298 0.09201 0.00006 MINI INTERN> 7.63326 36.66131 0.00000 20.27541 4.58340 MINI EXTERN> -172.38346 -92.41963 0.00000 0.00000 0.00000 MINI CONSTR> 23.40592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20094 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -172.24683 0.00303 0.09273 0.00006 MINI INTERN> 7.63513 36.65944 0.00000 20.27237 4.58319 MINI EXTERN> -172.39074 -92.41911 0.00000 0.00000 0.00000 MINI CONSTR> 23.41288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -172.25074 0.00391 0.02939 0.00003 MINI INTERN> 7.62884 36.66791 0.00000 20.27025 4.58217 MINI EXTERN> -172.39828 -92.42068 0.00000 0.00000 0.00000 MINI CONSTR> 23.41906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20093 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -172.25212 0.00138 0.10147 0.00007 MINI INTERN> 7.63734 36.65763 0.00000 20.26682 4.58288 MINI EXTERN> -172.40452 -92.41791 0.00000 0.00000 0.00000 MINI CONSTR> 23.42563 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -172.25499 0.00287 0.10374 0.00007 MINI INTERN> 7.63970 36.65543 0.00000 20.26391 4.58267 MINI EXTERN> -172.41198 -92.41715 0.00000 0.00000 0.00000 MINI CONSTR> 23.43243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20092 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -172.25788 0.00290 0.10683 0.00007 MINI INTERN> 7.64267 36.65268 0.00000 20.26097 4.58242 MINI EXTERN> -172.41974 -92.41630 0.00000 0.00000 0.00000 MINI CONSTR> 23.43941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -172.26074 0.00285 0.11166 0.00007 MINI INTERN> 7.64561 36.65012 0.00000 20.25801 4.58215 MINI EXTERN> -172.42772 -92.41537 0.00000 0.00000 0.00000 MINI CONSTR> 23.44646 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20092 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -172.26540 0.00467 0.03537 0.00003 MINI INTERN> 7.62819 36.67096 0.00000 20.25568 4.58122 MINI EXTERN> -172.43715 -92.41748 0.00000 0.00000 0.00000 MINI CONSTR> 23.45318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -172.26786 0.00246 0.02725 0.00003 MINI INTERN> 7.63051 36.66837 0.00000 20.25327 4.58116 MINI EXTERN> -172.44349 -92.41642 0.00000 0.00000 0.00000 MINI CONSTR> 23.45874 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20092 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -172.27077 0.00291 0.02696 0.00003 MINI INTERN> 7.63090 36.66843 0.00000 20.25039 4.58099 MINI EXTERN> -172.45152 -92.41551 0.00000 0.00000 0.00000 MINI CONSTR> 23.46556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -172.27374 0.00297 0.02688 0.00004 MINI INTERN> 7.63121 36.66861 0.00000 20.24745 4.58082 MINI EXTERN> -172.45985 -92.41456 0.00000 0.00000 0.00000 MINI CONSTR> 23.47257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20092 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -172.27673 0.00299 0.02720 0.00004 MINI INTERN> 7.63132 36.66907 0.00000 20.24449 4.58064 MINI EXTERN> -172.46832 -92.41359 0.00000 0.00000 0.00000 MINI CONSTR> 23.47966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -172.27968 0.00295 0.05364 0.00004 MINI INTERN> 7.62650 36.67602 0.00000 20.24139 4.58033 MINI EXTERN> -172.47799 -92.41342 0.00000 0.00000 0.00000 MINI CONSTR> 23.48751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20092 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -172.28248 0.00280 0.03510 0.00004 MINI INTERN> 7.62969 36.67228 0.00000 20.23877 4.58027 MINI EXTERN> -172.48509 -92.41194 0.00000 0.00000 0.00000 MINI CONSTR> 23.49353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -172.28531 0.00283 0.03606 0.00004 MINI INTERN> 7.63056 36.67197 0.00000 20.23597 4.58010 MINI EXTERN> -172.49338 -92.41088 0.00000 0.00000 0.00000 MINI CONSTR> 23.50034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20092 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -172.28800 0.00269 0.04508 0.00004 MINI INTERN> 7.62765 36.67579 0.00000 20.23320 4.57995 MINI EXTERN> -172.50141 -92.41023 0.00000 0.00000 0.00000 MINI CONSTR> 23.50706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -172.29016 0.00217 0.06536 0.00004 MINI INTERN> 7.62559 36.67942 0.00000 20.23081 4.57971 MINI EXTERN> -172.50904 -92.40982 0.00000 0.00000 0.00000 MINI CONSTR> 23.51317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20092 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -172.29315 0.00299 0.04155 0.00005 MINI INTERN> 7.63062 36.67367 0.00000 20.22813 4.57964 MINI EXTERN> -172.51660 -92.40798 0.00000 0.00000 0.00000 MINI CONSTR> 23.51937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -172.29525 0.00210 0.06937 0.00005 MINI INTERN> 7.62612 36.68006 0.00000 20.22568 4.57941 MINI EXTERN> -172.52438 -92.40782 0.00000 0.00000 0.00000 MINI CONSTR> 23.52569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20091 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -172.29795 0.00270 0.07403 0.00005 MINI INTERN> 7.62476 36.68208 0.00000 20.22290 4.57926 MINI EXTERN> -172.53248 -92.40699 0.00000 0.00000 0.00000 MINI CONSTR> 23.53250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -172.30038 0.00243 0.08466 0.00005 MINI INTERN> 7.62847 36.67930 0.00000 20.22033 4.57907 MINI EXTERN> -172.54092 -92.40566 0.00000 0.00000 0.00000 MINI CONSTR> 23.53903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20091 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -172.30281 0.00243 0.07815 0.00005 MINI INTERN> 7.62601 36.68202 0.00000 20.21797 4.57898 MINI EXTERN> -172.54752 -92.40487 0.00000 0.00000 0.00000 MINI CONSTR> 23.54460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -172.30538 0.00257 0.08305 0.00006 MINI INTERN> 7.62427 36.68439 0.00000 20.21530 4.57882 MINI EXTERN> -172.55524 -92.40412 0.00000 0.00000 0.00000 MINI CONSTR> 23.55119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20091 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -172.30760 0.00222 0.09773 0.00006 MINI INTERN> 7.62829 36.68148 0.00000 20.21277 4.57868 MINI EXTERN> -172.56381 -92.40264 0.00000 0.00000 0.00000 MINI CONSTR> 23.55763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -172.31001 0.00241 0.08950 0.00006 MINI INTERN> 7.62762 36.68229 0.00000 20.21050 4.57857 MINI EXTERN> -172.57036 -92.40162 0.00000 0.00000 0.00000 MINI CONSTR> 23.56300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20091 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -172.31349 0.00348 0.02855 0.00003 MINI INTERN> 7.63902 36.66781 0.00000 20.20754 4.57870 MINI EXTERN> -172.57727 -92.39796 0.00000 0.00000 0.00000 MINI CONSTR> 23.56867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -172.31457 0.00108 0.09754 0.00006 MINI INTERN> 7.62258 36.68845 0.00000 20.20564 4.57826 MINI EXTERN> -172.58402 -92.40023 0.00000 0.00000 0.00000 MINI CONSTR> 23.57475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20091 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -172.31671 0.00214 0.10958 0.00007 MINI INTERN> 7.63479 36.67674 0.00000 20.20322 4.57820 MINI EXTERN> -172.59297 -92.39751 0.00000 0.00000 0.00000 MINI CONSTR> 23.58081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -172.32059 0.00388 0.03111 0.00003 MINI INTERN> 7.64053 36.66757 0.00000 20.20027 4.57832 MINI EXTERN> -172.59910 -92.39451 0.00000 0.00000 0.00000 MINI CONSTR> 23.58633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20090 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -172.32133 0.00074 0.10504 0.00007 MINI INTERN> 7.62333 36.68977 0.00000 20.19857 4.57784 MINI EXTERN> -172.60603 -92.39709 0.00000 0.00000 0.00000 MINI CONSTR> 23.59228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -172.32547 0.00414 0.03470 0.00003 MINI INTERN> 7.64193 36.66702 0.00000 20.19521 4.57806 MINI EXTERN> -172.61430 -92.39197 0.00000 0.00000 0.00000 MINI CONSTR> 23.59858 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20089 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -172.32760 0.00213 0.02538 0.00003 MINI INTERN> 7.63943 36.67020 0.00000 20.19324 4.57791 MINI EXTERN> -172.62053 -92.39155 0.00000 0.00000 0.00000 MINI CONSTR> 23.60370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -172.33013 0.00253 0.02590 0.00003 MINI INTERN> 7.64035 36.66973 0.00000 20.19063 4.57776 MINI EXTERN> -172.62846 -92.39022 0.00000 0.00000 0.00000 MINI CONSTR> 23.61007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20089 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -172.33260 0.00247 0.04692 0.00003 MINI INTERN> 7.64506 36.66511 0.00000 20.18759 4.57769 MINI EXTERN> -172.63710 -92.38784 0.00000 0.00000 0.00000 MINI CONSTR> 23.61688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -172.33475 0.00215 0.02530 0.00004 MINI INTERN> 7.64039 36.67055 0.00000 20.18588 4.57751 MINI EXTERN> -172.64277 -92.38800 0.00000 0.00000 0.00000 MINI CONSTR> 23.62168 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20089 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -172.33732 0.00257 0.05231 0.00004 MINI INTERN> 7.64664 36.66442 0.00000 20.18256 4.57743 MINI EXTERN> -172.65223 -92.38516 0.00000 0.00000 0.00000 MINI CONSTR> 23.62902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -172.33980 0.00248 0.03344 0.00004 MINI INTERN> 7.64285 36.66883 0.00000 20.18044 4.57726 MINI EXTERN> -172.65894 -92.38489 0.00000 0.00000 0.00000 MINI CONSTR> 23.63465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20088 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -172.34219 0.00239 0.03988 0.00004 MINI INTERN> 7.64553 36.66651 0.00000 20.17786 4.57711 MINI EXTERN> -172.66690 -92.38322 0.00000 0.00000 0.00000 MINI CONSTR> 23.64091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -172.34412 0.00193 0.06028 0.00004 MINI INTERN> 7.64869 36.66362 0.00000 20.17527 4.57705 MINI EXTERN> -172.67417 -92.38123 0.00000 0.00000 0.00000 MINI CONSTR> 23.64666 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20088 ATOM PAIRS WERE FOUND FOR ATOM LIST 734 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -172.34674 0.00262 0.03737 0.00004 MINI INTERN> 7.64438 36.66852 0.00000 20.17313 4.57685 MINI EXTERN> -172.68095 -92.38110 0.00000 0.00000 0.00000 MINI CONSTR> 23.65243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -172.34865 0.00190 0.06414 0.00004 MINI INTERN> 7.64984 36.66333 0.00000 20.17041 4.57678 MINI EXTERN> -172.68878 -92.37863 0.00000 0.00000 0.00000 MINI CONSTR> 23.65841 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20088 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -172.35103 0.00238 0.06753 0.00005 MINI INTERN> 7.64917 36.66452 0.00000 20.16776 4.57664 MINI EXTERN> -172.69655 -92.37726 0.00000 0.00000 0.00000 MINI CONSTR> 23.66469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -172.35317 0.00214 0.07775 0.00005 MINI INTERN> 7.65442 36.65985 0.00000 20.16535 4.57642 MINI EXTERN> -172.70455 -92.37541 0.00000 0.00000 0.00000 MINI CONSTR> 23.67076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20087 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -172.35532 0.00215 0.07153 0.00005 MINI INTERN> 7.65151 36.66293 0.00000 20.16313 4.57638 MINI EXTERN> -172.71063 -92.37461 0.00000 0.00000 0.00000 MINI CONSTR> 23.67597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -172.35754 0.00222 0.08196 0.00005 MINI INTERN> 7.65263 36.66248 0.00000 20.16036 4.57620 MINI EXTERN> -172.71870 -92.37288 0.00000 0.00000 0.00000 MINI CONSTR> 23.68236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20087 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -172.35967 0.00213 0.07766 0.00005 MINI INTERN> 7.65298 36.66233 0.00000 20.15830 4.57610 MINI EXTERN> -172.72513 -92.37185 0.00000 0.00000 0.00000 MINI CONSTR> 23.68760 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -172.36200 0.00233 0.08002 0.00005 MINI INTERN> 7.65201 36.66385 0.00000 20.15568 4.57594 MINI EXTERN> -172.73276 -92.37053 0.00000 0.00000 0.00000 MINI CONSTR> 23.69380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20087 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -172.36502 0.00302 0.02572 0.00002 MINI INTERN> 7.64170 36.67467 0.00000 20.15447 4.57575 MINI EXTERN> -172.73789 -92.37297 0.00000 0.00000 0.00000 MINI CONSTR> 23.69925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -172.36613 0.00111 0.08689 0.00006 MINI INTERN> 7.65348 36.66315 0.00000 20.15101 4.57570 MINI EXTERN> -172.74674 -92.36775 0.00000 0.00000 0.00000 MINI CONSTR> 23.70502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20086 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -172.36831 0.00218 0.09156 0.00006 MINI INTERN> 7.65827 36.65896 0.00000 20.14872 4.57542 MINI EXTERN> -172.75455 -92.36613 0.00000 0.00000 0.00000 MINI CONSTR> 23.71099 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -172.37160 0.00328 0.02930 0.00003 MINI INTERN> 7.64178 36.67571 0.00000 20.14754 4.57536 MINI EXTERN> -172.75877 -92.36969 0.00000 0.00000 0.00000 MINI CONSTR> 23.71648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20086 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -172.37231 0.00072 0.09621 0.00007 MINI INTERN> 7.65522 36.66270 0.00000 20.14397 4.57528 MINI EXTERN> -172.76773 -92.36366 0.00000 0.00000 0.00000 MINI CONSTR> 23.72192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -172.37594 0.00363 0.02996 0.00003 MINI INTERN> 7.64249 36.67566 0.00000 20.14291 4.57509 MINI EXTERN> -172.77267 -92.36733 0.00000 0.00000 0.00000 MINI CONSTR> 23.72790 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20086 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -172.37784 0.00189 0.02457 0.00003 MINI INTERN> 7.64327 36.67500 0.00000 20.14079 4.57498 MINI EXTERN> -172.77879 -92.36584 0.00000 0.00000 0.00000 MINI CONSTR> 23.73276 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -172.37991 0.00207 0.02577 0.00003 MINI INTERN> 7.64339 36.67523 0.00000 20.13860 4.57485 MINI EXTERN> -172.78541 -92.36481 0.00000 0.00000 0.00000 MINI CONSTR> 23.73824 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20086 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -172.38205 0.00214 0.04083 0.00003 MINI INTERN> 7.64159 36.67773 0.00000 20.13640 4.57471 MINI EXTERN> -172.79226 -92.36455 0.00000 0.00000 0.00000 MINI CONSTR> 23.74433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -172.38393 0.00189 0.02372 0.00003 MINI INTERN> 7.64437 36.67476 0.00000 20.13422 4.57460 MINI EXTERN> -172.79841 -92.36231 0.00000 0.00000 0.00000 MINI CONSTR> 23.74884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20086 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -172.38625 0.00232 0.04672 0.00003 MINI INTERN> 7.64225 36.67779 0.00000 20.13188 4.57445 MINI EXTERN> -172.80590 -92.36243 0.00000 0.00000 0.00000 MINI CONSTR> 23.75571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -172.38835 0.00210 0.03482 0.00004 MINI INTERN> 7.64236 36.67766 0.00000 20.12953 4.57434 MINI EXTERN> -172.81240 -92.36070 0.00000 0.00000 0.00000 MINI CONSTR> 23.76086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20084 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -172.39029 0.00194 0.04151 0.00004 MINI INTERN> 7.64236 36.67812 0.00000 20.12749 4.57420 MINI EXTERN> -172.81873 -92.35997 0.00000 0.00000 0.00000 MINI CONSTR> 23.76625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -172.39207 0.00178 0.05601 0.00004 MINI INTERN> 7.64169 36.67941 0.00000 20.12553 4.57408 MINI EXTERN> -172.82484 -92.35956 0.00000 0.00000 0.00000 MINI CONSTR> 23.77163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20084 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -172.39437 0.00230 0.03489 0.00004 MINI INTERN> 7.64322 36.67762 0.00000 20.12299 4.57395 MINI EXTERN> -172.83182 -92.35727 0.00000 0.00000 0.00000 MINI CONSTR> 23.77693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -172.39606 0.00169 0.05903 0.00004 MINI INTERN> 7.64180 36.67991 0.00000 20.12115 4.57383 MINI EXTERN> -172.83778 -92.35746 0.00000 0.00000 0.00000 MINI CONSTR> 23.78248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20083 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -172.39821 0.00214 0.06033 0.00004 MINI INTERN> 7.64170 36.68024 0.00000 20.11879 4.57374 MINI EXTERN> -172.84468 -92.35631 0.00000 0.00000 0.00000 MINI CONSTR> 23.78831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -172.40030 0.00209 0.06540 0.00004 MINI INTERN> 7.64528 36.67733 0.00000 20.11649 4.57344 MINI EXTERN> -172.85177 -92.35527 0.00000 0.00000 0.00000 MINI CONSTR> 23.79420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20083 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -172.40210 0.00180 0.07472 0.00005 MINI INTERN> 7.63843 36.68405 0.00000 20.11422 4.57372 MINI EXTERN> -172.85778 -92.35434 0.00000 0.00000 0.00000 MINI CONSTR> 23.79960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -172.40400 0.00190 0.06833 0.00005 MINI INTERN> 7.64197 36.68090 0.00000 20.11234 4.57339 MINI EXTERN> -172.86374 -92.35327 0.00000 0.00000 0.00000 MINI CONSTR> 23.80440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20083 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -172.40590 0.00189 0.08045 0.00005 MINI INTERN> 7.64581 36.67808 0.00000 20.11014 4.57303 MINI EXTERN> -172.87059 -92.35265 0.00000 0.00000 0.00000 MINI CONSTR> 23.81029 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 -172.40590 0.00189 0.08045 0.00002 STPD INTERN> 7.64581 36.67808 0.00000 20.11014 4.57303 STPD EXTERN> -172.87059 -92.35265 0.00000 0.00000 0.00000 STPD CONSTR> 23.81029 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 20083 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 20083 ATOM PAIRS WERE FOUND FOR ATOM LIST 732 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 -172.40616 0.00026 0.03674 0.00000 MINI INTERN> 7.64922 36.67265 0.00000 20.10929 4.57314 MINI EXTERN> -172.87180 -92.34738 0.00000 0.00000 0.00000 MINI CONSTR> 23.80873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -172.77933 0.37318 0.03960 0.02018 MINI INTERN> 7.75301 36.74315 0.00000 19.33732 4.53388 MINI EXTERN> -175.19679 -91.81519 0.00000 0.00000 0.00000 MINI CONSTR> 25.86527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -172.78506 0.00572 0.07030 0.00659 MINI INTERN> 7.74414 36.77203 0.00000 19.32666 4.52215 MINI EXTERN> -175.18680 -91.84889 0.00000 0.00000 0.00000 MINI CONSTR> 25.88565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -172.83170 0.04664 0.11720 0.07312 MINI INTERN> 7.62959 36.45749 0.00000 19.24494 4.47631 MINI EXTERN> -175.11996 -91.55269 0.00000 0.00000 0.00000 MINI CONSTR> 26.03262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -172.87424 0.04254 0.11253 0.04928 MINI INTERN> 7.68072 36.41644 0.00000 19.21134 4.48392 MINI EXTERN> -175.31766 -91.51387 0.00000 0.00000 0.00000 MINI CONSTR> 26.16486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -172.89791 0.02366 0.07352 0.01815 MINI INTERN> 7.70410 36.39578 0.00000 19.13484 4.48005 MINI EXTERN> -175.26750 -91.58099 0.00000 0.00000 0.00000 MINI CONSTR> 26.23581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -172.90875 0.01084 0.06275 0.01537 MINI INTERN> 7.72597 36.38484 0.00000 19.08953 4.47632 MINI EXTERN> -175.21384 -91.63872 0.00000 0.00000 0.00000 MINI CONSTR> 26.26715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -172.91925 0.01051 0.05892 0.01210 MINI INTERN> 7.72950 36.39489 0.00000 19.02309 4.46800 MINI EXTERN> -175.14700 -91.68406 0.00000 0.00000 0.00000 MINI CONSTR> 26.29632 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -172.92895 0.00970 0.06018 0.01119 MINI INTERN> 7.72546 36.35850 0.00000 18.98794 4.46756 MINI EXTERN> -175.13596 -91.65784 0.00000 0.00000 0.00000 MINI CONSTR> 26.32540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -172.93965 0.01070 0.05902 0.01453 MINI INTERN> 7.74501 36.32885 0.00000 18.97577 4.45188 MINI EXTERN> -175.18182 -91.61760 0.00000 0.00000 0.00000 MINI CONSTR> 26.35827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -172.95125 0.01160 0.06760 0.01905 MINI INTERN> 7.71736 36.34434 0.00000 18.91646 4.45595 MINI EXTERN> -175.16876 -91.61075 0.00000 0.00000 0.00000 MINI CONSTR> 26.39414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -172.96282 0.01158 0.06310 0.01584 MINI INTERN> 7.73395 36.29602 0.00000 18.87972 4.46725 MINI EXTERN> -175.06823 -91.70129 0.00000 0.00000 0.00000 MINI CONSTR> 26.42976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -172.97278 0.00995 0.06282 0.01510 MINI INTERN> 7.70328 36.31148 0.00000 18.84881 4.46813 MINI EXTERN> -175.08645 -91.67891 0.00000 0.00000 0.00000 MINI CONSTR> 26.46088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -172.98185 0.00907 0.05706 0.01739 MINI INTERN> 7.72569 36.28404 0.00000 18.88426 4.47896 MINI EXTERN> -175.15454 -91.68993 0.00000 0.00000 0.00000 MINI CONSTR> 26.48967 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -172.98972 0.00787 0.05372 0.01279 MINI INTERN> 7.75054 36.26919 0.00000 18.92896 4.47633 MINI EXTERN> -175.34393 -91.58205 0.00000 0.00000 0.00000 MINI CONSTR> 26.51124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -172.99700 0.00728 0.05084 0.01351 MINI INTERN> 7.73725 36.27197 0.00000 18.97783 4.48177 MINI EXTERN> -175.43760 -91.55335 0.00000 0.00000 0.00000 MINI CONSTR> 26.52512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -173.00549 0.00849 0.05088 0.01712 MINI INTERN> 7.73496 36.24207 0.00000 19.00232 4.46781 MINI EXTERN> -175.34465 -91.63958 0.00000 0.00000 0.00000 MINI CONSTR> 26.53159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -173.01316 0.00767 0.05157 0.01950 MINI INTERN> 7.72652 36.27378 0.00000 18.98722 4.47160 MINI EXTERN> -175.34085 -91.66175 0.00000 0.00000 0.00000 MINI CONSTR> 26.53032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -173.01923 0.00607 0.04404 0.01217 MINI INTERN> 7.73470 36.30678 0.00000 18.97071 4.46272 MINI EXTERN> -175.29225 -91.72660 0.00000 0.00000 0.00000 MINI CONSTR> 26.52471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -173.02480 0.00557 0.04306 0.01083 MINI INTERN> 7.72663 36.30858 0.00000 18.96695 4.45714 MINI EXTERN> -175.29291 -91.70681 0.00000 0.00000 0.00000 MINI CONSTR> 26.51562 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -173.02998 0.00518 0.04309 0.01195 MINI INTERN> 7.71342 36.31209 0.00000 18.93950 4.46497 MINI EXTERN> -175.28797 -91.67544 0.00000 0.00000 0.00000 MINI CONSTR> 26.50344 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 -173.02998 0.00518 0.04309 0.02000 CONJ INTERN> 7.71342 36.31209 0.00000 18.93950 4.46497 CONJ EXTERN> -175.28797 -91.67544 0.00000 0.00000 0.00000 CONJ CONSTR> 26.50344 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 ASP 14 N ) 0.45311E-01 ( PROT ASP 14 H ) 0.36249E-01 ( PROT ASP 14 CA ) 0.45311E-01 ( PROT ASP 14 CB ) 0.36249E-01 ( PROT ASP 14 CG ) 0.36249E-01 ( PROT ASP 14 OD1 ) 0.36249E-01 ( PROT ASP 14 OD2 ) 0.36249E-01 ( PROT ASP 14 C ) 0.45311E-01 ( PROT ASP 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.61812 7.22726 -13.19937 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.02211 0.02010 -0.01209 ROTATION MATRIX 0.999996 -0.001663 -0.002104 0.001670 0.999992 0.003658 0.002098 -0.003662 0.999991 AXIS OF ROTATION IS 0.806622 0.463070 -0.367324 ANGLE IS 0.26 TOTAL SQUARE DIFF IS 439.3553 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 1.218322 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.2183" Parameter: A <- "1.2183" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.59490 7.32097 -13.47628 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.06667 -0.06542 0.03592 ROTATION MATRIX 0.999981 0.003770 0.004789 -0.003721 0.999940 -0.010278 -0.004828 0.010260 0.999936 AXIS OF ROTATION IS -0.859921 -0.402694 0.313645 ANGLE IS 0.68 TOTAL SQUARE DIFF IS 32.6749 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 1.026659 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.2183" RDCMND substituted energy or value "?RMS" to " 1.0267" Parameter: A <- "1.2183 1.0267" 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 1.2183 1.0267 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 " 26.50" Parameter: H <- "26.50" 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 -199.53342 26.50344 0.09398 ENER INTERN> 7.71342 36.31209 0.00000 18.93950 4.46497 ENER EXTERN> -175.28797 -91.67544 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 " -199.53" Parameter: B <- "-199.53" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -91.68" Parameter: C <- "-91.68" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -175.29" Parameter: C <- " -266.97" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -266.97" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.71" Parameter: D <- "7.71" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 36.31" Parameter: D <- " 44.02" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 18.94" Parameter: D <- " 62.96" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.46" Parameter: D <- " 67.42" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 67.42" 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= -199.53 GRMS= 0.09 ELEC= -91.68 VDW= -175.29 RDTITL> *EXTERNAL= -266.97 INTERNAL= 67.42 USER= 0.00 HARM= 26.50 RDTITL> *BOND= 7.71 ANGL= 36.31 DIHE= 18.94 IMPR= 4.46 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= -199.53 GRMS= 0.09 ELEC= -91.68 VDW= -175.29 RDTITL> *EXTERNAL= -266.97 INTERNAL= 67.42 USER= 0.00 HARM= 26.50 RDTITL> *BOND= 7.71 ANGL= 36.31 DIHE= 18.94 IMPR= 4.46 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= -199.53 GRMS= 0.09 ELEC= -91.68 VDW= -175.29 RDTITL> *EXTERNAL= -266.97 INTERNAL= 67.42 USER= 0.00 HARM= 26.50 RDTITL> *BOND= 7.71 ANGL= 36.31 DIHE= 18.94 IMPR= 4.46 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 12000 1.2183 1.0267 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 ASP 14 N ) 0.0000 ( PROT ASP 14 H ) 0.0000 ( PROT ASP 14 CA ) 0.0000 ( PROT ASP 14 CB ) 0.0000 ( PROT ASP 14 CG ) 0.0000 ( PROT ASP 14 OD1 ) 0.0000 ( PROT ASP 14 OD2 ) 0.0000 ( PROT ASP 14 C ) 0.0000 ( PROT ASP 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 20083 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19994 ATOM PAIRS WERE FOUND FOR ATOM LIST 733 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 -199.53342 26.50344 0.09398 0.00000 MINI INTERN> 7.71342 36.31209 0.00000 18.93950 4.46497 MINI EXTERN> -175.28797 -91.67544 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -205.53041 5.99700 0.19356 0.05311 MINI INTERN> 8.47752 36.17672 0.00000 15.91000 4.28178 MINI EXTERN> -185.50477 -84.87166 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19629 ATOM PAIRS WERE FOUND FOR ATOM LIST 706 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -205.53041 5.99700 0.19356 0.00000 MINI INTERN> 8.47752 36.17672 0.00000 15.91000 4.28178 MINI EXTERN> -185.50477 -84.87166 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -206.58049 1.05008 0.08070 0.03172 MINI INTERN> 8.39800 35.81554 0.00000 16.21639 4.35330 MINI EXTERN> -184.46783 -86.89589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19630 ATOM PAIRS WERE FOUND FOR ATOM LIST 715 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -206.58049 1.05008 0.08070 0.00000 MINI INTERN> 8.39800 35.81554 0.00000 16.21639 4.35330 MINI EXTERN> -184.46783 -86.89589 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -207.21294 0.63245 0.12648 0.02663 MINI INTERN> 8.65266 36.89424 0.00000 15.92485 4.33921 MINI EXTERN> -187.37904 -85.64487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19599 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -207.21294 0.63245 0.12648 0.00000 MINI INTERN> 8.65266 36.89424 0.00000 15.92485 4.33921 MINI EXTERN> -187.37904 -85.64487 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -207.64778 0.43483 0.04316 0.00829 MINI INTERN> 8.54119 36.40777 0.00000 16.30975 4.34847 MINI EXTERN> -186.19855 -87.05641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19620 ATOM PAIRS WERE FOUND FOR ATOM LIST 713 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -207.64778 0.43483 0.04316 0.00000 MINI INTERN> 8.54119 36.40777 0.00000 16.30975 4.34847 MINI EXTERN> -186.19855 -87.05641 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -207.83490 0.18713 0.09875 0.01441 MINI INTERN> 8.66420 36.63893 0.00000 16.36762 4.38162 MINI EXTERN> -187.32458 -86.56269 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19602 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -207.83490 0.18713 0.09875 0.00000 MINI INTERN> 8.66420 36.63893 0.00000 16.36762 4.38162 MINI EXTERN> -187.32458 -86.56269 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -207.96168 0.12677 0.03540 0.00737 MINI INTERN> 8.59765 36.37657 0.00000 16.58819 4.37577 MINI EXTERN> -186.77782 -87.12204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19620 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -207.96168 0.12677 0.03540 0.00000 MINI INTERN> 8.59765 36.37657 0.00000 16.58819 4.37577 MINI EXTERN> -186.77782 -87.12204 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -208.05788 0.09621 0.06718 0.01222 MINI INTERN> 8.68739 36.53494 0.00000 16.65736 4.40517 MINI EXTERN> -187.53104 -86.81170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19609 ATOM PAIRS WERE FOUND FOR ATOM LIST 708 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -208.05788 0.09621 0.06718 0.00000 MINI INTERN> 8.68739 36.53494 0.00000 16.65736 4.40517 MINI EXTERN> -187.53104 -86.81170 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -208.13350 0.07562 0.02653 0.00673 MINI INTERN> 8.63604 36.34660 0.00000 16.79167 4.39434 MINI EXTERN> -187.10706 -87.19510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19612 ATOM PAIRS WERE FOUND FOR ATOM LIST 712 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -208.13350 0.07562 0.02653 0.00000 MINI INTERN> 8.63604 36.34660 0.00000 16.79167 4.39434 MINI EXTERN> -187.10706 -87.19510 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -208.19441 0.06091 0.06963 0.01025 MINI INTERN> 8.70029 36.45237 0.00000 16.86803 4.42233 MINI EXTERN> -187.65412 -86.98331 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19609 ATOM PAIRS WERE FOUND FOR ATOM LIST 710 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -208.19441 0.06091 0.06963 0.00000 MINI INTERN> 8.70029 36.45237 0.00000 16.86803 4.42233 MINI EXTERN> -187.65412 -86.98331 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -208.24408 0.04967 0.03078 0.00576 MINI INTERN> 8.66156 36.32828 0.00000 16.94674 4.40991 MINI EXTERN> -187.33655 -87.25402 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19611 ATOM PAIRS WERE FOUND FOR ATOM LIST 715 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -208.24408 0.04967 0.03078 0.00000 MINI INTERN> 8.66156 36.32828 0.00000 16.94674 4.40991 MINI EXTERN> -187.33655 -87.25402 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -208.28458 0.04050 0.04174 0.00904 MINI INTERN> 8.70981 36.39239 0.00000 17.02121 4.43472 MINI EXTERN> -187.74393 -87.09879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19610 ATOM PAIRS WERE FOUND FOR ATOM LIST 708 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -208.28458 0.04050 0.04174 0.00000 MINI INTERN> 8.70981 36.39239 0.00000 17.02121 4.43472 MINI EXTERN> -187.74393 -87.09879 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -208.31814 0.03356 0.01824 0.00439 MINI INTERN> 8.68253 36.31564 0.00000 17.06945 4.42020 MINI EXTERN> -187.50531 -87.30066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19617 ATOM PAIRS WERE FOUND FOR ATOM LIST 711 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -208.31814 0.03356 0.01824 0.00000 MINI INTERN> 8.68253 36.31564 0.00000 17.06945 4.42020 MINI EXTERN> -187.50531 -87.30066 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -208.34613 0.02799 0.04401 0.00926 MINI INTERN> 8.71965 36.35191 0.00000 17.13777 4.44226 MINI EXTERN> -187.81945 -87.17826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19614 ATOM PAIRS WERE FOUND FOR ATOM LIST 708 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -208.34613 0.02799 0.04401 0.00000 MINI INTERN> 8.71965 36.35191 0.00000 17.13777 4.44226 MINI EXTERN> -187.81945 -87.17826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -208.36959 0.02346 0.01526 0.00387 MINI INTERN> 8.69788 36.30959 0.00000 17.16849 4.42861 MINI EXTERN> -187.63668 -87.33749 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19618 ATOM PAIRS WERE FOUND FOR ATOM LIST 706 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -208.36959 0.02346 0.01526 0.00000 MINI INTERN> 8.69788 36.30959 0.00000 17.16849 4.42861 MINI EXTERN> -187.63668 -87.33749 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -208.38962 0.02003 0.05176 0.00864 MINI INTERN> 8.73092 36.32073 0.00000 17.23123 4.44903 MINI EXTERN> -187.88447 -87.23706 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19619 ATOM PAIRS WERE FOUND FOR ATOM LIST 706 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -208.38962 0.02003 0.05176 0.00000 MINI INTERN> 8.73092 36.32073 0.00000 17.23123 4.44903 MINI EXTERN> -187.88447 -87.23706 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -208.40651 0.01689 0.01219 0.00347 MINI INTERN> 8.70995 36.30803 0.00000 17.24808 4.43552 MINI EXTERN> -187.74225 -87.36585 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19619 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -208.40651 0.01689 0.01219 0.00000 MINI INTERN> 8.70995 36.30803 0.00000 17.24808 4.43552 MINI EXTERN> -187.74225 -87.36585 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -208.42074 0.01423 0.03846 0.00670 MINI INTERN> 8.73372 36.31529 0.00000 17.30190 4.45184 MINI EXTERN> -187.93564 -87.28784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19621 ATOM PAIRS WERE FOUND FOR ATOM LIST 707 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -208.42074 0.01423 0.03846 0.00000 MINI INTERN> 8.73372 36.31529 0.00000 17.30190 4.45184 MINI EXTERN> -187.93564 -87.28784 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -208.43292 0.01218 0.01049 0.00302 MINI INTERN> 8.71879 36.31437 0.00000 17.31172 4.44063 MINI EXTERN> -187.82488 -87.39355 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19620 ATOM PAIRS WERE FOUND FOR ATOM LIST 706 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -208.43292 0.01218 0.01049 0.00000 MINI INTERN> 8.71879 36.31437 0.00000 17.31172 4.44063 MINI EXTERN> -187.82488 -87.39355 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -208.44345 0.01053 0.03406 0.00629 MINI INTERN> 8.73909 36.31728 0.00000 17.35804 4.45435 MINI EXTERN> -187.97985 -87.33235 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19624 ATOM PAIRS WERE FOUND FOR ATOM LIST 707 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -208.44345 0.01053 0.03406 0.00000 MINI INTERN> 8.73909 36.31728 0.00000 17.35804 4.45435 MINI EXTERN> -187.97985 -87.33235 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -208.45259 0.00914 0.00883 0.00274 MINI INTERN> 8.72587 36.32842 0.00000 17.36286 4.44413 MINI EXTERN> -187.89070 -87.42316 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 -208.45259 0.00914 0.00883 0.02000 CONJ INTERN> 8.72587 36.32842 0.00000 17.36286 4.44413 CONJ EXTERN> -187.89070 -87.42316 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 19624 atom pairs and 1255 atom exclusions. There are 0 group pairs and 278 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19624 ATOM PAIRS WERE FOUND FOR ATOM LIST 706 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 -208.45259 0.00914 0.00883 0.00000 MINI INTERN> 8.72587 36.32842 0.00000 17.36286 4.44413 MINI EXTERN> -187.89070 -87.42316 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -208.46083 0.00824 0.04773 0.00654 MINI INTERN> 8.73798 36.33698 0.00000 17.40370 4.45653 MINI EXTERN> -188.02004 -87.37598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19626 ATOM PAIRS WERE FOUND FOR ATOM LIST 704 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -208.46083 0.00824 0.04773 0.00000 MINI INTERN> 8.73798 36.33698 0.00000 17.40370 4.45653 MINI EXTERN> -188.02004 -87.37598 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -208.46801 0.00718 0.00750 0.00222 MINI INTERN> 8.73190 36.34998 0.00000 17.40354 4.44669 MINI EXTERN> -187.94596 -87.45415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19625 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -208.46801 0.00718 0.00750 0.00000 MINI INTERN> 8.73190 36.34998 0.00000 17.40354 4.44669 MINI EXTERN> -187.94596 -87.45415 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -208.47429 0.00628 0.03891 0.00508 MINI INTERN> 8.75031 36.34926 0.00000 17.44011 4.45842 MINI EXTERN> -188.05594 -87.41644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19629 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -208.47429 0.00628 0.03891 0.00000 MINI INTERN> 8.75031 36.34926 0.00000 17.44011 4.45842 MINI EXTERN> -188.05594 -87.41644 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -208.47977 0.00548 0.00638 0.00202 MINI INTERN> 8.73689 36.37448 0.00000 17.43647 4.44880 MINI EXTERN> -187.99190 -87.48450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19628 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -208.47977 0.00548 0.00638 0.00000 MINI INTERN> 8.73689 36.37448 0.00000 17.43647 4.44880 MINI EXTERN> -187.99190 -87.48450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -208.48452 0.00476 0.03387 0.00476 MINI INTERN> 8.74829 36.37877 0.00000 17.46746 4.45849 MINI EXTERN> -188.08141 -87.45613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19632 ATOM PAIRS WERE FOUND FOR ATOM LIST 706 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -208.48452 0.00476 0.03387 0.00000 MINI INTERN> 8.74829 36.37877 0.00000 17.46746 4.45849 MINI EXTERN> -188.08141 -87.45613 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -208.48865 0.00413 0.00537 0.00208 MINI INTERN> 8.74152 36.39612 0.00000 17.46384 4.45067 MINI EXTERN> -188.03007 -87.51074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19629 ATOM PAIRS WERE FOUND FOR ATOM LIST 707 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -208.48865 0.00413 0.00537 0.00000 MINI INTERN> 8.74152 36.39612 0.00000 17.46384 4.45067 MINI EXTERN> -188.03007 -87.51074 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -208.49227 0.00362 0.03090 0.00475 MINI INTERN> 8.74556 36.40448 0.00000 17.49221 4.45845 MINI EXTERN> -188.10643 -87.48655 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19635 ATOM PAIRS WERE FOUND FOR ATOM LIST 706 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -208.49227 0.00362 0.03090 0.00000 MINI INTERN> 8.74556 36.40448 0.00000 17.49221 4.45845 MINI EXTERN> -188.10643 -87.48655 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -208.49540 0.00313 0.00474 0.00168 MINI INTERN> 8.74494 36.41286 0.00000 17.48877 4.45220 MINI EXTERN> -188.06295 -87.53122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19632 ATOM PAIRS WERE FOUND FOR ATOM LIST 707 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -208.49540 0.00313 0.00474 0.00000 MINI INTERN> 8.74494 36.41286 0.00000 17.48877 4.45220 MINI EXTERN> -188.06295 -87.53122 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -208.49820 0.00280 0.03275 0.00452 MINI INTERN> 8.75183 36.41517 0.00000 17.51499 4.45859 MINI EXTERN> -188.12861 -87.51017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19637 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -208.49820 0.00280 0.03275 0.00000 MINI INTERN> 8.75183 36.41517 0.00000 17.51499 4.45859 MINI EXTERN> -188.12861 -87.51017 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -208.50062 0.00242 0.00390 0.00167 MINI INTERN> 8.74902 36.42572 0.00000 17.51087 4.45369 MINI EXTERN> -188.09200 -87.54793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19635 ATOM PAIRS WERE FOUND FOR ATOM LIST 706 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -208.50062 0.00242 0.00390 0.00000 MINI INTERN> 8.74902 36.42572 0.00000 17.51087 4.45369 MINI EXTERN> -188.09200 -87.54793 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -208.50272 0.00209 0.02180 0.00454 MINI INTERN> 8.75990 36.42368 0.00000 17.53328 4.45807 MINI EXTERN> -188.15019 -87.52745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19636 ATOM PAIRS WERE FOUND FOR ATOM LIST 704 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -208.50272 0.00209 0.02180 0.00000 MINI INTERN> 8.75990 36.42368 0.00000 17.53328 4.45807 MINI EXTERN> -188.15019 -87.52745 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -208.50453 0.00182 0.00308 0.00120 MINI INTERN> 8.75182 36.43551 0.00000 17.53062 4.45460 MINI EXTERN> -188.11571 -87.56138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19638 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -208.50453 0.00182 0.00308 0.00000 MINI INTERN> 8.75182 36.43551 0.00000 17.53062 4.45460 MINI EXTERN> -188.11571 -87.56138 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -208.50609 0.00156 0.01571 0.00439 MINI INTERN> 8.75990 36.43288 0.00000 17.55000 4.45784 MINI EXTERN> -188.16194 -87.54478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19638 ATOM PAIRS WERE FOUND FOR ATOM LIST 704 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -208.50609 0.00156 0.01571 0.00000 MINI INTERN> 8.75990 36.43288 0.00000 17.55000 4.45784 MINI EXTERN> -188.16194 -87.54478 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -208.50746 0.00136 0.00259 0.00098 MINI INTERN> 8.75371 36.44444 0.00000 17.54791 4.45510 MINI EXTERN> -188.13540 -87.57321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19639 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -208.50746 0.00136 0.00259 0.00000 MINI INTERN> 8.75371 36.44444 0.00000 17.54791 4.45510 MINI EXTERN> -188.13540 -87.57321 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -208.50865 0.00119 0.01356 0.00400 MINI INTERN> 8.75975 36.44389 0.00000 17.56490 4.45765 MINI EXTERN> -188.17633 -87.55851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19640 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -208.50865 0.00119 0.01356 0.00000 MINI INTERN> 8.75975 36.44389 0.00000 17.56490 4.45765 MINI EXTERN> -188.17633 -87.55851 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -208.50969 0.00104 0.00225 0.00082 MINI INTERN> 8.75562 36.45185 0.00000 17.56243 4.45575 MINI EXTERN> -188.15121 -87.58412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19640 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -208.50969 0.00104 0.00225 0.00000 MINI INTERN> 8.75562 36.45185 0.00000 17.56243 4.45575 MINI EXTERN> -188.15121 -87.58412 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -208.51059 0.00091 0.01270 0.00342 MINI INTERN> 8.76167 36.44979 0.00000 17.57708 4.45809 MINI EXTERN> -188.18352 -87.57370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19642 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -208.51059 0.00091 0.01270 0.00000 MINI INTERN> 8.76167 36.44979 0.00000 17.57708 4.45809 MINI EXTERN> -188.18352 -87.57370 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -208.51138 0.00079 0.00192 0.00063 MINI INTERN> 8.75740 36.45895 0.00000 17.57500 4.45597 MINI EXTERN> -188.16578 -87.59293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19641 ATOM PAIRS WERE FOUND FOR ATOM LIST 705 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -208.51138 0.00079 0.00192 0.00000 MINI INTERN> 8.75740 36.45895 0.00000 17.57500 4.45597 MINI EXTERN> -188.16578 -87.59293 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -208.51206 0.00068 0.01139 0.00286 MINI INTERN> 8.76238 36.45639 0.00000 17.58815 4.45784 MINI EXTERN> -188.19448 -87.58234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 43513 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 19642 ATOM PAIRS WERE FOUND FOR ATOM LIST 704 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -208.51206 0.00068 0.01139 0.00000 MINI INTERN> 8.76238 36.45639 0.00000 17.58815 4.45784 MINI EXTERN> -188.19448 -87.58234 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -208.51265 0.00059 0.00166 0.00050 MINI INTERN> 8.75869 36.46193 0.00000 17.58691 4.45634 MINI EXTERN> -188.17736 -87.59915 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 -208.51265 0.00059 0.00166 0.02000 CONJ INTERN> 8.75869 36.46193 0.00000 17.58691 4.45634 CONJ EXTERN> -188.17736 -87.59915 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> 296 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.57255 7.18484 -13.17458 CENTER OF REFERENCE COORDINATE SET 13.64023 7.24736 -13.21146 NET TRANSLATION OF ROTATED ATOMS 0.06768 0.06253 -0.03688 ROTATION MATRIX 0.999966 -0.004601 -0.006792 0.004682 0.999917 0.011982 0.006736 -0.012013 0.999905 AXIS OF ROTATION IS 0.825486 0.465404 -0.319331 ANGLE IS 0.83 TOTAL SQUARE DIFF IS 969.0862 DENOMINATOR IS 296.0000 THUS RMS DIFF IS 1.809403 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.8094" Parameter: A <- "1.8094" CHARMM> set a @a ?RMS Parameter: A -> "1.8094" RDCMND substituted energy or value "?RMS" to " 1.8094" Parameter: A <- "1.8094 1.8094" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 31 atoms have been selected out of 296 CENTER OF ATOMS BEFORE TRANSLATION 13.54675 7.38355 -13.47259 CENTER OF REFERENCE COORDINATE SET 13.52823 7.25555 -13.44035 NET TRANSLATION OF ROTATED ATOMS -0.01853 -0.12801 0.03223 ROTATION MATRIX 0.999957 -0.008962 -0.002482 0.008948 0.999943 -0.005769 0.002534 0.005746 0.999980 AXIS OF ROTATION IS -0.526389 0.229327 -0.818733 ANGLE IS 0.63 TOTAL SQUARE DIFF IS 63.4462 DENOMINATOR IS 31.0000 THUS RMS DIFF IS 1.430612 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.8094 1.8094" RDCMND substituted energy or value "?RMS" to " 1.4306" Parameter: A <- "1.8094 1.8094 1.4306" 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 1.8094 1.8094 1.4306 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" $$$$$$ New timer profile $$$$$ List time 0.00 Other: 0.00 Electrostatic & VDW 15.94 Other: 0.00 Nonbond force 15.99 Other: 0.04 Bond energy 0.14 Other: 0.00 Angle energy 1.07 Other: 0.00 Dihedral energy 0.73 Other: 0.00 Restraints energy 0.01 Other: 0.00 INTRNL energy 1.99 Other: 0.06 Energy time 18.12 Other: 0.14 Total time 19.02 Other: 0.90 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47522 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL 2 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 62660 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 19.02 SECONDS CPU TIME: 0.00 SECONDS