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-2.6.32-431.11.2.el6.x86_64(x86_64)@dog Created on 6/ 4/14 at 16:27:23 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: 6/ 4/14 16:26:43 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 = 19 Number of atoms = 183 Number of groups = 68 Number of bonds = 186 Number of angles = 263 Number of dihedrals = 103 Number of impropers = 89 Number of cross-terms = 0 Number of HB acceptors = 23 Number of HB donors = 28 Number of NB exclusions = 12 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: 6/ 4/14 16:26:43 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 461 exclusions and 307 interactions(1-4) found 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11486 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 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 11486 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11486 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 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 119802.13012 0.00000 29936.05346 ENER INTERN> 193.17966 108.25337 0.00000 8.72828 2.64933 ENER EXTERN> 119541.06250 -51.74302 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> 183 atoms have been selected out of 183 CHARMM> define water sele ( segid solv) end SELRPN> 0 atoms have been selected out of 183 CHARMM> define nonh sele ( .not. hydrogen ) end SELRPN> 155 atoms have been selected out of 183 CHARMM> define trace sele ( type ca ) end SELRPN> 19 atoms have been selected out of 183 CHARMM> define back sele ( type n .or. type ca .or. type c ) end SELRPN> 57 atoms have been selected out of 183 CHARMM> define main sele ( type n .or. type ca .or. type c .or. type o) end SELRPN> 75 atoms have been selected out of 183 CHARMM> define side sele ( (.not. main) ) end SELRPN> 108 atoms have been selected out of 183 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: 183 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 183 atoms are restrained. CHARMM> CHARMM> ! { very tight on backbone of pcna } CHARMM> SCALar CONSTraint SET 250. SELEct ( prot .AND. main ) END SELRPN> 75 atoms have been selected out of 183 CHARMM> CHARMM> ! { quite tight on sidechains of pcna } CHARMM> SCALar CONSTraint SET 200. SELEct ( prot .AND. side ) END SELRPN> 108 atoms have been selected out of 183 CHARMM> CHARMM> CHARMM> !SCALar CONSTraint SET 50. SELEct ( resname TIP3 ) END CHARMM> !SCALar CONSTraint SET 25. SELEct (side ) END CHARMM> CHARMM> ! to check CHARMM> SCAlar CONSTraint SHOW ( PROT LYS 1 HT1 ) 200.00 ( PROT LYS 1 HT2 ) 200.00 ( PROT LYS 1 N ) 250.00 ( PROT LYS 1 HT3 ) 200.00 ( PROT LYS 1 CA ) 250.00 ( PROT LYS 1 CB ) 200.00 ( PROT LYS 1 CG ) 200.00 ( PROT LYS 1 CD ) 200.00 ( PROT LYS 1 CE ) 200.00 ( PROT LYS 1 NZ ) 200.00 ( PROT LYS 1 HZ1 ) 200.00 ( PROT LYS 1 HZ2 ) 200.00 ( PROT LYS 1 HZ3 ) 200.00 ( PROT LYS 1 C ) 250.00 ( PROT LYS 1 O ) 250.00 ( PROT MET 2 N ) 250.00 ( PROT MET 2 H ) 200.00 ( PROT MET 2 CA ) 250.00 ( PROT MET 2 CB ) 200.00 ( PROT MET 2 CG ) 200.00 ( PROT MET 2 SD ) 200.00 ( PROT MET 2 CE ) 200.00 ( PROT MET 2 C ) 250.00 ( PROT MET 2 O ) 250.00 ( PROT LYS 3 N ) 250.00 ( PROT LYS 3 H ) 200.00 ( PROT LYS 3 CA ) 250.00 ( PROT LYS 3 CB ) 200.00 ( PROT LYS 3 CG ) 200.00 ( PROT LYS 3 CD ) 200.00 ( PROT LYS 3 CE ) 200.00 ( PROT LYS 3 NZ ) 200.00 ( PROT LYS 3 HZ1 ) 200.00 ( PROT LYS 3 HZ2 ) 200.00 ( PROT LYS 3 HZ3 ) 200.00 ( PROT LYS 3 C ) 250.00 ( PROT LYS 3 O ) 250.00 ( PROT ALA 4 N ) 250.00 ( PROT ALA 4 H ) 200.00 ( PROT ALA 4 CA ) 250.00 ( PROT ALA 4 CB ) 200.00 ( PROT ALA 4 C ) 250.00 ( PROT ALA 4 O ) 250.00 ( PROT VAL 5 N ) 250.00 ( PROT VAL 5 H ) 200.00 ( PROT VAL 5 CA ) 250.00 ( PROT VAL 5 CB ) 200.00 ( PROT VAL 5 CG1 ) 200.00 ( PROT VAL 5 CG2 ) 200.00 ( PROT VAL 5 C ) 250.00 ( PROT VAL 5 O ) 250.00 ( PROT MET 6 N ) 250.00 ( PROT MET 6 H ) 200.00 ( PROT MET 6 CA ) 250.00 ( PROT MET 6 CB ) 200.00 ( PROT MET 6 CG ) 200.00 ( PROT MET 6 SD ) 200.00 ( PROT MET 6 CE ) 200.00 ( PROT MET 6 C ) 250.00 ( PROT MET 6 O ) 250.00 ( PROT ILE 7 N ) 250.00 ( PROT ILE 7 H ) 200.00 ( PROT ILE 7 CA ) 250.00 ( PROT ILE 7 CB ) 200.00 ( PROT ILE 7 CG2 ) 200.00 ( PROT ILE 7 CG1 ) 200.00 ( PROT ILE 7 CD ) 200.00 ( PROT ILE 7 C ) 250.00 ( PROT ILE 7 O ) 250.00 ( PROT GLY 8 N ) 250.00 ( PROT GLY 8 H ) 200.00 ( PROT GLY 8 CA ) 250.00 ( PROT GLY 8 C ) 250.00 ( PROT GLY 8 O ) 250.00 ( PROT ALA 9 N ) 250.00 ( PROT ALA 9 H ) 200.00 ( PROT ALA 9 CA ) 250.00 ( PROT ALA 9 CB ) 200.00 ( PROT ALA 9 C ) 250.00 ( PROT ALA 9 O ) 250.00 ( PROT CYS 10 N ) 250.00 ( PROT CYS 10 H ) 200.00 ( PROT CYS 10 CA ) 250.00 ( PROT CYS 10 CB ) 200.00 ( PROT CYS 10 SG ) 200.00 ( PROT CYS 10 C ) 250.00 ( PROT CYS 10 O ) 250.00 ( PROT PHE 11 N ) 250.00 ( PROT PHE 11 H ) 200.00 ( PROT PHE 11 CA ) 250.00 ( PROT PHE 11 CB ) 200.00 ( PROT PHE 11 CG ) 200.00 ( PROT PHE 11 CD1 ) 200.00 ( PROT PHE 11 CD2 ) 200.00 ( PROT PHE 11 CE1 ) 200.00 ( PROT PHE 11 CE2 ) 200.00 ( PROT PHE 11 CZ ) 200.00 ( PROT PHE 11 C ) 250.00 ( PROT PHE 11 O ) 250.00 ( PROT LEU 12 N ) 250.00 ( PROT LEU 12 H ) 200.00 ( PROT LEU 12 CA ) 250.00 ( PROT LEU 12 CB ) 200.00 ( PROT LEU 12 CG ) 200.00 ( PROT LEU 12 CD1 ) 200.00 ( PROT LEU 12 CD2 ) 200.00 ( PROT LEU 12 C ) 250.00 ( PROT LEU 12 O ) 250.00 ( PROT ILE 13 N ) 250.00 ( PROT ILE 13 H ) 200.00 ( PROT ILE 13 CA ) 250.00 ( PROT ILE 13 CB ) 200.00 ( PROT ILE 13 CG2 ) 200.00 ( PROT ILE 13 CG1 ) 200.00 ( PROT ILE 13 CD ) 200.00 ( PROT ILE 13 C ) 250.00 ( PROT ILE 13 O ) 250.00 ( PROT ASH 14 N ) 250.00 ( PROT ASH 14 H ) 200.00 ( PROT ASH 14 CA ) 250.00 ( PROT ASH 14 CB ) 200.00 ( PROT ASH 14 CG ) 200.00 ( PROT ASH 14 OD1 ) 200.00 ( PROT ASH 14 OD2 ) 200.00 ( PROT ASH 14 HD2 ) 200.00 ( PROT ASH 14 C ) 250.00 ( PROT ASH 14 O ) 250.00 ( PROT PHE 15 N ) 250.00 ( PROT PHE 15 H ) 200.00 ( PROT PHE 15 CA ) 250.00 ( PROT PHE 15 CB ) 200.00 ( PROT PHE 15 CG ) 200.00 ( PROT PHE 15 CD1 ) 200.00 ( PROT PHE 15 CD2 ) 200.00 ( PROT PHE 15 CE1 ) 200.00 ( PROT PHE 15 CE2 ) 200.00 ( PROT PHE 15 CZ ) 200.00 ( PROT PHE 15 C ) 250.00 ( PROT PHE 15 O ) 250.00 ( PROT MET 16 N ) 250.00 ( PROT MET 16 H ) 200.00 ( PROT MET 16 CA ) 250.00 ( PROT MET 16 CB ) 200.00 ( PROT MET 16 CG ) 200.00 ( PROT MET 16 SD ) 200.00 ( PROT MET 16 CE ) 200.00 ( PROT MET 16 C ) 250.00 ( PROT MET 16 O ) 250.00 ( PROT PHE 17 N ) 250.00 ( PROT PHE 17 H ) 200.00 ( PROT PHE 17 CA ) 250.00 ( PROT PHE 17 CB ) 200.00 ( PROT PHE 17 CG ) 200.00 ( PROT PHE 17 CD1 ) 200.00 ( PROT PHE 17 CD2 ) 200.00 ( PROT PHE 17 CE1 ) 200.00 ( PROT PHE 17 CE2 ) 200.00 ( PROT PHE 17 CZ ) 200.00 ( PROT PHE 17 C ) 250.00 ( PROT PHE 17 O ) 250.00 ( PROT PHE 18 N ) 250.00 ( PROT PHE 18 H ) 200.00 ( PROT PHE 18 CA ) 250.00 ( PROT PHE 18 CB ) 200.00 ( PROT PHE 18 CG ) 200.00 ( PROT PHE 18 CD1 ) 200.00 ( PROT PHE 18 CD2 ) 200.00 ( PROT PHE 18 CE1 ) 200.00 ( PROT PHE 18 CE2 ) 200.00 ( PROT PHE 18 CZ ) 200.00 ( PROT PHE 18 C ) 250.00 ( PROT PHE 18 O ) 250.00 ( PROT GLU 19 N ) 250.00 ( PROT GLU 19 H ) 200.00 ( PROT GLU 19 CA ) 250.00 ( PROT GLU 19 CB ) 200.00 ( PROT GLU 19 CG ) 200.00 ( PROT GLU 19 CD ) 200.00 ( PROT GLU 19 OE1 ) 200.00 ( PROT GLU 19 OE2 ) 200.00 ( PROT GLU 19 C ) 250.00 ( PROT GLU 19 OT1 ) 200.00 ( PROT GLU 19 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: 6/ 4/14 16:26:43 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 11486 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11486 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 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 119802.13012 0.00000 29936.05346 0.02000 MINI INTERN> 193.17966 108.25337 0.00000 8.72828 2.64933 MINI EXTERN> 119541.06250 -51.74302 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 2134.44195 117667.68816 53.76186 0.02074 MINI INTERN> 309.61538 174.25805 0.00000 8.86034 95.43755 MINI EXTERN> 1035.50972 5.41160 0.00000 0.00000 0.00000 MINI CONSTR> 505.34932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11472 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1687.39855 447.04340 16.35030 0.00896 MINI INTERN> 50.06991 96.32951 0.00000 10.16932 32.71331 MINI EXTERN> 703.80382 4.24886 0.00000 0.00000 0.00000 MINI CONSTR> 790.06381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1671.77455 15.62400 9.06591 0.00387 MINI INTERN> 88.66100 90.31527 0.00000 10.52169 36.09544 MINI EXTERN> 597.82982 9.34769 0.00000 0.00000 0.00000 MINI CONSTR> 839.00365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11470 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1665.72072 6.05383 0.58615 0.00070 MINI INTERN> 67.40585 88.70207 0.00000 10.54315 33.85413 MINI EXTERN> 630.08198 6.99010 0.00000 0.00000 0.00000 MINI CONSTR> 828.14344 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1665.67235 0.04837 0.69060 0.00030 MINI INTERN> 66.55338 88.05990 0.00000 10.55076 33.57853 MINI EXTERN> 631.07043 6.88106 0.00000 0.00000 0.00000 MINI CONSTR> 828.97828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11471 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1665.63051 0.04184 0.06113 0.00005 MINI INTERN> 66.61736 88.05362 0.00000 10.56673 33.71182 MINI EXTERN> 630.47271 6.88036 0.00000 0.00000 0.00000 MINI CONSTR> 829.32793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1665.62984 0.00067 0.04566 0.00002 MINI INTERN> 66.57305 88.03916 0.00000 10.57074 33.71562 MINI EXTERN> 630.46537 6.88386 0.00000 0.00000 0.00000 MINI CONSTR> 829.38205 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> 38 1665.62964 0.00021 0.00619 0.00001 STPD INTERN> 66.57728 88.01999 0.00000 10.57039 33.71524 STPD EXTERN> 630.43868 6.87985 0.00000 0.00000 0.00000 STPD CONSTR> 829.42819 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 11471 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11471 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 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 1665.62964 0.00021 0.00619 0.00000 MINI INTERN> 66.57728 88.01999 0.00000 10.57039 33.71524 MINI EXTERN> 630.43868 6.87985 0.00000 0.00000 0.00000 MINI CONSTR> 829.42819 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> 1 1665.62963 0.00001 0.00380 0.02000 CONJ INTERN> 66.57397 88.02229 0.00000 10.57054 33.71509 CONJ EXTERN> 630.43560 6.88075 0.00000 0.00000 0.00000 CONJ CONSTR> 829.43139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 130.00 ( PROT LYS 1 HT2 ) 130.00 ( PROT LYS 1 N ) 162.50 ( PROT LYS 1 HT3 ) 130.00 ( PROT LYS 1 CA ) 162.50 ( PROT LYS 1 CB ) 130.00 ( PROT LYS 1 CG ) 130.00 ( PROT LYS 1 CD ) 130.00 ( PROT LYS 1 CE ) 130.00 ( PROT LYS 1 NZ ) 130.00 ( PROT LYS 1 HZ1 ) 130.00 ( PROT LYS 1 HZ2 ) 130.00 ( PROT LYS 1 HZ3 ) 130.00 ( PROT LYS 1 C ) 162.50 ( PROT LYS 1 O ) 162.50 ( PROT MET 2 N ) 162.50 ( PROT MET 2 H ) 130.00 ( PROT MET 2 CA ) 162.50 ( PROT MET 2 CB ) 130.00 ( PROT MET 2 CG ) 130.00 ( PROT MET 2 SD ) 130.00 ( PROT MET 2 CE ) 130.00 ( PROT MET 2 C ) 162.50 ( PROT MET 2 O ) 162.50 ( PROT LYS 3 N ) 162.50 ( PROT LYS 3 H ) 130.00 ( PROT LYS 3 CA ) 162.50 ( PROT LYS 3 CB ) 130.00 ( PROT LYS 3 CG ) 130.00 ( PROT LYS 3 CD ) 130.00 ( PROT LYS 3 CE ) 130.00 ( PROT LYS 3 NZ ) 130.00 ( PROT LYS 3 HZ1 ) 130.00 ( PROT LYS 3 HZ2 ) 130.00 ( PROT LYS 3 HZ3 ) 130.00 ( PROT LYS 3 C ) 162.50 ( PROT LYS 3 O ) 162.50 ( PROT ALA 4 N ) 162.50 ( PROT ALA 4 H ) 130.00 ( PROT ALA 4 CA ) 162.50 ( PROT ALA 4 CB ) 130.00 ( PROT ALA 4 C ) 162.50 ( PROT ALA 4 O ) 162.50 ( PROT VAL 5 N ) 162.50 ( PROT VAL 5 H ) 130.00 ( PROT VAL 5 CA ) 162.50 ( PROT VAL 5 CB ) 130.00 ( PROT VAL 5 CG1 ) 130.00 ( PROT VAL 5 CG2 ) 130.00 ( PROT VAL 5 C ) 162.50 ( PROT VAL 5 O ) 162.50 ( PROT MET 6 N ) 162.50 ( PROT MET 6 H ) 130.00 ( PROT MET 6 CA ) 162.50 ( PROT MET 6 CB ) 130.00 ( PROT MET 6 CG ) 130.00 ( PROT MET 6 SD ) 130.00 ( PROT MET 6 CE ) 130.00 ( PROT MET 6 C ) 162.50 ( PROT MET 6 O ) 162.50 ( PROT ILE 7 N ) 162.50 ( PROT ILE 7 H ) 130.00 ( PROT ILE 7 CA ) 162.50 ( PROT ILE 7 CB ) 130.00 ( PROT ILE 7 CG2 ) 130.00 ( PROT ILE 7 CG1 ) 130.00 ( PROT ILE 7 CD ) 130.00 ( PROT ILE 7 C ) 162.50 ( PROT ILE 7 O ) 162.50 ( PROT GLY 8 N ) 162.50 ( PROT GLY 8 H ) 130.00 ( PROT GLY 8 CA ) 162.50 ( PROT GLY 8 C ) 162.50 ( PROT GLY 8 O ) 162.50 ( PROT ALA 9 N ) 162.50 ( PROT ALA 9 H ) 130.00 ( PROT ALA 9 CA ) 162.50 ( PROT ALA 9 CB ) 130.00 ( PROT ALA 9 C ) 162.50 ( PROT ALA 9 O ) 162.50 ( PROT CYS 10 N ) 162.50 ( PROT CYS 10 H ) 130.00 ( PROT CYS 10 CA ) 162.50 ( PROT CYS 10 CB ) 130.00 ( PROT CYS 10 SG ) 130.00 ( PROT CYS 10 C ) 162.50 ( PROT CYS 10 O ) 162.50 ( PROT PHE 11 N ) 162.50 ( PROT PHE 11 H ) 130.00 ( PROT PHE 11 CA ) 162.50 ( PROT PHE 11 CB ) 130.00 ( PROT PHE 11 CG ) 130.00 ( PROT PHE 11 CD1 ) 130.00 ( PROT PHE 11 CD2 ) 130.00 ( PROT PHE 11 CE1 ) 130.00 ( PROT PHE 11 CE2 ) 130.00 ( PROT PHE 11 CZ ) 130.00 ( PROT PHE 11 C ) 162.50 ( PROT PHE 11 O ) 162.50 ( PROT LEU 12 N ) 162.50 ( PROT LEU 12 H ) 130.00 ( PROT LEU 12 CA ) 162.50 ( PROT LEU 12 CB ) 130.00 ( PROT LEU 12 CG ) 130.00 ( PROT LEU 12 CD1 ) 130.00 ( PROT LEU 12 CD2 ) 130.00 ( PROT LEU 12 C ) 162.50 ( PROT LEU 12 O ) 162.50 ( PROT ILE 13 N ) 162.50 ( PROT ILE 13 H ) 130.00 ( PROT ILE 13 CA ) 162.50 ( PROT ILE 13 CB ) 130.00 ( PROT ILE 13 CG2 ) 130.00 ( PROT ILE 13 CG1 ) 130.00 ( PROT ILE 13 CD ) 130.00 ( PROT ILE 13 C ) 162.50 ( PROT ILE 13 O ) 162.50 ( PROT ASH 14 N ) 162.50 ( PROT ASH 14 H ) 130.00 ( PROT ASH 14 CA ) 162.50 ( PROT ASH 14 CB ) 130.00 ( PROT ASH 14 CG ) 130.00 ( PROT ASH 14 OD1 ) 130.00 ( PROT ASH 14 OD2 ) 130.00 ( PROT ASH 14 HD2 ) 130.00 ( PROT ASH 14 C ) 162.50 ( PROT ASH 14 O ) 162.50 ( PROT PHE 15 N ) 162.50 ( PROT PHE 15 H ) 130.00 ( PROT PHE 15 CA ) 162.50 ( PROT PHE 15 CB ) 130.00 ( PROT PHE 15 CG ) 130.00 ( PROT PHE 15 CD1 ) 130.00 ( PROT PHE 15 CD2 ) 130.00 ( PROT PHE 15 CE1 ) 130.00 ( PROT PHE 15 CE2 ) 130.00 ( PROT PHE 15 CZ ) 130.00 ( PROT PHE 15 C ) 162.50 ( PROT PHE 15 O ) 162.50 ( PROT MET 16 N ) 162.50 ( PROT MET 16 H ) 130.00 ( PROT MET 16 CA ) 162.50 ( PROT MET 16 CB ) 130.00 ( PROT MET 16 CG ) 130.00 ( PROT MET 16 SD ) 130.00 ( PROT MET 16 CE ) 130.00 ( PROT MET 16 C ) 162.50 ( PROT MET 16 O ) 162.50 ( PROT PHE 17 N ) 162.50 ( PROT PHE 17 H ) 130.00 ( PROT PHE 17 CA ) 162.50 ( PROT PHE 17 CB ) 130.00 ( PROT PHE 17 CG ) 130.00 ( PROT PHE 17 CD1 ) 130.00 ( PROT PHE 17 CD2 ) 130.00 ( PROT PHE 17 CE1 ) 130.00 ( PROT PHE 17 CE2 ) 130.00 ( PROT PHE 17 CZ ) 130.00 ( PROT PHE 17 C ) 162.50 ( PROT PHE 17 O ) 162.50 ( PROT PHE 18 N ) 162.50 ( PROT PHE 18 H ) 130.00 ( PROT PHE 18 CA ) 162.50 ( PROT PHE 18 CB ) 130.00 ( PROT PHE 18 CG ) 130.00 ( PROT PHE 18 CD1 ) 130.00 ( PROT PHE 18 CD2 ) 130.00 ( PROT PHE 18 CE1 ) 130.00 ( PROT PHE 18 CE2 ) 130.00 ( PROT PHE 18 CZ ) 130.00 ( PROT PHE 18 C ) 162.50 ( PROT PHE 18 O ) 162.50 ( PROT GLU 19 N ) 162.50 ( PROT GLU 19 H ) 130.00 ( PROT GLU 19 CA ) 162.50 ( PROT GLU 19 CB ) 130.00 ( PROT GLU 19 CG ) 130.00 ( PROT GLU 19 CD ) 130.00 ( PROT GLU 19 OE1 ) 130.00 ( PROT GLU 19 OE2 ) 130.00 ( PROT GLU 19 C ) 162.50 ( PROT GLU 19 OT1 ) 130.00 ( PROT GLU 19 OT2 ) 130.00 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40607 5.29404 -8.69463 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS -0.00153 -0.00162 0.00142 ROTATION MATRIX 1.000000 -0.000026 -0.000029 0.000026 1.000000 0.000041 0.000029 -0.000041 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 3.9300 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.146545 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1465" Parameter: A <- "0.1465" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70609 5.25152 -8.78390 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00875 0.01290 -0.01047 ROTATION MATRIX 0.999953 0.006978 0.006800 -0.006929 0.999950 -0.007188 -0.006850 0.007141 0.999951 AXIS OF ROTATION IS -0.592400 -0.564362 0.574941 ANGLE IS 0.69 TOTAL SQUARE DIFF IS 0.0261 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.037088 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1465" RDCMND substituted energy or value "?RMS" to " 0.0371" Parameter: A <- "0.1465 0.0371" 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 0.1465 0.0371 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 " 829.43" Parameter: H <- "829.43" 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> 0 836.19824 829.43139 35.87924 ENER INTERN> 66.57397 88.02229 0.00000 10.57054 33.71509 ENER EXTERN> 630.43560 6.88075 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 " 836.20" Parameter: B <- "836.20" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 6.88" Parameter: C <- "6.88" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 630.44" Parameter: C <- " 637.32" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 637.32" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 66.57" Parameter: D <- "66.57" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 88.02" Parameter: D <- " 154.59" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.57" Parameter: D <- " 165.16" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 33.72" Parameter: D <- " 198.88" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 198.88" 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= 836.20 GRMS= 35.88 ELEC= 6.88 VDW= 630.44 RDTITL> *EXTERNAL= 637.32 INTERNAL= 198.88 USER= 0.00 HARM= 829.43 RDTITL> *BOND= 66.57 ANGL= 88.02 DIHE= 10.57 IMPR= 33.72 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11471 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11471 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 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 1438.81639 -602.61815 14.87521 0.02000 MINI INTERN> 66.57397 88.02229 0.00000 10.57054 33.71509 MINI EXTERN> 630.43560 6.88075 0.00000 0.00000 0.00000 MINI CONSTR> 602.61815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1373.49667 65.31972 17.58010 0.00864 MINI INTERN> 69.45760 84.88912 0.00000 11.93695 28.94826 MINI EXTERN> 514.99419 7.51586 0.00000 0.00000 0.00000 MINI CONSTR> 655.75470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11456 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1343.71821 29.77847 1.32872 0.00156 MINI INTERN> 55.64083 84.68569 0.00000 11.71501 27.61958 MINI EXTERN> 486.05535 8.03562 0.00000 0.00000 0.00000 MINI CONSTR> 669.96612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1342.97203 0.74618 0.76830 0.00067 MINI INTERN> 55.52280 84.71706 0.00000 11.76073 28.06482 MINI EXTERN> 479.42321 8.10034 0.00000 0.00000 0.00000 MINI CONSTR> 675.38306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11457 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1342.89480 0.07723 0.08618 0.00012 MINI INTERN> 55.50820 84.48649 0.00000 11.74277 27.86420 MINI EXTERN> 481.21051 8.03325 0.00000 0.00000 0.00000 MINI CONSTR> 674.04938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1342.89344 0.00136 0.09263 0.00005 MINI INTERN> 55.51276 84.39827 0.00000 11.74474 27.88871 MINI EXTERN> 481.13607 8.01571 0.00000 0.00000 0.00000 MINI CONSTR> 674.19719 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11457 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1342.89248 0.00097 0.00765 0.00001 MINI INTERN> 55.44258 84.41983 0.00000 11.74483 27.86255 MINI EXTERN> 481.26057 8.01848 0.00000 0.00000 0.00000 MINI CONSTR> 674.14365 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> 30 1342.89248 0.00097 0.00765 0.00001 STPD INTERN> 55.44258 84.41983 0.00000 11.74483 27.86255 STPD EXTERN> 481.26057 8.01848 0.00000 0.00000 0.00000 STPD CONSTR> 674.14365 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 11457 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11457 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 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 1342.89248 0.00097 0.00765 0.00000 MINI INTERN> 55.44258 84.41983 0.00000 11.74483 27.86255 MINI EXTERN> 481.26057 8.01848 0.00000 0.00000 0.00000 MINI CONSTR> 674.14365 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> 1 1342.89247 0.00001 0.00405 0.02000 CONJ INTERN> 55.44013 84.42015 0.00000 11.74502 27.85956 CONJ EXTERN> 481.26739 8.01983 0.00000 0.00000 0.00000 CONJ CONSTR> 674.14039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "1200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 84.500 ( PROT LYS 1 HT2 ) 84.500 ( PROT LYS 1 N ) 105.63 ( PROT LYS 1 HT3 ) 84.500 ( PROT LYS 1 CA ) 105.63 ( PROT LYS 1 CB ) 84.500 ( PROT LYS 1 CG ) 84.500 ( PROT LYS 1 CD ) 84.500 ( PROT LYS 1 CE ) 84.500 ( PROT LYS 1 NZ ) 84.500 ( PROT LYS 1 HZ1 ) 84.500 ( PROT LYS 1 HZ2 ) 84.500 ( PROT LYS 1 HZ3 ) 84.500 ( PROT LYS 1 C ) 105.63 ( PROT LYS 1 O ) 105.63 ( PROT MET 2 N ) 105.63 ( PROT MET 2 H ) 84.500 ( PROT MET 2 CA ) 105.63 ( PROT MET 2 CB ) 84.500 ( PROT MET 2 CG ) 84.500 ( PROT MET 2 SD ) 84.500 ( PROT MET 2 CE ) 84.500 ( PROT MET 2 C ) 105.63 ( PROT MET 2 O ) 105.63 ( PROT LYS 3 N ) 105.63 ( PROT LYS 3 H ) 84.500 ( PROT LYS 3 CA ) 105.63 ( PROT LYS 3 CB ) 84.500 ( PROT LYS 3 CG ) 84.500 ( PROT LYS 3 CD ) 84.500 ( PROT LYS 3 CE ) 84.500 ( PROT LYS 3 NZ ) 84.500 ( PROT LYS 3 HZ1 ) 84.500 ( PROT LYS 3 HZ2 ) 84.500 ( PROT LYS 3 HZ3 ) 84.500 ( PROT LYS 3 C ) 105.63 ( PROT LYS 3 O ) 105.63 ( PROT ALA 4 N ) 105.63 ( PROT ALA 4 H ) 84.500 ( PROT ALA 4 CA ) 105.63 ( PROT ALA 4 CB ) 84.500 ( PROT ALA 4 C ) 105.63 ( PROT ALA 4 O ) 105.63 ( PROT VAL 5 N ) 105.63 ( PROT VAL 5 H ) 84.500 ( PROT VAL 5 CA ) 105.63 ( PROT VAL 5 CB ) 84.500 ( PROT VAL 5 CG1 ) 84.500 ( PROT VAL 5 CG2 ) 84.500 ( PROT VAL 5 C ) 105.63 ( PROT VAL 5 O ) 105.63 ( PROT MET 6 N ) 105.63 ( PROT MET 6 H ) 84.500 ( PROT MET 6 CA ) 105.63 ( PROT MET 6 CB ) 84.500 ( PROT MET 6 CG ) 84.500 ( PROT MET 6 SD ) 84.500 ( PROT MET 6 CE ) 84.500 ( PROT MET 6 C ) 105.63 ( PROT MET 6 O ) 105.63 ( PROT ILE 7 N ) 105.63 ( PROT ILE 7 H ) 84.500 ( PROT ILE 7 CA ) 105.63 ( PROT ILE 7 CB ) 84.500 ( PROT ILE 7 CG2 ) 84.500 ( PROT ILE 7 CG1 ) 84.500 ( PROT ILE 7 CD ) 84.500 ( PROT ILE 7 C ) 105.63 ( PROT ILE 7 O ) 105.63 ( PROT GLY 8 N ) 105.63 ( PROT GLY 8 H ) 84.500 ( PROT GLY 8 CA ) 105.63 ( PROT GLY 8 C ) 105.63 ( PROT GLY 8 O ) 105.63 ( PROT ALA 9 N ) 105.63 ( PROT ALA 9 H ) 84.500 ( PROT ALA 9 CA ) 105.63 ( PROT ALA 9 CB ) 84.500 ( PROT ALA 9 C ) 105.63 ( PROT ALA 9 O ) 105.63 ( PROT CYS 10 N ) 105.63 ( PROT CYS 10 H ) 84.500 ( PROT CYS 10 CA ) 105.63 ( PROT CYS 10 CB ) 84.500 ( PROT CYS 10 SG ) 84.500 ( PROT CYS 10 C ) 105.63 ( PROT CYS 10 O ) 105.63 ( PROT PHE 11 N ) 105.63 ( PROT PHE 11 H ) 84.500 ( PROT PHE 11 CA ) 105.63 ( PROT PHE 11 CB ) 84.500 ( PROT PHE 11 CG ) 84.500 ( PROT PHE 11 CD1 ) 84.500 ( PROT PHE 11 CD2 ) 84.500 ( PROT PHE 11 CE1 ) 84.500 ( PROT PHE 11 CE2 ) 84.500 ( PROT PHE 11 CZ ) 84.500 ( PROT PHE 11 C ) 105.63 ( PROT PHE 11 O ) 105.63 ( PROT LEU 12 N ) 105.63 ( PROT LEU 12 H ) 84.500 ( PROT LEU 12 CA ) 105.63 ( PROT LEU 12 CB ) 84.500 ( PROT LEU 12 CG ) 84.500 ( PROT LEU 12 CD1 ) 84.500 ( PROT LEU 12 CD2 ) 84.500 ( PROT LEU 12 C ) 105.63 ( PROT LEU 12 O ) 105.63 ( PROT ILE 13 N ) 105.63 ( PROT ILE 13 H ) 84.500 ( PROT ILE 13 CA ) 105.63 ( PROT ILE 13 CB ) 84.500 ( PROT ILE 13 CG2 ) 84.500 ( PROT ILE 13 CG1 ) 84.500 ( PROT ILE 13 CD ) 84.500 ( PROT ILE 13 C ) 105.63 ( PROT ILE 13 O ) 105.63 ( PROT ASH 14 N ) 105.63 ( PROT ASH 14 H ) 84.500 ( PROT ASH 14 CA ) 105.63 ( PROT ASH 14 CB ) 84.500 ( PROT ASH 14 CG ) 84.500 ( PROT ASH 14 OD1 ) 84.500 ( PROT ASH 14 OD2 ) 84.500 ( PROT ASH 14 HD2 ) 84.500 ( PROT ASH 14 C ) 105.63 ( PROT ASH 14 O ) 105.63 ( PROT PHE 15 N ) 105.63 ( PROT PHE 15 H ) 84.500 ( PROT PHE 15 CA ) 105.63 ( PROT PHE 15 CB ) 84.500 ( PROT PHE 15 CG ) 84.500 ( PROT PHE 15 CD1 ) 84.500 ( PROT PHE 15 CD2 ) 84.500 ( PROT PHE 15 CE1 ) 84.500 ( PROT PHE 15 CE2 ) 84.500 ( PROT PHE 15 CZ ) 84.500 ( PROT PHE 15 C ) 105.63 ( PROT PHE 15 O ) 105.63 ( PROT MET 16 N ) 105.63 ( PROT MET 16 H ) 84.500 ( PROT MET 16 CA ) 105.63 ( PROT MET 16 CB ) 84.500 ( PROT MET 16 CG ) 84.500 ( PROT MET 16 SD ) 84.500 ( PROT MET 16 CE ) 84.500 ( PROT MET 16 C ) 105.63 ( PROT MET 16 O ) 105.63 ( PROT PHE 17 N ) 105.63 ( PROT PHE 17 H ) 84.500 ( PROT PHE 17 CA ) 105.63 ( PROT PHE 17 CB ) 84.500 ( PROT PHE 17 CG ) 84.500 ( PROT PHE 17 CD1 ) 84.500 ( PROT PHE 17 CD2 ) 84.500 ( PROT PHE 17 CE1 ) 84.500 ( PROT PHE 17 CE2 ) 84.500 ( PROT PHE 17 CZ ) 84.500 ( PROT PHE 17 C ) 105.63 ( PROT PHE 17 O ) 105.63 ( PROT PHE 18 N ) 105.63 ( PROT PHE 18 H ) 84.500 ( PROT PHE 18 CA ) 105.63 ( PROT PHE 18 CB ) 84.500 ( PROT PHE 18 CG ) 84.500 ( PROT PHE 18 CD1 ) 84.500 ( PROT PHE 18 CD2 ) 84.500 ( PROT PHE 18 CE1 ) 84.500 ( PROT PHE 18 CE2 ) 84.500 ( PROT PHE 18 CZ ) 84.500 ( PROT PHE 18 C ) 105.63 ( PROT PHE 18 O ) 105.63 ( PROT GLU 19 N ) 105.63 ( PROT GLU 19 H ) 84.500 ( PROT GLU 19 CA ) 105.63 ( PROT GLU 19 CB ) 84.500 ( PROT GLU 19 CG ) 84.500 ( PROT GLU 19 CD ) 84.500 ( PROT GLU 19 OE1 ) 84.500 ( PROT GLU 19 OE2 ) 84.500 ( PROT GLU 19 C ) 105.63 ( PROT GLU 19 OT1 ) 84.500 ( PROT GLU 19 OT2 ) 84.500 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40608 5.29415 -8.69464 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS -0.00153 -0.00173 0.00142 ROTATION MATRIX 1.000000 -0.000028 -0.000030 0.000028 1.000000 0.000047 0.000030 -0.000047 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 4.8996 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.163628 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1636" Parameter: A <- "0.1636" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70613 5.24901 -8.78288 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00871 0.01542 -0.01148 ROTATION MATRIX 0.999930 0.008481 0.008204 -0.008410 0.999927 -0.008647 -0.008277 0.008577 0.999929 AXIS OF ROTATION IS -0.589517 -0.564098 0.578155 ANGLE IS 0.84 TOTAL SQUARE DIFF IS 0.0437 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.047948 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1636" RDCMND substituted energy or value "?RMS" to " 0.0479" Parameter: A <- "0.1636 0.0479" 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 0.1636 0.0479 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 " 674.14" Parameter: H <- "674.14" 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> 0 668.75208 674.14039 26.12273 ENER INTERN> 55.44013 84.42015 0.00000 11.74502 27.85956 ENER EXTERN> 481.26739 8.01983 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 " 668.75" Parameter: B <- "668.75" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 8.02" Parameter: C <- "8.02" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 481.27" Parameter: C <- " 489.29" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 489.29" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 55.44" Parameter: D <- "55.44" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 84.42" Parameter: D <- " 139.86" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.75" Parameter: D <- " 151.61" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 27.86" Parameter: D <- " 179.47" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 179.47" 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= 668.75 GRMS= 26.12 ELEC= 8.02 VDW= 481.27 RDTITL> *EXTERNAL= 489.29 INTERNAL= 179.47 USER= 0.00 HARM= 674.14 RDTITL> *BOND= 55.44 ANGL= 84.42 DIHE= 11.75 IMPR= 27.86 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= 668.75 GRMS= 26.12 ELEC= 8.02 VDW= 481.27 RDTITL> *EXTERNAL= 489.29 INTERNAL= 179.47 USER= 0.00 HARM= 674.14 RDTITL> *BOND= 55.44 ANGL= 84.42 DIHE= 11.75 IMPR= 27.86 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= 668.75 GRMS= 26.12 ELEC= 8.02 VDW= 481.27 RDTITL> *EXTERNAL= 489.29 INTERNAL= 179.47 USER= 0.00 HARM= 674.14 RDTITL> *BOND= 55.44 ANGL= 84.42 DIHE= 11.75 IMPR= 27.86 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 1200 0.1636 0.0479 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11457 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11457 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 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 1166.51937 -497.76728 11.04959 0.02000 MINI INTERN> 55.44013 84.42015 0.00000 11.74502 27.85956 MINI EXTERN> 481.26739 8.01983 0.00000 0.00000 0.00000 MINI CONSTR> 497.76728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1115.96054 50.55882 18.00283 0.00864 MINI INTERN> 98.36395 76.79281 0.00000 13.07669 21.46503 MINI EXTERN> 350.02618 12.76858 0.00000 0.00000 0.00000 MINI CONSTR> 543.46730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11445 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1086.55773 29.40281 6.70333 0.00373 MINI INTERN> 40.75161 86.09888 0.00000 13.21827 22.31654 MINI EXTERN> 370.46982 7.08555 0.00000 0.00000 0.00000 MINI CONSTR> 546.61706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1081.63746 4.92028 2.57725 0.00161 MINI INTERN> 47.11131 81.98367 0.00000 13.31257 21.29641 MINI EXTERN> 365.39522 7.91926 0.00000 0.00000 0.00000 MINI CONSTR> 544.61903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11443 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1080.75431 0.88315 0.83618 0.00070 MINI INTERN> 46.74138 82.12798 0.00000 13.33153 22.27995 MINI EXTERN> 359.49785 7.90137 0.00000 0.00000 0.00000 MINI CONSTR> 548.87426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1080.63157 0.12274 0.11620 0.00013 MINI INTERN> 46.55461 81.63123 0.00000 13.31768 21.74393 MINI EXTERN> 361.60797 7.89083 0.00000 0.00000 0.00000 MINI CONSTR> 547.88533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11443 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1080.62484 0.00674 0.04622 0.00005 MINI INTERN> 46.37821 81.60097 0.00000 13.31955 21.69379 MINI EXTERN> 361.91591 7.86287 0.00000 0.00000 0.00000 MINI CONSTR> 547.85355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1080.62313 0.00171 0.01891 0.00002 MINI INTERN> 46.39826 81.57186 0.00000 13.32087 21.70510 MINI EXTERN> 361.79208 7.86467 0.00000 0.00000 0.00000 MINI CONSTR> 547.97029 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11443 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1080.62276 0.00038 0.00917 0.00001 MINI INTERN> 46.37904 81.55746 0.00000 13.32164 21.69556 MINI EXTERN> 361.82333 7.86236 0.00000 0.00000 0.00000 MINI CONSTR> 547.98337 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> 40 1080.62276 0.00038 0.00917 0.00001 STPD INTERN> 46.37904 81.55746 0.00000 13.32164 21.69556 STPD EXTERN> 361.82333 7.86236 0.00000 0.00000 0.00000 STPD CONSTR> 547.98337 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 11443 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11443 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 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 1080.62276 0.00038 0.00917 0.00000 MINI INTERN> 46.37904 81.55746 0.00000 13.32164 21.69556 MINI EXTERN> 361.82333 7.86236 0.00000 0.00000 0.00000 MINI CONSTR> 547.98337 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 1080.62265 0.00011 0.00115 0.02000 CONJ INTERN> 46.37116 81.54617 0.00000 13.32242 21.69707 CONJ EXTERN> 361.79910 7.86152 0.00000 0.00000 0.00000 CONJ CONSTR> 548.02521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "1800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 54.925 ( PROT LYS 1 HT2 ) 54.925 ( PROT LYS 1 N ) 68.656 ( PROT LYS 1 HT3 ) 54.925 ( PROT LYS 1 CA ) 68.656 ( PROT LYS 1 CB ) 54.925 ( PROT LYS 1 CG ) 54.925 ( PROT LYS 1 CD ) 54.925 ( PROT LYS 1 CE ) 54.925 ( PROT LYS 1 NZ ) 54.925 ( PROT LYS 1 HZ1 ) 54.925 ( PROT LYS 1 HZ2 ) 54.925 ( PROT LYS 1 HZ3 ) 54.925 ( PROT LYS 1 C ) 68.656 ( PROT LYS 1 O ) 68.656 ( PROT MET 2 N ) 68.656 ( PROT MET 2 H ) 54.925 ( PROT MET 2 CA ) 68.656 ( PROT MET 2 CB ) 54.925 ( PROT MET 2 CG ) 54.925 ( PROT MET 2 SD ) 54.925 ( PROT MET 2 CE ) 54.925 ( PROT MET 2 C ) 68.656 ( PROT MET 2 O ) 68.656 ( PROT LYS 3 N ) 68.656 ( PROT LYS 3 H ) 54.925 ( PROT LYS 3 CA ) 68.656 ( PROT LYS 3 CB ) 54.925 ( PROT LYS 3 CG ) 54.925 ( PROT LYS 3 CD ) 54.925 ( PROT LYS 3 CE ) 54.925 ( PROT LYS 3 NZ ) 54.925 ( PROT LYS 3 HZ1 ) 54.925 ( PROT LYS 3 HZ2 ) 54.925 ( PROT LYS 3 HZ3 ) 54.925 ( PROT LYS 3 C ) 68.656 ( PROT LYS 3 O ) 68.656 ( PROT ALA 4 N ) 68.656 ( PROT ALA 4 H ) 54.925 ( PROT ALA 4 CA ) 68.656 ( PROT ALA 4 CB ) 54.925 ( PROT ALA 4 C ) 68.656 ( PROT ALA 4 O ) 68.656 ( PROT VAL 5 N ) 68.656 ( PROT VAL 5 H ) 54.925 ( PROT VAL 5 CA ) 68.656 ( PROT VAL 5 CB ) 54.925 ( PROT VAL 5 CG1 ) 54.925 ( PROT VAL 5 CG2 ) 54.925 ( PROT VAL 5 C ) 68.656 ( PROT VAL 5 O ) 68.656 ( PROT MET 6 N ) 68.656 ( PROT MET 6 H ) 54.925 ( PROT MET 6 CA ) 68.656 ( PROT MET 6 CB ) 54.925 ( PROT MET 6 CG ) 54.925 ( PROT MET 6 SD ) 54.925 ( PROT MET 6 CE ) 54.925 ( PROT MET 6 C ) 68.656 ( PROT MET 6 O ) 68.656 ( PROT ILE 7 N ) 68.656 ( PROT ILE 7 H ) 54.925 ( PROT ILE 7 CA ) 68.656 ( PROT ILE 7 CB ) 54.925 ( PROT ILE 7 CG2 ) 54.925 ( PROT ILE 7 CG1 ) 54.925 ( PROT ILE 7 CD ) 54.925 ( PROT ILE 7 C ) 68.656 ( PROT ILE 7 O ) 68.656 ( PROT GLY 8 N ) 68.656 ( PROT GLY 8 H ) 54.925 ( PROT GLY 8 CA ) 68.656 ( PROT GLY 8 C ) 68.656 ( PROT GLY 8 O ) 68.656 ( PROT ALA 9 N ) 68.656 ( PROT ALA 9 H ) 54.925 ( PROT ALA 9 CA ) 68.656 ( PROT ALA 9 CB ) 54.925 ( PROT ALA 9 C ) 68.656 ( PROT ALA 9 O ) 68.656 ( PROT CYS 10 N ) 68.656 ( PROT CYS 10 H ) 54.925 ( PROT CYS 10 CA ) 68.656 ( PROT CYS 10 CB ) 54.925 ( PROT CYS 10 SG ) 54.925 ( PROT CYS 10 C ) 68.656 ( PROT CYS 10 O ) 68.656 ( PROT PHE 11 N ) 68.656 ( PROT PHE 11 H ) 54.925 ( PROT PHE 11 CA ) 68.656 ( PROT PHE 11 CB ) 54.925 ( PROT PHE 11 CG ) 54.925 ( PROT PHE 11 CD1 ) 54.925 ( PROT PHE 11 CD2 ) 54.925 ( PROT PHE 11 CE1 ) 54.925 ( PROT PHE 11 CE2 ) 54.925 ( PROT PHE 11 CZ ) 54.925 ( PROT PHE 11 C ) 68.656 ( PROT PHE 11 O ) 68.656 ( PROT LEU 12 N ) 68.656 ( PROT LEU 12 H ) 54.925 ( PROT LEU 12 CA ) 68.656 ( PROT LEU 12 CB ) 54.925 ( PROT LEU 12 CG ) 54.925 ( PROT LEU 12 CD1 ) 54.925 ( PROT LEU 12 CD2 ) 54.925 ( PROT LEU 12 C ) 68.656 ( PROT LEU 12 O ) 68.656 ( PROT ILE 13 N ) 68.656 ( PROT ILE 13 H ) 54.925 ( PROT ILE 13 CA ) 68.656 ( PROT ILE 13 CB ) 54.925 ( PROT ILE 13 CG2 ) 54.925 ( PROT ILE 13 CG1 ) 54.925 ( PROT ILE 13 CD ) 54.925 ( PROT ILE 13 C ) 68.656 ( PROT ILE 13 O ) 68.656 ( PROT ASH 14 N ) 68.656 ( PROT ASH 14 H ) 54.925 ( PROT ASH 14 CA ) 68.656 ( PROT ASH 14 CB ) 54.925 ( PROT ASH 14 CG ) 54.925 ( PROT ASH 14 OD1 ) 54.925 ( PROT ASH 14 OD2 ) 54.925 ( PROT ASH 14 HD2 ) 54.925 ( PROT ASH 14 C ) 68.656 ( PROT ASH 14 O ) 68.656 ( PROT PHE 15 N ) 68.656 ( PROT PHE 15 H ) 54.925 ( PROT PHE 15 CA ) 68.656 ( PROT PHE 15 CB ) 54.925 ( PROT PHE 15 CG ) 54.925 ( PROT PHE 15 CD1 ) 54.925 ( PROT PHE 15 CD2 ) 54.925 ( PROT PHE 15 CE1 ) 54.925 ( PROT PHE 15 CE2 ) 54.925 ( PROT PHE 15 CZ ) 54.925 ( PROT PHE 15 C ) 68.656 ( PROT PHE 15 O ) 68.656 ( PROT MET 16 N ) 68.656 ( PROT MET 16 H ) 54.925 ( PROT MET 16 CA ) 68.656 ( PROT MET 16 CB ) 54.925 ( PROT MET 16 CG ) 54.925 ( PROT MET 16 SD ) 54.925 ( PROT MET 16 CE ) 54.925 ( PROT MET 16 C ) 68.656 ( PROT MET 16 O ) 68.656 ( PROT PHE 17 N ) 68.656 ( PROT PHE 17 H ) 54.925 ( PROT PHE 17 CA ) 68.656 ( PROT PHE 17 CB ) 54.925 ( PROT PHE 17 CG ) 54.925 ( PROT PHE 17 CD1 ) 54.925 ( PROT PHE 17 CD2 ) 54.925 ( PROT PHE 17 CE1 ) 54.925 ( PROT PHE 17 CE2 ) 54.925 ( PROT PHE 17 CZ ) 54.925 ( PROT PHE 17 C ) 68.656 ( PROT PHE 17 O ) 68.656 ( PROT PHE 18 N ) 68.656 ( PROT PHE 18 H ) 54.925 ( PROT PHE 18 CA ) 68.656 ( PROT PHE 18 CB ) 54.925 ( PROT PHE 18 CG ) 54.925 ( PROT PHE 18 CD1 ) 54.925 ( PROT PHE 18 CD2 ) 54.925 ( PROT PHE 18 CE1 ) 54.925 ( PROT PHE 18 CE2 ) 54.925 ( PROT PHE 18 CZ ) 54.925 ( PROT PHE 18 C ) 68.656 ( PROT PHE 18 O ) 68.656 ( PROT GLU 19 N ) 68.656 ( PROT GLU 19 H ) 54.925 ( PROT GLU 19 CA ) 68.656 ( PROT GLU 19 CB ) 54.925 ( PROT GLU 19 CG ) 54.925 ( PROT GLU 19 CD ) 54.925 ( PROT GLU 19 OE1 ) 54.925 ( PROT GLU 19 OE2 ) 54.925 ( PROT GLU 19 C ) 68.656 ( PROT GLU 19 OT1 ) 54.925 ( PROT GLU 19 OT2 ) 54.925 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40599 5.29421 -8.69454 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS -0.00145 -0.00180 0.00133 ROTATION MATRIX 1.000000 -0.000032 -0.000028 0.000032 1.000000 0.000053 0.000028 -0.000053 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 6.1134 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.182775 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1828" Parameter: A <- "0.1828" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70659 5.24603 -8.78203 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00825 0.01839 -0.01234 ROTATION MATRIX 0.999905 0.009975 0.009534 -0.009879 0.999901 -0.010047 -0.009633 0.009952 0.999904 AXIS OF ROTATION IS -0.586816 -0.562395 0.582545 ANGLE IS 0.98 TOTAL SQUARE DIFF IS 0.0696 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.060528 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1828" RDCMND substituted energy or value "?RMS" to " 0.0605" Parameter: A <- "0.1828 0.0605" 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 0.1828 0.0605 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 " 548.03" Parameter: H <- "548.03" 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> 0 532.59744 548.02521 19.01340 ENER INTERN> 46.37116 81.54617 0.00000 13.32242 21.69707 ENER EXTERN> 361.79910 7.86152 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 " 532.60" Parameter: B <- "532.60" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 7.86" Parameter: C <- "7.86" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 361.80" Parameter: C <- " 369.66" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 369.66" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 46.37" Parameter: D <- "46.37" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 81.55" Parameter: D <- " 127.92" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 13.32" Parameter: D <- " 141.24" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 21.70" Parameter: D <- " 162.94" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 162.94" 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= 532.60 GRMS= 19.01 ELEC= 7.86 VDW= 361.80 RDTITL> *EXTERNAL= 369.66 INTERNAL= 162.94 USER= 0.00 HARM= 548.03 RDTITL> *BOND= 46.37 ANGL= 81.55 DIHE= 13.32 IMPR= 21.70 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11443 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11443 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 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> 0 941.32747 -408.73003 8.13731 0.02000 MINI INTERN> 46.37116 81.54617 0.00000 13.32242 21.69707 MINI EXTERN> 361.79910 7.86152 0.00000 0.00000 0.00000 MINI CONSTR> 408.73003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 905.08571 36.24176 17.13844 0.00864 MINI INTERN> 89.55806 73.81932 0.00000 14.64543 15.83009 MINI EXTERN> 254.53487 12.30815 0.00000 0.00000 0.00000 MINI CONSTR> 444.38979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11433 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 876.09382 28.99190 6.77307 0.00373 MINI INTERN> 32.40256 83.46951 0.00000 15.40527 17.04097 MINI EXTERN> 278.94022 5.55947 0.00000 0.00000 0.00000 MINI CONSTR> 443.27583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 869.35803 6.73579 2.09196 0.00161 MINI INTERN> 40.33788 79.38284 0.00000 15.21632 16.42374 MINI EXTERN> 265.90485 6.99854 0.00000 0.00000 0.00000 MINI CONSTR> 445.09386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11429 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 867.83532 1.52271 0.67665 0.00070 MINI INTERN> 38.52086 78.36070 0.00000 15.34745 16.38500 MINI EXTERN> 267.01618 6.66071 0.00000 0.00000 0.00000 MINI CONSTR> 445.54442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 867.38318 0.45214 1.17863 0.00072 MINI INTERN> 37.95516 77.69179 0.00000 15.40643 16.29109 MINI EXTERN> 267.37076 6.49382 0.00000 0.00000 0.00000 MINI CONSTR> 446.17414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11429 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 867.09727 0.28591 0.30211 0.00031 MINI INTERN> 38.31304 77.66252 0.00000 15.36737 16.24840 MINI EXTERN> 266.02384 6.51041 0.00000 0.00000 0.00000 MINI CONSTR> 446.97168 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 867.03378 0.06349 0.36523 0.00032 MINI INTERN> 38.26148 77.47224 0.00000 15.37386 16.21800 MINI EXTERN> 265.85138 6.47593 0.00000 0.00000 0.00000 MINI CONSTR> 447.38087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11428 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 867.00489 0.02888 0.18119 0.00014 MINI INTERN> 38.01056 77.41968 0.00000 15.39229 16.24399 MINI EXTERN> 265.89504 6.43561 0.00000 0.00000 0.00000 MINI CONSTR> 447.60773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 866.99518 0.00972 0.05119 0.00006 MINI INTERN> 38.03224 77.33664 0.00000 15.39069 16.22074 MINI EXTERN> 265.86853 6.43289 0.00000 0.00000 0.00000 MINI CONSTR> 447.71343 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11428 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 866.99320 0.00198 0.09159 0.00006 MINI INTERN> 38.00131 77.28928 0.00000 15.39244 16.21371 MINI EXTERN> 265.87013 6.42627 0.00000 0.00000 0.00000 MINI CONSTR> 447.80006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 866.99166 0.00154 0.02893 0.00003 MINI INTERN> 38.00242 77.29038 0.00000 15.39427 16.22032 MINI EXTERN> 265.78992 6.42233 0.00000 0.00000 0.00000 MINI CONSTR> 447.87201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11428 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 866.99139 0.00027 0.01017 0.00001 MINI INTERN> 37.98346 77.28036 0.00000 15.39478 16.21870 MINI EXTERN> 265.80540 6.41943 0.00000 0.00000 0.00000 MINI CONSTR> 447.88926 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> 63 866.99132 0.00007 0.00765 0.00001 STPD INTERN> 37.97905 77.27708 0.00000 15.39504 16.21860 STPD EXTERN> 265.80248 6.41838 0.00000 0.00000 0.00000 STPD CONSTR> 447.90069 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 11428 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11428 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 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> 0 866.99132 0.00007 0.00765 0.00000 MINI INTERN> 37.97905 77.27708 0.00000 15.39504 16.21860 MINI EXTERN> 265.80248 6.41838 0.00000 0.00000 0.00000 MINI CONSTR> 447.90069 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> 1 866.99130 0.00002 0.00928 0.02000 CONJ INTERN> 37.97407 77.27960 0.00000 15.39513 16.21919 CONJ EXTERN> 265.79977 6.41712 0.00000 0.00000 0.00000 CONJ CONSTR> 447.90641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "2400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 35.701 ( PROT LYS 1 HT2 ) 35.701 ( PROT LYS 1 N ) 44.627 ( PROT LYS 1 HT3 ) 35.701 ( PROT LYS 1 CA ) 44.627 ( PROT LYS 1 CB ) 35.701 ( PROT LYS 1 CG ) 35.701 ( PROT LYS 1 CD ) 35.701 ( PROT LYS 1 CE ) 35.701 ( PROT LYS 1 NZ ) 35.701 ( PROT LYS 1 HZ1 ) 35.701 ( PROT LYS 1 HZ2 ) 35.701 ( PROT LYS 1 HZ3 ) 35.701 ( PROT LYS 1 C ) 44.627 ( PROT LYS 1 O ) 44.627 ( PROT MET 2 N ) 44.627 ( PROT MET 2 H ) 35.701 ( PROT MET 2 CA ) 44.627 ( PROT MET 2 CB ) 35.701 ( PROT MET 2 CG ) 35.701 ( PROT MET 2 SD ) 35.701 ( PROT MET 2 CE ) 35.701 ( PROT MET 2 C ) 44.627 ( PROT MET 2 O ) 44.627 ( PROT LYS 3 N ) 44.627 ( PROT LYS 3 H ) 35.701 ( PROT LYS 3 CA ) 44.627 ( PROT LYS 3 CB ) 35.701 ( PROT LYS 3 CG ) 35.701 ( PROT LYS 3 CD ) 35.701 ( PROT LYS 3 CE ) 35.701 ( PROT LYS 3 NZ ) 35.701 ( PROT LYS 3 HZ1 ) 35.701 ( PROT LYS 3 HZ2 ) 35.701 ( PROT LYS 3 HZ3 ) 35.701 ( PROT LYS 3 C ) 44.627 ( PROT LYS 3 O ) 44.627 ( PROT ALA 4 N ) 44.627 ( PROT ALA 4 H ) 35.701 ( PROT ALA 4 CA ) 44.627 ( PROT ALA 4 CB ) 35.701 ( PROT ALA 4 C ) 44.627 ( PROT ALA 4 O ) 44.627 ( PROT VAL 5 N ) 44.627 ( PROT VAL 5 H ) 35.701 ( PROT VAL 5 CA ) 44.627 ( PROT VAL 5 CB ) 35.701 ( PROT VAL 5 CG1 ) 35.701 ( PROT VAL 5 CG2 ) 35.701 ( PROT VAL 5 C ) 44.627 ( PROT VAL 5 O ) 44.627 ( PROT MET 6 N ) 44.627 ( PROT MET 6 H ) 35.701 ( PROT MET 6 CA ) 44.627 ( PROT MET 6 CB ) 35.701 ( PROT MET 6 CG ) 35.701 ( PROT MET 6 SD ) 35.701 ( PROT MET 6 CE ) 35.701 ( PROT MET 6 C ) 44.627 ( PROT MET 6 O ) 44.627 ( PROT ILE 7 N ) 44.627 ( PROT ILE 7 H ) 35.701 ( PROT ILE 7 CA ) 44.627 ( PROT ILE 7 CB ) 35.701 ( PROT ILE 7 CG2 ) 35.701 ( PROT ILE 7 CG1 ) 35.701 ( PROT ILE 7 CD ) 35.701 ( PROT ILE 7 C ) 44.627 ( PROT ILE 7 O ) 44.627 ( PROT GLY 8 N ) 44.627 ( PROT GLY 8 H ) 35.701 ( PROT GLY 8 CA ) 44.627 ( PROT GLY 8 C ) 44.627 ( PROT GLY 8 O ) 44.627 ( PROT ALA 9 N ) 44.627 ( PROT ALA 9 H ) 35.701 ( PROT ALA 9 CA ) 44.627 ( PROT ALA 9 CB ) 35.701 ( PROT ALA 9 C ) 44.627 ( PROT ALA 9 O ) 44.627 ( PROT CYS 10 N ) 44.627 ( PROT CYS 10 H ) 35.701 ( PROT CYS 10 CA ) 44.627 ( PROT CYS 10 CB ) 35.701 ( PROT CYS 10 SG ) 35.701 ( PROT CYS 10 C ) 44.627 ( PROT CYS 10 O ) 44.627 ( PROT PHE 11 N ) 44.627 ( PROT PHE 11 H ) 35.701 ( PROT PHE 11 CA ) 44.627 ( PROT PHE 11 CB ) 35.701 ( PROT PHE 11 CG ) 35.701 ( PROT PHE 11 CD1 ) 35.701 ( PROT PHE 11 CD2 ) 35.701 ( PROT PHE 11 CE1 ) 35.701 ( PROT PHE 11 CE2 ) 35.701 ( PROT PHE 11 CZ ) 35.701 ( PROT PHE 11 C ) 44.627 ( PROT PHE 11 O ) 44.627 ( PROT LEU 12 N ) 44.627 ( PROT LEU 12 H ) 35.701 ( PROT LEU 12 CA ) 44.627 ( PROT LEU 12 CB ) 35.701 ( PROT LEU 12 CG ) 35.701 ( PROT LEU 12 CD1 ) 35.701 ( PROT LEU 12 CD2 ) 35.701 ( PROT LEU 12 C ) 44.627 ( PROT LEU 12 O ) 44.627 ( PROT ILE 13 N ) 44.627 ( PROT ILE 13 H ) 35.701 ( PROT ILE 13 CA ) 44.627 ( PROT ILE 13 CB ) 35.701 ( PROT ILE 13 CG2 ) 35.701 ( PROT ILE 13 CG1 ) 35.701 ( PROT ILE 13 CD ) 35.701 ( PROT ILE 13 C ) 44.627 ( PROT ILE 13 O ) 44.627 ( PROT ASH 14 N ) 44.627 ( PROT ASH 14 H ) 35.701 ( PROT ASH 14 CA ) 44.627 ( PROT ASH 14 CB ) 35.701 ( PROT ASH 14 CG ) 35.701 ( PROT ASH 14 OD1 ) 35.701 ( PROT ASH 14 OD2 ) 35.701 ( PROT ASH 14 HD2 ) 35.701 ( PROT ASH 14 C ) 44.627 ( PROT ASH 14 O ) 44.627 ( PROT PHE 15 N ) 44.627 ( PROT PHE 15 H ) 35.701 ( PROT PHE 15 CA ) 44.627 ( PROT PHE 15 CB ) 35.701 ( PROT PHE 15 CG ) 35.701 ( PROT PHE 15 CD1 ) 35.701 ( PROT PHE 15 CD2 ) 35.701 ( PROT PHE 15 CE1 ) 35.701 ( PROT PHE 15 CE2 ) 35.701 ( PROT PHE 15 CZ ) 35.701 ( PROT PHE 15 C ) 44.627 ( PROT PHE 15 O ) 44.627 ( PROT MET 16 N ) 44.627 ( PROT MET 16 H ) 35.701 ( PROT MET 16 CA ) 44.627 ( PROT MET 16 CB ) 35.701 ( PROT MET 16 CG ) 35.701 ( PROT MET 16 SD ) 35.701 ( PROT MET 16 CE ) 35.701 ( PROT MET 16 C ) 44.627 ( PROT MET 16 O ) 44.627 ( PROT PHE 17 N ) 44.627 ( PROT PHE 17 H ) 35.701 ( PROT PHE 17 CA ) 44.627 ( PROT PHE 17 CB ) 35.701 ( PROT PHE 17 CG ) 35.701 ( PROT PHE 17 CD1 ) 35.701 ( PROT PHE 17 CD2 ) 35.701 ( PROT PHE 17 CE1 ) 35.701 ( PROT PHE 17 CE2 ) 35.701 ( PROT PHE 17 CZ ) 35.701 ( PROT PHE 17 C ) 44.627 ( PROT PHE 17 O ) 44.627 ( PROT PHE 18 N ) 44.627 ( PROT PHE 18 H ) 35.701 ( PROT PHE 18 CA ) 44.627 ( PROT PHE 18 CB ) 35.701 ( PROT PHE 18 CG ) 35.701 ( PROT PHE 18 CD1 ) 35.701 ( PROT PHE 18 CD2 ) 35.701 ( PROT PHE 18 CE1 ) 35.701 ( PROT PHE 18 CE2 ) 35.701 ( PROT PHE 18 CZ ) 35.701 ( PROT PHE 18 C ) 44.627 ( PROT PHE 18 O ) 44.627 ( PROT GLU 19 N ) 44.627 ( PROT GLU 19 H ) 35.701 ( PROT GLU 19 CA ) 44.627 ( PROT GLU 19 CB ) 35.701 ( PROT GLU 19 CG ) 35.701 ( PROT GLU 19 CD ) 35.701 ( PROT GLU 19 OE1 ) 35.701 ( PROT GLU 19 OE2 ) 35.701 ( PROT GLU 19 C ) 44.627 ( PROT GLU 19 OT1 ) 35.701 ( PROT GLU 19 OT2 ) 35.701 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40581 5.29424 -8.69434 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS -0.00127 -0.00182 0.00112 ROTATION MATRIX 1.000000 -0.000057 -0.000040 0.000057 1.000000 0.000080 0.000040 -0.000080 1.000000 AXIS OF ROTATION IS 0.756726 0.375899 -0.534850 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 7.6696 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.204721 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2047" Parameter: A <- "0.2047" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70732 5.24245 -8.78126 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00752 0.02198 -0.01311 ROTATION MATRIX 0.999876 0.011476 0.010792 -0.011353 0.999871 -0.011400 -0.010921 0.011276 0.999877 AXIS OF ROTATION IS -0.584180 -0.559356 0.588094 ANGLE IS 1.11 CENTER OF ROTATION 9.423103 5.086774 -9.232389 SHIFT IS -0.024398 TOTAL SQUARE DIFF IS 0.1054 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.074472 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2047" RDCMND substituted energy or value "?RMS" to " 0.0745" Parameter: A <- "0.2047 0.0745" 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 0.2047 0.0745 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 " 447.91" Parameter: H <- "447.91" 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> 0 419.08489 447.90641 13.87617 ENER INTERN> 37.97407 77.27960 0.00000 15.39513 16.21919 ENER EXTERN> 265.79977 6.41712 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 " 419.08" Parameter: B <- "419.08" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 6.42" Parameter: C <- "6.42" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 265.80" Parameter: C <- " 272.22" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 272.22" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 37.97" Parameter: D <- "37.97" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 77.28" Parameter: D <- " 115.25" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 15.40" Parameter: D <- " 130.65" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 16.22" Parameter: D <- " 146.87" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 146.87" 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= 419.08 GRMS= 13.88 ELEC= 6.42 VDW= 265.80 RDTITL> *EXTERNAL= 272.22 INTERNAL= 146.87 USER= 0.00 HARM= 447.91 RDTITL> *BOND= 37.97 ANGL= 77.28 DIHE= 15.40 IMPR= 16.22 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= 419.08 GRMS= 13.88 ELEC= 6.42 VDW= 265.80 RDTITL> *EXTERNAL= 272.22 INTERNAL= 146.87 USER= 0.00 HARM= 447.91 RDTITL> *BOND= 37.97 ANGL= 77.28 DIHE= 15.40 IMPR= 16.22 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= 419.08 GRMS= 13.88 ELEC= 6.42 VDW= 265.80 RDTITL> *EXTERNAL= 272.22 INTERNAL= 146.87 USER= 0.00 HARM= 447.91 RDTITL> *BOND= 37.97 ANGL= 77.28 DIHE= 15.40 IMPR= 16.22 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 2400 0.2047 0.0745 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11428 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11428 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 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> 0 754.62260 -335.53771 5.96599 0.02000 MINI INTERN> 37.97407 77.27960 0.00000 15.39513 16.21919 MINI EXTERN> 265.79977 6.41712 0.00000 0.00000 0.00000 MINI CONSTR> 335.53771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 728.55367 26.06893 15.03934 0.00864 MINI INTERN> 66.54347 70.31171 0.00000 16.82354 11.80050 MINI EXTERN> 192.36964 8.77116 0.00000 0.00000 0.00000 MINI CONSTR> 361.93364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11424 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 703.64741 24.90626 6.90296 0.00373 MINI INTERN> 43.81614 72.32637 0.00000 17.58322 12.71075 MINI EXTERN> 184.07927 7.03241 0.00000 0.00000 0.00000 MINI CONSTR> 366.09926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 696.31775 7.32966 2.08076 0.00161 MINI INTERN> 29.33671 74.04399 0.00000 17.87441 12.39778 MINI EXTERN> 193.01962 4.42776 0.00000 0.00000 0.00000 MINI CONSTR> 365.21748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11420 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 694.57213 1.74562 2.80258 0.00167 MINI INTERN> 28.28071 73.35011 0.00000 17.98304 12.32478 MINI EXTERN> 192.51901 4.02240 0.00000 0.00000 0.00000 MINI CONSTR> 366.09206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 692.81761 1.75452 0.77497 0.00072 MINI INTERN> 30.54210 71.82318 0.00000 17.91396 12.29056 MINI EXTERN> 188.28747 4.52739 0.00000 0.00000 0.00000 MINI CONSTR> 367.43294 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11420 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 692.21119 0.60643 0.52473 0.00075 MINI INTERN> 30.10870 71.40784 0.00000 17.95431 12.26162 MINI EXTERN> 188.03040 4.38446 0.00000 0.00000 0.00000 MINI CONSTR> 368.06386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 691.91428 0.29691 1.22305 0.00078 MINI INTERN> 30.53483 71.05744 0.00000 17.92807 12.26025 MINI EXTERN> 186.75699 4.39744 0.00000 0.00000 0.00000 MINI CONSTR> 368.97925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11420 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 691.61198 0.30230 0.34790 0.00034 MINI INTERN> 29.46598 70.77098 0.00000 18.02138 12.21955 MINI EXTERN> 187.80849 4.17403 0.00000 0.00000 0.00000 MINI CONSTR> 369.15157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 691.51199 0.09999 0.36927 0.00035 MINI INTERN> 29.31747 70.61095 0.00000 18.03397 12.21094 MINI EXTERN> 187.69513 4.12052 0.00000 0.00000 0.00000 MINI CONSTR> 369.52300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11420 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 691.48350 0.02849 0.56671 0.00036 MINI INTERN> 29.13512 70.50787 0.00000 18.05176 12.20149 MINI EXTERN> 187.79465 4.06926 0.00000 0.00000 0.00000 MINI CONSTR> 369.72336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 691.43006 0.05344 0.24011 0.00016 MINI INTERN> 29.56902 70.46317 0.00000 18.00553 12.21241 MINI EXTERN> 186.97247 4.12175 0.00000 0.00000 0.00000 MINI CONSTR> 370.08571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11420 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 691.41748 0.01258 0.28903 0.00016 MINI INTERN> 29.58857 70.40772 0.00000 18.00315 12.21094 MINI EXTERN> 186.84511 4.11040 0.00000 0.00000 0.00000 MINI CONSTR> 370.25159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 691.40391 0.01357 0.05197 0.00007 MINI INTERN> 29.37724 70.36840 0.00000 18.02251 12.20661 MINI EXTERN> 187.08330 4.07075 0.00000 0.00000 0.00000 MINI CONSTR> 370.27510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11421 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 691.39935 0.00456 0.11997 0.00007 MINI INTERN> 29.29944 70.33224 0.00000 18.02923 12.20559 MINI EXTERN> 187.12442 4.04701 0.00000 0.00000 0.00000 MINI CONSTR> 370.36142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 691.39714 0.00222 0.11698 0.00007 MINI INTERN> 29.29282 70.31568 0.00000 18.02892 12.20491 MINI EXTERN> 187.10112 4.03917 0.00000 0.00000 0.00000 MINI CONSTR> 370.41450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11421 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 691.39452 0.00262 0.04297 0.00003 MINI INTERN> 29.37685 70.30856 0.00000 18.01886 12.20516 MINI EXTERN> 186.95175 4.04587 0.00000 0.00000 0.00000 MINI CONSTR> 370.48746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 691.39361 0.00091 0.03589 0.00003 MINI INTERN> 29.36908 70.29966 0.00000 18.01884 12.20522 MINI EXTERN> 186.94032 4.03924 0.00000 0.00000 0.00000 MINI CONSTR> 370.52125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11421 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 691.39323 0.00037 0.05264 0.00003 MINI INTERN> 29.37761 70.29498 0.00000 18.01724 12.20551 MINI EXTERN> 186.91146 4.03617 0.00000 0.00000 0.00000 MINI CONSTR> 370.55026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 691.39263 0.00060 0.01551 0.00002 MINI INTERN> 29.34055 70.28828 0.00000 18.02068 12.20590 MINI EXTERN> 186.94884 4.02606 0.00000 0.00000 0.00000 MINI CONSTR> 370.56232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11421 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 691.39236 0.00026 0.01324 0.00002 MINI INTERN> 29.34069 70.28464 0.00000 18.02012 12.20605 MINI EXTERN> 186.93783 4.02223 0.00000 0.00000 0.00000 MINI CONSTR> 370.58081 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> 102 691.39228 0.00008 0.00911 0.00001 STPD INTERN> 29.34691 70.28284 0.00000 18.01923 12.20562 STPD EXTERN> 186.92810 4.02199 0.00000 0.00000 0.00000 STPD CONSTR> 370.58759 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 11421 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11421 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 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> 0 691.39228 0.00008 0.00911 0.00000 MINI INTERN> 29.34691 70.28284 0.00000 18.01923 12.20562 MINI EXTERN> 186.92810 4.02199 0.00000 0.00000 0.00000 MINI CONSTR> 370.58759 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> 3 691.39176 0.00052 0.00353 0.02000 CONJ INTERN> 29.34262 70.26685 0.00000 18.01700 12.20624 CONJ EXTERN> 186.88699 4.00222 0.00000 0.00000 0.00000 CONJ CONSTR> 370.66986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "3000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 23.206 ( PROT LYS 1 HT2 ) 23.206 ( PROT LYS 1 N ) 29.007 ( PROT LYS 1 HT3 ) 23.206 ( PROT LYS 1 CA ) 29.007 ( PROT LYS 1 CB ) 23.206 ( PROT LYS 1 CG ) 23.206 ( PROT LYS 1 CD ) 23.206 ( PROT LYS 1 CE ) 23.206 ( PROT LYS 1 NZ ) 23.206 ( PROT LYS 1 HZ1 ) 23.206 ( PROT LYS 1 HZ2 ) 23.206 ( PROT LYS 1 HZ3 ) 23.206 ( PROT LYS 1 C ) 29.007 ( PROT LYS 1 O ) 29.007 ( PROT MET 2 N ) 29.007 ( PROT MET 2 H ) 23.206 ( PROT MET 2 CA ) 29.007 ( PROT MET 2 CB ) 23.206 ( PROT MET 2 CG ) 23.206 ( PROT MET 2 SD ) 23.206 ( PROT MET 2 CE ) 23.206 ( PROT MET 2 C ) 29.007 ( PROT MET 2 O ) 29.007 ( PROT LYS 3 N ) 29.007 ( PROT LYS 3 H ) 23.206 ( PROT LYS 3 CA ) 29.007 ( PROT LYS 3 CB ) 23.206 ( PROT LYS 3 CG ) 23.206 ( PROT LYS 3 CD ) 23.206 ( PROT LYS 3 CE ) 23.206 ( PROT LYS 3 NZ ) 23.206 ( PROT LYS 3 HZ1 ) 23.206 ( PROT LYS 3 HZ2 ) 23.206 ( PROT LYS 3 HZ3 ) 23.206 ( PROT LYS 3 C ) 29.007 ( PROT LYS 3 O ) 29.007 ( PROT ALA 4 N ) 29.007 ( PROT ALA 4 H ) 23.206 ( PROT ALA 4 CA ) 29.007 ( PROT ALA 4 CB ) 23.206 ( PROT ALA 4 C ) 29.007 ( PROT ALA 4 O ) 29.007 ( PROT VAL 5 N ) 29.007 ( PROT VAL 5 H ) 23.206 ( PROT VAL 5 CA ) 29.007 ( PROT VAL 5 CB ) 23.206 ( PROT VAL 5 CG1 ) 23.206 ( PROT VAL 5 CG2 ) 23.206 ( PROT VAL 5 C ) 29.007 ( PROT VAL 5 O ) 29.007 ( PROT MET 6 N ) 29.007 ( PROT MET 6 H ) 23.206 ( PROT MET 6 CA ) 29.007 ( PROT MET 6 CB ) 23.206 ( PROT MET 6 CG ) 23.206 ( PROT MET 6 SD ) 23.206 ( PROT MET 6 CE ) 23.206 ( PROT MET 6 C ) 29.007 ( PROT MET 6 O ) 29.007 ( PROT ILE 7 N ) 29.007 ( PROT ILE 7 H ) 23.206 ( PROT ILE 7 CA ) 29.007 ( PROT ILE 7 CB ) 23.206 ( PROT ILE 7 CG2 ) 23.206 ( PROT ILE 7 CG1 ) 23.206 ( PROT ILE 7 CD ) 23.206 ( PROT ILE 7 C ) 29.007 ( PROT ILE 7 O ) 29.007 ( PROT GLY 8 N ) 29.007 ( PROT GLY 8 H ) 23.206 ( PROT GLY 8 CA ) 29.007 ( PROT GLY 8 C ) 29.007 ( PROT GLY 8 O ) 29.007 ( PROT ALA 9 N ) 29.007 ( PROT ALA 9 H ) 23.206 ( PROT ALA 9 CA ) 29.007 ( PROT ALA 9 CB ) 23.206 ( PROT ALA 9 C ) 29.007 ( PROT ALA 9 O ) 29.007 ( PROT CYS 10 N ) 29.007 ( PROT CYS 10 H ) 23.206 ( PROT CYS 10 CA ) 29.007 ( PROT CYS 10 CB ) 23.206 ( PROT CYS 10 SG ) 23.206 ( PROT CYS 10 C ) 29.007 ( PROT CYS 10 O ) 29.007 ( PROT PHE 11 N ) 29.007 ( PROT PHE 11 H ) 23.206 ( PROT PHE 11 CA ) 29.007 ( PROT PHE 11 CB ) 23.206 ( PROT PHE 11 CG ) 23.206 ( PROT PHE 11 CD1 ) 23.206 ( PROT PHE 11 CD2 ) 23.206 ( PROT PHE 11 CE1 ) 23.206 ( PROT PHE 11 CE2 ) 23.206 ( PROT PHE 11 CZ ) 23.206 ( PROT PHE 11 C ) 29.007 ( PROT PHE 11 O ) 29.007 ( PROT LEU 12 N ) 29.007 ( PROT LEU 12 H ) 23.206 ( PROT LEU 12 CA ) 29.007 ( PROT LEU 12 CB ) 23.206 ( PROT LEU 12 CG ) 23.206 ( PROT LEU 12 CD1 ) 23.206 ( PROT LEU 12 CD2 ) 23.206 ( PROT LEU 12 C ) 29.007 ( PROT LEU 12 O ) 29.007 ( PROT ILE 13 N ) 29.007 ( PROT ILE 13 H ) 23.206 ( PROT ILE 13 CA ) 29.007 ( PROT ILE 13 CB ) 23.206 ( PROT ILE 13 CG2 ) 23.206 ( PROT ILE 13 CG1 ) 23.206 ( PROT ILE 13 CD ) 23.206 ( PROT ILE 13 C ) 29.007 ( PROT ILE 13 O ) 29.007 ( PROT ASH 14 N ) 29.007 ( PROT ASH 14 H ) 23.206 ( PROT ASH 14 CA ) 29.007 ( PROT ASH 14 CB ) 23.206 ( PROT ASH 14 CG ) 23.206 ( PROT ASH 14 OD1 ) 23.206 ( PROT ASH 14 OD2 ) 23.206 ( PROT ASH 14 HD2 ) 23.206 ( PROT ASH 14 C ) 29.007 ( PROT ASH 14 O ) 29.007 ( PROT PHE 15 N ) 29.007 ( PROT PHE 15 H ) 23.206 ( PROT PHE 15 CA ) 29.007 ( PROT PHE 15 CB ) 23.206 ( PROT PHE 15 CG ) 23.206 ( PROT PHE 15 CD1 ) 23.206 ( PROT PHE 15 CD2 ) 23.206 ( PROT PHE 15 CE1 ) 23.206 ( PROT PHE 15 CE2 ) 23.206 ( PROT PHE 15 CZ ) 23.206 ( PROT PHE 15 C ) 29.007 ( PROT PHE 15 O ) 29.007 ( PROT MET 16 N ) 29.007 ( PROT MET 16 H ) 23.206 ( PROT MET 16 CA ) 29.007 ( PROT MET 16 CB ) 23.206 ( PROT MET 16 CG ) 23.206 ( PROT MET 16 SD ) 23.206 ( PROT MET 16 CE ) 23.206 ( PROT MET 16 C ) 29.007 ( PROT MET 16 O ) 29.007 ( PROT PHE 17 N ) 29.007 ( PROT PHE 17 H ) 23.206 ( PROT PHE 17 CA ) 29.007 ( PROT PHE 17 CB ) 23.206 ( PROT PHE 17 CG ) 23.206 ( PROT PHE 17 CD1 ) 23.206 ( PROT PHE 17 CD2 ) 23.206 ( PROT PHE 17 CE1 ) 23.206 ( PROT PHE 17 CE2 ) 23.206 ( PROT PHE 17 CZ ) 23.206 ( PROT PHE 17 C ) 29.007 ( PROT PHE 17 O ) 29.007 ( PROT PHE 18 N ) 29.007 ( PROT PHE 18 H ) 23.206 ( PROT PHE 18 CA ) 29.007 ( PROT PHE 18 CB ) 23.206 ( PROT PHE 18 CG ) 23.206 ( PROT PHE 18 CD1 ) 23.206 ( PROT PHE 18 CD2 ) 23.206 ( PROT PHE 18 CE1 ) 23.206 ( PROT PHE 18 CE2 ) 23.206 ( PROT PHE 18 CZ ) 23.206 ( PROT PHE 18 C ) 29.007 ( PROT PHE 18 O ) 29.007 ( PROT GLU 19 N ) 29.007 ( PROT GLU 19 H ) 23.206 ( PROT GLU 19 CA ) 29.007 ( PROT GLU 19 CB ) 23.206 ( PROT GLU 19 CG ) 23.206 ( PROT GLU 19 CD ) 23.206 ( PROT GLU 19 OE1 ) 23.206 ( PROT GLU 19 OE2 ) 23.206 ( PROT GLU 19 C ) 29.007 ( PROT GLU 19 OT1 ) 23.206 ( PROT GLU 19 OT2 ) 23.206 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40554 5.29418 -8.69398 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS -0.00099 -0.00176 0.00076 ROTATION MATRIX 1.000000 -0.000066 -0.000026 0.000066 1.000000 0.000091 0.000026 -0.000091 1.000000 AXIS OF ROTATION IS 0.789101 0.228453 -0.570201 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 9.7316 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.230604 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2306" Parameter: A <- "0.2306" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70799 5.23824 -8.78052 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00686 0.02618 -0.01385 ROTATION MATRIX 0.999846 0.012890 0.011894 -0.012740 0.999839 -0.012632 -0.012055 0.012478 0.999849 AXIS OF ROTATION IS -0.582080 -0.555162 0.594119 ANGLE IS 1.24 CENTER OF ROTATION 9.346739 5.066389 -9.317542 SHIFT IS -0.026756 TOTAL SQUARE DIFF IS 0.1528 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.089665 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2306" RDCMND substituted energy or value "?RMS" to " 0.0897" Parameter: A <- "0.2306 0.0897" 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 0.2306 0.0897 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 " 370.67" Parameter: H <- "370.67" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 320.72190 370.66986 10.19626 ENER INTERN> 29.34262 70.26685 0.00000 18.01700 12.20624 ENER EXTERN> 186.88699 4.00222 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 " 320.72" Parameter: B <- "320.72" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 4.00" Parameter: C <- "4.00" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 186.89" Parameter: C <- " 190.89" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 190.89" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 29.34" Parameter: D <- "29.34" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 70.27" Parameter: D <- " 99.61" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 18.02" Parameter: D <- " 117.63" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 12.21" Parameter: D <- " 129.84" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 129.84" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 3000 ENER= 320.72 GRMS= 10.20 ELEC= 4.00 VDW= 186.89 RDTITL> *EXTERNAL= 190.89 INTERNAL= 129.84 USER= 0.00 HARM= 370.67 RDTITL> *BOND= 29.34 ANGL= 70.27 DIHE= 18.02 IMPR= 12.21 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11421 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11421 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 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> 0 597.63104 -276.90914 4.36397 0.02000 MINI INTERN> 29.34262 70.26685 0.00000 18.01700 12.20624 MINI EXTERN> 186.88699 4.00222 0.00000 0.00000 0.00000 MINI CONSTR> 276.90914 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 578.77396 18.85709 11.70236 0.00864 MINI INTERN> 32.95387 67.37113 0.00000 20.29115 9.63805 MINI EXTERN> 147.48145 3.02914 0.00000 0.00000 0.00000 MINI CONSTR> 298.00917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11413 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 560.36057 18.41339 6.71724 0.00373 MINI INTERN> 25.26269 68.35822 0.00000 20.63442 10.27039 MINI EXTERN> 130.52717 2.08066 0.00000 0.00000 0.00000 MINI CONSTR> 303.22701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 553.22937 7.13120 2.17841 0.00161 MINI INTERN> 23.38539 65.38459 0.00000 20.83314 10.05814 MINI EXTERN> 126.88996 2.79769 0.00000 0.00000 0.00000 MINI CONSTR> 303.88045 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11407 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 551.16256 2.06681 2.93279 0.00167 MINI INTERN> 23.24702 64.43349 0.00000 20.94284 10.03921 MINI EXTERN> 125.02035 2.72964 0.00000 0.00000 0.00000 MINI CONSTR> 304.75002 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 549.73000 1.43256 3.43502 0.00173 MINI INTERN> 23.09993 63.71704 0.00000 21.01829 10.02538 MINI EXTERN> 123.73829 2.63314 0.00000 0.00000 0.00000 MINI CONSTR> 305.49793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11406 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 548.61806 1.11194 3.12055 0.00180 MINI INTERN> 22.88018 63.21517 0.00000 21.04291 10.01951 MINI EXTERN> 122.94952 2.52504 0.00000 0.00000 0.00000 MINI CONSTR> 305.98573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 547.11903 1.49903 1.27049 0.00078 MINI INTERN> 21.74317 62.91482 0.00000 21.04426 10.03394 MINI EXTERN> 123.04171 1.93846 0.00000 0.00000 0.00000 MINI CONSTR> 306.40266 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 546.53589 0.58314 0.88511 0.00080 MINI INTERN> 21.58002 62.60466 0.00000 21.06226 10.02280 MINI EXTERN> 122.53739 1.91311 0.00000 0.00000 0.00000 MINI CONSTR> 306.81564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 546.31029 0.22560 1.41630 0.00083 MINI INTERN> 21.53131 62.43852 0.00000 21.06774 10.01773 MINI EXTERN> 122.33804 1.79102 0.00000 0.00000 0.00000 MINI CONSTR> 307.12594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 545.90865 0.40164 0.42366 0.00036 MINI INTERN> 21.34232 62.25685 0.00000 21.08032 10.00449 MINI EXTERN> 121.85491 1.91973 0.00000 0.00000 0.00000 MINI CONSTR> 307.45003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 545.75069 0.15796 0.27830 0.00037 MINI INTERN> 21.30948 62.14515 0.00000 21.07702 9.99993 MINI EXTERN> 121.68981 1.86923 0.00000 0.00000 0.00000 MINI CONSTR> 307.66007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 545.63871 0.11198 0.65845 0.00039 MINI INTERN> 21.25592 62.05792 0.00000 21.07620 9.99323 MINI EXTERN> 121.45334 1.87747 0.00000 0.00000 0.00000 MINI CONSTR> 307.92465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 545.56678 0.07194 0.79507 0.00040 MINI INTERN> 21.20244 62.00360 0.00000 21.07203 9.98863 MINI EXTERN> 121.32011 1.85481 0.00000 0.00000 0.00000 MINI CONSTR> 308.12515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 545.50676 0.06002 0.71265 0.00042 MINI INTERN> 21.21895 61.94240 0.00000 21.06454 9.98602 MINI EXTERN> 121.20452 1.83358 0.00000 0.00000 0.00000 MINI CONSTR> 308.25674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 545.42452 0.08223 0.28519 0.00018 MINI INTERN> 21.27565 61.83350 0.00000 21.05347 9.98092 MINI EXTERN> 121.17157 1.73576 0.00000 0.00000 0.00000 MINI CONSTR> 308.37366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 545.39072 0.03380 0.20029 0.00019 MINI INTERN> 21.25149 61.80417 0.00000 21.04844 9.97781 MINI EXTERN> 121.09286 1.72488 0.00000 0.00000 0.00000 MINI CONSTR> 308.49108 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 545.37415 0.01657 0.31933 0.00019 MINI INTERN> 21.26740 61.76590 0.00000 21.04265 9.97464 MINI EXTERN> 121.03705 1.69988 0.00000 0.00000 0.00000 MINI CONSTR> 308.58663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 545.34948 0.02467 0.09755 0.00008 MINI INTERN> 21.19253 61.77589 0.00000 21.03943 9.97345 MINI EXTERN> 120.97593 1.70859 0.00000 0.00000 0.00000 MINI CONSTR> 308.68366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 545.33700 0.01248 0.07834 0.00009 MINI INTERN> 21.19625 61.75523 0.00000 21.03423 9.97181 MINI EXTERN> 120.92587 1.69560 0.00000 0.00000 0.00000 MINI CONSTR> 308.75800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 545.32551 0.01149 0.14068 0.00009 MINI INTERN> 21.16916 61.74731 0.00000 21.02901 9.97014 MINI EXTERN> 120.87427 1.68576 0.00000 0.00000 0.00000 MINI CONSTR> 308.84985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 545.31648 0.00902 0.09763 0.00009 MINI INTERN> 21.17911 61.72833 0.00000 21.02372 9.96887 MINI EXTERN> 120.82846 1.67299 0.00000 0.00000 0.00000 MINI CONSTR> 308.91499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 545.31105 0.00543 0.15869 0.00010 MINI INTERN> 21.16472 61.72487 0.00000 21.01932 9.96825 MINI EXTERN> 120.78857 1.66648 0.00000 0.00000 0.00000 MINI CONSTR> 308.97885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 545.30537 0.00569 0.16683 0.00010 MINI INTERN> 21.16073 61.71571 0.00000 21.01486 9.96738 MINI EXTERN> 120.75164 1.65683 0.00000 0.00000 0.00000 MINI CONSTR> 309.03822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 545.29846 0.00691 0.05024 0.00004 MINI INTERN> 21.20784 61.68422 0.00000 21.00919 9.96612 MINI EXTERN> 120.70348 1.64183 0.00000 0.00000 0.00000 MINI CONSTR> 309.08578 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 545.29688 0.00158 0.18073 0.00011 MINI INTERN> 21.15950 61.70062 0.00000 21.00659 9.96635 MINI EXTERN> 120.68280 1.64103 0.00000 0.00000 0.00000 MINI CONSTR> 309.14000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 545.29043 0.00645 0.05918 0.00005 MINI INTERN> 21.21644 61.66582 0.00000 21.00078 9.96497 MINI EXTERN> 120.63234 1.62557 0.00000 0.00000 0.00000 MINI CONSTR> 309.18449 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 545.28756 0.00286 0.03881 0.00005 MINI INTERN> 21.20571 61.66451 0.00000 20.99839 9.96456 MINI EXTERN> 120.61347 1.62060 0.00000 0.00000 0.00000 MINI CONSTR> 309.22032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 545.28453 0.00304 0.08280 0.00005 MINI INTERN> 21.22815 61.65011 0.00000 20.99315 9.96417 MINI EXTERN> 120.56776 1.61145 0.00000 0.00000 0.00000 MINI CONSTR> 309.26973 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 545.28169 0.00284 0.05005 0.00005 MINI INTERN> 21.21654 61.64956 0.00000 20.99064 9.96388 MINI EXTERN> 120.54814 1.60661 0.00000 0.00000 0.00000 MINI CONSTR> 309.30632 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 545.27977 0.00192 0.08836 0.00005 MINI INTERN> 21.23150 61.63999 0.00000 20.98679 9.96358 MINI EXTERN> 120.51468 1.59983 0.00000 0.00000 0.00000 MINI CONSTR> 309.34339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 545.27770 0.00207 0.09794 0.00006 MINI INTERN> 21.23776 61.63483 0.00000 20.98318 9.96353 MINI EXTERN> 120.48366 1.59444 0.00000 0.00000 0.00000 MINI CONSTR> 309.38031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 545.27589 0.00181 0.09446 0.00006 MINI INTERN> 21.23523 61.63176 0.00000 20.98094 9.96318 MINI EXTERN> 120.46562 1.58970 0.00000 0.00000 0.00000 MINI CONSTR> 309.40946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 545.27351 0.00238 0.02890 0.00002 MINI INTERN> 21.20175 61.63742 0.00000 20.98054 9.96271 MINI EXTERN> 120.46681 1.58676 0.00000 0.00000 0.00000 MINI CONSTR> 309.43752 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 545.27272 0.00079 0.10307 0.00006 MINI INTERN> 21.24062 61.62496 0.00000 20.97533 9.96299 MINI EXTERN> 120.41826 1.58094 0.00000 0.00000 0.00000 MINI CONSTR> 309.46962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 545.27128 0.00143 0.10712 0.00006 MINI INTERN> 21.24517 61.62210 0.00000 20.97229 9.96311 MINI EXTERN> 120.39211 1.57721 0.00000 0.00000 0.00000 MINI CONSTR> 309.49929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 545.26901 0.00228 0.03431 0.00003 MINI INTERN> 21.19684 61.62814 0.00000 20.97387 9.96190 MINI EXTERN> 120.41279 1.57372 0.00000 0.00000 0.00000 MINI CONSTR> 309.52175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 545.26790 0.00111 0.02398 0.00003 MINI INTERN> 21.20571 61.62441 0.00000 20.97125 9.96207 MINI EXTERN> 120.38960 1.57091 0.00000 0.00000 0.00000 MINI CONSTR> 309.54393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 545.26666 0.00123 0.02376 0.00003 MINI INTERN> 21.20514 61.62165 0.00000 20.96914 9.96185 MINI EXTERN> 120.37233 1.56710 0.00000 0.00000 0.00000 MINI CONSTR> 309.56945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 545.26560 0.00106 0.04812 0.00003 MINI INTERN> 21.18740 61.62101 0.00000 20.96871 9.96081 MINI EXTERN> 120.37229 1.56210 0.00000 0.00000 0.00000 MINI CONSTR> 309.59328 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 545.26452 0.00108 0.02944 0.00003 MINI INTERN> 21.19863 61.61743 0.00000 20.96577 9.96113 MINI EXTERN> 120.34590 1.55967 0.00000 0.00000 0.00000 MINI CONSTR> 309.61599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 545.26372 0.00080 0.05245 0.00003 MINI INTERN> 21.18186 61.61740 0.00000 20.96558 9.96006 MINI EXTERN> 120.34783 1.55499 0.00000 0.00000 0.00000 MINI CONSTR> 309.63600 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 545.26287 0.00085 0.05539 0.00003 MINI INTERN> 21.17851 61.61597 0.00000 20.96410 9.95966 MINI EXTERN> 120.33649 1.55160 0.00000 0.00000 0.00000 MINI CONSTR> 309.65654 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 545.26212 0.00075 0.06063 0.00004 MINI INTERN> 21.17423 61.61472 0.00000 20.96282 9.95922 MINI EXTERN> 120.32687 1.54839 0.00000 0.00000 0.00000 MINI CONSTR> 309.67587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 545.26144 0.00068 0.05714 0.00004 MINI INTERN> 21.17730 61.61261 0.00000 20.96106 9.95926 MINI EXTERN> 120.31177 1.54648 0.00000 0.00000 0.00000 MINI CONSTR> 309.69296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 545.26073 0.00071 0.05760 0.00004 MINI INTERN> 21.17594 61.61110 0.00000 20.95956 9.95897 MINI EXTERN> 120.29975 1.54372 0.00000 0.00000 0.00000 MINI CONSTR> 309.71169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11403 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 545.25986 0.00087 0.01822 0.00002 MINI INTERN> 21.22204 61.60265 0.00000 20.95337 9.96142 MINI EXTERN> 120.23867 1.54620 0.00000 0.00000 0.00000 MINI CONSTR> 309.73550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 545.25964 0.00021 0.06331 0.00004 MINI INTERN> 21.17218 61.60859 0.00000 20.95716 9.95845 MINI EXTERN> 120.28096 1.53919 0.00000 0.00000 0.00000 MINI CONSTR> 309.74311 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 545.25873 0.00092 0.01911 0.00002 MINI INTERN> 21.22542 61.59906 0.00000 20.95016 9.96131 MINI EXTERN> 120.21155 1.54243 0.00000 0.00000 0.00000 MINI CONSTR> 309.76880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 545.25829 0.00044 0.01470 0.00002 MINI INTERN> 21.21991 61.59870 0.00000 20.94961 9.96086 MINI EXTERN> 120.20821 1.54030 0.00000 0.00000 0.00000 MINI CONSTR> 309.78070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 545.25779 0.00049 0.02689 0.00002 MINI INTERN> 21.23449 61.59493 0.00000 20.94658 9.96155 MINI EXTERN> 120.18027 1.53972 0.00000 0.00000 0.00000 MINI CONSTR> 309.80026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 545.25736 0.00043 0.01849 0.00002 MINI INTERN> 21.22726 61.59486 0.00000 20.94621 9.96099 MINI EXTERN> 120.17875 1.53746 0.00000 0.00000 0.00000 MINI CONSTR> 309.81183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 545.25696 0.00040 0.02020 0.00002 MINI INTERN> 21.22973 61.59323 0.00000 20.94472 9.96099 MINI EXTERN> 120.16612 1.53610 0.00000 0.00000 0.00000 MINI CONSTR> 309.82606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 545.25666 0.00029 0.03249 0.00002 MINI INTERN> 21.24093 61.59043 0.00000 20.94244 9.96153 MINI EXTERN> 120.14512 1.53582 0.00000 0.00000 0.00000 MINI CONSTR> 309.84039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 545.25633 0.00034 0.03485 0.00002 MINI INTERN> 21.24348 61.58886 0.00000 20.94103 9.96155 MINI EXTERN> 120.13317 1.53463 0.00000 0.00000 0.00000 MINI CONSTR> 309.85360 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 545.25603 0.00029 0.03895 0.00002 MINI INTERN> 21.24727 61.58721 0.00000 20.93955 9.96166 MINI EXTERN> 120.12044 1.53368 0.00000 0.00000 0.00000 MINI CONSTR> 309.86624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 545.25576 0.00027 0.03660 0.00002 MINI INTERN> 21.24565 61.58666 0.00000 20.93886 9.96142 MINI EXTERN> 120.11507 1.53247 0.00000 0.00000 0.00000 MINI CONSTR> 309.87561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 545.25538 0.00038 0.01080 0.00001 MINI INTERN> 21.21611 61.59048 0.00000 20.94111 9.95946 MINI EXTERN> 120.13914 1.52835 0.00000 0.00000 0.00000 MINI CONSTR> 309.88073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 545.25526 0.00012 0.03972 0.00003 MINI INTERN> 21.24891 61.58429 0.00000 20.93661 9.96139 MINI EXTERN> 120.09630 1.53053 0.00000 0.00000 0.00000 MINI CONSTR> 309.89723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 545.25489 0.00037 0.01181 0.00001 MINI INTERN> 21.21381 61.58920 0.00000 20.93954 9.95904 MINI EXTERN> 120.12662 1.52598 0.00000 0.00000 0.00000 MINI CONSTR> 309.90070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 545.25470 0.00019 0.00965 0.00001 MINI INTERN> 21.21711 61.58798 0.00000 20.93845 9.95915 MINI EXTERN> 120.11713 1.52547 0.00000 0.00000 0.00000 MINI CONSTR> 309.90941 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> 300 545.25470 0.00019 0.00965 0.00001 STPD INTERN> 21.21711 61.58798 0.00000 20.93845 9.95915 STPD EXTERN> 120.11713 1.52547 0.00000 0.00000 0.00000 STPD CONSTR> 309.90941 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 11404 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 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> 0 545.25470 0.00019 0.00965 0.00000 MINI INTERN> 21.21711 61.58798 0.00000 20.93845 9.95915 MINI EXTERN> 120.11713 1.52547 0.00000 0.00000 0.00000 MINI CONSTR> 309.90941 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> 3 545.25183 0.00287 0.00401 0.02000 CONJ INTERN> 21.21831 61.56495 0.00000 20.91520 9.95874 CONJ EXTERN> 119.91150 1.50488 0.00000 0.00000 0.00000 CONJ CONSTR> 310.17825 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "3600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 15.084 ( PROT LYS 1 HT2 ) 15.084 ( PROT LYS 1 N ) 18.855 ( PROT LYS 1 HT3 ) 15.084 ( PROT LYS 1 CA ) 18.855 ( PROT LYS 1 CB ) 15.084 ( PROT LYS 1 CG ) 15.084 ( PROT LYS 1 CD ) 15.084 ( PROT LYS 1 CE ) 15.084 ( PROT LYS 1 NZ ) 15.084 ( PROT LYS 1 HZ1 ) 15.084 ( PROT LYS 1 HZ2 ) 15.084 ( PROT LYS 1 HZ3 ) 15.084 ( PROT LYS 1 C ) 18.855 ( PROT LYS 1 O ) 18.855 ( PROT MET 2 N ) 18.855 ( PROT MET 2 H ) 15.084 ( PROT MET 2 CA ) 18.855 ( PROT MET 2 CB ) 15.084 ( PROT MET 2 CG ) 15.084 ( PROT MET 2 SD ) 15.084 ( PROT MET 2 CE ) 15.084 ( PROT MET 2 C ) 18.855 ( PROT MET 2 O ) 18.855 ( PROT LYS 3 N ) 18.855 ( PROT LYS 3 H ) 15.084 ( PROT LYS 3 CA ) 18.855 ( PROT LYS 3 CB ) 15.084 ( PROT LYS 3 CG ) 15.084 ( PROT LYS 3 CD ) 15.084 ( PROT LYS 3 CE ) 15.084 ( PROT LYS 3 NZ ) 15.084 ( PROT LYS 3 HZ1 ) 15.084 ( PROT LYS 3 HZ2 ) 15.084 ( PROT LYS 3 HZ3 ) 15.084 ( PROT LYS 3 C ) 18.855 ( PROT LYS 3 O ) 18.855 ( PROT ALA 4 N ) 18.855 ( PROT ALA 4 H ) 15.084 ( PROT ALA 4 CA ) 18.855 ( PROT ALA 4 CB ) 15.084 ( PROT ALA 4 C ) 18.855 ( PROT ALA 4 O ) 18.855 ( PROT VAL 5 N ) 18.855 ( PROT VAL 5 H ) 15.084 ( PROT VAL 5 CA ) 18.855 ( PROT VAL 5 CB ) 15.084 ( PROT VAL 5 CG1 ) 15.084 ( PROT VAL 5 CG2 ) 15.084 ( PROT VAL 5 C ) 18.855 ( PROT VAL 5 O ) 18.855 ( PROT MET 6 N ) 18.855 ( PROT MET 6 H ) 15.084 ( PROT MET 6 CA ) 18.855 ( PROT MET 6 CB ) 15.084 ( PROT MET 6 CG ) 15.084 ( PROT MET 6 SD ) 15.084 ( PROT MET 6 CE ) 15.084 ( PROT MET 6 C ) 18.855 ( PROT MET 6 O ) 18.855 ( PROT ILE 7 N ) 18.855 ( PROT ILE 7 H ) 15.084 ( PROT ILE 7 CA ) 18.855 ( PROT ILE 7 CB ) 15.084 ( PROT ILE 7 CG2 ) 15.084 ( PROT ILE 7 CG1 ) 15.084 ( PROT ILE 7 CD ) 15.084 ( PROT ILE 7 C ) 18.855 ( PROT ILE 7 O ) 18.855 ( PROT GLY 8 N ) 18.855 ( PROT GLY 8 H ) 15.084 ( PROT GLY 8 CA ) 18.855 ( PROT GLY 8 C ) 18.855 ( PROT GLY 8 O ) 18.855 ( PROT ALA 9 N ) 18.855 ( PROT ALA 9 H ) 15.084 ( PROT ALA 9 CA ) 18.855 ( PROT ALA 9 CB ) 15.084 ( PROT ALA 9 C ) 18.855 ( PROT ALA 9 O ) 18.855 ( PROT CYS 10 N ) 18.855 ( PROT CYS 10 H ) 15.084 ( PROT CYS 10 CA ) 18.855 ( PROT CYS 10 CB ) 15.084 ( PROT CYS 10 SG ) 15.084 ( PROT CYS 10 C ) 18.855 ( PROT CYS 10 O ) 18.855 ( PROT PHE 11 N ) 18.855 ( PROT PHE 11 H ) 15.084 ( PROT PHE 11 CA ) 18.855 ( PROT PHE 11 CB ) 15.084 ( PROT PHE 11 CG ) 15.084 ( PROT PHE 11 CD1 ) 15.084 ( PROT PHE 11 CD2 ) 15.084 ( PROT PHE 11 CE1 ) 15.084 ( PROT PHE 11 CE2 ) 15.084 ( PROT PHE 11 CZ ) 15.084 ( PROT PHE 11 C ) 18.855 ( PROT PHE 11 O ) 18.855 ( PROT LEU 12 N ) 18.855 ( PROT LEU 12 H ) 15.084 ( PROT LEU 12 CA ) 18.855 ( PROT LEU 12 CB ) 15.084 ( PROT LEU 12 CG ) 15.084 ( PROT LEU 12 CD1 ) 15.084 ( PROT LEU 12 CD2 ) 15.084 ( PROT LEU 12 C ) 18.855 ( PROT LEU 12 O ) 18.855 ( PROT ILE 13 N ) 18.855 ( PROT ILE 13 H ) 15.084 ( PROT ILE 13 CA ) 18.855 ( PROT ILE 13 CB ) 15.084 ( PROT ILE 13 CG2 ) 15.084 ( PROT ILE 13 CG1 ) 15.084 ( PROT ILE 13 CD ) 15.084 ( PROT ILE 13 C ) 18.855 ( PROT ILE 13 O ) 18.855 ( PROT ASH 14 N ) 18.855 ( PROT ASH 14 H ) 15.084 ( PROT ASH 14 CA ) 18.855 ( PROT ASH 14 CB ) 15.084 ( PROT ASH 14 CG ) 15.084 ( PROT ASH 14 OD1 ) 15.084 ( PROT ASH 14 OD2 ) 15.084 ( PROT ASH 14 HD2 ) 15.084 ( PROT ASH 14 C ) 18.855 ( PROT ASH 14 O ) 18.855 ( PROT PHE 15 N ) 18.855 ( PROT PHE 15 H ) 15.084 ( PROT PHE 15 CA ) 18.855 ( PROT PHE 15 CB ) 15.084 ( PROT PHE 15 CG ) 15.084 ( PROT PHE 15 CD1 ) 15.084 ( PROT PHE 15 CD2 ) 15.084 ( PROT PHE 15 CE1 ) 15.084 ( PROT PHE 15 CE2 ) 15.084 ( PROT PHE 15 CZ ) 15.084 ( PROT PHE 15 C ) 18.855 ( PROT PHE 15 O ) 18.855 ( PROT MET 16 N ) 18.855 ( PROT MET 16 H ) 15.084 ( PROT MET 16 CA ) 18.855 ( PROT MET 16 CB ) 15.084 ( PROT MET 16 CG ) 15.084 ( PROT MET 16 SD ) 15.084 ( PROT MET 16 CE ) 15.084 ( PROT MET 16 C ) 18.855 ( PROT MET 16 O ) 18.855 ( PROT PHE 17 N ) 18.855 ( PROT PHE 17 H ) 15.084 ( PROT PHE 17 CA ) 18.855 ( PROT PHE 17 CB ) 15.084 ( PROT PHE 17 CG ) 15.084 ( PROT PHE 17 CD1 ) 15.084 ( PROT PHE 17 CD2 ) 15.084 ( PROT PHE 17 CE1 ) 15.084 ( PROT PHE 17 CE2 ) 15.084 ( PROT PHE 17 CZ ) 15.084 ( PROT PHE 17 C ) 18.855 ( PROT PHE 17 O ) 18.855 ( PROT PHE 18 N ) 18.855 ( PROT PHE 18 H ) 15.084 ( PROT PHE 18 CA ) 18.855 ( PROT PHE 18 CB ) 15.084 ( PROT PHE 18 CG ) 15.084 ( PROT PHE 18 CD1 ) 15.084 ( PROT PHE 18 CD2 ) 15.084 ( PROT PHE 18 CE1 ) 15.084 ( PROT PHE 18 CE2 ) 15.084 ( PROT PHE 18 CZ ) 15.084 ( PROT PHE 18 C ) 18.855 ( PROT PHE 18 O ) 18.855 ( PROT GLU 19 N ) 18.855 ( PROT GLU 19 H ) 15.084 ( PROT GLU 19 CA ) 18.855 ( PROT GLU 19 CB ) 15.084 ( PROT GLU 19 CG ) 15.084 ( PROT GLU 19 CD ) 15.084 ( PROT GLU 19 OE1 ) 15.084 ( PROT GLU 19 OE2 ) 15.084 ( PROT GLU 19 C ) 18.855 ( PROT GLU 19 OT1 ) 15.084 ( PROT GLU 19 OT2 ) 15.084 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40516 5.29412 -8.69359 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS -0.00061 -0.00171 0.00038 ROTATION MATRIX 1.000000 -0.000107 -0.000024 0.000107 1.000000 0.000138 0.000024 -0.000138 1.000000 AXIS OF ROTATION IS 0.783704 0.136994 -0.605839 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 12.4421 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.260748 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2607" Parameter: A <- "0.2607" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70866 5.23395 -8.77964 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00618 0.03047 -0.01473 ROTATION MATRIX 0.999828 0.013800 0.012428 -0.013632 0.999817 -0.013450 -0.012611 0.013278 0.999832 AXIS OF ROTATION IS -0.584105 -0.547192 0.599501 ANGLE IS 1.31 CENTER OF ROTATION 9.265674 5.035171 -9.416964 SHIFT IS -0.029116 TOTAL SQUARE DIFF IS 0.2171 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.106904 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2607" RDCMND substituted energy or value "?RMS" to " 0.1069" Parameter: A <- "0.2607 0.1069" 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 0.2607 0.1069 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 " 310.18" Parameter: H <- "310.18" 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> 0 235.07359 310.17825 7.54749 ENER INTERN> 21.21831 61.56495 0.00000 20.91520 9.95874 ENER EXTERN> 119.91150 1.50488 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 " 235.07" Parameter: B <- "235.07" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 1.50" Parameter: C <- "1.50" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 119.91" Parameter: C <- " 121.41" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 121.41" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 21.22" Parameter: D <- "21.22" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 61.56" Parameter: D <- " 82.78" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 20.92" Parameter: D <- " 103.70" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 9.96" Parameter: D <- " 113.66" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 113.66" 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= 235.07 GRMS= 7.55 ELEC= 1.50 VDW= 119.91 RDTITL> *EXTERNAL= 121.41 INTERNAL= 113.66 USER= 0.00 HARM= 310.18 RDTITL> *BOND= 21.22 ANGL= 61.56 DIHE= 20.92 IMPR= 9.96 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 "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= 235.07 GRMS= 7.55 ELEC= 1.50 VDW= 119.91 RDTITL> *EXTERNAL= 121.41 INTERNAL= 113.66 USER= 0.00 HARM= 310.18 RDTITL> *BOND= 21.22 ANGL= 61.56 DIHE= 20.92 IMPR= 9.96 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= 235.07 GRMS= 7.55 ELEC= 1.50 VDW= 119.91 RDTITL> *EXTERNAL= 121.41 INTERNAL= 113.66 USER= 0.00 HARM= 310.18 RDTITL> *BOND= 21.22 ANGL= 61.56 DIHE= 20.92 IMPR= 9.96 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 3600 0.2607 0.1069 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11404 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11404 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 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> 0 463.53114 -228.45756 3.16783 0.02000 MINI INTERN> 21.21831 61.56495 0.00000 20.91520 9.95874 MINI EXTERN> 119.91150 1.50488 0.00000 0.00000 0.00000 MINI CONSTR> 228.45756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 442.27840 21.25274 2.41603 0.00360 MINI INTERN> 19.03128 62.10211 0.00000 23.58184 9.43782 MINI EXTERN> 76.11993 2.03348 0.00000 0.00000 0.00000 MINI CONSTR> 249.97194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11393 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 436.19963 6.07877 1.50394 0.00156 MINI INTERN> 16.67297 58.09904 0.00000 23.65886 9.01474 MINI EXTERN> 76.28648 1.20850 0.00000 0.00000 0.00000 MINI CONSTR> 251.25905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 433.05692 3.14272 1.19241 0.00161 MINI INTERN> 16.06468 57.09019 0.00000 23.87952 9.02956 MINI EXTERN> 73.37121 1.14423 0.00000 0.00000 0.00000 MINI CONSTR> 252.47752 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11394 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 430.94327 2.11365 2.65538 0.00167 MINI INTERN> 15.59331 55.98863 0.00000 24.20616 8.87188 MINI EXTERN> 72.06444 1.06048 0.00000 0.00000 0.00000 MINI CONSTR> 253.15837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 429.36484 1.57843 2.94162 0.00173 MINI INTERN> 14.31676 55.93425 0.00000 24.33109 8.81986 MINI EXTERN> 71.47628 0.84221 0.00000 0.00000 0.00000 MINI CONSTR> 253.64441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11390 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 428.11813 1.24671 2.77039 0.00180 MINI INTERN> 14.13725 55.49728 0.00000 24.35363 8.80611 MINI EXTERN> 70.54960 0.80660 0.00000 0.00000 0.00000 MINI CONSTR> 253.96766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 426.43049 1.68765 0.86200 0.00078 MINI INTERN> 15.62504 54.49180 0.00000 24.05141 9.00884 MINI EXTERN> 67.75821 0.96392 0.00000 0.00000 0.00000 MINI CONSTR> 254.53127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 425.73995 0.69054 0.55427 0.00080 MINI INTERN> 15.11278 54.37382 0.00000 24.10251 8.95744 MINI EXTERN> 67.61185 0.91041 0.00000 0.00000 0.00000 MINI CONSTR> 254.67115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 425.17289 0.56706 1.28557 0.00083 MINI INTERN> 15.99620 53.83773 0.00000 23.99899 9.00145 MINI EXTERN> 66.39033 0.97087 0.00000 0.00000 0.00000 MINI CONSTR> 254.97733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 424.76523 0.40767 1.44820 0.00087 MINI INTERN> 16.14392 53.60122 0.00000 23.97056 8.99341 MINI EXTERN> 65.91918 0.97855 0.00000 0.00000 0.00000 MINI CONSTR> 255.15839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 424.45133 0.31389 1.36769 0.00090 MINI INTERN> 16.02430 53.49882 0.00000 23.96647 8.97311 MINI EXTERN> 65.73914 0.97181 0.00000 0.00000 0.00000 MINI CONSTR> 255.27769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11385 ATOM PAIRS WERE FOUND FOR ATOM LIST 342 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 424.02227 0.42907 0.41129 0.00039 MINI INTERN> 14.47720 53.82141 0.00000 24.10985 8.84775 MINI EXTERN> 66.63885 0.85034 0.00000 0.00000 0.00000 MINI CONSTR> 255.27687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 423.84097 0.18129 0.28574 0.00040 MINI INTERN> 14.60405 53.68542 0.00000 24.07786 8.84890 MINI EXTERN> 66.35583 0.86682 0.00000 0.00000 0.00000 MINI CONSTR> 255.40210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 342 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 423.68824 0.15274 0.64224 0.00042 MINI INTERN> 14.18519 53.73796 0.00000 24.10795 8.80239 MINI EXTERN> 66.51059 0.83834 0.00000 0.00000 0.00000 MINI CONSTR> 255.50582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 423.57211 0.11612 0.70039 0.00043 MINI INTERN> 14.11384 53.69133 0.00000 24.09758 8.78857 MINI EXTERN> 66.41738 0.84155 0.00000 0.00000 0.00000 MINI CONSTR> 255.62187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 342 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 423.48282 0.08930 0.67228 0.00045 MINI INTERN> 14.11802 53.63064 0.00000 24.08069 8.78325 MINI EXTERN> 66.29393 0.85113 0.00000 0.00000 0.00000 MINI CONSTR> 255.72516 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 423.36692 0.11589 0.19742 0.00019 MINI INTERN> 14.69722 53.36136 0.00000 23.99100 8.82733 MINI EXTERN> 65.68347 0.91179 0.00000 0.00000 0.00000 MINI CONSTR> 255.89475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 342 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 423.31121 0.05571 0.15826 0.00020 MINI INTERN> 14.63824 53.33828 0.00000 23.98328 8.81920 MINI EXTERN> 65.63450 0.91733 0.00000 0.00000 0.00000 MINI CONSTR> 255.98037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 423.25969 0.05152 0.29999 0.00021 MINI INTERN> 14.80250 53.23394 0.00000 23.94611 8.82831 MINI EXTERN> 65.39344 0.94309 0.00000 0.00000 0.00000 MINI CONSTR> 256.11230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 423.21602 0.04367 0.19218 0.00022 MINI INTERN> 14.68954 53.23400 0.00000 23.94475 8.81755 MINI EXTERN> 65.39290 0.94654 0.00000 0.00000 0.00000 MINI CONSTR> 256.19073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 423.18962 0.02640 0.32604 0.00022 MINI INTERN> 14.80834 53.16165 0.00000 23.91709 8.82524 MINI EXTERN> 65.21811 0.96746 0.00000 0.00000 0.00000 MINI CONSTR> 256.29173 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 423.16236 0.02726 0.34377 0.00023 MINI INTERN> 14.81274 53.12832 0.00000 23.90304 8.82455 MINI EXTERN> 65.13486 0.98040 0.00000 0.00000 0.00000 MINI CONSTR> 256.37846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 423.12909 0.03327 0.10241 0.00010 MINI INTERN> 14.50791 53.20104 0.00000 23.92650 8.80015 MINI EXTERN> 65.29821 0.97237 0.00000 0.00000 0.00000 MINI CONSTR> 256.42291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 423.12139 0.00770 0.37123 0.00025 MINI INTERN> 14.81423 53.07510 0.00000 23.87859 8.82435 MINI EXTERN> 64.99252 1.00522 0.00000 0.00000 0.00000 MINI CONSTR> 256.53139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 423.09081 0.03058 0.12287 0.00011 MINI INTERN> 14.45741 53.16625 0.00000 23.90857 8.79637 MINI EXTERN> 65.19760 0.99643 0.00000 0.00000 0.00000 MINI CONSTR> 256.56819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 423.07728 0.01353 0.07938 0.00011 MINI INTERN> 14.50020 53.13263 0.00000 23.89449 8.80025 MINI EXTERN> 65.11156 1.00978 0.00000 0.00000 0.00000 MINI CONSTR> 256.62837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 423.06294 0.01434 0.17135 0.00012 MINI INTERN> 14.40432 53.14031 0.00000 23.89368 8.79345 MINI EXTERN> 65.11552 1.02042 0.00000 0.00000 0.00000 MINI CONSTR> 256.69526 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 423.04945 0.01349 0.10214 0.00012 MINI INTERN> 14.45133 53.10490 0.00000 23.87838 8.79836 MINI EXTERN> 65.02248 1.03565 0.00000 0.00000 0.00000 MINI CONSTR> 256.75836 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 423.04035 0.00911 0.18168 0.00012 MINI INTERN> 14.38770 53.10799 0.00000 23.87659 8.79425 MINI EXTERN> 65.01822 1.04570 0.00000 0.00000 0.00000 MINI CONSTR> 256.80990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 423.03043 0.00992 0.20136 0.00013 MINI INTERN> 14.37456 53.09321 0.00000 23.86851 8.79472 MINI EXTERN> 64.97317 1.06011 0.00000 0.00000 0.00000 MINI CONSTR> 256.86615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 423.02167 0.00876 0.19436 0.00013 MINI INTERN> 14.37479 53.07879 0.00000 23.86061 8.79576 MINI EXTERN> 64.92823 1.07021 0.00000 0.00000 0.00000 MINI CONSTR> 256.91328 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 423.01018 0.01149 0.06050 0.00006 MINI INTERN> 14.48366 53.02770 0.00000 23.83938 8.80610 MINI EXTERN> 64.79254 1.08758 0.00000 0.00000 0.00000 MINI CONSTR> 256.97320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 423.00637 0.00381 0.22118 0.00014 MINI INTERN> 14.37616 53.05251 0.00000 23.84468 8.79809 MINI EXTERN> 64.84115 1.08759 0.00000 0.00000 0.00000 MINI CONSTR> 257.00620 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 422.99526 0.01110 0.06928 0.00006 MINI INTERN> 14.48275 53.00120 0.00000 23.82416 8.80898 MINI EXTERN> 64.70465 1.11135 0.00000 0.00000 0.00000 MINI CONSTR> 257.06217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 422.98913 0.00614 0.05444 0.00006 MINI INTERN> 14.46418 52.99633 0.00000 23.81997 8.80886 MINI EXTERN> 64.68379 1.12021 0.00000 0.00000 0.00000 MINI CONSTR> 257.09579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 422.98261 0.00651 0.05587 0.00007 MINI INTERN> 14.46175 52.98487 0.00000 23.81308 8.81027 MINI EXTERN> 64.64458 1.13239 0.00000 0.00000 0.00000 MINI CONSTR> 257.13567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 422.97630 0.00631 0.08966 0.00007 MINI INTERN> 14.47883 52.96845 0.00000 23.80359 8.81314 MINI EXTERN> 64.58788 1.14436 0.00000 0.00000 0.00000 MINI CONSTR> 257.18006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 422.97051 0.00579 0.07002 0.00007 MINI INTERN> 14.45784 52.96300 0.00000 23.79960 8.81317 MINI EXTERN> 64.56779 1.15716 0.00000 0.00000 0.00000 MINI CONSTR> 257.21194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 422.96530 0.00521 0.08218 0.00007 MINI INTERN> 14.46326 52.95242 0.00000 23.79261 8.81506 MINI EXTERN> 64.52845 1.16685 0.00000 0.00000 0.00000 MINI CONSTR> 257.24664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 422.96006 0.00523 0.08297 0.00008 MINI INTERN> 14.45893 52.94529 0.00000 23.78692 8.81599 MINI EXTERN> 64.49858 1.17536 0.00000 0.00000 0.00000 MINI CONSTR> 257.27899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 422.95587 0.00419 0.11600 0.00008 MINI INTERN> 14.46883 52.93293 0.00000 23.77965 8.81855 MINI EXTERN> 64.45530 1.18870 0.00000 0.00000 0.00000 MINI CONSTR> 257.31191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 422.95119 0.00468 0.13104 0.00008 MINI INTERN> 14.46530 52.92883 0.00000 23.77426 8.81901 MINI EXTERN> 64.42866 1.19277 0.00000 0.00000 0.00000 MINI CONSTR> 257.34235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 422.94703 0.00416 0.13456 0.00009 MINI INTERN> 14.46697 52.91897 0.00000 23.76822 8.82100 MINI EXTERN> 64.39445 1.20627 0.00000 0.00000 0.00000 MINI CONSTR> 257.37115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 422.94280 0.00423 0.12897 0.00009 MINI INTERN> 14.45564 52.91236 0.00000 23.76396 8.82175 MINI EXTERN> 64.37233 1.22011 0.00000 0.00000 0.00000 MINI CONSTR> 257.39665 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 422.93880 0.00400 0.14172 0.00009 MINI INTERN> 14.44931 52.91185 0.00000 23.75967 8.82141 MINI EXTERN> 64.35606 1.21937 0.00000 0.00000 0.00000 MINI CONSTR> 257.42111 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 422.93373 0.00507 0.04333 0.00004 MINI INTERN> 14.39764 52.91234 0.00000 23.76062 8.81856 MINI EXTERN> 64.37238 1.23564 0.00000 0.00000 0.00000 MINI CONSTR> 257.43656 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 422.93182 0.00192 0.15146 0.00010 MINI INTERN> 14.44329 52.89363 0.00000 23.74941 8.82476 MINI EXTERN> 64.29805 1.25188 0.00000 0.00000 0.00000 MINI CONSTR> 257.47079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 422.92879 0.00302 0.17643 0.00010 MINI INTERN> 14.44179 52.89625 0.00000 23.74545 8.82387 MINI EXTERN> 64.28774 1.24307 0.00000 0.00000 0.00000 MINI CONSTR> 257.49062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 422.92304 0.00575 0.04878 0.00004 MINI INTERN> 14.38144 52.89648 0.00000 23.74734 8.82020 MINI EXTERN> 64.30977 1.26354 0.00000 0.00000 0.00000 MINI CONSTR> 257.50427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 422.92002 0.00302 0.03956 0.00005 MINI INTERN> 14.38294 52.89070 0.00000 23.74276 8.82133 MINI EXTERN> 64.28574 1.27242 0.00000 0.00000 0.00000 MINI CONSTR> 257.52412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 422.91689 0.00313 0.04079 0.00005 MINI INTERN> 14.37754 52.88630 0.00000 23.73870 8.82170 MINI EXTERN> 64.26749 1.28114 0.00000 0.00000 0.00000 MINI CONSTR> 257.54402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 422.91376 0.00313 0.06542 0.00005 MINI INTERN> 14.36350 52.88336 0.00000 23.73526 8.82105 MINI EXTERN> 64.25678 1.28986 0.00000 0.00000 0.00000 MINI CONSTR> 257.56395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 422.91083 0.00293 0.05312 0.00005 MINI INTERN> 14.36400 52.87733 0.00000 23.73066 8.82218 MINI EXTERN> 64.23300 1.30051 0.00000 0.00000 0.00000 MINI CONSTR> 257.58315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 422.90816 0.00268 0.05980 0.00005 MINI INTERN> 14.35677 52.87431 0.00000 23.72717 8.82208 MINI EXTERN> 64.21926 1.30820 0.00000 0.00000 0.00000 MINI CONSTR> 257.60036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 422.90547 0.00268 0.06186 0.00006 MINI INTERN> 14.35473 52.87077 0.00000 23.72305 8.82236 MINI EXTERN> 64.20193 1.31470 0.00000 0.00000 0.00000 MINI CONSTR> 257.61793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 422.90324 0.00223 0.08352 0.00006 MINI INTERN> 14.34106 52.86796 0.00000 23.72041 8.82173 MINI EXTERN> 64.19349 1.32528 0.00000 0.00000 0.00000 MINI CONSTR> 257.63331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 422.90080 0.00245 0.09450 0.00006 MINI INTERN> 14.34467 52.86429 0.00000 23.71566 8.82216 MINI EXTERN> 64.17463 1.32884 0.00000 0.00000 0.00000 MINI CONSTR> 257.65056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 422.89860 0.00220 0.09704 0.00006 MINI INTERN> 14.33426 52.86165 0.00000 23.71289 8.82176 MINI EXTERN> 64.16433 1.33874 0.00000 0.00000 0.00000 MINI CONSTR> 257.66497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 422.89636 0.00223 0.09303 0.00006 MINI INTERN> 14.32939 52.85707 0.00000 23.70938 8.82220 MINI EXTERN> 64.14798 1.35044 0.00000 0.00000 0.00000 MINI CONSTR> 257.67992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 422.89427 0.00209 0.10185 0.00007 MINI INTERN> 14.33892 52.85479 0.00000 23.70448 8.82280 MINI EXTERN> 64.12804 1.35002 0.00000 0.00000 0.00000 MINI CONSTR> 257.69521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 422.89161 0.00266 0.03150 0.00003 MINI INTERN> 14.35520 52.84730 0.00000 23.69850 8.82597 MINI EXTERN> 64.09063 1.36163 0.00000 0.00000 0.00000 MINI CONSTR> 257.71238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 422.89055 0.00106 0.10849 0.00007 MINI INTERN> 14.31635 52.84846 0.00000 23.69945 8.82208 MINI EXTERN> 64.10890 1.37446 0.00000 0.00000 0.00000 MINI CONSTR> 257.72085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 422.88892 0.00163 0.12547 0.00007 MINI INTERN> 14.33197 52.84766 0.00000 23.69431 8.82272 MINI EXTERN> 64.08874 1.36896 0.00000 0.00000 0.00000 MINI CONSTR> 257.73455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 422.88592 0.00300 0.03457 0.00003 MINI INTERN> 14.34963 52.83885 0.00000 23.68779 8.82638 MINI EXTERN> 64.04801 1.38304 0.00000 0.00000 0.00000 MINI CONSTR> 257.75222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 422.88432 0.00160 0.02871 0.00003 MINI INTERN> 14.34373 52.83680 0.00000 23.68524 8.82596 MINI EXTERN> 64.04008 1.38994 0.00000 0.00000 0.00000 MINI CONSTR> 257.76257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11386 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 422.88267 0.00165 0.02938 0.00003 MINI INTERN> 14.34248 52.83432 0.00000 23.68185 8.82600 MINI EXTERN> 64.02712 1.39648 0.00000 0.00000 0.00000 MINI CONSTR> 257.77442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 422.88108 0.00159 0.02871 0.00004 MINI INTERN> 14.34020 52.83223 0.00000 23.67866 8.82584 MINI EXTERN> 64.01575 1.40271 0.00000 0.00000 0.00000 MINI CONSTR> 257.78568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11387 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 422.87953 0.00155 0.05121 0.00004 MINI INTERN> 14.34611 52.82861 0.00000 23.67389 8.82685 MINI EXTERN> 63.99365 1.41046 0.00000 0.00000 0.00000 MINI CONSTR> 257.79996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 422.87798 0.00155 0.03616 0.00004 MINI INTERN> 14.33851 52.82803 0.00000 23.67170 8.82581 MINI EXTERN> 63.98949 1.41548 0.00000 0.00000 0.00000 MINI CONSTR> 257.80895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 422.87663 0.00134 0.04575 0.00004 MINI INTERN> 14.34025 52.82538 0.00000 23.66802 8.82614 MINI EXTERN> 63.97446 1.42215 0.00000 0.00000 0.00000 MINI CONSTR> 257.82024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 422.87546 0.00118 0.06044 0.00004 MINI INTERN> 14.34137 52.82272 0.00000 23.66450 8.82650 MINI EXTERN> 63.95961 1.42966 0.00000 0.00000 0.00000 MINI CONSTR> 257.83110 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 422.87423 0.00123 0.06889 0.00004 MINI INTERN> 14.34145 52.82264 0.00000 23.66143 8.82600 MINI EXTERN> 63.95029 1.43181 0.00000 0.00000 0.00000 MINI CONSTR> 257.84060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 422.87310 0.00113 0.07026 0.00004 MINI INTERN> 14.34188 52.82000 0.00000 23.65826 8.82610 MINI EXTERN> 63.93842 1.43846 0.00000 0.00000 0.00000 MINI CONSTR> 257.84998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 422.87196 0.00114 0.06694 0.00005 MINI INTERN> 14.33649 52.81743 0.00000 23.65586 8.82577 MINI EXTERN> 63.93034 1.44767 0.00000 0.00000 0.00000 MINI CONSTR> 257.85840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 422.87088 0.00107 0.07284 0.00005 MINI INTERN> 14.33598 52.81830 0.00000 23.65327 8.82481 MINI EXTERN> 63.92496 1.44754 0.00000 0.00000 0.00000 MINI CONSTR> 257.86603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 422.86952 0.00136 0.02251 0.00002 MINI INTERN> 14.31521 52.81731 0.00000 23.65336 8.82235 MINI EXTERN> 63.93413 1.45713 0.00000 0.00000 0.00000 MINI CONSTR> 257.87003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 422.86899 0.00053 0.07752 0.00005 MINI INTERN> 14.33296 52.81253 0.00000 23.64760 8.82490 MINI EXTERN> 63.90321 1.46478 0.00000 0.00000 0.00000 MINI CONSTR> 257.88301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 422.86816 0.00083 0.08994 0.00005 MINI INTERN> 14.33341 52.81476 0.00000 23.64531 8.82357 MINI EXTERN> 63.90057 1.46134 0.00000 0.00000 0.00000 MINI CONSTR> 257.88918 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 422.86663 0.00153 0.02486 0.00002 MINI INTERN> 14.30835 52.81395 0.00000 23.64588 8.82069 MINI EXTERN> 63.91228 1.47291 0.00000 0.00000 0.00000 MINI CONSTR> 257.89257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 422.86583 0.00081 0.02033 0.00002 MINI INTERN> 14.30865 52.81278 0.00000 23.64339 8.82055 MINI EXTERN> 63.90337 1.47768 0.00000 0.00000 0.00000 MINI CONSTR> 257.89941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 422.86499 0.00083 0.02091 0.00002 MINI INTERN> 14.30636 52.81197 0.00000 23.64110 8.81990 MINI EXTERN> 63.89708 1.48250 0.00000 0.00000 0.00000 MINI CONSTR> 257.90607 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 422.86416 0.00083 0.03349 0.00003 MINI INTERN> 14.30065 52.81144 0.00000 23.63907 8.81860 MINI EXTERN> 63.89435 1.48760 0.00000 0.00000 0.00000 MINI CONSTR> 257.91245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 422.86339 0.00078 0.02675 0.00003 MINI INTERN> 14.30080 52.81006 0.00000 23.63653 8.81844 MINI EXTERN> 63.88526 1.49312 0.00000 0.00000 0.00000 MINI CONSTR> 257.91917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 422.86268 0.00070 0.03070 0.00003 MINI INTERN> 14.29765 52.80974 0.00000 23.63456 8.81756 MINI EXTERN> 63.88093 1.49739 0.00000 0.00000 0.00000 MINI CONSTR> 257.92486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 422.86206 0.00062 0.04215 0.00003 MINI INTERN> 14.29405 52.80960 0.00000 23.63272 8.81645 MINI EXTERN> 63.87813 1.50100 0.00000 0.00000 0.00000 MINI CONSTR> 257.93011 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 422.86141 0.00065 0.04646 0.00003 MINI INTERN> 14.29112 52.80792 0.00000 23.63055 8.81594 MINI EXTERN> 63.87152 1.50820 0.00000 0.00000 0.00000 MINI CONSTR> 257.93617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 422.86082 0.00060 0.04753 0.00003 MINI INTERN> 14.28848 52.80824 0.00000 23.62879 8.81497 MINI EXTERN> 63.86819 1.51115 0.00000 0.00000 0.00000 MINI CONSTR> 257.94100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 422.86024 0.00058 0.05124 0.00003 MINI INTERN> 14.28889 52.80823 0.00000 23.62658 8.81422 MINI EXTERN> 63.86291 1.51319 0.00000 0.00000 0.00000 MINI CONSTR> 257.94622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 422.85967 0.00057 0.04767 0.00003 MINI INTERN> 14.28580 52.80740 0.00000 23.62482 8.81365 MINI EXTERN> 63.85772 1.51913 0.00000 0.00000 0.00000 MINI CONSTR> 257.95115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 422.85911 0.00056 0.05202 0.00003 MINI INTERN> 14.28978 52.80704 0.00000 23.62215 8.81315 MINI EXTERN> 63.85042 1.51998 0.00000 0.00000 0.00000 MINI CONSTR> 257.95658 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 422.85842 0.00069 0.01573 0.00001 MINI INTERN> 14.29679 52.80551 0.00000 23.61898 8.81424 MINI EXTERN> 63.83416 1.52533 0.00000 0.00000 0.00000 MINI CONSTR> 257.96340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 422.85815 0.00027 0.05366 0.00004 MINI INTERN> 14.28178 52.80613 0.00000 23.61909 8.81135 MINI EXTERN> 63.84431 1.53036 0.00000 0.00000 0.00000 MINI CONSTR> 257.96513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 422.85764 0.00050 0.05502 0.00004 MINI INTERN> 14.28232 52.80481 0.00000 23.61681 8.81064 MINI EXTERN> 63.83896 1.53411 0.00000 0.00000 0.00000 MINI CONSTR> 257.96999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 422.85718 0.00047 0.05910 0.00004 MINI INTERN> 14.28168 52.80254 0.00000 23.61452 8.81008 MINI EXTERN> 63.83294 1.54037 0.00000 0.00000 0.00000 MINI CONSTR> 257.97505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 422.85644 0.00073 0.02045 0.00002 MINI INTERN> 14.29300 52.80489 0.00000 23.61095 8.81147 MINI EXTERN> 63.81283 1.54087 0.00000 0.00000 0.00000 MINI CONSTR> 257.98243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 422.85607 0.00038 0.01384 0.00002 MINI INTERN> 14.29094 52.80429 0.00000 23.60966 8.81053 MINI EXTERN> 63.81172 1.54366 0.00000 0.00000 0.00000 MINI CONSTR> 257.98528 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 422.85566 0.00040 0.02522 0.00002 MINI INTERN> 14.29214 52.80502 0.00000 23.60738 8.81018 MINI EXTERN> 63.80353 1.54701 0.00000 0.00000 0.00000 MINI CONSTR> 257.99041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 422.85528 0.00038 0.01956 0.00002 MINI INTERN> 14.28933 52.80421 0.00000 23.60601 8.80927 MINI EXTERN> 63.80165 1.55124 0.00000 0.00000 0.00000 MINI CONSTR> 257.99356 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 422.85497 0.00032 0.02836 0.00002 MINI INTERN> 14.29078 52.80498 0.00000 23.60408 8.80886 MINI EXTERN> 63.79527 1.55333 0.00000 0.00000 0.00000 MINI CONSTR> 257.99767 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 422.85458 0.00038 0.01985 0.00002 MINI INTERN> 14.28743 52.80413 0.00000 23.60281 8.80780 MINI EXTERN> 63.79432 1.55756 0.00000 0.00000 0.00000 MINI CONSTR> 258.00054 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> 500 422.85458 0.00038 0.01985 0.00002 STPD INTERN> 14.28743 52.80413 0.00000 23.60281 8.80780 STPD EXTERN> 63.79432 1.55756 0.00000 0.00000 0.00000 STPD CONSTR> 258.00054 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 11388 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 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> 0 422.85458 0.00038 0.01985 0.00000 MINI INTERN> 14.28743 52.80413 0.00000 23.60281 8.80780 MINI EXTERN> 63.79432 1.55756 0.00000 0.00000 0.00000 MINI CONSTR> 258.00054 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> 4 422.84794 0.00665 0.00938 0.02000 CONJ INTERN> 14.24283 52.79644 0.00000 23.54306 8.78109 CONJ EXTERN> 63.63473 1.68719 0.00000 0.00000 0.00000 CONJ CONSTR> 258.16259 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "4200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 9.8045 ( PROT LYS 1 HT2 ) 9.8045 ( PROT LYS 1 N ) 12.256 ( PROT LYS 1 HT3 ) 9.8045 ( PROT LYS 1 CA ) 12.256 ( PROT LYS 1 CB ) 9.8045 ( PROT LYS 1 CG ) 9.8045 ( PROT LYS 1 CD ) 9.8045 ( PROT LYS 1 CE ) 9.8045 ( PROT LYS 1 NZ ) 9.8045 ( PROT LYS 1 HZ1 ) 9.8045 ( PROT LYS 1 HZ2 ) 9.8045 ( PROT LYS 1 HZ3 ) 9.8045 ( PROT LYS 1 C ) 12.256 ( PROT LYS 1 O ) 12.256 ( PROT MET 2 N ) 12.256 ( PROT MET 2 H ) 9.8045 ( PROT MET 2 CA ) 12.256 ( PROT MET 2 CB ) 9.8045 ( PROT MET 2 CG ) 9.8045 ( PROT MET 2 SD ) 9.8045 ( PROT MET 2 CE ) 9.8045 ( PROT MET 2 C ) 12.256 ( PROT MET 2 O ) 12.256 ( PROT LYS 3 N ) 12.256 ( PROT LYS 3 H ) 9.8045 ( PROT LYS 3 CA ) 12.256 ( PROT LYS 3 CB ) 9.8045 ( PROT LYS 3 CG ) 9.8045 ( PROT LYS 3 CD ) 9.8045 ( PROT LYS 3 CE ) 9.8045 ( PROT LYS 3 NZ ) 9.8045 ( PROT LYS 3 HZ1 ) 9.8045 ( PROT LYS 3 HZ2 ) 9.8045 ( PROT LYS 3 HZ3 ) 9.8045 ( PROT LYS 3 C ) 12.256 ( PROT LYS 3 O ) 12.256 ( PROT ALA 4 N ) 12.256 ( PROT ALA 4 H ) 9.8045 ( PROT ALA 4 CA ) 12.256 ( PROT ALA 4 CB ) 9.8045 ( PROT ALA 4 C ) 12.256 ( PROT ALA 4 O ) 12.256 ( PROT VAL 5 N ) 12.256 ( PROT VAL 5 H ) 9.8045 ( PROT VAL 5 CA ) 12.256 ( PROT VAL 5 CB ) 9.8045 ( PROT VAL 5 CG1 ) 9.8045 ( PROT VAL 5 CG2 ) 9.8045 ( PROT VAL 5 C ) 12.256 ( PROT VAL 5 O ) 12.256 ( PROT MET 6 N ) 12.256 ( PROT MET 6 H ) 9.8045 ( PROT MET 6 CA ) 12.256 ( PROT MET 6 CB ) 9.8045 ( PROT MET 6 CG ) 9.8045 ( PROT MET 6 SD ) 9.8045 ( PROT MET 6 CE ) 9.8045 ( PROT MET 6 C ) 12.256 ( PROT MET 6 O ) 12.256 ( PROT ILE 7 N ) 12.256 ( PROT ILE 7 H ) 9.8045 ( PROT ILE 7 CA ) 12.256 ( PROT ILE 7 CB ) 9.8045 ( PROT ILE 7 CG2 ) 9.8045 ( PROT ILE 7 CG1 ) 9.8045 ( PROT ILE 7 CD ) 9.8045 ( PROT ILE 7 C ) 12.256 ( PROT ILE 7 O ) 12.256 ( PROT GLY 8 N ) 12.256 ( PROT GLY 8 H ) 9.8045 ( PROT GLY 8 CA ) 12.256 ( PROT GLY 8 C ) 12.256 ( PROT GLY 8 O ) 12.256 ( PROT ALA 9 N ) 12.256 ( PROT ALA 9 H ) 9.8045 ( PROT ALA 9 CA ) 12.256 ( PROT ALA 9 CB ) 9.8045 ( PROT ALA 9 C ) 12.256 ( PROT ALA 9 O ) 12.256 ( PROT CYS 10 N ) 12.256 ( PROT CYS 10 H ) 9.8045 ( PROT CYS 10 CA ) 12.256 ( PROT CYS 10 CB ) 9.8045 ( PROT CYS 10 SG ) 9.8045 ( PROT CYS 10 C ) 12.256 ( PROT CYS 10 O ) 12.256 ( PROT PHE 11 N ) 12.256 ( PROT PHE 11 H ) 9.8045 ( PROT PHE 11 CA ) 12.256 ( PROT PHE 11 CB ) 9.8045 ( PROT PHE 11 CG ) 9.8045 ( PROT PHE 11 CD1 ) 9.8045 ( PROT PHE 11 CD2 ) 9.8045 ( PROT PHE 11 CE1 ) 9.8045 ( PROT PHE 11 CE2 ) 9.8045 ( PROT PHE 11 CZ ) 9.8045 ( PROT PHE 11 C ) 12.256 ( PROT PHE 11 O ) 12.256 ( PROT LEU 12 N ) 12.256 ( PROT LEU 12 H ) 9.8045 ( PROT LEU 12 CA ) 12.256 ( PROT LEU 12 CB ) 9.8045 ( PROT LEU 12 CG ) 9.8045 ( PROT LEU 12 CD1 ) 9.8045 ( PROT LEU 12 CD2 ) 9.8045 ( PROT LEU 12 C ) 12.256 ( PROT LEU 12 O ) 12.256 ( PROT ILE 13 N ) 12.256 ( PROT ILE 13 H ) 9.8045 ( PROT ILE 13 CA ) 12.256 ( PROT ILE 13 CB ) 9.8045 ( PROT ILE 13 CG2 ) 9.8045 ( PROT ILE 13 CG1 ) 9.8045 ( PROT ILE 13 CD ) 9.8045 ( PROT ILE 13 C ) 12.256 ( PROT ILE 13 O ) 12.256 ( PROT ASH 14 N ) 12.256 ( PROT ASH 14 H ) 9.8045 ( PROT ASH 14 CA ) 12.256 ( PROT ASH 14 CB ) 9.8045 ( PROT ASH 14 CG ) 9.8045 ( PROT ASH 14 OD1 ) 9.8045 ( PROT ASH 14 OD2 ) 9.8045 ( PROT ASH 14 HD2 ) 9.8045 ( PROT ASH 14 C ) 12.256 ( PROT ASH 14 O ) 12.256 ( PROT PHE 15 N ) 12.256 ( PROT PHE 15 H ) 9.8045 ( PROT PHE 15 CA ) 12.256 ( PROT PHE 15 CB ) 9.8045 ( PROT PHE 15 CG ) 9.8045 ( PROT PHE 15 CD1 ) 9.8045 ( PROT PHE 15 CD2 ) 9.8045 ( PROT PHE 15 CE1 ) 9.8045 ( PROT PHE 15 CE2 ) 9.8045 ( PROT PHE 15 CZ ) 9.8045 ( PROT PHE 15 C ) 12.256 ( PROT PHE 15 O ) 12.256 ( PROT MET 16 N ) 12.256 ( PROT MET 16 H ) 9.8045 ( PROT MET 16 CA ) 12.256 ( PROT MET 16 CB ) 9.8045 ( PROT MET 16 CG ) 9.8045 ( PROT MET 16 SD ) 9.8045 ( PROT MET 16 CE ) 9.8045 ( PROT MET 16 C ) 12.256 ( PROT MET 16 O ) 12.256 ( PROT PHE 17 N ) 12.256 ( PROT PHE 17 H ) 9.8045 ( PROT PHE 17 CA ) 12.256 ( PROT PHE 17 CB ) 9.8045 ( PROT PHE 17 CG ) 9.8045 ( PROT PHE 17 CD1 ) 9.8045 ( PROT PHE 17 CD2 ) 9.8045 ( PROT PHE 17 CE1 ) 9.8045 ( PROT PHE 17 CE2 ) 9.8045 ( PROT PHE 17 CZ ) 9.8045 ( PROT PHE 17 C ) 12.256 ( PROT PHE 17 O ) 12.256 ( PROT PHE 18 N ) 12.256 ( PROT PHE 18 H ) 9.8045 ( PROT PHE 18 CA ) 12.256 ( PROT PHE 18 CB ) 9.8045 ( PROT PHE 18 CG ) 9.8045 ( PROT PHE 18 CD1 ) 9.8045 ( PROT PHE 18 CD2 ) 9.8045 ( PROT PHE 18 CE1 ) 9.8045 ( PROT PHE 18 CE2 ) 9.8045 ( PROT PHE 18 CZ ) 9.8045 ( PROT PHE 18 C ) 12.256 ( PROT PHE 18 O ) 12.256 ( PROT GLU 19 N ) 12.256 ( PROT GLU 19 H ) 9.8045 ( PROT GLU 19 CA ) 12.256 ( PROT GLU 19 CB ) 9.8045 ( PROT GLU 19 CG ) 9.8045 ( PROT GLU 19 CD ) 9.8045 ( PROT GLU 19 OE1 ) 9.8045 ( PROT GLU 19 OE2 ) 9.8045 ( PROT GLU 19 C ) 12.256 ( PROT GLU 19 OT1 ) 9.8045 ( PROT GLU 19 OT2 ) 9.8045 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40475 5.29420 -8.69307 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS -0.00021 -0.00178 -0.00015 ROTATION MATRIX 1.000000 -0.000133 -0.000001 0.000133 1.000000 0.000170 0.000001 -0.000170 1.000000 AXIS OF ROTATION IS 0.787069 0.003180 -0.616856 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 15.8084 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.293913 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2939" Parameter: A <- "0.2939" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70951 5.22862 -8.77920 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00533 0.03580 -0.01517 ROTATION MATRIX 0.999825 0.014181 0.012234 -0.014013 0.999807 -0.013747 -0.012426 0.013573 0.999831 AXIS OF ROTATION IS -0.589291 -0.531904 0.608124 ANGLE IS 1.33 CENTER OF ROTATION 9.121312 5.000761 -9.574305 SHIFT IS -0.031411 TOTAL SQUARE DIFF IS 0.3077 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.127253 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2939" RDCMND substituted energy or value "?RMS" to " 0.1273" Parameter: A <- "0.2939 0.1273" 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 0.2939 0.1273 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 " 258.16" Parameter: H <- "258.16" 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> 0 164.68535 258.16259 5.57347 ENER INTERN> 14.24283 52.79644 0.00000 23.54306 8.78109 ENER EXTERN> 63.63473 1.68719 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 " 164.69" Parameter: B <- "164.69" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 1.69" Parameter: C <- "1.69" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 63.63" Parameter: C <- " 65.32" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 65.32" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 14.24" Parameter: D <- "14.24" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 52.80" Parameter: D <- " 67.04" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 23.54" Parameter: D <- " 90.58" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.78" Parameter: D <- " 99.36" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 99.36" 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= 164.69 GRMS= 5.57 ELEC= 1.69 VDW= 63.63 RDTITL> *EXTERNAL= 65.32 INTERNAL= 99.36 USER= 0.00 HARM= 258.16 RDTITL> *BOND= 14.24 ANGL= 52.80 DIHE= 23.54 IMPR= 8.78 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11388 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11388 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 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> 0 351.13590 -186.45055 2.27755 0.02000 MINI INTERN> 14.24283 52.79644 0.00000 23.54306 8.78109 MINI EXTERN> 63.63473 1.68719 0.00000 0.00000 0.00000 MINI CONSTR> 186.45055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 337.59446 13.54144 1.95442 0.00360 MINI INTERN> 13.14529 51.63658 0.00000 25.91257 8.51702 MINI EXTERN> 32.54463 2.76860 0.00000 0.00000 0.00000 MINI CONSTR> 203.06977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11368 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 333.95691 3.63754 1.19861 0.00156 MINI INTERN> 11.29333 50.14222 0.00000 26.10727 8.30523 MINI EXTERN> 30.72360 2.54467 0.00000 0.00000 0.00000 MINI CONSTR> 204.84060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 331.61297 2.34394 1.66794 0.00161 MINI INTERN> 11.77599 48.70430 0.00000 26.33024 8.21736 MINI EXTERN> 28.02233 2.61552 0.00000 0.00000 0.00000 MINI CONSTR> 205.94723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11363 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 330.42701 1.18596 2.93223 0.00167 MINI INTERN> 11.10604 48.56645 0.00000 26.43399 8.19580 MINI EXTERN> 26.72031 2.82378 0.00000 0.00000 0.00000 MINI CONSTR> 206.58065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 328.68464 1.74237 0.73303 0.00072 MINI INTERN> 10.58531 48.17220 0.00000 26.51941 8.10353 MINI EXTERN> 25.79992 2.64736 0.00000 0.00000 0.00000 MINI CONSTR> 206.85691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11361 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 327.74763 0.93701 0.64855 0.00075 MINI INTERN> 10.48097 47.83588 0.00000 26.55530 8.06277 MINI EXTERN> 25.13179 2.65972 0.00000 0.00000 0.00000 MINI CONSTR> 207.02121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 326.89315 0.85449 1.21227 0.00078 MINI INTERN> 10.47073 47.51396 0.00000 26.61618 7.98777 MINI EXTERN> 24.54800 2.63303 0.00000 0.00000 0.00000 MINI CONSTR> 207.12347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11361 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 326.23140 0.66175 0.90686 0.00080 MINI INTERN> 10.44077 47.25527 0.00000 26.60395 7.96865 MINI EXTERN> 24.10978 2.66631 0.00000 0.00000 0.00000 MINI CONSTR> 207.18667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 325.82065 0.41074 1.43329 0.00083 MINI INTERN> 10.67061 46.99690 0.00000 26.60593 7.93504 MINI EXTERN> 23.74112 2.65975 0.00000 0.00000 0.00000 MINI CONSTR> 207.21131 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11360 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 325.37799 0.44266 1.50800 0.00087 MINI INTERN> 10.75067 46.77692 0.00000 26.59884 7.90745 MINI EXTERN> 23.42953 2.68188 0.00000 0.00000 0.00000 MINI CONSTR> 207.23270 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 324.83659 0.54140 0.44991 0.00037 MINI INTERN> 10.18113 46.87805 0.00000 26.54818 7.91801 MINI EXTERN> 23.30456 2.71469 0.00000 0.00000 0.00000 MINI CONSTR> 207.29197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11360 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 324.71266 0.12393 1.63670 0.00093 MINI INTERN> 10.92378 46.42498 0.00000 26.56760 7.86771 MINI EXTERN> 22.94415 2.71951 0.00000 0.00000 0.00000 MINI CONSTR> 207.26493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 324.22010 0.49257 0.54414 0.00040 MINI INTERN> 10.02245 46.73665 0.00000 26.51310 7.88201 MINI EXTERN> 23.01342 2.72009 0.00000 0.00000 0.00000 MINI CONSTR> 207.33237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11360 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 323.98300 0.23710 0.42981 0.00042 MINI INTERN> 10.02800 46.62731 0.00000 26.50261 7.86235 MINI EXTERN> 22.88992 2.72813 0.00000 0.00000 0.00000 MINI CONSTR> 207.34467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 323.76508 0.21792 0.41921 0.00043 MINI INTERN> 9.99007 46.56179 0.00000 26.48313 7.84756 MINI EXTERN> 22.78574 2.72883 0.00000 0.00000 0.00000 MINI CONSTR> 207.36795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11360 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 323.61126 0.15382 0.77675 0.00045 MINI INTERN> 9.75824 46.67693 0.00000 26.44748 7.84549 MINI EXTERN> 22.78067 2.69026 0.00000 0.00000 0.00000 MINI CONSTR> 207.41219 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 323.46995 0.14131 0.85363 0.00046 MINI INTERN> 9.67929 46.67272 0.00000 26.42653 7.83569 MINI EXTERN> 22.73449 2.67769 0.00000 0.00000 0.00000 MINI CONSTR> 207.44354 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11360 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 323.35037 0.11959 0.81257 0.00048 MINI INTERN> 9.64276 46.62371 0.00000 26.41797 7.82192 MINI EXTERN> 22.69232 2.68636 0.00000 0.00000 0.00000 MINI CONSTR> 207.46533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 323.19091 0.15946 0.23834 0.00021 MINI INTERN> 10.15622 46.14698 0.00000 26.43268 7.78954 MINI EXTERN> 22.39906 2.80723 0.00000 0.00000 0.00000 MINI CONSTR> 207.45921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 323.15803 0.03288 0.86887 0.00052 MINI INTERN> 9.55520 46.58490 0.00000 26.38551 7.80460 MINI EXTERN> 22.61911 2.67930 0.00000 0.00000 0.00000 MINI CONSTR> 207.52941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 323.01445 0.14357 0.29936 0.00022 MINI INTERN> 10.22613 45.98865 0.00000 26.40566 7.76902 MINI EXTERN> 22.25758 2.84595 0.00000 0.00000 0.00000 MINI CONSTR> 207.52146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 322.94684 0.06761 0.23518 0.00023 MINI INTERN> 10.18066 45.98228 0.00000 26.38806 7.76523 MINI EXTERN> 22.22908 2.84436 0.00000 0.00000 0.00000 MINI CONSTR> 207.55717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 322.88603 0.06081 0.24555 0.00024 MINI INTERN> 10.18940 45.93247 0.00000 26.37458 7.75800 MINI EXTERN> 22.18185 2.85738 0.00000 0.00000 0.00000 MINI CONSTR> 207.59235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 322.84601 0.04002 0.41028 0.00025 MINI INTERN> 10.32341 45.80115 0.00000 26.36798 7.74759 MINI EXTERN> 22.08995 2.89669 0.00000 0.00000 0.00000 MINI CONSTR> 207.61924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 322.80521 0.04080 0.46883 0.00026 MINI INTERN> 10.34953 45.74318 0.00000 26.35817 7.73988 MINI EXTERN> 22.04610 2.91519 0.00000 0.00000 0.00000 MINI CONSTR> 207.65317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 322.77137 0.03383 0.45089 0.00027 MINI INTERN> 10.36664 45.71089 0.00000 26.34382 7.73842 MINI EXTERN> 22.00345 2.92279 0.00000 0.00000 0.00000 MINI CONSTR> 207.68537 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 322.74028 0.03109 0.46021 0.00028 MINI INTERN> 10.36421 45.68161 0.00000 26.33318 7.73400 MINI EXTERN> 21.97570 2.93270 0.00000 0.00000 0.00000 MINI CONSTR> 207.71888 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 322.71388 0.02641 0.48615 0.00029 MINI INTERN> 10.35277 45.65530 0.00000 26.32469 7.72862 MINI EXTERN> 21.95635 2.94376 0.00000 0.00000 0.00000 MINI CONSTR> 207.75238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 322.67238 0.04150 0.17304 0.00012 MINI INTERN> 10.03481 45.89137 0.00000 26.28461 7.74668 MINI EXTERN> 22.04291 2.85959 0.00000 0.00000 0.00000 MINI CONSTR> 207.81242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 322.65259 0.01979 0.12971 0.00013 MINI INTERN> 10.05051 45.85272 0.00000 26.27851 7.74223 MINI EXTERN> 22.01629 2.87306 0.00000 0.00000 0.00000 MINI CONSTR> 207.83928 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 322.63500 0.01759 0.14153 0.00013 MINI INTERN> 10.05412 45.83222 0.00000 26.26726 7.74085 MINI EXTERN> 21.98954 2.87902 0.00000 0.00000 0.00000 MINI CONSTR> 207.87198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 322.62313 0.01187 0.22030 0.00014 MINI INTERN> 10.02924 45.84254 0.00000 26.25371 7.74216 MINI EXTERN> 21.97691 2.87372 0.00000 0.00000 0.00000 MINI CONSTR> 207.90486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 322.61077 0.01236 0.24803 0.00014 MINI INTERN> 10.06954 45.80529 0.00000 26.24136 7.74210 MINI EXTERN> 21.93259 2.88342 0.00000 0.00000 0.00000 MINI CONSTR> 207.93647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 322.60020 0.01057 0.23764 0.00015 MINI INTERN> 10.06106 45.79172 0.00000 26.23582 7.73975 MINI EXTERN> 21.92222 2.88904 0.00000 0.00000 0.00000 MINI CONSTR> 207.96058 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 322.58600 0.01420 0.06982 0.00006 MINI INTERN> 10.04635 45.74233 0.00000 26.24622 7.72826 MINI EXTERN> 21.93047 2.91744 0.00000 0.00000 0.00000 MINI CONSTR> 207.97492 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 322.58278 0.00322 0.24997 0.00016 MINI INTERN> 10.13248 45.71916 0.00000 26.21907 7.73804 MINI EXTERN> 21.85067 2.91148 0.00000 0.00000 0.00000 MINI CONSTR> 208.01188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 322.56963 0.01315 0.08070 0.00007 MINI INTERN> 10.02010 45.72249 0.00000 26.23465 7.72478 MINI EXTERN> 21.91345 2.92801 0.00000 0.00000 0.00000 MINI CONSTR> 208.02614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 322.56375 0.00588 0.05309 0.00007 MINI INTERN> 10.04949 45.69945 0.00000 26.22536 7.72638 MINI EXTERN> 21.88065 2.93442 0.00000 0.00000 0.00000 MINI CONSTR> 208.04799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 322.55766 0.00609 0.11121 0.00007 MINI INTERN> 9.98644 45.70830 0.00000 26.22616 7.72081 MINI EXTERN> 21.90667 2.93688 0.00000 0.00000 0.00000 MINI CONSTR> 208.07240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 322.55202 0.00564 0.06721 0.00008 MINI INTERN> 10.02241 45.68167 0.00000 26.21591 7.72312 MINI EXTERN> 21.86822 2.94477 0.00000 0.00000 0.00000 MINI CONSTR> 208.09591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 322.54836 0.00365 0.11756 0.00008 MINI INTERN> 9.97783 45.68725 0.00000 26.21621 7.71917 MINI EXTERN> 21.88610 2.94670 0.00000 0.00000 0.00000 MINI CONSTR> 208.11510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 322.54452 0.00384 0.13378 0.00008 MINI INTERN> 9.96321 45.68109 0.00000 26.21260 7.71769 MINI EXTERN> 21.88254 2.95104 0.00000 0.00000 0.00000 MINI CONSTR> 208.13636 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 322.54127 0.00325 0.12872 0.00009 MINI INTERN> 9.96648 45.66976 0.00000 26.20774 7.71794 MINI EXTERN> 21.86908 2.95613 0.00000 0.00000 0.00000 MINI CONSTR> 208.15413 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 322.53674 0.00453 0.03771 0.00004 MINI INTERN> 10.07273 45.61620 0.00000 26.18901 7.72688 MINI EXTERN> 21.78215 2.97079 0.00000 0.00000 0.00000 MINI CONSTR> 208.17898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 322.53570 0.00104 0.13741 0.00009 MINI INTERN> 9.95801 45.65314 0.00000 26.20002 7.71735 MINI EXTERN> 21.85192 2.96550 0.00000 0.00000 0.00000 MINI CONSTR> 208.18977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 322.53142 0.00428 0.04429 0.00004 MINI INTERN> 10.08439 45.59121 0.00000 26.17870 7.72819 MINI EXTERN> 21.75128 2.98206 0.00000 0.00000 0.00000 MINI CONSTR> 208.21559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 322.52947 0.00195 0.03027 0.00004 MINI INTERN> 10.06614 45.59098 0.00000 26.17790 7.72687 MINI EXTERN> 21.75521 2.98445 0.00000 0.00000 0.00000 MINI CONSTR> 208.22792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 322.52734 0.00213 0.06219 0.00004 MINI INTERN> 10.10209 45.56574 0.00000 26.16863 7.73025 MINI EXTERN> 21.71857 2.99309 0.00000 0.00000 0.00000 MINI CONSTR> 208.24897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 322.52540 0.00193 0.03883 0.00004 MINI INTERN> 10.08082 45.56641 0.00000 26.16818 7.72882 MINI EXTERN> 21.72406 2.99552 0.00000 0.00000 0.00000 MINI CONSTR> 208.26160 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 322.52403 0.00138 0.06897 0.00005 MINI INTERN> 10.10802 45.54698 0.00000 26.16113 7.73151 MINI EXTERN> 21.69610 3.00230 0.00000 0.00000 0.00000 MINI CONSTR> 208.27800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 322.52255 0.00148 0.07466 0.00005 MINI INTERN> 10.11261 45.53699 0.00000 26.15725 7.73236 MINI EXTERN> 21.68394 3.00700 0.00000 0.00000 0.00000 MINI CONSTR> 208.29240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 322.52124 0.00130 0.07214 0.00005 MINI INTERN> 10.11054 45.53091 0.00000 26.15479 7.73262 MINI EXTERN> 21.67743 3.01070 0.00000 0.00000 0.00000 MINI CONSTR> 208.30424 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 322.51998 0.00126 0.07416 0.00005 MINI INTERN> 10.11203 45.52302 0.00000 26.15171 7.73326 MINI EXTERN> 21.66823 3.01471 0.00000 0.00000 0.00000 MINI CONSTR> 208.31703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 322.51841 0.00157 0.02369 0.00002 MINI INTERN> 10.04944 45.54238 0.00000 26.15772 7.72843 MINI EXTERN> 21.70283 3.01354 0.00000 0.00000 0.00000 MINI CONSTR> 208.32406 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 322.51796 0.00045 0.08204 0.00006 MINI INTERN> 10.11820 45.50753 0.00000 26.14592 7.73478 MINI EXTERN> 21.64929 3.02257 0.00000 0.00000 0.00000 MINI CONSTR> 208.33967 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 322.51697 0.00099 0.08655 0.00006 MINI INTERN> 10.12090 45.49939 0.00000 26.14295 7.73564 MINI EXTERN> 21.63971 3.02687 0.00000 0.00000 0.00000 MINI CONSTR> 208.35150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 322.51538 0.00159 0.02979 0.00002 MINI INTERN> 10.04016 45.52684 0.00000 26.15169 7.72928 MINI EXTERN> 21.68641 3.02418 0.00000 0.00000 0.00000 MINI CONSTR> 208.35682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 322.51462 0.00076 0.01903 0.00003 MINI INTERN> 10.05306 45.51659 0.00000 26.14814 7.73086 MINI EXTERN> 21.67218 3.02795 0.00000 0.00000 0.00000 MINI CONSTR> 208.36584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 322.51370 0.00092 0.03534 0.00003 MINI INTERN> 10.03472 45.51722 0.00000 26.14814 7.72995 MINI EXTERN> 21.67607 3.03095 0.00000 0.00000 0.00000 MINI CONSTR> 208.37664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 322.51292 0.00078 0.02541 0.00003 MINI INTERN> 10.04319 45.50847 0.00000 26.14510 7.73125 MINI EXTERN> 21.66437 3.03460 0.00000 0.00000 0.00000 MINI CONSTR> 208.38594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 322.51220 0.00072 0.02861 0.00003 MINI INTERN> 10.03982 45.50424 0.00000 26.14361 7.73157 MINI EXTERN> 21.65999 3.03792 0.00000 0.00000 0.00000 MINI CONSTR> 208.39504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 322.51166 0.00054 0.04347 0.00003 MINI INTERN> 10.02768 45.50453 0.00000 26.14360 7.73104 MINI EXTERN> 21.66230 3.03997 0.00000 0.00000 0.00000 MINI CONSTR> 208.40253 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 322.51101 0.00065 0.04626 0.00003 MINI INTERN> 10.02567 45.49996 0.00000 26.14208 7.73148 MINI EXTERN> 21.65723 3.04338 0.00000 0.00000 0.00000 MINI CONSTR> 208.41121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 322.51045 0.00057 0.05193 0.00003 MINI INTERN> 10.02281 45.49658 0.00000 26.14084 7.73174 MINI EXTERN> 21.65362 3.04556 0.00000 0.00000 0.00000 MINI CONSTR> 208.41928 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 322.50992 0.00053 0.04892 0.00003 MINI INTERN> 10.02348 45.49172 0.00000 26.13929 7.73242 MINI EXTERN> 21.64785 3.04892 0.00000 0.00000 0.00000 MINI CONSTR> 208.42625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 322.50937 0.00055 0.04996 0.00003 MINI INTERN> 10.02409 45.48704 0.00000 26.13768 7.73299 MINI EXTERN> 21.64216 3.05132 0.00000 0.00000 0.00000 MINI CONSTR> 208.43408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 322.50868 0.00069 0.01599 0.00001 MINI INTERN> 10.06081 45.46701 0.00000 26.13103 7.73694 MINI EXTERN> 21.61306 3.05651 0.00000 0.00000 0.00000 MINI CONSTR> 208.44332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 322.50848 0.00020 0.05449 0.00004 MINI INTERN> 10.01955 45.48022 0.00000 26.13557 7.73377 MINI EXTERN> 21.63485 3.05715 0.00000 0.00000 0.00000 MINI CONSTR> 208.44737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 322.50804 0.00044 0.05828 0.00004 MINI INTERN> 10.02096 45.47621 0.00000 26.13411 7.73429 MINI EXTERN> 21.62975 3.05833 0.00000 0.00000 0.00000 MINI CONSTR> 208.45438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 322.50733 0.00071 0.02005 0.00002 MINI INTERN> 10.06510 45.45272 0.00000 26.12637 7.73907 MINI EXTERN> 21.59570 3.06447 0.00000 0.00000 0.00000 MINI CONSTR> 208.46390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 322.50698 0.00035 0.01316 0.00002 MINI INTERN> 10.05740 45.45266 0.00000 26.12647 7.73882 MINI EXTERN> 21.59685 3.06627 0.00000 0.00000 0.00000 MINI CONSTR> 208.46850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 322.50656 0.00042 0.02413 0.00002 MINI INTERN> 10.06805 45.44393 0.00000 26.12353 7.74045 MINI EXTERN> 21.58498 3.06921 0.00000 0.00000 0.00000 MINI CONSTR> 208.47641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 322.50620 0.00036 0.01844 0.00002 MINI INTERN> 10.06265 45.44240 0.00000 26.12322 7.74051 MINI EXTERN> 21.58410 3.07181 0.00000 0.00000 0.00000 MINI CONSTR> 208.48151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 322.50588 0.00032 0.02186 0.00002 MINI INTERN> 10.06633 45.43757 0.00000 26.12165 7.74133 MINI EXTERN> 21.57792 3.07382 0.00000 0.00000 0.00000 MINI CONSTR> 208.48726 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 322.50560 0.00028 0.02945 0.00002 MINI INTERN> 10.07177 45.43196 0.00000 26.11984 7.74234 MINI EXTERN> 21.57058 3.07615 0.00000 0.00000 0.00000 MINI CONSTR> 208.49297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 322.50527 0.00033 0.02973 0.00002 MINI INTERN> 10.07139 45.42853 0.00000 26.11880 7.74288 MINI EXTERN> 21.56665 3.07848 0.00000 0.00000 0.00000 MINI CONSTR> 208.49854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 322.50496 0.00031 0.03200 0.00002 MINI INTERN> 10.07238 45.42502 0.00000 26.11762 7.74348 MINI EXTERN> 21.56230 3.08002 0.00000 0.00000 0.00000 MINI CONSTR> 208.50414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 322.50471 0.00025 0.03719 0.00002 MINI INTERN> 10.07217 45.42085 0.00000 26.11656 7.74416 MINI EXTERN> 21.55766 3.08391 0.00000 0.00000 0.00000 MINI CONSTR> 208.50940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 322.50445 0.00026 0.03397 0.00002 MINI INTERN> 10.07280 45.41824 0.00000 26.11573 7.74456 MINI EXTERN> 21.55455 3.08498 0.00000 0.00000 0.00000 MINI CONSTR> 208.51360 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 322.50411 0.00034 0.01086 0.00001 MINI INTERN> 10.05153 45.42465 0.00000 26.11810 7.74291 MINI EXTERN> 21.56509 3.08545 0.00000 0.00000 0.00000 MINI CONSTR> 208.51639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 322.50398 0.00013 0.03688 0.00002 MINI INTERN> 10.07386 45.41187 0.00000 26.11384 7.74562 MINI EXTERN> 21.54705 3.08891 0.00000 0.00000 0.00000 MINI CONSTR> 208.52282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 322.50376 0.00022 0.04067 0.00003 MINI INTERN> 10.07338 45.41077 0.00000 26.11326 7.74579 MINI EXTERN> 21.54557 3.08800 0.00000 0.00000 0.00000 MINI CONSTR> 208.52700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 322.50341 0.00035 0.01219 0.00001 MINI INTERN> 10.04911 45.41713 0.00000 26.11600 7.74406 MINI EXTERN> 21.55670 3.09094 0.00000 0.00000 0.00000 MINI CONSTR> 208.52946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 322.50322 0.00019 0.00959 0.00001 MINI INTERN> 10.05194 45.41367 0.00000 26.11490 7.74472 MINI EXTERN> 21.55224 3.09246 0.00000 0.00000 0.00000 MINI CONSTR> 208.53329 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> 420 322.50322 0.00019 0.00959 0.00001 STPD INTERN> 10.05194 45.41367 0.00000 26.11490 7.74472 STPD EXTERN> 21.55224 3.09246 0.00000 0.00000 0.00000 STPD CONSTR> 208.53329 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 11358 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11358 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 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> 0 322.50322 0.00019 0.00959 0.00000 MINI INTERN> 10.05194 45.41367 0.00000 26.11490 7.74472 MINI EXTERN> 21.55224 3.09246 0.00000 0.00000 0.00000 MINI CONSTR> 208.53329 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> 3 322.49884 0.00438 0.00548 0.02000 CONJ INTERN> 10.04250 45.30216 0.00000 26.08449 7.76486 CONJ EXTERN> 21.40972 3.17254 0.00000 0.00000 0.00000 CONJ CONSTR> 208.72257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "4800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 6.3729 ( PROT LYS 1 HT2 ) 6.3729 ( PROT LYS 1 N ) 7.9661 ( PROT LYS 1 HT3 ) 6.3729 ( PROT LYS 1 CA ) 7.9661 ( PROT LYS 1 CB ) 6.3729 ( PROT LYS 1 CG ) 6.3729 ( PROT LYS 1 CD ) 6.3729 ( PROT LYS 1 CE ) 6.3729 ( PROT LYS 1 NZ ) 6.3729 ( PROT LYS 1 HZ1 ) 6.3729 ( PROT LYS 1 HZ2 ) 6.3729 ( PROT LYS 1 HZ3 ) 6.3729 ( PROT LYS 1 C ) 7.9661 ( PROT LYS 1 O ) 7.9661 ( PROT MET 2 N ) 7.9661 ( PROT MET 2 H ) 6.3729 ( PROT MET 2 CA ) 7.9661 ( PROT MET 2 CB ) 6.3729 ( PROT MET 2 CG ) 6.3729 ( PROT MET 2 SD ) 6.3729 ( PROT MET 2 CE ) 6.3729 ( PROT MET 2 C ) 7.9661 ( PROT MET 2 O ) 7.9661 ( PROT LYS 3 N ) 7.9661 ( PROT LYS 3 H ) 6.3729 ( PROT LYS 3 CA ) 7.9661 ( PROT LYS 3 CB ) 6.3729 ( PROT LYS 3 CG ) 6.3729 ( PROT LYS 3 CD ) 6.3729 ( PROT LYS 3 CE ) 6.3729 ( PROT LYS 3 NZ ) 6.3729 ( PROT LYS 3 HZ1 ) 6.3729 ( PROT LYS 3 HZ2 ) 6.3729 ( PROT LYS 3 HZ3 ) 6.3729 ( PROT LYS 3 C ) 7.9661 ( PROT LYS 3 O ) 7.9661 ( PROT ALA 4 N ) 7.9661 ( PROT ALA 4 H ) 6.3729 ( PROT ALA 4 CA ) 7.9661 ( PROT ALA 4 CB ) 6.3729 ( PROT ALA 4 C ) 7.9661 ( PROT ALA 4 O ) 7.9661 ( PROT VAL 5 N ) 7.9661 ( PROT VAL 5 H ) 6.3729 ( PROT VAL 5 CA ) 7.9661 ( PROT VAL 5 CB ) 6.3729 ( PROT VAL 5 CG1 ) 6.3729 ( PROT VAL 5 CG2 ) 6.3729 ( PROT VAL 5 C ) 7.9661 ( PROT VAL 5 O ) 7.9661 ( PROT MET 6 N ) 7.9661 ( PROT MET 6 H ) 6.3729 ( PROT MET 6 CA ) 7.9661 ( PROT MET 6 CB ) 6.3729 ( PROT MET 6 CG ) 6.3729 ( PROT MET 6 SD ) 6.3729 ( PROT MET 6 CE ) 6.3729 ( PROT MET 6 C ) 7.9661 ( PROT MET 6 O ) 7.9661 ( PROT ILE 7 N ) 7.9661 ( PROT ILE 7 H ) 6.3729 ( PROT ILE 7 CA ) 7.9661 ( PROT ILE 7 CB ) 6.3729 ( PROT ILE 7 CG2 ) 6.3729 ( PROT ILE 7 CG1 ) 6.3729 ( PROT ILE 7 CD ) 6.3729 ( PROT ILE 7 C ) 7.9661 ( PROT ILE 7 O ) 7.9661 ( PROT GLY 8 N ) 7.9661 ( PROT GLY 8 H ) 6.3729 ( PROT GLY 8 CA ) 7.9661 ( PROT GLY 8 C ) 7.9661 ( PROT GLY 8 O ) 7.9661 ( PROT ALA 9 N ) 7.9661 ( PROT ALA 9 H ) 6.3729 ( PROT ALA 9 CA ) 7.9661 ( PROT ALA 9 CB ) 6.3729 ( PROT ALA 9 C ) 7.9661 ( PROT ALA 9 O ) 7.9661 ( PROT CYS 10 N ) 7.9661 ( PROT CYS 10 H ) 6.3729 ( PROT CYS 10 CA ) 7.9661 ( PROT CYS 10 CB ) 6.3729 ( PROT CYS 10 SG ) 6.3729 ( PROT CYS 10 C ) 7.9661 ( PROT CYS 10 O ) 7.9661 ( PROT PHE 11 N ) 7.9661 ( PROT PHE 11 H ) 6.3729 ( PROT PHE 11 CA ) 7.9661 ( PROT PHE 11 CB ) 6.3729 ( PROT PHE 11 CG ) 6.3729 ( PROT PHE 11 CD1 ) 6.3729 ( PROT PHE 11 CD2 ) 6.3729 ( PROT PHE 11 CE1 ) 6.3729 ( PROT PHE 11 CE2 ) 6.3729 ( PROT PHE 11 CZ ) 6.3729 ( PROT PHE 11 C ) 7.9661 ( PROT PHE 11 O ) 7.9661 ( PROT LEU 12 N ) 7.9661 ( PROT LEU 12 H ) 6.3729 ( PROT LEU 12 CA ) 7.9661 ( PROT LEU 12 CB ) 6.3729 ( PROT LEU 12 CG ) 6.3729 ( PROT LEU 12 CD1 ) 6.3729 ( PROT LEU 12 CD2 ) 6.3729 ( PROT LEU 12 C ) 7.9661 ( PROT LEU 12 O ) 7.9661 ( PROT ILE 13 N ) 7.9661 ( PROT ILE 13 H ) 6.3729 ( PROT ILE 13 CA ) 7.9661 ( PROT ILE 13 CB ) 6.3729 ( PROT ILE 13 CG2 ) 6.3729 ( PROT ILE 13 CG1 ) 6.3729 ( PROT ILE 13 CD ) 6.3729 ( PROT ILE 13 C ) 7.9661 ( PROT ILE 13 O ) 7.9661 ( PROT ASH 14 N ) 7.9661 ( PROT ASH 14 H ) 6.3729 ( PROT ASH 14 CA ) 7.9661 ( PROT ASH 14 CB ) 6.3729 ( PROT ASH 14 CG ) 6.3729 ( PROT ASH 14 OD1 ) 6.3729 ( PROT ASH 14 OD2 ) 6.3729 ( PROT ASH 14 HD2 ) 6.3729 ( PROT ASH 14 C ) 7.9661 ( PROT ASH 14 O ) 7.9661 ( PROT PHE 15 N ) 7.9661 ( PROT PHE 15 H ) 6.3729 ( PROT PHE 15 CA ) 7.9661 ( PROT PHE 15 CB ) 6.3729 ( PROT PHE 15 CG ) 6.3729 ( PROT PHE 15 CD1 ) 6.3729 ( PROT PHE 15 CD2 ) 6.3729 ( PROT PHE 15 CE1 ) 6.3729 ( PROT PHE 15 CE2 ) 6.3729 ( PROT PHE 15 CZ ) 6.3729 ( PROT PHE 15 C ) 7.9661 ( PROT PHE 15 O ) 7.9661 ( PROT MET 16 N ) 7.9661 ( PROT MET 16 H ) 6.3729 ( PROT MET 16 CA ) 7.9661 ( PROT MET 16 CB ) 6.3729 ( PROT MET 16 CG ) 6.3729 ( PROT MET 16 SD ) 6.3729 ( PROT MET 16 CE ) 6.3729 ( PROT MET 16 C ) 7.9661 ( PROT MET 16 O ) 7.9661 ( PROT PHE 17 N ) 7.9661 ( PROT PHE 17 H ) 6.3729 ( PROT PHE 17 CA ) 7.9661 ( PROT PHE 17 CB ) 6.3729 ( PROT PHE 17 CG ) 6.3729 ( PROT PHE 17 CD1 ) 6.3729 ( PROT PHE 17 CD2 ) 6.3729 ( PROT PHE 17 CE1 ) 6.3729 ( PROT PHE 17 CE2 ) 6.3729 ( PROT PHE 17 CZ ) 6.3729 ( PROT PHE 17 C ) 7.9661 ( PROT PHE 17 O ) 7.9661 ( PROT PHE 18 N ) 7.9661 ( PROT PHE 18 H ) 6.3729 ( PROT PHE 18 CA ) 7.9661 ( PROT PHE 18 CB ) 6.3729 ( PROT PHE 18 CG ) 6.3729 ( PROT PHE 18 CD1 ) 6.3729 ( PROT PHE 18 CD2 ) 6.3729 ( PROT PHE 18 CE1 ) 6.3729 ( PROT PHE 18 CE2 ) 6.3729 ( PROT PHE 18 CZ ) 6.3729 ( PROT PHE 18 C ) 7.9661 ( PROT PHE 18 O ) 7.9661 ( PROT GLU 19 N ) 7.9661 ( PROT GLU 19 H ) 6.3729 ( PROT GLU 19 CA ) 7.9661 ( PROT GLU 19 CB ) 6.3729 ( PROT GLU 19 CG ) 6.3729 ( PROT GLU 19 CD ) 6.3729 ( PROT GLU 19 OE1 ) 6.3729 ( PROT GLU 19 OE2 ) 6.3729 ( PROT GLU 19 C ) 7.9661 ( PROT GLU 19 OT1 ) 6.3729 ( PROT GLU 19 OT2 ) 6.3729 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40446 5.29410 -8.69270 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00009 -0.00168 -0.00051 ROTATION MATRIX 1.000000 -0.000137 0.000018 0.000137 1.000000 0.000166 -0.000018 -0.000166 1.000000 AXIS OF ROTATION IS 0.769640 -0.082276 -0.633155 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 19.5681 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.327000 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3270" Parameter: A <- "0.3270" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70904 5.22477 -8.77922 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00580 0.03965 -0.01515 ROTATION MATRIX 0.999813 0.014935 0.012313 -0.014761 0.999791 -0.014126 -0.012522 0.013941 0.999824 AXIS OF ROTATION IS -0.586973 -0.519389 0.621046 ANGLE IS 1.37 CENTER OF ROTATION 9.011234 5.023206 -9.634208 SHIFT IS -0.033408 TOTAL SQUARE DIFF IS 0.4409 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.152329 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3270" RDCMND substituted energy or value "?RMS" to " 0.1523" Parameter: A <- "0.3270 0.1523" 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 0.3270 0.1523 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 " 208.72" Parameter: H <- "208.72" 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> 0 113.77627 208.72257 4.05081 ENER INTERN> 10.04250 45.30216 0.00000 26.08449 7.76486 ENER EXTERN> 21.40972 3.17254 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 " 113.78" Parameter: B <- "113.78" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 3.17" Parameter: C <- "3.17" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 21.41" Parameter: C <- " 24.58" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 24.58" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 10.04" Parameter: D <- "10.04" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 45.30" Parameter: D <- " 55.34" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 26.08" Parameter: D <- " 81.42" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.76" Parameter: D <- " 89.18" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 89.18" 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= 113.78 GRMS= 4.05 ELEC= 3.17 VDW= 21.41 RDTITL> *EXTERNAL= 24.58 INTERNAL= 89.18 USER= 0.00 HARM= 208.72 RDTITL> *BOND= 10.04 ANGL= 45.30 DIHE= 26.08 IMPR= 7.76 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= 113.78 GRMS= 4.05 ELEC= 3.17 VDW= 21.41 RDTITL> *EXTERNAL= 24.58 INTERNAL= 89.18 USER= 0.00 HARM= 208.72 RDTITL> *BOND= 10.04 ANGL= 45.30 DIHE= 26.08 IMPR= 7.76 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= 113.78 GRMS= 4.05 ELEC= 3.17 VDW= 21.41 RDTITL> *EXTERNAL= 24.58 INTERNAL= 89.18 USER= 0.00 HARM= 208.72 RDTITL> *BOND= 10.04 ANGL= 45.30 DIHE= 26.08 IMPR= 7.76 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 4800 0.3270 0.1523 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11358 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11359 ATOM PAIRS WERE FOUND FOR ATOM LIST 341 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> 0 262.67689 -148.90062 1.62744 0.02000 MINI INTERN> 10.04250 45.30216 0.00000 26.08449 7.76486 MINI EXTERN> 21.40972 3.17254 0.00000 0.00000 0.00000 MINI CONSTR> 148.90062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 254.07688 8.60001 1.69236 0.00360 MINI INTERN> 9.39154 43.33050 0.00000 28.13723 7.59242 MINI EXTERN> 0.68753 4.23907 0.00000 0.00000 0.00000 MINI CONSTR> 160.69858 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11341 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 251.85319 2.22369 1.47533 0.00156 MINI INTERN> 8.89772 43.28167 0.00000 28.38041 7.54542 MINI EXTERN> -3.08602 4.48748 0.00000 0.00000 0.00000 MINI CONSTR> 162.34652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 250.92961 0.92358 2.76323 0.00161 MINI INTERN> 9.55465 42.53379 0.00000 28.61979 7.42817 MINI EXTERN> -4.73441 4.49788 0.00000 0.00000 0.00000 MINI CONSTR> 163.02973 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11340 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 249.43064 1.49897 0.66353 0.00070 MINI INTERN> 8.18688 42.47714 0.00000 28.67973 7.39448 MINI EXTERN> -5.40263 4.63893 0.00000 0.00000 0.00000 MINI CONSTR> 163.45612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 248.61973 0.81090 0.60374 0.00072 MINI INTERN> 8.08965 42.19447 0.00000 28.73059 7.34679 MINI EXTERN> -6.11154 4.65074 0.00000 0.00000 0.00000 MINI CONSTR> 163.71905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11340 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 247.84286 0.77687 1.00498 0.00075 MINI INTERN> 7.93264 41.94917 0.00000 28.75142 7.28788 MINI EXTERN> -6.66045 4.64518 0.00000 0.00000 0.00000 MINI CONSTR> 163.93702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 247.21125 0.63161 0.77868 0.00078 MINI INTERN> 7.91614 41.71732 0.00000 28.77046 7.25617 MINI EXTERN> -7.16380 4.66934 0.00000 0.00000 0.00000 MINI CONSTR> 164.04562 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11341 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 246.71142 0.49984 1.18956 0.00080 MINI INTERN> 7.98640 41.44941 0.00000 28.76604 7.20749 MINI EXTERN> -7.51574 4.69604 0.00000 0.00000 0.00000 MINI CONSTR> 164.12178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 246.21450 0.49692 1.22793 0.00083 MINI INTERN> 8.34492 40.97224 0.00000 28.76840 7.15992 MINI EXTERN> -7.98608 4.79912 0.00000 0.00000 0.00000 MINI CONSTR> 164.15598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11339 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 245.76784 0.44665 1.31988 0.00087 MINI INTERN> 8.25074 40.84535 0.00000 28.74840 7.12694 MINI EXTERN> -8.19599 4.80162 0.00000 0.00000 0.00000 MINI CONSTR> 164.19079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 245.37820 0.38964 1.25523 0.00090 MINI INTERN> 8.29345 40.65955 0.00000 28.73456 7.10394 MINI EXTERN> -8.44658 4.82577 0.00000 0.00000 0.00000 MINI CONSTR> 164.20751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11335 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 244.88364 0.49456 0.38282 0.00039 MINI INTERN> 7.80111 40.92465 0.00000 28.72513 7.12932 MINI EXTERN> -8.69131 4.74652 0.00000 0.00000 0.00000 MINI CONSTR> 164.24822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 244.73488 0.14876 1.38923 0.00096 MINI INTERN> 8.43488 40.26614 0.00000 28.68139 7.05485 MINI EXTERN> -8.81967 4.88678 0.00000 0.00000 0.00000 MINI CONSTR> 164.23051 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11334 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 244.28824 0.44664 0.46894 0.00042 MINI INTERN> 7.70748 40.78339 0.00000 28.67963 7.09784 MINI EXTERN> -9.00833 4.75279 0.00000 0.00000 0.00000 MINI CONSTR> 164.27545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 244.07013 0.21811 0.32418 0.00043 MINI INTERN> 7.74999 40.62034 0.00000 28.65217 7.07508 MINI EXTERN> -9.08969 4.78118 0.00000 0.00000 0.00000 MINI CONSTR> 164.28105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11333 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 243.86249 0.20764 0.62511 0.00045 MINI INTERN> 7.58267 40.71223 0.00000 28.63285 7.07485 MINI EXTERN> -9.20931 4.76411 0.00000 0.00000 0.00000 MINI CONSTR> 164.30509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 243.67398 0.18851 0.50997 0.00046 MINI INTERN> 7.66522 40.56676 0.00000 28.60618 7.05729 MINI EXTERN> -9.30338 4.76732 0.00000 0.00000 0.00000 MINI CONSTR> 164.31459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11332 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 243.53383 0.14015 0.67962 0.00048 MINI INTERN> 7.59851 40.56074 0.00000 28.58662 7.05282 MINI EXTERN> -9.38961 4.78901 0.00000 0.00000 0.00000 MINI CONSTR> 164.33574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 243.40715 0.12668 0.83552 0.00050 MINI INTERN> 7.66016 40.50789 0.00000 28.56068 7.04135 MINI EXTERN> -9.46131 4.74638 0.00000 0.00000 0.00000 MINI CONSTR> 164.35200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11332 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 243.27784 0.12931 0.73929 0.00052 MINI INTERN> 7.62644 40.45367 0.00000 28.54022 7.03405 MINI EXTERN> -9.52333 4.77431 0.00000 0.00000 0.00000 MINI CONSTR> 164.37247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 243.12235 0.15549 0.24684 0.00022 MINI INTERN> 7.79807 40.12450 0.00000 28.50531 6.99769 MINI EXTERN> -9.52684 4.84591 0.00000 0.00000 0.00000 MINI CONSTR> 164.37772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 243.08701 0.03534 0.89685 0.00056 MINI INTERN> 7.62396 40.28640 0.00000 28.49749 7.01280 MINI EXTERN> -9.61617 4.86669 0.00000 0.00000 0.00000 MINI CONSTR> 164.41585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 242.93012 0.15690 0.25228 0.00024 MINI INTERN> 7.79665 40.02000 0.00000 28.46360 6.98109 MINI EXTERN> -9.61814 4.86320 0.00000 0.00000 0.00000 MINI CONSTR> 164.42373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 242.85437 0.07575 0.19982 0.00025 MINI INTERN> 7.76069 40.00990 0.00000 28.44819 6.97794 MINI EXTERN> -9.65946 4.86925 0.00000 0.00000 0.00000 MINI CONSTR> 164.44786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 242.78168 0.07269 0.35037 0.00026 MINI INTERN> 7.82420 39.89764 0.00000 28.42328 6.96373 MINI EXTERN> -9.68770 4.88776 0.00000 0.00000 0.00000 MINI CONSTR> 164.47278 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 242.70873 0.07296 0.22044 0.00027 MINI INTERN> 7.78015 39.90515 0.00000 28.40761 6.96301 MINI EXTERN> -9.73387 4.88440 0.00000 0.00000 0.00000 MINI CONSTR> 164.50227 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 242.64958 0.05914 0.31818 0.00028 MINI INTERN> 7.79992 39.83201 0.00000 28.38670 6.95416 MINI EXTERN> -9.76331 4.90849 0.00000 0.00000 0.00000 MINI CONSTR> 164.53161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 242.60729 0.04230 0.39982 0.00029 MINI INTERN> 7.83299 39.77011 0.00000 28.36921 6.94618 MINI EXTERN> -9.78336 4.91654 0.00000 0.00000 0.00000 MINI CONSTR> 164.55562 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 242.56881 0.03847 0.52657 0.00030 MINI INTERN> 7.86458 39.74848 0.00000 28.35252 6.94184 MINI EXTERN> -9.81667 4.89437 0.00000 0.00000 0.00000 MINI CONSTR> 164.58370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 242.53080 0.03801 0.50294 0.00031 MINI INTERN> 7.83376 39.75120 0.00000 28.34210 6.94079 MINI EXTERN> -9.83991 4.89455 0.00000 0.00000 0.00000 MINI CONSTR> 164.60831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 242.49344 0.03736 0.46228 0.00032 MINI INTERN> 7.82914 39.68139 0.00000 28.32698 6.93366 MINI EXTERN> -9.85037 4.93822 0.00000 0.00000 0.00000 MINI CONSTR> 164.63441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 242.44029 0.05316 0.14836 0.00014 MINI INTERN> 7.68760 39.81132 0.00000 28.32316 6.94588 MINI EXTERN> -9.90702 4.90923 0.00000 0.00000 0.00000 MINI CONSTR> 164.67012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 242.41406 0.02622 0.11969 0.00014 MINI INTERN> 7.69699 39.77521 0.00000 28.31139 6.94185 MINI EXTERN> -9.92310 4.91917 0.00000 0.00000 0.00000 MINI CONSTR> 164.69256 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 242.38680 0.02726 0.19315 0.00015 MINI INTERN> 7.67315 39.78310 0.00000 28.30003 6.94174 MINI EXTERN> -9.95086 4.91603 0.00000 0.00000 0.00000 MINI CONSTR> 164.72361 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 242.36391 0.02289 0.16859 0.00015 MINI INTERN> 7.67440 39.75210 0.00000 28.28913 6.93850 MINI EXTERN> -9.96705 4.92920 0.00000 0.00000 0.00000 MINI CONSTR> 164.74762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 242.34557 0.01834 0.23690 0.00016 MINI INTERN> 7.67102 39.75074 0.00000 28.27899 6.93768 MINI EXTERN> -9.98828 4.92202 0.00000 0.00000 0.00000 MINI CONSTR> 164.77340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 242.32810 0.01747 0.24986 0.00017 MINI INTERN> 7.65621 39.73608 0.00000 28.27021 6.93634 MINI EXTERN> -10.00655 4.93749 0.00000 0.00000 0.00000 MINI CONSTR> 164.79832 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 242.31244 0.01566 0.27670 0.00017 MINI INTERN> 7.67129 39.71876 0.00000 28.25970 6.93407 MINI EXTERN> -10.02212 4.92915 0.00000 0.00000 0.00000 MINI CONSTR> 164.82159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 242.29747 0.01497 0.25445 0.00018 MINI INTERN> 7.65878 39.69825 0.00000 28.25205 6.93243 MINI EXTERN> -10.03641 4.94845 0.00000 0.00000 0.00000 MINI CONSTR> 164.84391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11331 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 242.27886 0.01861 0.08532 0.00008 MINI INTERN> 7.71554 39.60966 0.00000 28.23901 6.92369 MINI EXTERN> -10.03069 4.96127 0.00000 0.00000 0.00000 MINI CONSTR> 164.86039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 242.27481 0.00405 0.31011 0.00019 MINI INTERN> 7.69360 39.65584 0.00000 28.23359 6.92765 MINI EXTERN> -10.05945 4.93865 0.00000 0.00000 0.00000 MINI CONSTR> 164.88492 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 242.25607 0.01873 0.08742 0.00008 MINI INTERN> 7.71578 39.57718 0.00000 28.22344 6.92065 MINI EXTERN> -10.05446 4.97085 0.00000 0.00000 0.00000 MINI CONSTR> 164.90263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 242.24692 0.00916 0.06875 0.00009 MINI INTERN> 7.70960 39.57293 0.00000 28.21748 6.92032 MINI EXTERN> -10.06684 4.97204 0.00000 0.00000 0.00000 MINI CONSTR> 164.92138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 242.23805 0.00887 0.12145 0.00009 MINI INTERN> 7.72453 39.53913 0.00000 28.20863 6.91727 MINI EXTERN> -10.07384 4.97994 0.00000 0.00000 0.00000 MINI CONSTR> 164.94238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 242.22953 0.00851 0.09260 0.00009 MINI INTERN> 7.71135 39.53644 0.00000 28.20331 6.91738 MINI EXTERN> -10.08731 4.98629 0.00000 0.00000 0.00000 MINI CONSTR> 164.96207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 242.22345 0.00608 0.13682 0.00010 MINI INTERN> 7.72144 39.51141 0.00000 28.19642 6.91524 MINI EXTERN> -10.09309 4.99235 0.00000 0.00000 0.00000 MINI CONSTR> 164.97968 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 242.21757 0.00588 0.16311 0.00010 MINI INTERN> 7.73051 39.50134 0.00000 28.19002 6.91433 MINI EXTERN> -10.10255 4.98663 0.00000 0.00000 0.00000 MINI CONSTR> 164.99728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 242.21168 0.00589 0.14360 0.00010 MINI INTERN> 7.72335 39.48832 0.00000 28.18543 6.91359 MINI EXTERN> -10.10981 4.99727 0.00000 0.00000 0.00000 MINI CONSTR> 165.01353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 242.20602 0.00566 0.15292 0.00011 MINI INTERN> 7.72648 39.47155 0.00000 28.17931 6.91254 MINI EXTERN> -10.11950 5.00344 0.00000 0.00000 0.00000 MINI CONSTR> 165.03220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 242.19889 0.00713 0.04677 0.00005 MINI INTERN> 7.69491 39.50013 0.00000 28.17713 6.91558 MINI EXTERN> -10.13929 4.99941 0.00000 0.00000 0.00000 MINI CONSTR> 165.05102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 242.19739 0.00151 0.18765 0.00011 MINI INTERN> 7.71199 39.45616 0.00000 28.17063 6.91225 MINI EXTERN> -10.13903 5.01935 0.00000 0.00000 0.00000 MINI CONSTR> 165.06603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 242.19066 0.00673 0.05151 0.00005 MINI INTERN> 7.69122 39.48399 0.00000 28.16854 6.91495 MINI EXTERN> -10.15623 5.00618 0.00000 0.00000 0.00000 MINI CONSTR> 165.08200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 242.18732 0.00334 0.03903 0.00005 MINI INTERN> 7.69519 39.46984 0.00000 28.16449 6.91408 MINI EXTERN> -10.16158 5.01051 0.00000 0.00000 0.00000 MINI CONSTR> 165.09480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 242.18377 0.00354 0.07181 0.00005 MINI INTERN> 7.68657 39.47181 0.00000 28.16068 6.91479 MINI EXTERN> -10.17306 5.01068 0.00000 0.00000 0.00000 MINI CONSTR> 165.11230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 242.18092 0.00285 0.05965 0.00006 MINI INTERN> 7.68752 39.46039 0.00000 28.15726 6.91425 MINI EXTERN> -10.17906 5.01591 0.00000 0.00000 0.00000 MINI CONSTR> 165.12465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 242.17810 0.00281 0.05645 0.00006 MINI INTERN> 7.68832 39.45119 0.00000 28.15366 6.91393 MINI EXTERN> -10.18572 5.01865 0.00000 0.00000 0.00000 MINI CONSTR> 165.13807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 242.17604 0.00206 0.08345 0.00006 MINI INTERN> 7.68118 39.45011 0.00000 28.15110 6.91440 MINI EXTERN> -10.19420 5.02223 0.00000 0.00000 0.00000 MINI CONSTR> 165.15121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 242.17410 0.00194 0.10644 0.00006 MINI INTERN> 7.68762 39.44263 0.00000 28.14755 6.91412 MINI EXTERN> -10.20030 5.01914 0.00000 0.00000 0.00000 MINI CONSTR> 165.16334 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 242.17219 0.00192 0.09864 0.00006 MINI INTERN> 7.68873 39.43413 0.00000 28.14498 6.91384 MINI EXTERN> -10.20558 5.02261 0.00000 0.00000 0.00000 MINI CONSTR> 165.17347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 242.16970 0.00249 0.02892 0.00003 MINI INTERN> 7.69876 39.40741 0.00000 28.14147 6.91206 MINI EXTERN> -10.20513 5.03277 0.00000 0.00000 0.00000 MINI CONSTR> 165.18236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 242.16881 0.00088 0.10131 0.00007 MINI INTERN> 7.68553 39.42288 0.00000 28.14026 6.91394 MINI EXTERN> -10.21796 5.02906 0.00000 0.00000 0.00000 MINI CONSTR> 165.19510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 242.16640 0.00241 0.03333 0.00003 MINI INTERN> 7.70058 39.39101 0.00000 28.13637 6.91173 MINI EXTERN> -10.21533 5.03847 0.00000 0.00000 0.00000 MINI CONSTR> 165.20358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 242.16507 0.00133 0.02493 0.00003 MINI INTERN> 7.69723 39.38887 0.00000 28.13472 6.91206 MINI EXTERN> -10.22089 5.04046 0.00000 0.00000 0.00000 MINI CONSTR> 165.21261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 242.16371 0.00136 0.02581 0.00003 MINI INTERN> 7.69776 39.38154 0.00000 28.13254 6.91199 MINI EXTERN> -10.22561 5.04314 0.00000 0.00000 0.00000 MINI CONSTR> 165.22234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 242.16247 0.00124 0.04462 0.00003 MINI INTERN> 7.70293 39.36911 0.00000 28.12987 6.91152 MINI EXTERN> -10.22919 5.04591 0.00000 0.00000 0.00000 MINI CONSTR> 165.23233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 242.16134 0.00114 0.03740 0.00003 MINI INTERN> 7.69913 39.36582 0.00000 28.12846 6.91183 MINI EXTERN> -10.23426 5.04937 0.00000 0.00000 0.00000 MINI CONSTR> 165.24099 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 242.16043 0.00091 0.05032 0.00004 MINI INTERN> 7.70295 39.35698 0.00000 28.12642 6.91159 MINI EXTERN> -10.23736 5.05070 0.00000 0.00000 0.00000 MINI CONSTR> 165.24915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 242.15948 0.00095 0.05872 0.00004 MINI INTERN> 7.69963 39.35128 0.00000 28.12501 6.91178 MINI EXTERN> -10.24220 5.05596 0.00000 0.00000 0.00000 MINI CONSTR> 165.25802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 242.15868 0.00081 0.06241 0.00004 MINI INTERN> 7.69964 39.34572 0.00000 28.12357 6.91185 MINI EXTERN> -10.24568 5.05804 0.00000 0.00000 0.00000 MINI CONSTR> 165.26553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 242.15784 0.00084 0.05540 0.00004 MINI INTERN> 7.70218 39.34095 0.00000 28.12206 6.91192 MINI EXTERN> -10.24906 5.05729 0.00000 0.00000 0.00000 MINI CONSTR> 165.27251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 242.15702 0.00082 0.06037 0.00004 MINI INTERN> 7.70073 39.33464 0.00000 28.12071 6.91206 MINI EXTERN> -10.25355 5.06161 0.00000 0.00000 0.00000 MINI CONSTR> 165.28083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 242.15604 0.00098 0.01956 0.00002 MINI INTERN> 7.69293 39.34320 0.00000 28.12048 6.91328 MINI EXTERN> -10.26145 5.05964 0.00000 0.00000 0.00000 MINI CONSTR> 165.28795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 242.15575 0.00029 0.06731 0.00004 MINI INTERN> 7.70408 39.32700 0.00000 28.11822 6.91240 MINI EXTERN> -10.26065 5.06057 0.00000 0.00000 0.00000 MINI CONSTR> 165.29413 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 242.15476 0.00099 0.02135 0.00002 MINI INTERN> 7.69231 39.33485 0.00000 28.11839 6.91369 MINI EXTERN> -10.26898 5.06312 0.00000 0.00000 0.00000 MINI CONSTR> 165.30139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 242.15458 0.00017 0.06702 0.00005 MINI INTERN> 7.70224 39.31616 0.00000 28.11630 6.91266 MINI EXTERN> -10.26644 5.06680 0.00000 0.00000 0.00000 MINI CONSTR> 165.30688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 242.15354 0.00104 0.02340 0.00002 MINI INTERN> 7.69135 39.32637 0.00000 28.11646 6.91418 MINI EXTERN> -10.27655 5.06683 0.00000 0.00000 0.00000 MINI CONSTR> 165.31491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 242.15306 0.00049 0.01573 0.00002 MINI INTERN> 7.69338 39.32024 0.00000 28.11551 6.91413 MINI EXTERN> -10.27850 5.06833 0.00000 0.00000 0.00000 MINI CONSTR> 165.31997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 242.15258 0.00047 0.03223 0.00002 MINI INTERN> 7.69144 39.31962 0.00000 28.11487 6.91470 MINI EXTERN> -10.28358 5.06880 0.00000 0.00000 0.00000 MINI CONSTR> 165.32674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 242.15214 0.00044 0.03228 0.00002 MINI INTERN> 7.68979 39.31583 0.00000 28.11430 6.91495 MINI EXTERN> -10.28681 5.07180 0.00000 0.00000 0.00000 MINI CONSTR> 165.33228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 242.15168 0.00045 0.02712 0.00002 MINI INTERN> 7.69180 39.31096 0.00000 28.11347 6.91504 MINI EXTERN> -10.28926 5.07227 0.00000 0.00000 0.00000 MINI CONSTR> 165.33740 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 242.15133 0.00035 0.03433 0.00002 MINI INTERN> 7.68994 39.30872 0.00000 28.11305 6.91540 MINI EXTERN> -10.29289 5.07439 0.00000 0.00000 0.00000 MINI CONSTR> 165.34271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 242.15095 0.00038 0.04197 0.00003 MINI INTERN> 7.69178 39.30511 0.00000 28.11230 6.91565 MINI EXTERN> -10.29593 5.07387 0.00000 0.00000 0.00000 MINI CONSTR> 165.34818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 242.15058 0.00037 0.03698 0.00003 MINI INTERN> 7.68998 39.30198 0.00000 28.11196 6.91592 MINI EXTERN> -10.29884 5.07669 0.00000 0.00000 0.00000 MINI CONSTR> 165.35290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 242.15022 0.00036 0.04087 0.00003 MINI INTERN> 7.68817 39.29794 0.00000 28.11156 6.91622 MINI EXTERN> -10.30172 5.07978 0.00000 0.00000 0.00000 MINI CONSTR> 165.35826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 242.14977 0.00044 0.01293 0.00001 MINI INTERN> 7.69399 39.28797 0.00000 28.11053 6.91582 MINI EXTERN> -10.30100 5.08064 0.00000 0.00000 0.00000 MINI CONSTR> 165.36183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 242.14961 0.00017 0.04183 0.00003 MINI INTERN> 7.68879 39.29229 0.00000 28.11075 6.91674 MINI EXTERN> -10.30726 5.08118 0.00000 0.00000 0.00000 MINI CONSTR> 165.36712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 242.14933 0.00028 0.04922 0.00003 MINI INTERN> 7.69250 39.28789 0.00000 28.11005 6.91686 MINI EXTERN> -10.30915 5.07962 0.00000 0.00000 0.00000 MINI CONSTR> 165.37155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 242.14885 0.00048 0.01388 0.00001 MINI INTERN> 7.69394 39.27755 0.00000 28.10941 6.91656 MINI EXTERN> -10.30847 5.08458 0.00000 0.00000 0.00000 MINI CONSTR> 165.37528 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 242.14860 0.00025 0.01145 0.00001 MINI INTERN> 7.69353 39.27568 0.00000 28.10921 6.91686 MINI EXTERN> -10.31091 5.08524 0.00000 0.00000 0.00000 MINI CONSTR> 165.37899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 242.14833 0.00027 0.01814 0.00001 MINI INTERN> 7.69439 39.27055 0.00000 28.10881 6.91700 MINI EXTERN> -10.31263 5.08695 0.00000 0.00000 0.00000 MINI CONSTR> 165.38327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 242.14810 0.00023 0.01062 0.00001 MINI INTERN> 7.69323 39.27013 0.00000 28.10876 6.91738 MINI EXTERN> -10.31542 5.08734 0.00000 0.00000 0.00000 MINI CONSTR> 165.38667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 242.14786 0.00024 0.02172 0.00002 MINI INTERN> 7.69504 39.26437 0.00000 28.10832 6.91747 MINI EXTERN> -10.31679 5.08861 0.00000 0.00000 0.00000 MINI CONSTR> 165.39085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 242.14763 0.00023 0.01712 0.00002 MINI INTERN> 7.69369 39.26254 0.00000 28.10829 6.91780 MINI EXTERN> -10.31912 5.09009 0.00000 0.00000 0.00000 MINI CONSTR> 165.39435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 242.14744 0.00019 0.02385 0.00002 MINI INTERN> 7.69500 39.25891 0.00000 28.10801 6.91797 MINI EXTERN> -10.32069 5.09042 0.00000 0.00000 0.00000 MINI CONSTR> 165.39782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 242.14725 0.00019 0.02643 0.00002 MINI INTERN> 7.69354 39.25600 0.00000 28.10799 6.91824 MINI EXTERN> -10.32258 5.09278 0.00000 0.00000 0.00000 MINI CONSTR> 165.40127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 242.14706 0.00019 0.02637 0.00002 MINI INTERN> 7.69422 39.25329 0.00000 28.10783 6.91847 MINI EXTERN> -10.32421 5.09304 0.00000 0.00000 0.00000 MINI CONSTR> 165.40442 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> 483 242.14691 0.00015 0.00966 0.00002 STPD INTERN> 7.69274 39.25531 0.00000 28.10801 6.91883 STPD EXTERN> -10.32674 5.09265 0.00000 0.00000 0.00000 STPD CONSTR> 165.40611 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 11330 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11330 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 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> 0 242.14691 0.00015 0.00966 0.00000 MINI INTERN> 7.69274 39.25531 0.00000 28.10801 6.91883 MINI EXTERN> -10.32674 5.09265 0.00000 0.00000 0.00000 MINI CONSTR> 165.40611 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> 3 242.14245 0.00447 0.00658 0.02000 CONJ INTERN> 7.68354 39.13778 0.00000 28.10599 6.93276 CONJ EXTERN> -10.42910 5.14056 0.00000 0.00000 0.00000 CONJ CONSTR> 165.57092 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "5400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 4.1424 ( PROT LYS 1 HT2 ) 4.1424 ( PROT LYS 1 N ) 5.1780 ( PROT LYS 1 HT3 ) 4.1424 ( PROT LYS 1 CA ) 5.1780 ( PROT LYS 1 CB ) 4.1424 ( PROT LYS 1 CG ) 4.1424 ( PROT LYS 1 CD ) 4.1424 ( PROT LYS 1 CE ) 4.1424 ( PROT LYS 1 NZ ) 4.1424 ( PROT LYS 1 HZ1 ) 4.1424 ( PROT LYS 1 HZ2 ) 4.1424 ( PROT LYS 1 HZ3 ) 4.1424 ( PROT LYS 1 C ) 5.1780 ( PROT LYS 1 O ) 5.1780 ( PROT MET 2 N ) 5.1780 ( PROT MET 2 H ) 4.1424 ( PROT MET 2 CA ) 5.1780 ( PROT MET 2 CB ) 4.1424 ( PROT MET 2 CG ) 4.1424 ( PROT MET 2 SD ) 4.1424 ( PROT MET 2 CE ) 4.1424 ( PROT MET 2 C ) 5.1780 ( PROT MET 2 O ) 5.1780 ( PROT LYS 3 N ) 5.1780 ( PROT LYS 3 H ) 4.1424 ( PROT LYS 3 CA ) 5.1780 ( PROT LYS 3 CB ) 4.1424 ( PROT LYS 3 CG ) 4.1424 ( PROT LYS 3 CD ) 4.1424 ( PROT LYS 3 CE ) 4.1424 ( PROT LYS 3 NZ ) 4.1424 ( PROT LYS 3 HZ1 ) 4.1424 ( PROT LYS 3 HZ2 ) 4.1424 ( PROT LYS 3 HZ3 ) 4.1424 ( PROT LYS 3 C ) 5.1780 ( PROT LYS 3 O ) 5.1780 ( PROT ALA 4 N ) 5.1780 ( PROT ALA 4 H ) 4.1424 ( PROT ALA 4 CA ) 5.1780 ( PROT ALA 4 CB ) 4.1424 ( PROT ALA 4 C ) 5.1780 ( PROT ALA 4 O ) 5.1780 ( PROT VAL 5 N ) 5.1780 ( PROT VAL 5 H ) 4.1424 ( PROT VAL 5 CA ) 5.1780 ( PROT VAL 5 CB ) 4.1424 ( PROT VAL 5 CG1 ) 4.1424 ( PROT VAL 5 CG2 ) 4.1424 ( PROT VAL 5 C ) 5.1780 ( PROT VAL 5 O ) 5.1780 ( PROT MET 6 N ) 5.1780 ( PROT MET 6 H ) 4.1424 ( PROT MET 6 CA ) 5.1780 ( PROT MET 6 CB ) 4.1424 ( PROT MET 6 CG ) 4.1424 ( PROT MET 6 SD ) 4.1424 ( PROT MET 6 CE ) 4.1424 ( PROT MET 6 C ) 5.1780 ( PROT MET 6 O ) 5.1780 ( PROT ILE 7 N ) 5.1780 ( PROT ILE 7 H ) 4.1424 ( PROT ILE 7 CA ) 5.1780 ( PROT ILE 7 CB ) 4.1424 ( PROT ILE 7 CG2 ) 4.1424 ( PROT ILE 7 CG1 ) 4.1424 ( PROT ILE 7 CD ) 4.1424 ( PROT ILE 7 C ) 5.1780 ( PROT ILE 7 O ) 5.1780 ( PROT GLY 8 N ) 5.1780 ( PROT GLY 8 H ) 4.1424 ( PROT GLY 8 CA ) 5.1780 ( PROT GLY 8 C ) 5.1780 ( PROT GLY 8 O ) 5.1780 ( PROT ALA 9 N ) 5.1780 ( PROT ALA 9 H ) 4.1424 ( PROT ALA 9 CA ) 5.1780 ( PROT ALA 9 CB ) 4.1424 ( PROT ALA 9 C ) 5.1780 ( PROT ALA 9 O ) 5.1780 ( PROT CYS 10 N ) 5.1780 ( PROT CYS 10 H ) 4.1424 ( PROT CYS 10 CA ) 5.1780 ( PROT CYS 10 CB ) 4.1424 ( PROT CYS 10 SG ) 4.1424 ( PROT CYS 10 C ) 5.1780 ( PROT CYS 10 O ) 5.1780 ( PROT PHE 11 N ) 5.1780 ( PROT PHE 11 H ) 4.1424 ( PROT PHE 11 CA ) 5.1780 ( PROT PHE 11 CB ) 4.1424 ( PROT PHE 11 CG ) 4.1424 ( PROT PHE 11 CD1 ) 4.1424 ( PROT PHE 11 CD2 ) 4.1424 ( PROT PHE 11 CE1 ) 4.1424 ( PROT PHE 11 CE2 ) 4.1424 ( PROT PHE 11 CZ ) 4.1424 ( PROT PHE 11 C ) 5.1780 ( PROT PHE 11 O ) 5.1780 ( PROT LEU 12 N ) 5.1780 ( PROT LEU 12 H ) 4.1424 ( PROT LEU 12 CA ) 5.1780 ( PROT LEU 12 CB ) 4.1424 ( PROT LEU 12 CG ) 4.1424 ( PROT LEU 12 CD1 ) 4.1424 ( PROT LEU 12 CD2 ) 4.1424 ( PROT LEU 12 C ) 5.1780 ( PROT LEU 12 O ) 5.1780 ( PROT ILE 13 N ) 5.1780 ( PROT ILE 13 H ) 4.1424 ( PROT ILE 13 CA ) 5.1780 ( PROT ILE 13 CB ) 4.1424 ( PROT ILE 13 CG2 ) 4.1424 ( PROT ILE 13 CG1 ) 4.1424 ( PROT ILE 13 CD ) 4.1424 ( PROT ILE 13 C ) 5.1780 ( PROT ILE 13 O ) 5.1780 ( PROT ASH 14 N ) 5.1780 ( PROT ASH 14 H ) 4.1424 ( PROT ASH 14 CA ) 5.1780 ( PROT ASH 14 CB ) 4.1424 ( PROT ASH 14 CG ) 4.1424 ( PROT ASH 14 OD1 ) 4.1424 ( PROT ASH 14 OD2 ) 4.1424 ( PROT ASH 14 HD2 ) 4.1424 ( PROT ASH 14 C ) 5.1780 ( PROT ASH 14 O ) 5.1780 ( PROT PHE 15 N ) 5.1780 ( PROT PHE 15 H ) 4.1424 ( PROT PHE 15 CA ) 5.1780 ( PROT PHE 15 CB ) 4.1424 ( PROT PHE 15 CG ) 4.1424 ( PROT PHE 15 CD1 ) 4.1424 ( PROT PHE 15 CD2 ) 4.1424 ( PROT PHE 15 CE1 ) 4.1424 ( PROT PHE 15 CE2 ) 4.1424 ( PROT PHE 15 CZ ) 4.1424 ( PROT PHE 15 C ) 5.1780 ( PROT PHE 15 O ) 5.1780 ( PROT MET 16 N ) 5.1780 ( PROT MET 16 H ) 4.1424 ( PROT MET 16 CA ) 5.1780 ( PROT MET 16 CB ) 4.1424 ( PROT MET 16 CG ) 4.1424 ( PROT MET 16 SD ) 4.1424 ( PROT MET 16 CE ) 4.1424 ( PROT MET 16 C ) 5.1780 ( PROT MET 16 O ) 5.1780 ( PROT PHE 17 N ) 5.1780 ( PROT PHE 17 H ) 4.1424 ( PROT PHE 17 CA ) 5.1780 ( PROT PHE 17 CB ) 4.1424 ( PROT PHE 17 CG ) 4.1424 ( PROT PHE 17 CD1 ) 4.1424 ( PROT PHE 17 CD2 ) 4.1424 ( PROT PHE 17 CE1 ) 4.1424 ( PROT PHE 17 CE2 ) 4.1424 ( PROT PHE 17 CZ ) 4.1424 ( PROT PHE 17 C ) 5.1780 ( PROT PHE 17 O ) 5.1780 ( PROT PHE 18 N ) 5.1780 ( PROT PHE 18 H ) 4.1424 ( PROT PHE 18 CA ) 5.1780 ( PROT PHE 18 CB ) 4.1424 ( PROT PHE 18 CG ) 4.1424 ( PROT PHE 18 CD1 ) 4.1424 ( PROT PHE 18 CD2 ) 4.1424 ( PROT PHE 18 CE1 ) 4.1424 ( PROT PHE 18 CE2 ) 4.1424 ( PROT PHE 18 CZ ) 4.1424 ( PROT PHE 18 C ) 5.1780 ( PROT PHE 18 O ) 5.1780 ( PROT GLU 19 N ) 5.1780 ( PROT GLU 19 H ) 4.1424 ( PROT GLU 19 CA ) 5.1780 ( PROT GLU 19 CB ) 4.1424 ( PROT GLU 19 CG ) 4.1424 ( PROT GLU 19 CD ) 4.1424 ( PROT GLU 19 OE1 ) 4.1424 ( PROT GLU 19 OE2 ) 4.1424 ( PROT GLU 19 C ) 5.1780 ( PROT GLU 19 OT1 ) 4.1424 ( PROT GLU 19 OT2 ) 4.1424 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40425 5.29391 -8.69236 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00029 -0.00149 -0.00086 ROTATION MATRIX 1.000000 -0.000101 0.000067 0.000101 1.000000 0.000134 -0.000067 -0.000134 1.000000 AXIS OF ROTATION IS 0.742347 -0.371648 -0.557493 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 23.8192 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.360776 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3608" Parameter: A <- "0.3608" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70796 5.22187 -8.77930 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00689 0.04255 -0.01507 ROTATION MATRIX 0.999793 0.015955 0.012657 -0.015768 0.999767 -0.014757 -0.012889 0.014554 0.999811 AXIS OF ROTATION IS -0.584114 -0.509077 0.632181 ANGLE IS 1.44 CENTER OF ROTATION 8.945286 5.065792 -9.637515 SHIFT IS -0.035209 TOTAL SQUARE DIFF IS 0.6370 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.183099 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3608" RDCMND substituted energy or value "?RMS" to " 0.1831" Parameter: A <- "0.3608 0.1831" 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 0.3608 0.1831 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 " 165.57" Parameter: H <- "165.57" 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 76.57153 165.57092 2.91257 ENER INTERN> 7.68354 39.13778 0.00000 28.10599 6.93276 ENER EXTERN> -10.42910 5.14056 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 " 76.57" Parameter: B <- "76.57" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 5.14" Parameter: C <- "5.14" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -10.43" Parameter: C <- " -5.29" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -5.29" 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 " 39.14" Parameter: D <- " 46.82" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 28.11" Parameter: D <- " 74.93" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.93" Parameter: D <- " 81.86" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 81.86" 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= 76.57 GRMS= 2.91 ELEC= 5.14 VDW= -10.43 RDTITL> *EXTERNAL= -5.29 INTERNAL= 81.86 USER= 0.00 HARM= 165.57 RDTITL> *BOND= 7.68 ANGL= 39.14 DIHE= 28.11 IMPR= 6.93 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11330 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11332 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 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> 0 193.78718 -117.21565 1.15767 0.02000 MINI INTERN> 7.68354 39.13778 0.00000 28.10599 6.93276 MINI EXTERN> -10.42910 5.14056 0.00000 0.00000 0.00000 MINI CONSTR> 117.21565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 188.31088 5.47630 1.39157 0.00360 MINI INTERN> 7.53005 36.89039 0.00000 29.88172 6.81518 MINI EXTERN> -24.37958 6.17718 0.00000 0.00000 0.00000 MINI CONSTR> 125.39594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11322 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 187.06458 1.24630 1.73058 0.00156 MINI INTERN> 7.66095 37.63227 0.00000 30.10122 6.82527 MINI EXTERN> -28.34646 6.61298 0.00000 0.00000 0.00000 MINI CONSTR> 126.57835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 186.07719 0.98740 0.60590 0.00067 MINI INTERN> 7.03289 37.52376 0.00000 30.22663 6.79586 MINI EXTERN> -29.20326 6.70833 0.00000 0.00000 0.00000 MINI CONSTR> 126.99298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11321 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 185.48501 0.59217 0.94019 0.00070 MINI INTERN> 7.38336 37.06646 0.00000 30.23160 6.77188 MINI EXTERN> -30.08605 6.79288 0.00000 0.00000 0.00000 MINI CONSTR> 127.32488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 184.97699 0.50802 0.79499 0.00072 MINI INTERN> 7.28066 36.90164 0.00000 30.26069 6.73268 MINI EXTERN> -30.52076 6.79357 0.00000 0.00000 0.00000 MINI CONSTR> 127.52850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11319 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 184.57971 0.39729 1.14636 0.00075 MINI INTERN> 7.63997 36.54273 0.00000 30.23442 6.72330 MINI EXTERN> -31.12052 6.85357 0.00000 0.00000 0.00000 MINI CONSTR> 127.70624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 184.15687 0.42284 1.21349 0.00078 MINI INTERN> 7.70341 36.39586 0.00000 30.20921 6.71082 MINI EXTERN> -31.53477 6.81873 0.00000 0.00000 0.00000 MINI CONSTR> 127.85362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11319 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 183.77010 0.38677 1.30009 0.00080 MINI INTERN> 7.62367 36.30464 0.00000 30.18406 6.69909 MINI EXTERN> -31.85679 6.84014 0.00000 0.00000 0.00000 MINI CONSTR> 127.97529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 183.40897 0.36113 1.22150 0.00083 MINI INTERN> 7.56279 36.20674 0.00000 30.17124 6.67392 MINI EXTERN> -32.08351 6.82156 0.00000 0.00000 0.00000 MINI CONSTR> 128.05624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11316 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 183.05027 0.35871 1.26369 0.00087 MINI INTERN> 7.48008 36.10803 0.00000 30.14485 6.65471 MINI EXTERN> -32.32005 6.84451 0.00000 0.00000 0.00000 MINI CONSTR> 128.13813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 182.61356 0.43670 0.40457 0.00037 MINI INTERN> 6.52076 36.36050 0.00000 30.26564 6.53656 MINI EXTERN> -32.02501 6.78956 0.00000 0.00000 0.00000 MINI CONSTR> 128.16555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11315 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 182.49423 0.11933 1.37511 0.00093 MINI INTERN> 7.62953 35.83180 0.00000 30.07537 6.62382 MINI EXTERN> -32.74795 6.83822 0.00000 0.00000 0.00000 MINI CONSTR> 128.24345 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 182.04517 0.44906 0.43763 0.00040 MINI INTERN> 6.43001 36.17852 0.00000 30.21494 6.49211 MINI EXTERN> -32.33271 6.80408 0.00000 0.00000 0.00000 MINI CONSTR> 128.25823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11312 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 181.82351 0.22166 0.32882 0.00042 MINI INTERN> 6.53480 36.04240 0.00000 30.16704 6.49099 MINI EXTERN> -32.51870 6.81347 0.00000 0.00000 0.00000 MINI CONSTR> 128.29351 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 181.58244 0.24107 0.58962 0.00043 MINI INTERN> 6.28117 36.06562 0.00000 30.17248 6.44491 MINI EXTERN> -32.51932 6.81227 0.00000 0.00000 0.00000 MINI CONSTR> 128.32530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11310 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 181.36551 0.21693 0.40998 0.00045 MINI INTERN> 6.40792 35.92119 0.00000 30.11626 6.44715 MINI EXTERN> -32.70296 6.81792 0.00000 0.00000 0.00000 MINI CONSTR> 128.35804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 181.17608 0.18943 0.51589 0.00046 MINI INTERN> 6.29938 35.89018 0.00000 30.09915 6.42306 MINI EXTERN> -32.75132 6.83020 0.00000 0.00000 0.00000 MINI CONSTR> 128.38544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11309 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 181.02678 0.14930 0.70383 0.00048 MINI INTERN> 6.17692 35.89453 0.00000 30.09085 6.39539 MINI EXTERN> -32.75837 6.81989 0.00000 0.00000 0.00000 MINI CONSTR> 128.40757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 180.85765 0.16913 0.75860 0.00050 MINI INTERN> 6.13725 35.83488 0.00000 30.06139 6.38033 MINI EXTERN> -32.83275 6.84034 0.00000 0.00000 0.00000 MINI CONSTR> 128.43621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11309 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 180.72019 0.13746 0.85997 0.00052 MINI INTERN> 6.13594 35.79841 0.00000 30.03385 6.36451 MINI EXTERN> -32.88376 6.81102 0.00000 0.00000 0.00000 MINI CONSTR> 128.46022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 180.58515 0.13504 0.79035 0.00054 MINI INTERN> 6.10694 35.74475 0.00000 30.00683 6.35604 MINI EXTERN> -32.94450 6.83085 0.00000 0.00000 0.00000 MINI CONSTR> 128.48426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11310 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 180.40081 0.18434 0.24166 0.00023 MINI INTERN> 6.57473 35.43293 0.00000 29.88764 6.40492 MINI EXTERN> -33.29483 6.86991 0.00000 0.00000 0.00000 MINI CONSTR> 128.52551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 180.34521 0.05560 0.87881 0.00058 MINI INTERN> 6.11522 35.64790 0.00000 29.94658 6.33603 MINI EXTERN> -33.05942 6.82288 0.00000 0.00000 0.00000 MINI CONSTR> 128.53603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11310 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 180.17049 0.17472 0.28136 0.00025 MINI INTERN> 6.62581 35.30658 0.00000 29.81869 6.39407 MINI EXTERN> -33.43620 6.88165 0.00000 0.00000 0.00000 MINI CONSTR> 128.57990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 180.07814 0.09235 0.20820 0.00026 MINI INTERN> 6.53718 35.30570 0.00000 29.80860 6.37811 MINI EXTERN> -33.43330 6.88180 0.00000 0.00000 0.00000 MINI CONSTR> 128.60006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11310 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 179.97517 0.10297 0.19958 0.00027 MINI INTERN> 6.52941 35.26161 0.00000 29.77999 6.36974 MINI EXTERN> -33.47987 6.88583 0.00000 0.00000 0.00000 MINI CONSTR> 128.62847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 179.87837 0.09680 0.20188 0.00028 MINI INTERN> 6.53754 35.21067 0.00000 29.74879 6.36363 MINI EXTERN> -33.53347 6.89273 0.00000 0.00000 0.00000 MINI CONSTR> 128.65848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11310 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 179.80039 0.07798 0.42496 0.00029 MINI INTERN> 6.72299 35.08565 0.00000 29.68919 6.37626 MINI EXTERN> -33.67445 6.90585 0.00000 0.00000 0.00000 MINI CONSTR> 128.69490 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 179.71659 0.08380 0.26671 0.00030 MINI INTERN> 6.60078 35.10530 0.00000 29.68491 6.35709 MINI EXTERN> -33.64605 6.89721 0.00000 0.00000 0.00000 MINI CONSTR> 128.71734 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11310 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 179.65964 0.05695 0.44696 0.00031 MINI INTERN> 6.73575 35.01099 0.00000 29.63860 6.36593 MINI EXTERN> -33.75096 6.91012 0.00000 0.00000 0.00000 MINI CONSTR> 128.74921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 179.59400 0.06564 0.49160 0.00032 MINI INTERN> 6.74143 34.96928 0.00000 29.61178 6.36182 MINI EXTERN> -33.79354 6.92326 0.00000 0.00000 0.00000 MINI CONSTR> 128.77997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11310 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 179.53693 0.05707 0.49019 0.00033 MINI INTERN> 6.74115 34.95104 0.00000 29.59249 6.35453 MINI EXTERN> -33.81191 6.90509 0.00000 0.00000 0.00000 MINI CONSTR> 128.80455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 179.46752 0.06941 0.15926 0.00014 MINI INTERN> 6.43387 35.04788 0.00000 29.62235 6.31902 MINI EXTERN> -33.68690 6.91135 0.00000 0.00000 0.00000 MINI CONSTR> 128.81997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11310 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 179.44086 0.02666 0.52972 0.00036 MINI INTERN> 6.78052 34.87460 0.00000 29.54523 6.35053 MINI EXTERN> -33.88764 6.91982 0.00000 0.00000 0.00000 MINI CONSTR> 128.85779 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 179.39673 0.04413 0.58893 0.00037 MINI INTERN> 6.70953 34.86428 0.00000 29.53416 6.34186 MINI EXTERN> -33.89120 6.95241 0.00000 0.00000 0.00000 MINI CONSTR> 128.88567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11309 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 179.32581 0.07092 0.17881 0.00016 MINI INTERN> 6.39696 34.98328 0.00000 29.56867 6.30201 MINI EXTERN> -33.74444 6.91979 0.00000 0.00000 0.00000 MINI CONSTR> 128.89953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 179.28926 0.03654 0.13193 0.00017 MINI INTERN> 6.43805 34.94168 0.00000 29.54516 6.30377 MINI EXTERN> -33.78834 6.92515 0.00000 0.00000 0.00000 MINI CONSTR> 128.92380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11309 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 179.24975 0.03952 0.13633 0.00017 MINI INTERN> 6.42524 34.92356 0.00000 29.52884 6.29835 MINI EXTERN> -33.80369 6.92673 0.00000 0.00000 0.00000 MINI CONSTR> 128.95071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 179.21536 0.03438 0.25362 0.00018 MINI INTERN> 6.33887 34.93956 0.00000 29.52538 6.28431 MINI EXTERN> -33.77831 6.92880 0.00000 0.00000 0.00000 MINI CONSTR> 128.97674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11308 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 179.18024 0.03513 0.16112 0.00019 MINI INTERN> 6.39841 34.89069 0.00000 29.49870 6.28807 MINI EXTERN> -33.83024 6.93124 0.00000 0.00000 0.00000 MINI CONSTR> 129.00336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 179.15043 0.02981 0.21772 0.00019 MINI INTERN> 6.35657 34.88619 0.00000 29.48897 6.28040 MINI EXTERN> -33.82920 6.93826 0.00000 0.00000 0.00000 MINI CONSTR> 129.02924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11308 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 179.12733 0.02310 0.28621 0.00020 MINI INTERN> 6.31666 34.88993 0.00000 29.48228 6.27223 MINI EXTERN> -33.82111 6.93588 0.00000 0.00000 0.00000 MINI CONSTR> 129.05144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 179.10036 0.02696 0.31242 0.00021 MINI INTERN> 6.30599 34.87167 0.00000 29.46803 6.26791 MINI EXTERN> -33.83433 6.94278 0.00000 0.00000 0.00000 MINI CONSTR> 129.07831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11308 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 179.07825 0.02211 0.35559 0.00021 MINI INTERN> 6.30772 34.85938 0.00000 29.45471 6.26357 MINI EXTERN> -33.84440 6.93472 0.00000 0.00000 0.00000 MINI CONSTR> 129.10255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 179.05662 0.02163 0.32579 0.00022 MINI INTERN> 6.29911 34.84455 0.00000 29.44316 6.26150 MINI EXTERN> -33.85861 6.94275 0.00000 0.00000 0.00000 MINI CONSTR> 129.12415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11307 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 179.02628 0.03034 0.09920 0.00010 MINI INTERN> 6.46427 34.74722 0.00000 29.39917 6.27984 MINI EXTERN> -33.97037 6.95240 0.00000 0.00000 0.00000 MINI CONSTR> 129.15374 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 179.01783 0.00845 0.35274 0.00024 MINI INTERN> 6.29944 34.81387 0.00000 29.41799 6.25587 MINI EXTERN> -33.88462 6.94453 0.00000 0.00000 0.00000 MINI CONSTR> 129.17074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11307 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 178.98874 0.02908 0.11648 0.00010 MINI INTERN> 6.47943 34.70925 0.00000 29.37140 6.27711 MINI EXTERN> -34.00720 6.95787 0.00000 0.00000 0.00000 MINI CONSTR> 129.20087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 178.97372 0.01503 0.08385 0.00011 MINI INTERN> 6.45198 34.70799 0.00000 29.36626 6.27203 MINI EXTERN> -34.00318 6.95977 0.00000 0.00000 0.00000 MINI CONSTR> 129.21888 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11307 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 178.95679 0.01693 0.08135 0.00011 MINI INTERN> 6.45105 34.69331 0.00000 29.35432 6.26976 MINI EXTERN> -34.01627 6.96220 0.00000 0.00000 0.00000 MINI CONSTR> 129.24242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 178.94098 0.01581 0.15865 0.00011 MINI INTERN> 6.49304 34.65991 0.00000 29.33353 6.27296 MINI EXTERN> -34.05644 6.96736 0.00000 0.00000 0.00000 MINI CONSTR> 129.27061 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11305 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 178.92724 0.01373 0.12166 0.00012 MINI INTERN> 6.47639 34.65584 0.00000 29.32713 6.26861 MINI EXTERN> -34.05545 6.96539 0.00000 0.00000 0.00000 MINI CONSTR> 129.28935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 178.91686 0.01038 0.17820 0.00012 MINI INTERN> 6.50557 34.63128 0.00000 29.31221 6.27071 MINI EXTERN> -34.08357 6.97003 0.00000 0.00000 0.00000 MINI CONSTR> 129.31063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11305 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 178.90483 0.01203 0.18801 0.00013 MINI INTERN> 6.49569 34.62111 0.00000 29.30332 6.26857 MINI EXTERN> -34.09288 6.97696 0.00000 0.00000 0.00000 MINI CONSTR> 129.33206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 178.89521 0.00962 0.21727 0.00013 MINI INTERN> 6.51378 34.60780 0.00000 29.29225 6.26772 MINI EXTERN> -34.10706 6.96936 0.00000 0.00000 0.00000 MINI CONSTR> 129.35136 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11305 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 178.88543 0.00977 0.19771 0.00014 MINI INTERN> 6.51045 34.59467 0.00000 29.28415 6.26678 MINI EXTERN> -34.11749 6.97790 0.00000 0.00000 0.00000 MINI CONSTR> 129.36896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 178.87553 0.00990 0.20575 0.00014 MINI INTERN> 6.50584 34.58612 0.00000 29.27564 6.26500 MINI EXTERN> -34.12695 6.98053 0.00000 0.00000 0.00000 MINI CONSTR> 129.38936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 178.86281 0.01272 0.06193 0.00006 MINI INTERN> 6.43052 34.60159 0.00000 29.28099 6.25375 MINI EXTERN> -34.09085 6.98280 0.00000 0.00000 0.00000 MINI CONSTR> 129.40400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 178.85890 0.00391 0.22966 0.00015 MINI INTERN> 6.49272 34.56948 0.00000 29.26084 6.26165 MINI EXTERN> -34.14300 6.99027 0.00000 0.00000 0.00000 MINI CONSTR> 129.42695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 178.84687 0.01203 0.07494 0.00007 MINI INTERN> 6.42239 34.58336 0.00000 29.26697 6.24992 MINI EXTERN> -34.10318 6.98801 0.00000 0.00000 0.00000 MINI CONSTR> 129.43939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 178.84040 0.00647 0.05478 0.00007 MINI INTERN> 6.43098 34.57256 0.00000 29.25905 6.25023 MINI EXTERN> -34.11677 6.98974 0.00000 0.00000 0.00000 MINI CONSTR> 129.45461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 178.83308 0.00732 0.05284 0.00007 MINI INTERN> 6.43111 34.56211 0.00000 29.25143 6.24904 MINI EXTERN> -34.12584 6.99258 0.00000 0.00000 0.00000 MINI CONSTR> 129.47265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 178.82632 0.00676 0.05681 0.00007 MINI INTERN> 6.42871 34.55287 0.00000 29.24475 6.24735 MINI EXTERN> -34.13217 6.99482 0.00000 0.00000 0.00000 MINI CONSTR> 129.48999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 178.82057 0.00575 0.10779 0.00008 MINI INTERN> 6.41736 34.54426 0.00000 29.23980 6.24413 MINI EXTERN> -34.13105 6.99907 0.00000 0.00000 0.00000 MINI CONSTR> 129.50700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 178.81464 0.00593 0.07621 0.00008 MINI INTERN> 6.42733 34.53489 0.00000 29.23216 6.24449 MINI EXTERN> -34.14488 6.99824 0.00000 0.00000 0.00000 MINI CONSTR> 129.52242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 178.81041 0.00423 0.11721 0.00008 MINI INTERN> 6.41849 34.52807 0.00000 29.22817 6.24194 MINI EXTERN> -34.14437 7.00157 0.00000 0.00000 0.00000 MINI CONSTR> 129.53653 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 178.80597 0.00444 0.14119 0.00009 MINI INTERN> 6.41335 34.51813 0.00000 29.22235 6.24126 MINI EXTERN> -34.15201 7.01096 0.00000 0.00000 0.00000 MINI CONSTR> 129.55194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 178.80155 0.00442 0.12548 0.00009 MINI INTERN> 6.41392 34.51268 0.00000 29.21785 6.23992 MINI EXTERN> -34.15628 7.00891 0.00000 0.00000 0.00000 MINI CONSTR> 129.56455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 178.79742 0.00413 0.14202 0.00009 MINI INTERN> 6.42686 34.50415 0.00000 29.21118 6.23972 MINI EXTERN> -34.16711 7.00370 0.00000 0.00000 0.00000 MINI CONSTR> 129.57893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 178.79219 0.00523 0.04247 0.00004 MINI INTERN> 6.43193 34.49784 0.00000 29.20429 6.24189 MINI EXTERN> -34.18633 7.01020 0.00000 0.00000 0.00000 MINI CONSTR> 129.59238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 178.79008 0.00211 0.14431 0.00010 MINI INTERN> 6.41179 34.49011 0.00000 29.20311 6.23722 MINI EXTERN> -34.17400 7.01708 0.00000 0.00000 0.00000 MINI CONSTR> 129.60477 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 178.78701 0.00308 0.17069 0.00010 MINI INTERN> 6.43025 34.48356 0.00000 29.19685 6.23753 MINI EXTERN> -34.18671 7.00772 0.00000 0.00000 0.00000 MINI CONSTR> 129.61781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 178.78143 0.00558 0.04688 0.00004 MINI INTERN> 6.43240 34.47753 0.00000 29.19008 6.23988 MINI EXTERN> -34.20637 7.01649 0.00000 0.00000 0.00000 MINI CONSTR> 129.63142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11303 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 178.77852 0.00291 0.03867 0.00005 MINI INTERN> 6.43017 34.47128 0.00000 29.18658 6.23894 MINI EXTERN> -34.20985 7.01926 0.00000 0.00000 0.00000 MINI CONSTR> 129.64213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 178.77558 0.00294 0.03975 0.00005 MINI INTERN> 6.43065 34.46506 0.00000 29.18244 6.23841 MINI EXTERN> -34.21604 7.02126 0.00000 0.00000 0.00000 MINI CONSTR> 129.65382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11304 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 178.77269 0.00289 0.06520 0.00005 MINI INTERN> 6.43511 34.45896 0.00000 29.17728 6.23851 MINI EXTERN> -34.22642 7.02218 0.00000 0.00000 0.00000 MINI CONSTR> 129.66707 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 178.76997 0.00272 0.05336 0.00005 MINI INTERN> 6.43105 34.45269 0.00000 29.17409 6.23756 MINI EXTERN> -34.22953 7.02639 0.00000 0.00000 0.00000 MINI CONSTR> 129.67773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11304 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 178.76755 0.00242 0.06088 0.00005 MINI INTERN> 6.43311 34.44671 0.00000 29.17011 6.23732 MINI EXTERN> -34.23645 7.02804 0.00000 0.00000 0.00000 MINI CONSTR> 129.68871 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 178.76539 0.00216 0.08019 0.00005 MINI INTERN> 6.43781 34.44136 0.00000 29.16603 6.23724 MINI EXTERN> -34.24433 7.02764 0.00000 0.00000 0.00000 MINI CONSTR> 129.69963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11304 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 178.76320 0.00219 0.09000 0.00006 MINI INTERN> 6.43324 34.43525 0.00000 29.16277 6.23677 MINI EXTERN> -34.24935 7.03413 0.00000 0.00000 0.00000 MINI CONSTR> 129.71040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 178.76111 0.00209 0.09059 0.00006 MINI INTERN> 6.43697 34.42943 0.00000 29.15909 6.23663 MINI EXTERN> -34.25600 7.03460 0.00000 0.00000 0.00000 MINI CONSTR> 129.72039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11304 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 178.75903 0.00209 0.08831 0.00006 MINI INTERN> 6.43959 34.42466 0.00000 29.15612 6.23597 MINI EXTERN> -34.26030 7.03319 0.00000 0.00000 0.00000 MINI CONSTR> 129.72980 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 178.75710 0.00192 0.09552 0.00006 MINI INTERN> 6.43155 34.41877 0.00000 29.15363 6.23530 MINI EXTERN> -34.26348 7.04165 0.00000 0.00000 0.00000 MINI CONSTR> 129.73969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 178.75464 0.00246 0.02983 0.00003 MINI INTERN> 6.42571 34.41452 0.00000 29.15288 6.23298 MINI EXTERN> -34.25881 7.04046 0.00000 0.00000 0.00000 MINI CONSTR> 129.74690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 178.75362 0.00102 0.10409 0.00007 MINI INTERN> 6.44254 34.40892 0.00000 29.14709 6.23492 MINI EXTERN> -34.27584 7.03799 0.00000 0.00000 0.00000 MINI CONSTR> 129.75800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 178.75208 0.00155 0.11742 0.00007 MINI INTERN> 6.43046 34.40312 0.00000 29.14524 6.23421 MINI EXTERN> -34.27796 7.04977 0.00000 0.00000 0.00000 MINI CONSTR> 129.76724 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 178.75037 0.00171 0.11062 0.00007 MINI INTERN> 6.43920 34.39747 0.00000 29.14137 6.23472 MINI EXTERN> -34.28696 7.04820 0.00000 0.00000 0.00000 MINI CONSTR> 129.77638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11301 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 178.74766 0.00270 0.03537 0.00003 MINI INTERN> 6.42346 34.39470 0.00000 29.14245 6.23105 MINI EXTERN> -34.27622 7.04899 0.00000 0.00000 0.00000 MINI CONSTR> 129.78323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 178.74621 0.00146 0.02664 0.00003 MINI INTERN> 6.42473 34.39050 0.00000 29.13990 6.23113 MINI EXTERN> -34.28213 7.05102 0.00000 0.00000 0.00000 MINI CONSTR> 129.79104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 178.74465 0.00155 0.02806 0.00003 MINI INTERN> 6.42395 34.38578 0.00000 29.13761 6.23067 MINI EXTERN> -34.28617 7.05322 0.00000 0.00000 0.00000 MINI CONSTR> 129.79960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 178.74314 0.00151 0.04663 0.00004 MINI INTERN> 6.42187 34.38055 0.00000 29.13561 6.22971 MINI EXTERN> -34.28836 7.05525 0.00000 0.00000 0.00000 MINI CONSTR> 129.80852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 178.74171 0.00143 0.03778 0.00004 MINI INTERN> 6.42153 34.37618 0.00000 29.13328 6.22974 MINI EXTERN> -34.29396 7.05853 0.00000 0.00000 0.00000 MINI CONSTR> 129.81642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 178.74042 0.00130 0.04289 0.00004 MINI INTERN> 6.42029 34.37211 0.00000 29.13146 6.22922 MINI EXTERN> -34.29720 7.06050 0.00000 0.00000 0.00000 MINI CONSTR> 129.82404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 178.73924 0.00118 0.05762 0.00004 MINI INTERN> 6.42022 34.36802 0.00000 29.12972 6.22855 MINI EXTERN> -34.29985 7.06106 0.00000 0.00000 0.00000 MINI CONSTR> 129.83151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 178.73802 0.00122 0.06328 0.00004 MINI INTERN> 6.41673 34.36348 0.00000 29.12795 6.22832 MINI EXTERN> -34.30393 7.06631 0.00000 0.00000 0.00000 MINI CONSTR> 129.83918 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 178.73684 0.00118 0.06379 0.00004 MINI INTERN> 6.41643 34.36003 0.00000 29.12636 6.22779 MINI EXTERN> -34.30691 7.06696 0.00000 0.00000 0.00000 MINI CONSTR> 129.84618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 178.73564 0.00120 0.06914 0.00004 MINI INTERN> 6.41911 34.35558 0.00000 29.12424 6.22756 MINI EXTERN> -34.31155 7.06703 0.00000 0.00000 0.00000 MINI CONSTR> 129.85367 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 178.73449 0.00115 0.06535 0.00005 MINI INTERN> 6.41556 34.35164 0.00000 29.12274 6.22741 MINI EXTERN> -34.31546 7.07208 0.00000 0.00000 0.00000 MINI CONSTR> 129.86052 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 178.73341 0.00108 0.07262 0.00005 MINI INTERN> 6.42211 34.34782 0.00000 29.12039 6.22746 MINI EXTERN> -34.32123 7.06941 0.00000 0.00000 0.00000 MINI CONSTR> 129.86746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 178.73234 0.00107 0.07065 0.00005 MINI INTERN> 6.41911 34.34447 0.00000 29.11923 6.22699 MINI EXTERN> -34.32388 7.07246 0.00000 0.00000 0.00000 MINI CONSTR> 129.87395 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> 500 178.73234 0.00107 0.07065 0.00006 STPD INTERN> 6.41911 34.34447 0.00000 29.11923 6.22699 STPD EXTERN> -34.32388 7.07246 0.00000 0.00000 0.00000 STPD CONSTR> 129.87395 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 11302 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11302 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 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> 0 178.73234 0.00107 0.07065 0.00000 MINI INTERN> 6.41911 34.34447 0.00000 29.11923 6.22699 MINI EXTERN> -34.32388 7.07246 0.00000 0.00000 0.00000 MINI CONSTR> 129.87395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 178.69128 0.04106 0.05428 0.00848 MINI INTERN> 6.38658 34.04653 0.00000 29.02084 6.23283 MINI EXTERN> -34.72530 7.28795 0.00000 0.00000 0.00000 MINI CONSTR> 130.44186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 178.68018 0.01110 0.11873 0.01445 MINI INTERN> 6.39272 34.00756 0.00000 28.97896 6.24087 MINI EXTERN> -34.68900 7.32453 0.00000 0.00000 0.00000 MINI CONSTR> 130.42454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 178.66120 0.01897 0.07868 0.02137 MINI INTERN> 6.35148 33.80354 0.00000 29.01216 6.28154 MINI EXTERN> -34.78634 7.49167 0.00000 0.00000 0.00000 MINI CONSTR> 130.50716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 178.65637 0.00483 0.03736 0.00372 MINI INTERN> 6.34719 33.77227 0.00000 29.03245 6.30031 MINI EXTERN> -35.01881 7.58335 0.00000 0.00000 0.00000 MINI CONSTR> 130.63961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 178.65414 0.00223 0.03841 0.00405 MINI INTERN> 6.33642 33.76604 0.00000 29.08385 6.30688 MINI EXTERN> -35.14979 7.61704 0.00000 0.00000 0.00000 MINI CONSTR> 130.69368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 178.65193 0.00221 0.02623 0.00320 MINI INTERN> 6.33559 33.79133 0.00000 29.10610 6.30070 MINI EXTERN> -35.11359 7.59755 0.00000 0.00000 0.00000 MINI CONSTR> 130.63424 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 178.65120 0.00073 0.01742 0.00149 MINI INTERN> 6.34809 33.80536 0.00000 29.10417 6.30412 MINI EXTERN> -35.05998 7.58318 0.00000 0.00000 0.00000 MINI CONSTR> 130.56626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 178.65074 0.00046 0.01743 0.00171 MINI INTERN> 6.35432 33.82546 0.00000 29.10251 6.30781 MINI EXTERN> -35.03153 7.56803 0.00000 0.00000 0.00000 MINI CONSTR> 130.52413 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 178.65023 0.00051 0.01744 0.00220 MINI INTERN> 6.35596 33.83426 0.00000 29.11210 6.30198 MINI EXTERN> -35.01885 7.55435 0.00000 0.00000 0.00000 MINI CONSTR> 130.51042 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 178.64983 0.00039 0.01326 0.00140 MINI INTERN> 6.35401 33.85148 0.00000 29.12992 6.30205 MINI EXTERN> -35.04748 7.54280 0.00000 0.00000 0.00000 MINI CONSTR> 130.51705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 178.64959 0.00024 0.01105 0.00142 MINI INTERN> 6.35486 33.86159 0.00000 29.12480 6.30509 MINI EXTERN> -35.02782 7.52286 0.00000 0.00000 0.00000 MINI CONSTR> 130.50821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 58 178.64947 0.00013 0.00961 0.02000 CONJ INTERN> 6.35534 33.86205 0.00000 29.12526 6.30227 CONJ EXTERN> -35.01229 7.51570 0.00000 0.00000 0.00000 CONJ CONSTR> 130.50113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "6000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 2.6925 ( PROT LYS 1 HT2 ) 2.6925 ( PROT LYS 1 N ) 3.3657 ( PROT LYS 1 HT3 ) 2.6925 ( PROT LYS 1 CA ) 3.3657 ( PROT LYS 1 CB ) 2.6925 ( PROT LYS 1 CG ) 2.6925 ( PROT LYS 1 CD ) 2.6925 ( PROT LYS 1 CE ) 2.6925 ( PROT LYS 1 NZ ) 2.6925 ( PROT LYS 1 HZ1 ) 2.6925 ( PROT LYS 1 HZ2 ) 2.6925 ( PROT LYS 1 HZ3 ) 2.6925 ( PROT LYS 1 C ) 3.3657 ( PROT LYS 1 O ) 3.3657 ( PROT MET 2 N ) 3.3657 ( PROT MET 2 H ) 2.6925 ( PROT MET 2 CA ) 3.3657 ( PROT MET 2 CB ) 2.6925 ( PROT MET 2 CG ) 2.6925 ( PROT MET 2 SD ) 2.6925 ( PROT MET 2 CE ) 2.6925 ( PROT MET 2 C ) 3.3657 ( PROT MET 2 O ) 3.3657 ( PROT LYS 3 N ) 3.3657 ( PROT LYS 3 H ) 2.6925 ( PROT LYS 3 CA ) 3.3657 ( PROT LYS 3 CB ) 2.6925 ( PROT LYS 3 CG ) 2.6925 ( PROT LYS 3 CD ) 2.6925 ( PROT LYS 3 CE ) 2.6925 ( PROT LYS 3 NZ ) 2.6925 ( PROT LYS 3 HZ1 ) 2.6925 ( PROT LYS 3 HZ2 ) 2.6925 ( PROT LYS 3 HZ3 ) 2.6925 ( PROT LYS 3 C ) 3.3657 ( PROT LYS 3 O ) 3.3657 ( PROT ALA 4 N ) 3.3657 ( PROT ALA 4 H ) 2.6925 ( PROT ALA 4 CA ) 3.3657 ( PROT ALA 4 CB ) 2.6925 ( PROT ALA 4 C ) 3.3657 ( PROT ALA 4 O ) 3.3657 ( PROT VAL 5 N ) 3.3657 ( PROT VAL 5 H ) 2.6925 ( PROT VAL 5 CA ) 3.3657 ( PROT VAL 5 CB ) 2.6925 ( PROT VAL 5 CG1 ) 2.6925 ( PROT VAL 5 CG2 ) 2.6925 ( PROT VAL 5 C ) 3.3657 ( PROT VAL 5 O ) 3.3657 ( PROT MET 6 N ) 3.3657 ( PROT MET 6 H ) 2.6925 ( PROT MET 6 CA ) 3.3657 ( PROT MET 6 CB ) 2.6925 ( PROT MET 6 CG ) 2.6925 ( PROT MET 6 SD ) 2.6925 ( PROT MET 6 CE ) 2.6925 ( PROT MET 6 C ) 3.3657 ( PROT MET 6 O ) 3.3657 ( PROT ILE 7 N ) 3.3657 ( PROT ILE 7 H ) 2.6925 ( PROT ILE 7 CA ) 3.3657 ( PROT ILE 7 CB ) 2.6925 ( PROT ILE 7 CG2 ) 2.6925 ( PROT ILE 7 CG1 ) 2.6925 ( PROT ILE 7 CD ) 2.6925 ( PROT ILE 7 C ) 3.3657 ( PROT ILE 7 O ) 3.3657 ( PROT GLY 8 N ) 3.3657 ( PROT GLY 8 H ) 2.6925 ( PROT GLY 8 CA ) 3.3657 ( PROT GLY 8 C ) 3.3657 ( PROT GLY 8 O ) 3.3657 ( PROT ALA 9 N ) 3.3657 ( PROT ALA 9 H ) 2.6925 ( PROT ALA 9 CA ) 3.3657 ( PROT ALA 9 CB ) 2.6925 ( PROT ALA 9 C ) 3.3657 ( PROT ALA 9 O ) 3.3657 ( PROT CYS 10 N ) 3.3657 ( PROT CYS 10 H ) 2.6925 ( PROT CYS 10 CA ) 3.3657 ( PROT CYS 10 CB ) 2.6925 ( PROT CYS 10 SG ) 2.6925 ( PROT CYS 10 C ) 3.3657 ( PROT CYS 10 O ) 3.3657 ( PROT PHE 11 N ) 3.3657 ( PROT PHE 11 H ) 2.6925 ( PROT PHE 11 CA ) 3.3657 ( PROT PHE 11 CB ) 2.6925 ( PROT PHE 11 CG ) 2.6925 ( PROT PHE 11 CD1 ) 2.6925 ( PROT PHE 11 CD2 ) 2.6925 ( PROT PHE 11 CE1 ) 2.6925 ( PROT PHE 11 CE2 ) 2.6925 ( PROT PHE 11 CZ ) 2.6925 ( PROT PHE 11 C ) 3.3657 ( PROT PHE 11 O ) 3.3657 ( PROT LEU 12 N ) 3.3657 ( PROT LEU 12 H ) 2.6925 ( PROT LEU 12 CA ) 3.3657 ( PROT LEU 12 CB ) 2.6925 ( PROT LEU 12 CG ) 2.6925 ( PROT LEU 12 CD1 ) 2.6925 ( PROT LEU 12 CD2 ) 2.6925 ( PROT LEU 12 C ) 3.3657 ( PROT LEU 12 O ) 3.3657 ( PROT ILE 13 N ) 3.3657 ( PROT ILE 13 H ) 2.6925 ( PROT ILE 13 CA ) 3.3657 ( PROT ILE 13 CB ) 2.6925 ( PROT ILE 13 CG2 ) 2.6925 ( PROT ILE 13 CG1 ) 2.6925 ( PROT ILE 13 CD ) 2.6925 ( PROT ILE 13 C ) 3.3657 ( PROT ILE 13 O ) 3.3657 ( PROT ASH 14 N ) 3.3657 ( PROT ASH 14 H ) 2.6925 ( PROT ASH 14 CA ) 3.3657 ( PROT ASH 14 CB ) 2.6925 ( PROT ASH 14 CG ) 2.6925 ( PROT ASH 14 OD1 ) 2.6925 ( PROT ASH 14 OD2 ) 2.6925 ( PROT ASH 14 HD2 ) 2.6925 ( PROT ASH 14 C ) 3.3657 ( PROT ASH 14 O ) 3.3657 ( PROT PHE 15 N ) 3.3657 ( PROT PHE 15 H ) 2.6925 ( PROT PHE 15 CA ) 3.3657 ( PROT PHE 15 CB ) 2.6925 ( PROT PHE 15 CG ) 2.6925 ( PROT PHE 15 CD1 ) 2.6925 ( PROT PHE 15 CD2 ) 2.6925 ( PROT PHE 15 CE1 ) 2.6925 ( PROT PHE 15 CE2 ) 2.6925 ( PROT PHE 15 CZ ) 2.6925 ( PROT PHE 15 C ) 3.3657 ( PROT PHE 15 O ) 3.3657 ( PROT MET 16 N ) 3.3657 ( PROT MET 16 H ) 2.6925 ( PROT MET 16 CA ) 3.3657 ( PROT MET 16 CB ) 2.6925 ( PROT MET 16 CG ) 2.6925 ( PROT MET 16 SD ) 2.6925 ( PROT MET 16 CE ) 2.6925 ( PROT MET 16 C ) 3.3657 ( PROT MET 16 O ) 3.3657 ( PROT PHE 17 N ) 3.3657 ( PROT PHE 17 H ) 2.6925 ( PROT PHE 17 CA ) 3.3657 ( PROT PHE 17 CB ) 2.6925 ( PROT PHE 17 CG ) 2.6925 ( PROT PHE 17 CD1 ) 2.6925 ( PROT PHE 17 CD2 ) 2.6925 ( PROT PHE 17 CE1 ) 2.6925 ( PROT PHE 17 CE2 ) 2.6925 ( PROT PHE 17 CZ ) 2.6925 ( PROT PHE 17 C ) 3.3657 ( PROT PHE 17 O ) 3.3657 ( PROT PHE 18 N ) 3.3657 ( PROT PHE 18 H ) 2.6925 ( PROT PHE 18 CA ) 3.3657 ( PROT PHE 18 CB ) 2.6925 ( PROT PHE 18 CG ) 2.6925 ( PROT PHE 18 CD1 ) 2.6925 ( PROT PHE 18 CD2 ) 2.6925 ( PROT PHE 18 CE1 ) 2.6925 ( PROT PHE 18 CE2 ) 2.6925 ( PROT PHE 18 CZ ) 2.6925 ( PROT PHE 18 C ) 3.3657 ( PROT PHE 18 O ) 3.3657 ( PROT GLU 19 N ) 3.3657 ( PROT GLU 19 H ) 2.6925 ( PROT GLU 19 CA ) 3.3657 ( PROT GLU 19 CB ) 2.6925 ( PROT GLU 19 CG ) 2.6925 ( PROT GLU 19 CD ) 2.6925 ( PROT GLU 19 OE1 ) 2.6925 ( PROT GLU 19 OE2 ) 2.6925 ( PROT GLU 19 C ) 3.3657 ( PROT GLU 19 OT1 ) 2.6925 ( PROT GLU 19 OT2 ) 2.6925 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40395 5.29407 -8.69215 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00059 -0.00166 -0.00106 ROTATION MATRIX 1.000000 -0.000246 -0.000031 0.000246 1.000000 0.000265 0.000030 -0.000265 1.000000 AXIS OF ROTATION IS 0.730200 0.084128 -0.678034 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 28.8328 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.396933 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3969" Parameter: A <- "0.3969" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70689 5.21976 -8.78013 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00796 0.04466 -0.01424 ROTATION MATRIX 0.999776 0.016833 0.012860 -0.016635 0.999744 -0.015334 -0.013115 0.015116 0.999800 AXIS OF ROTATION IS -0.583636 -0.497875 0.641474 ANGLE IS 1.49 CENTER OF ROTATION 8.884559 5.119220 -9.634417 SHIFT IS -0.036011 TOTAL SQUARE DIFF IS 0.9312 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.221386 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3969" RDCMND substituted energy or value "?RMS" to " 0.2214" Parameter: A <- "0.3969 0.2214" 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 0.3969 0.2214 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 " 130.50" Parameter: H <- "130.50" 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 48.14833 130.50113 2.08744 ENER INTERN> 6.35534 33.86205 0.00000 29.12526 6.30227 ENER EXTERN> -35.01229 7.51570 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 " 48.15" Parameter: B <- "48.15" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 7.52" Parameter: C <- "7.52" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -35.01" Parameter: C <- " -27.49" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -27.49" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 6.36" Parameter: D <- "6.36" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 33.86" Parameter: D <- " 40.22" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 29.13" Parameter: D <- " 69.35" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.30" Parameter: D <- " 75.65" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 75.65" 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= 6000 ENER= 48.15 GRMS= 2.09 ELEC= 7.52 VDW= -35.01 RDTITL> *EXTERNAL= -27.49 INTERNAL= 75.65 USER= 0.00 HARM= 130.50 RDTITL> *BOND= 6.36 ANGL= 33.86 DIHE= 29.13 IMPR= 6.30 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= 48.15 GRMS= 2.09 ELEC= 7.52 VDW= -35.01 RDTITL> *EXTERNAL= -27.49 INTERNAL= 75.65 USER= 0.00 HARM= 130.50 RDTITL> *BOND= 6.36 ANGL= 33.86 DIHE= 29.13 IMPR= 6.30 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= 48.15 GRMS= 2.09 ELEC= 7.52 VDW= -35.01 RDTITL> *EXTERNAL= -27.49 INTERNAL= 75.65 USER= 0.00 HARM= 130.50 RDTITL> *BOND= 6.36 ANGL= 33.86 DIHE= 29.13 IMPR= 6.30 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 6000 0.3969 0.2214 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11302 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11304 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 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> 0 139.76778 -91.61945 0.82056 0.02000 MINI INTERN> 6.35534 33.86205 0.00000 29.12526 6.30227 MINI EXTERN> -35.01229 7.51570 0.00000 0.00000 0.00000 MINI CONSTR> 91.61945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 156.95161 -17.18383 15.06478 0.00864 MINI INTERN> 27.43697 30.79050 0.00000 31.54691 5.54963 MINI EXTERN> -45.78337 10.16671 0.00000 0.00000 0.00000 MINI CONSTR> 97.24426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11292 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 139.65681 17.29480 6.69296 0.00373 MINI INTERN> 8.30573 35.66876 0.00000 30.36214 6.69064 MINI EXTERN> -47.76849 8.30471 0.00000 0.00000 0.00000 MINI CONSTR> 98.09333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 135.21855 4.43826 0.44562 0.00067 MINI INTERN> 6.13980 33.02192 0.00000 30.77250 6.28090 MINI EXTERN> -48.18144 9.00797 0.00000 0.00000 0.00000 MINI CONSTR> 98.17690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11287 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 134.86577 0.35278 1.03178 0.00070 MINI INTERN> 6.43386 32.81564 0.00000 30.72775 6.29709 MINI EXTERN> -48.92576 9.02047 0.00000 0.00000 0.00000 MINI CONSTR> 98.49673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 134.51599 0.34978 1.08636 0.00072 MINI INTERN> 6.50038 32.60926 0.00000 30.72836 6.26978 MINI EXTERN> -49.37836 9.05983 0.00000 0.00000 0.00000 MINI CONSTR> 98.72673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11284 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 134.20448 0.31151 1.18120 0.00075 MINI INTERN> 6.43829 32.54453 0.00000 30.70795 6.25633 MINI EXTERN> -49.72610 9.05499 0.00000 0.00000 0.00000 MINI CONSTR> 98.92849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 133.91647 0.28800 1.11759 0.00078 MINI INTERN> 6.44273 32.38577 0.00000 30.69339 6.23145 MINI EXTERN> -49.99505 9.08081 0.00000 0.00000 0.00000 MINI CONSTR> 99.07737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11282 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 133.61939 0.29709 1.13191 0.00080 MINI INTERN> 6.41191 32.27071 0.00000 30.67289 6.20810 MINI EXTERN> -50.27798 9.10047 0.00000 0.00000 0.00000 MINI CONSTR> 99.23329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 133.25027 0.36912 0.35723 0.00035 MINI INTERN> 5.92921 32.20807 0.00000 30.73696 6.10335 MINI EXTERN> -50.19481 9.12890 0.00000 0.00000 0.00000 MINI CONSTR> 99.33858 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11280 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 133.14630 0.10396 1.24624 0.00087 MINI INTERN> 6.39053 32.09635 0.00000 30.60139 6.18153 MINI EXTERN> -50.71401 9.11597 0.00000 0.00000 0.00000 MINI CONSTR> 99.47454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 132.75966 0.38664 0.37494 0.00037 MINI INTERN> 5.91357 31.98618 0.00000 30.66567 6.06505 MINI EXTERN> -50.59032 9.15867 0.00000 0.00000 0.00000 MINI CONSTR> 99.56084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11280 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 132.56847 0.19119 0.32277 0.00039 MINI INTERN> 5.88703 31.92962 0.00000 30.63031 6.05595 MINI EXTERN> -50.74037 9.16466 0.00000 0.00000 0.00000 MINI CONSTR> 99.64128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 132.36824 0.20023 0.31108 0.00040 MINI INTERN> 5.87358 31.84988 0.00000 30.59171 6.04241 MINI EXTERN> -50.88718 9.17432 0.00000 0.00000 0.00000 MINI CONSTR> 99.72351 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11279 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 132.17795 0.19029 0.56891 0.00042 MINI INTERN> 5.84275 31.73141 0.00000 30.56534 6.00365 MINI EXTERN> -50.96783 9.19822 0.00000 0.00000 0.00000 MINI CONSTR> 99.80440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 131.98954 0.18840 0.40782 0.00043 MINI INTERN> 5.84954 31.67232 0.00000 30.51515 6.00578 MINI EXTERN> -51.12787 9.20020 0.00000 0.00000 0.00000 MINI CONSTR> 99.87442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11278 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 131.84314 0.14640 0.64108 0.00045 MINI INTERN> 5.82451 31.58224 0.00000 30.48797 5.97430 MINI EXTERN> -51.18144 9.21870 0.00000 0.00000 0.00000 MINI CONSTR> 99.93685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 131.69093 0.15221 0.72687 0.00046 MINI INTERN> 5.83839 31.50881 0.00000 30.44678 5.96508 MINI EXTERN> -51.29626 9.22903 0.00000 0.00000 0.00000 MINI CONSTR> 99.99910 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11274 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 131.55404 0.13689 0.75435 0.00048 MINI INTERN> 5.78011 31.47616 0.00000 30.41801 5.94774 MINI EXTERN> -51.35379 9.23389 0.00000 0.00000 0.00000 MINI CONSTR> 100.05192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 131.41652 0.13752 0.71841 0.00050 MINI INTERN> 5.75123 31.43736 0.00000 30.37829 5.93922 MINI EXTERN> -51.42858 9.23650 0.00000 0.00000 0.00000 MINI CONSTR> 100.10249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11274 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 131.28945 0.12707 0.78189 0.00052 MINI INTERN> 5.75786 31.38834 0.00000 30.33916 5.93625 MINI EXTERN> -51.53223 9.24525 0.00000 0.00000 0.00000 MINI CONSTR> 100.15481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 131.12825 0.16120 0.24206 0.00022 MINI INTERN> 5.80308 31.36346 0.00000 30.26813 5.96673 MINI EXTERN> -51.70826 9.23034 0.00000 0.00000 0.00000 MINI CONSTR> 100.20478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11273 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 131.06490 0.06336 0.83825 0.00056 MINI INTERN> 5.67240 31.32923 0.00000 30.27592 5.90760 MINI EXTERN> -51.61449 9.25011 0.00000 0.00000 0.00000 MINI CONSTR> 100.24413 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 130.96724 0.09766 0.96099 0.00058 MINI INTERN> 5.70312 31.28194 0.00000 30.23743 5.90914 MINI EXTERN> -51.71691 9.26139 0.00000 0.00000 0.00000 MINI CONSTR> 100.29113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11273 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 130.78887 0.17837 0.26486 0.00025 MINI INTERN> 5.80127 31.21511 0.00000 30.15258 5.94566 MINI EXTERN> -51.91346 9.24700 0.00000 0.00000 0.00000 MINI CONSTR> 100.34071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 130.69497 0.09390 0.21632 0.00026 MINI INTERN> 5.77908 31.17287 0.00000 30.12526 5.93335 MINI EXTERN> -51.94637 9.25364 0.00000 0.00000 0.00000 MINI CONSTR> 100.37715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11275 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 130.59824 0.09673 0.22298 0.00027 MINI INTERN> 5.78345 31.12748 0.00000 30.08820 5.92785 MINI EXTERN> -52.00568 9.25858 0.00000 0.00000 0.00000 MINI CONSTR> 100.41835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 130.50332 0.09492 0.36352 0.00028 MINI INTERN> 5.82906 31.07881 0.00000 30.03813 5.93173 MINI EXTERN> -52.10052 9.26058 0.00000 0.00000 0.00000 MINI CONSTR> 100.46552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11275 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 130.41367 0.08964 0.28011 0.00029 MINI INTERN> 5.79225 31.04469 0.00000 30.01229 5.91830 MINI EXTERN> -52.12105 9.26592 0.00000 0.00000 0.00000 MINI CONSTR> 100.50126 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 130.33380 0.07988 0.33225 0.00030 MINI INTERN> 5.81907 30.99781 0.00000 29.97347 5.91687 MINI EXTERN> -52.18417 9.27043 0.00000 0.00000 0.00000 MINI CONSTR> 100.54032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11274 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 130.26395 0.06985 0.45149 0.00031 MINI INTERN> 5.85957 30.95410 0.00000 29.93323 5.91830 MINI EXTERN> -52.25379 9.27329 0.00000 0.00000 0.00000 MINI CONSTR> 100.57926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 130.18935 0.07460 0.49372 0.00032 MINI INTERN> 5.84863 30.92528 0.00000 29.90055 5.91114 MINI EXTERN> -52.28808 9.27504 0.00000 0.00000 0.00000 MINI CONSTR> 100.61678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11272 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 130.12288 0.06646 0.51213 0.00033 MINI INTERN> 5.88106 30.87796 0.00000 29.86538 5.91040 MINI EXTERN> -52.34515 9.28077 0.00000 0.00000 0.00000 MINI CONSTR> 100.65247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 130.05581 0.06707 0.48769 0.00034 MINI INTERN> 5.87335 30.84626 0.00000 29.83842 5.90371 MINI EXTERN> -52.37496 9.28368 0.00000 0.00000 0.00000 MINI CONSTR> 100.68535 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11271 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 129.99005 0.06576 0.52307 0.00036 MINI INTERN> 5.85366 30.82676 0.00000 29.80788 5.89856 MINI EXTERN> -52.40890 9.28947 0.00000 0.00000 0.00000 MINI CONSTR> 100.72262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 129.90779 0.08226 0.17110 0.00015 MINI INTERN> 5.70658 30.81641 0.00000 29.81331 5.86455 MINI EXTERN> -52.33813 9.29752 0.00000 0.00000 0.00000 MINI CONSTR> 100.74754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11271 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 129.87640 0.03139 0.55894 0.00038 MINI INTERN> 5.86818 30.76790 0.00000 29.75153 5.89060 MINI EXTERN> -52.47997 9.28929 0.00000 0.00000 0.00000 MINI CONSTR> 100.78887 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 129.82452 0.05187 0.63216 0.00040 MINI INTERN> 5.81458 30.75668 0.00000 29.72901 5.87993 MINI EXTERN> -52.48220 9.30445 0.00000 0.00000 0.00000 MINI CONSTR> 100.82207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11269 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 129.74049 0.08403 0.18378 0.00017 MINI INTERN> 5.69210 30.73492 0.00000 29.73304 5.84910 MINI EXTERN> -52.42123 9.30663 0.00000 0.00000 0.00000 MINI CONSTR> 100.84594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 129.69507 0.04542 0.15019 0.00018 MINI INTERN> 5.69560 30.71500 0.00000 29.70755 5.84845 MINI EXTERN> -52.45445 9.30834 0.00000 0.00000 0.00000 MINI CONSTR> 100.87458 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11269 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 129.64829 0.04679 0.15455 0.00019 MINI INTERN> 5.68780 30.69317 0.00000 29.68413 5.84354 MINI EXTERN> -52.47604 9.31077 0.00000 0.00000 0.00000 MINI CONSTR> 100.90491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 129.60201 0.04627 0.24878 0.00019 MINI INTERN> 5.66730 30.66834 0.00000 29.66335 5.83309 MINI EXTERN> -52.48212 9.31473 0.00000 0.00000 0.00000 MINI CONSTR> 100.93732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11268 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 129.55894 0.04308 0.19840 0.00020 MINI INTERN> 5.67200 30.64707 0.00000 29.63710 5.83303 MINI EXTERN> -52.51515 9.31820 0.00000 0.00000 0.00000 MINI CONSTR> 100.96669 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 129.52020 0.03874 0.22891 0.00021 MINI INTERN> 5.65705 30.63119 0.00000 29.61767 5.82710 MINI EXTERN> -52.52787 9.31991 0.00000 0.00000 0.00000 MINI CONSTR> 100.99515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11268 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 129.48597 0.03423 0.31231 0.00021 MINI INTERN> 5.64261 30.61477 0.00000 29.60014 5.81962 MINI EXTERN> -52.53521 9.32085 0.00000 0.00000 0.00000 MINI CONSTR> 101.02318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 129.45053 0.03544 0.34637 0.00022 MINI INTERN> 5.63850 30.59319 0.00000 29.57627 5.81687 MINI EXTERN> -52.55569 9.32899 0.00000 0.00000 0.00000 MINI CONSTR> 101.05242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11267 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 129.41792 0.03262 0.35383 0.00023 MINI INTERN> 5.62086 30.58387 0.00000 29.56011 5.81132 MINI EXTERN> -52.56501 9.32803 0.00000 0.00000 0.00000 MINI CONSTR> 101.07872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 129.38524 0.03267 0.34058 0.00024 MINI INTERN> 5.62554 30.56714 0.00000 29.54045 5.80940 MINI EXTERN> -52.58772 9.32542 0.00000 0.00000 0.00000 MINI CONSTR> 101.10502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11266 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 129.35503 0.03022 0.37599 0.00025 MINI INTERN> 5.62715 30.54569 0.00000 29.51608 5.80863 MINI EXTERN> -52.61100 9.33532 0.00000 0.00000 0.00000 MINI CONSTR> 101.13316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 129.32522 0.02981 0.35476 0.00026 MINI INTERN> 5.60798 30.53826 0.00000 29.50207 5.80298 MINI EXTERN> -52.61732 9.33308 0.00000 0.00000 0.00000 MINI CONSTR> 101.15818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11266 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 129.28757 0.03765 0.11867 0.00011 MINI INTERN> 5.68590 30.50083 0.00000 29.46590 5.81687 MINI EXTERN> -52.69633 9.32831 0.00000 0.00000 0.00000 MINI CONSTR> 101.18609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 129.27399 0.01358 0.40004 0.00028 MINI INTERN> 5.59023 30.51441 0.00000 29.46877 5.79557 MINI EXTERN> -52.64022 9.33660 0.00000 0.00000 0.00000 MINI CONSTR> 101.20862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11266 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 129.25021 0.02378 0.46217 0.00029 MINI INTERN> 5.63338 30.48661 0.00000 29.44606 5.79667 MINI EXTERN> -52.67582 9.32747 0.00000 0.00000 0.00000 MINI CONSTR> 101.23584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 129.20837 0.04184 0.13101 0.00012 MINI INTERN> 5.68611 30.45352 0.00000 29.40978 5.81024 MINI EXTERN> -52.74827 9.33295 0.00000 0.00000 0.00000 MINI CONSTR> 101.26405 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 129.18662 0.02176 0.10072 0.00013 MINI INTERN> 5.67414 30.44198 0.00000 29.39704 5.80586 MINI EXTERN> -52.75265 9.33487 0.00000 0.00000 0.00000 MINI CONSTR> 101.28539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 129.16237 0.02425 0.10244 0.00013 MINI INTERN> 5.67232 30.42727 0.00000 29.37887 5.80365 MINI EXTERN> -52.76854 9.33714 0.00000 0.00000 0.00000 MINI CONSTR> 101.31165 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 129.14101 0.02137 0.19028 0.00014 MINI INTERN> 5.69100 30.41211 0.00000 29.35622 5.80563 MINI EXTERN> -52.80070 9.33703 0.00000 0.00000 0.00000 MINI CONSTR> 101.33972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 129.11976 0.02124 0.13744 0.00014 MINI INTERN> 5.67981 30.40025 0.00000 29.34422 5.80078 MINI EXTERN> -52.80324 9.33666 0.00000 0.00000 0.00000 MINI CONSTR> 101.36127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 129.10281 0.01695 0.21236 0.00015 MINI INTERN> 5.69180 30.38705 0.00000 29.32499 5.80215 MINI EXTERN> -52.82877 9.33973 0.00000 0.00000 0.00000 MINI CONSTR> 101.38586 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 129.08225 0.02056 0.15084 0.00015 MINI INTERN> 5.67986 30.37589 0.00000 29.31362 5.79700 MINI EXTERN> -52.82942 9.33808 0.00000 0.00000 0.00000 MINI CONSTR> 101.40722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 129.06843 0.01382 0.23059 0.00016 MINI INTERN> 5.69731 30.36285 0.00000 29.29647 5.79807 MINI EXTERN> -52.85276 9.33702 0.00000 0.00000 0.00000 MINI CONSTR> 101.42947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 129.05335 0.01508 0.26099 0.00016 MINI INTERN> 5.69344 30.34988 0.00000 29.28094 5.79751 MINI EXTERN> -52.86737 9.34705 0.00000 0.00000 0.00000 MINI CONSTR> 101.45191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 129.03784 0.01551 0.24412 0.00017 MINI INTERN> 5.70332 30.33727 0.00000 29.26802 5.79557 MINI EXTERN> -52.87842 9.34064 0.00000 0.00000 0.00000 MINI CONSTR> 101.47143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 129.02324 0.01460 0.27092 0.00018 MINI INTERN> 5.67609 30.32942 0.00000 29.25697 5.79216 MINI EXTERN> -52.88009 9.35581 0.00000 0.00000 0.00000 MINI CONSTR> 101.49288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 129.00473 0.01851 0.08289 0.00008 MINI INTERN> 5.65398 30.31999 0.00000 29.25239 5.78386 MINI EXTERN> -52.86344 9.34978 0.00000 0.00000 0.00000 MINI CONSTR> 101.50816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 128.99762 0.00711 0.28152 0.00019 MINI INTERN> 5.71363 30.30304 0.00000 29.22866 5.79139 MINI EXTERN> -52.91243 9.34151 0.00000 0.00000 0.00000 MINI CONSTR> 101.53183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 128.98675 0.01087 0.33553 0.00020 MINI INTERN> 5.67346 30.29735 0.00000 29.22042 5.78744 MINI EXTERN> -52.90843 9.36477 0.00000 0.00000 0.00000 MINI CONSTR> 101.55175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 128.96599 0.02076 0.09356 0.00009 MINI INTERN> 5.64700 30.29126 0.00000 29.21695 5.77829 MINI EXTERN> -52.88832 9.35384 0.00000 0.00000 0.00000 MINI CONSTR> 101.56697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 128.95514 0.01085 0.07333 0.00009 MINI INTERN> 5.65239 30.28260 0.00000 29.20549 5.77810 MINI EXTERN> -52.90101 9.35342 0.00000 0.00000 0.00000 MINI CONSTR> 101.58415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 128.94390 0.01124 0.07627 0.00009 MINI INTERN> 5.64950 30.27408 0.00000 29.19473 5.77629 MINI EXTERN> -52.90812 9.35470 0.00000 0.00000 0.00000 MINI CONSTR> 101.60272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 128.93301 0.01089 0.12616 0.00010 MINI INTERN> 5.63700 30.26584 0.00000 29.18503 5.77261 MINI EXTERN> -52.90832 9.35835 0.00000 0.00000 0.00000 MINI CONSTR> 101.62250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 128.92253 0.01048 0.09874 0.00010 MINI INTERN> 5.64600 30.25651 0.00000 29.17328 5.77252 MINI EXTERN> -52.92163 9.35585 0.00000 0.00000 0.00000 MINI CONSTR> 101.64000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 128.91328 0.00925 0.11601 0.00010 MINI INTERN> 5.63989 30.24998 0.00000 29.16422 5.77034 MINI EXTERN> -52.92573 9.35738 0.00000 0.00000 0.00000 MINI CONSTR> 101.65720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 128.90510 0.00818 0.15364 0.00011 MINI INTERN> 5.62743 30.24409 0.00000 29.15614 5.76775 MINI EXTERN> -52.92712 9.36269 0.00000 0.00000 0.00000 MINI CONSTR> 101.67412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 128.89661 0.00848 0.17443 0.00011 MINI INTERN> 5.63809 30.23516 0.00000 29.14542 5.76655 MINI EXTERN> -52.93609 9.35631 0.00000 0.00000 0.00000 MINI CONSTR> 101.69117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 128.88875 0.00787 0.17861 0.00011 MINI INTERN> 5.62914 30.23060 0.00000 29.13769 5.76457 MINI EXTERN> -52.93933 9.35908 0.00000 0.00000 0.00000 MINI CONSTR> 101.70698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 128.88084 0.00791 0.17056 0.00012 MINI INTERN> 5.61956 30.22424 0.00000 29.12931 5.76377 MINI EXTERN> -52.94603 9.36725 0.00000 0.00000 0.00000 MINI CONSTR> 101.72275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 128.87351 0.00733 0.18624 0.00012 MINI INTERN> 5.63682 30.21558 0.00000 29.11872 5.76318 MINI EXTERN> -52.95669 9.35741 0.00000 0.00000 0.00000 MINI CONSTR> 101.73849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 128.86632 0.00719 0.17878 0.00013 MINI INTERN> 5.62457 30.21194 0.00000 29.11202 5.76109 MINI EXTERN> -52.95846 9.36163 0.00000 0.00000 0.00000 MINI CONSTR> 101.75352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 128.85717 0.00916 0.05821 0.00005 MINI INTERN> 5.65135 30.19631 0.00000 29.09745 5.76601 MINI EXTERN> -52.98805 9.36497 0.00000 0.00000 0.00000 MINI CONSTR> 101.76913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 128.85382 0.00334 0.20288 0.00014 MINI INTERN> 5.61863 30.20152 0.00000 29.09678 5.75816 MINI EXTERN> -52.96735 9.36300 0.00000 0.00000 0.00000 MINI CONSTR> 101.78308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 128.84391 0.00991 0.06506 0.00006 MINI INTERN> 5.65320 30.18238 0.00000 29.08023 5.76441 MINI EXTERN> -53.00272 9.36672 0.00000 0.00000 0.00000 MINI CONSTR> 101.79970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 128.84190 0.00201 0.21049 0.00015 MINI INTERN> 5.60900 30.19071 0.00000 29.08227 5.75549 MINI EXTERN> -52.97578 9.36824 0.00000 0.00000 0.00000 MINI CONSTR> 101.81197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 128.83150 0.01041 0.07127 0.00006 MINI INTERN> 5.65260 30.16974 0.00000 29.06386 5.76261 MINI EXTERN> -53.01599 9.36875 0.00000 0.00000 0.00000 MINI CONSTR> 101.82994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 128.82637 0.00512 0.05023 0.00007 MINI INTERN> 5.64757 30.16516 0.00000 29.05841 5.76080 MINI EXTERN> -53.01671 9.36936 0.00000 0.00000 0.00000 MINI CONSTR> 101.84179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 128.82081 0.00556 0.09301 0.00007 MINI INTERN> 5.65608 30.15754 0.00000 29.04815 5.76143 MINI EXTERN> -53.03035 9.36965 0.00000 0.00000 0.00000 MINI CONSTR> 101.85831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 128.81544 0.00537 0.06549 0.00007 MINI INTERN> 5.64754 30.15294 0.00000 29.04269 5.75957 MINI EXTERN> -53.03100 9.37264 0.00000 0.00000 0.00000 MINI CONSTR> 101.87106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 128.81078 0.00466 0.08192 0.00007 MINI INTERN> 5.65139 30.14665 0.00000 29.03492 5.75938 MINI EXTERN> -53.03921 9.37303 0.00000 0.00000 0.00000 MINI CONSTR> 101.88464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 128.80673 0.00405 0.11018 0.00008 MINI INTERN> 5.65850 30.14069 0.00000 29.02715 5.75930 MINI EXTERN> -53.04779 9.37120 0.00000 0.00000 0.00000 MINI CONSTR> 101.89768 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 128.80259 0.00414 0.12626 0.00008 MINI INTERN> 5.65146 30.13580 0.00000 29.02122 5.75856 MINI EXTERN> -53.05243 9.37734 0.00000 0.00000 0.00000 MINI CONSTR> 101.91065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 128.79870 0.00389 0.12864 0.00008 MINI INTERN> 5.65564 30.12956 0.00000 29.01448 5.75827 MINI EXTERN> -53.05895 9.37720 0.00000 0.00000 0.00000 MINI CONSTR> 101.92250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 128.79476 0.00394 0.12203 0.00008 MINI INTERN> 5.66175 30.12420 0.00000 29.00817 5.75742 MINI EXTERN> -53.06339 9.37294 0.00000 0.00000 0.00000 MINI CONSTR> 101.93367 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 128.79111 0.00366 0.13359 0.00009 MINI INTERN> 5.64942 30.12026 0.00000 29.00360 5.75633 MINI EXTERN> -53.06550 9.38138 0.00000 0.00000 0.00000 MINI CONSTR> 101.94561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 128.78644 0.00467 0.04158 0.00004 MINI INTERN> 5.63969 30.11778 0.00000 29.00115 5.75293 MINI EXTERN> -53.05796 9.37832 0.00000 0.00000 0.00000 MINI CONSTR> 101.95452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11263 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 128.78455 0.00189 0.14267 0.00009 MINI INTERN> 5.66652 30.10862 0.00000 28.99045 5.75577 MINI EXTERN> -53.07827 9.37388 0.00000 0.00000 0.00000 MINI CONSTR> 101.96758 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 128.78169 0.00287 0.16421 0.00010 MINI INTERN> 5.64853 30.10560 0.00000 28.98707 5.75460 MINI EXTERN> -53.07895 9.38608 0.00000 0.00000 0.00000 MINI CONSTR> 101.97875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11263 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 128.77644 0.00524 0.04497 0.00004 MINI INTERN> 5.63706 30.10444 0.00000 28.98515 5.75069 MINI EXTERN> -53.06968 9.38114 0.00000 0.00000 0.00000 MINI CONSTR> 101.98764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 128.77363 0.00281 0.03818 0.00004 MINI INTERN> 5.63900 30.10030 0.00000 28.98011 5.75043 MINI EXTERN> -53.07474 9.38124 0.00000 0.00000 0.00000 MINI CONSTR> 101.99729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11263 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 128.77075 0.00288 0.03871 0.00005 MINI INTERN> 5.63782 30.09633 0.00000 28.97532 5.74974 MINI EXTERN> -53.07827 9.38228 0.00000 0.00000 0.00000 MINI CONSTR> 102.00752 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 128.76792 0.00283 0.03689 0.00005 MINI INTERN> 5.63773 30.09202 0.00000 28.97033 5.74925 MINI EXTERN> -53.08258 9.38336 0.00000 0.00000 0.00000 MINI CONSTR> 102.01781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11263 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 128.76513 0.00278 0.06644 0.00005 MINI INTERN> 5.63234 30.08845 0.00000 28.96605 5.74750 MINI EXTERN> -53.08241 9.38420 0.00000 0.00000 0.00000 MINI CONSTR> 102.02900 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> 500 128.76513 0.00278 0.06644 0.00006 STPD INTERN> 5.63234 30.08845 0.00000 28.96605 5.74750 STPD EXTERN> -53.08241 9.38420 0.00000 0.00000 0.00000 STPD CONSTR> 102.02900 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 11263 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11263 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 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> 0 128.76513 0.00278 0.06644 0.00000 MINI INTERN> 5.63234 30.08845 0.00000 28.96605 5.74750 MINI EXTERN> -53.08241 9.38420 0.00000 0.00000 0.00000 MINI CONSTR> 102.02900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 128.70567 0.05946 0.02718 0.00150 MINI INTERN> 5.62267 29.91115 0.00000 28.76008 5.72505 MINI EXTERN> -53.27989 9.43069 0.00000 0.00000 0.00000 MINI CONSTR> 102.53592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 128.69969 0.00599 0.06775 0.01231 MINI INTERN> 5.62609 29.91329 0.00000 28.78045 5.69778 MINI EXTERN> -53.08787 9.39346 0.00000 0.00000 0.00000 MINI CONSTR> 102.37648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 128.69415 0.00554 0.03920 0.01199 MINI INTERN> 5.62286 29.87775 0.00000 28.80985 5.74774 MINI EXTERN> -53.19366 9.48041 0.00000 0.00000 0.00000 MINI CONSTR> 102.34920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 128.69266 0.00149 0.02224 0.00183 MINI INTERN> 5.63618 29.86225 0.00000 28.85114 5.74360 MINI EXTERN> -53.32985 9.51454 0.00000 0.00000 0.00000 MINI CONSTR> 102.41480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 128.69202 0.00063 0.01973 0.00176 MINI INTERN> 5.63361 29.84543 0.00000 28.86616 5.73862 MINI EXTERN> -53.39765 9.52511 0.00000 0.00000 0.00000 MINI CONSTR> 102.48074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 128.69140 0.00062 0.01838 0.00175 MINI INTERN> 5.62269 29.83116 0.00000 28.87003 5.74668 MINI EXTERN> -53.44682 9.52558 0.00000 0.00000 0.00000 MINI CONSTR> 102.54208 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 128.69103 0.00037 0.01001 0.00108 MINI INTERN> 5.61882 29.81572 0.00000 28.86557 5.74374 MINI EXTERN> -53.43384 9.51841 0.00000 0.00000 0.00000 MINI CONSTR> 102.56261 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> 36 128.69099 0.00004 0.00960 0.02000 CONJ INTERN> 5.61885 29.81179 0.00000 28.86688 5.74289 CONJ EXTERN> -53.43065 9.51784 0.00000 0.00000 0.00000 CONJ CONSTR> 102.56340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "6600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 1.7502 ( PROT LYS 1 HT2 ) 1.7502 ( PROT LYS 1 N ) 2.1877 ( PROT LYS 1 HT3 ) 1.7502 ( PROT LYS 1 CA ) 2.1877 ( PROT LYS 1 CB ) 1.7502 ( PROT LYS 1 CG ) 1.7502 ( PROT LYS 1 CD ) 1.7502 ( PROT LYS 1 CE ) 1.7502 ( PROT LYS 1 NZ ) 1.7502 ( PROT LYS 1 HZ1 ) 1.7502 ( PROT LYS 1 HZ2 ) 1.7502 ( PROT LYS 1 HZ3 ) 1.7502 ( PROT LYS 1 C ) 2.1877 ( PROT LYS 1 O ) 2.1877 ( PROT MET 2 N ) 2.1877 ( PROT MET 2 H ) 1.7502 ( PROT MET 2 CA ) 2.1877 ( PROT MET 2 CB ) 1.7502 ( PROT MET 2 CG ) 1.7502 ( PROT MET 2 SD ) 1.7502 ( PROT MET 2 CE ) 1.7502 ( PROT MET 2 C ) 2.1877 ( PROT MET 2 O ) 2.1877 ( PROT LYS 3 N ) 2.1877 ( PROT LYS 3 H ) 1.7502 ( PROT LYS 3 CA ) 2.1877 ( PROT LYS 3 CB ) 1.7502 ( PROT LYS 3 CG ) 1.7502 ( PROT LYS 3 CD ) 1.7502 ( PROT LYS 3 CE ) 1.7502 ( PROT LYS 3 NZ ) 1.7502 ( PROT LYS 3 HZ1 ) 1.7502 ( PROT LYS 3 HZ2 ) 1.7502 ( PROT LYS 3 HZ3 ) 1.7502 ( PROT LYS 3 C ) 2.1877 ( PROT LYS 3 O ) 2.1877 ( PROT ALA 4 N ) 2.1877 ( PROT ALA 4 H ) 1.7502 ( PROT ALA 4 CA ) 2.1877 ( PROT ALA 4 CB ) 1.7502 ( PROT ALA 4 C ) 2.1877 ( PROT ALA 4 O ) 2.1877 ( PROT VAL 5 N ) 2.1877 ( PROT VAL 5 H ) 1.7502 ( PROT VAL 5 CA ) 2.1877 ( PROT VAL 5 CB ) 1.7502 ( PROT VAL 5 CG1 ) 1.7502 ( PROT VAL 5 CG2 ) 1.7502 ( PROT VAL 5 C ) 2.1877 ( PROT VAL 5 O ) 2.1877 ( PROT MET 6 N ) 2.1877 ( PROT MET 6 H ) 1.7502 ( PROT MET 6 CA ) 2.1877 ( PROT MET 6 CB ) 1.7502 ( PROT MET 6 CG ) 1.7502 ( PROT MET 6 SD ) 1.7502 ( PROT MET 6 CE ) 1.7502 ( PROT MET 6 C ) 2.1877 ( PROT MET 6 O ) 2.1877 ( PROT ILE 7 N ) 2.1877 ( PROT ILE 7 H ) 1.7502 ( PROT ILE 7 CA ) 2.1877 ( PROT ILE 7 CB ) 1.7502 ( PROT ILE 7 CG2 ) 1.7502 ( PROT ILE 7 CG1 ) 1.7502 ( PROT ILE 7 CD ) 1.7502 ( PROT ILE 7 C ) 2.1877 ( PROT ILE 7 O ) 2.1877 ( PROT GLY 8 N ) 2.1877 ( PROT GLY 8 H ) 1.7502 ( PROT GLY 8 CA ) 2.1877 ( PROT GLY 8 C ) 2.1877 ( PROT GLY 8 O ) 2.1877 ( PROT ALA 9 N ) 2.1877 ( PROT ALA 9 H ) 1.7502 ( PROT ALA 9 CA ) 2.1877 ( PROT ALA 9 CB ) 1.7502 ( PROT ALA 9 C ) 2.1877 ( PROT ALA 9 O ) 2.1877 ( PROT CYS 10 N ) 2.1877 ( PROT CYS 10 H ) 1.7502 ( PROT CYS 10 CA ) 2.1877 ( PROT CYS 10 CB ) 1.7502 ( PROT CYS 10 SG ) 1.7502 ( PROT CYS 10 C ) 2.1877 ( PROT CYS 10 O ) 2.1877 ( PROT PHE 11 N ) 2.1877 ( PROT PHE 11 H ) 1.7502 ( PROT PHE 11 CA ) 2.1877 ( PROT PHE 11 CB ) 1.7502 ( PROT PHE 11 CG ) 1.7502 ( PROT PHE 11 CD1 ) 1.7502 ( PROT PHE 11 CD2 ) 1.7502 ( PROT PHE 11 CE1 ) 1.7502 ( PROT PHE 11 CE2 ) 1.7502 ( PROT PHE 11 CZ ) 1.7502 ( PROT PHE 11 C ) 2.1877 ( PROT PHE 11 O ) 2.1877 ( PROT LEU 12 N ) 2.1877 ( PROT LEU 12 H ) 1.7502 ( PROT LEU 12 CA ) 2.1877 ( PROT LEU 12 CB ) 1.7502 ( PROT LEU 12 CG ) 1.7502 ( PROT LEU 12 CD1 ) 1.7502 ( PROT LEU 12 CD2 ) 1.7502 ( PROT LEU 12 C ) 2.1877 ( PROT LEU 12 O ) 2.1877 ( PROT ILE 13 N ) 2.1877 ( PROT ILE 13 H ) 1.7502 ( PROT ILE 13 CA ) 2.1877 ( PROT ILE 13 CB ) 1.7502 ( PROT ILE 13 CG2 ) 1.7502 ( PROT ILE 13 CG1 ) 1.7502 ( PROT ILE 13 CD ) 1.7502 ( PROT ILE 13 C ) 2.1877 ( PROT ILE 13 O ) 2.1877 ( PROT ASH 14 N ) 2.1877 ( PROT ASH 14 H ) 1.7502 ( PROT ASH 14 CA ) 2.1877 ( PROT ASH 14 CB ) 1.7502 ( PROT ASH 14 CG ) 1.7502 ( PROT ASH 14 OD1 ) 1.7502 ( PROT ASH 14 OD2 ) 1.7502 ( PROT ASH 14 HD2 ) 1.7502 ( PROT ASH 14 C ) 2.1877 ( PROT ASH 14 O ) 2.1877 ( PROT PHE 15 N ) 2.1877 ( PROT PHE 15 H ) 1.7502 ( PROT PHE 15 CA ) 2.1877 ( PROT PHE 15 CB ) 1.7502 ( PROT PHE 15 CG ) 1.7502 ( PROT PHE 15 CD1 ) 1.7502 ( PROT PHE 15 CD2 ) 1.7502 ( PROT PHE 15 CE1 ) 1.7502 ( PROT PHE 15 CE2 ) 1.7502 ( PROT PHE 15 CZ ) 1.7502 ( PROT PHE 15 C ) 2.1877 ( PROT PHE 15 O ) 2.1877 ( PROT MET 16 N ) 2.1877 ( PROT MET 16 H ) 1.7502 ( PROT MET 16 CA ) 2.1877 ( PROT MET 16 CB ) 1.7502 ( PROT MET 16 CG ) 1.7502 ( PROT MET 16 SD ) 1.7502 ( PROT MET 16 CE ) 1.7502 ( PROT MET 16 C ) 2.1877 ( PROT MET 16 O ) 2.1877 ( PROT PHE 17 N ) 2.1877 ( PROT PHE 17 H ) 1.7502 ( PROT PHE 17 CA ) 2.1877 ( PROT PHE 17 CB ) 1.7502 ( PROT PHE 17 CG ) 1.7502 ( PROT PHE 17 CD1 ) 1.7502 ( PROT PHE 17 CD2 ) 1.7502 ( PROT PHE 17 CE1 ) 1.7502 ( PROT PHE 17 CE2 ) 1.7502 ( PROT PHE 17 CZ ) 1.7502 ( PROT PHE 17 C ) 2.1877 ( PROT PHE 17 O ) 2.1877 ( PROT PHE 18 N ) 2.1877 ( PROT PHE 18 H ) 1.7502 ( PROT PHE 18 CA ) 2.1877 ( PROT PHE 18 CB ) 1.7502 ( PROT PHE 18 CG ) 1.7502 ( PROT PHE 18 CD1 ) 1.7502 ( PROT PHE 18 CD2 ) 1.7502 ( PROT PHE 18 CE1 ) 1.7502 ( PROT PHE 18 CE2 ) 1.7502 ( PROT PHE 18 CZ ) 1.7502 ( PROT PHE 18 C ) 2.1877 ( PROT PHE 18 O ) 2.1877 ( PROT GLU 19 N ) 2.1877 ( PROT GLU 19 H ) 1.7502 ( PROT GLU 19 CA ) 2.1877 ( PROT GLU 19 CB ) 1.7502 ( PROT GLU 19 CG ) 1.7502 ( PROT GLU 19 CD ) 1.7502 ( PROT GLU 19 OE1 ) 1.7502 ( PROT GLU 19 OE2 ) 1.7502 ( PROT GLU 19 C ) 2.1877 ( PROT GLU 19 OT1 ) 1.7502 ( PROT GLU 19 OT2 ) 1.7502 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40374 5.29393 -8.69194 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00081 -0.00152 -0.00128 ROTATION MATRIX 1.000000 -0.000200 0.000042 0.000200 1.000000 0.000238 -0.000042 -0.000238 1.000000 AXIS OF ROTATION IS 0.758323 -0.133029 -0.638162 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 34.8633 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.436475 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4365" Parameter: A <- "0.4365" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70629 5.22024 -8.78088 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00855 0.04418 -0.01348 ROTATION MATRIX 0.999766 0.017350 0.012892 -0.017146 0.999729 -0.015734 -0.013161 0.015509 0.999793 AXIS OF ROTATION IS -0.585761 -0.488458 0.646756 ANGLE IS 1.53 CENTER OF ROTATION 8.886141 5.153536 -9.601362 SHIFT IS -0.035311 TOTAL SQUARE DIFF IS 1.3231 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.263888 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4365" RDCMND substituted energy or value "?RMS" to " 0.2639" Parameter: A <- "0.4365 0.2639" 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 0.4365 0.2639 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 102.56" Parameter: H <- "102.56" 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 26.12759 102.56340 1.49140 ENER INTERN> 5.61885 29.81179 0.00000 28.86688 5.74289 ENER EXTERN> -53.43065 9.51784 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 " 26.13" Parameter: B <- "26.13" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 9.52" Parameter: C <- "9.52" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -53.43" Parameter: C <- " -43.91" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -43.91" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.62" Parameter: D <- "5.62" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 29.81" Parameter: D <- " 35.43" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 28.87" Parameter: D <- " 64.30" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.74" Parameter: D <- " 70.04" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 70.04" 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= 26.13 GRMS= 1.49 ELEC= 9.52 VDW= -53.43 RDTITL> *EXTERNAL= -43.91 INTERNAL= 70.04 USER= 0.00 HARM= 102.56 RDTITL> *BOND= 5.62 ANGL= 29.81 DIHE= 28.87 IMPR= 5.74 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11263 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11263 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 97.39824 -71.27065 0.57765 0.02000 MINI INTERN> 5.61885 29.81179 0.00000 28.86688 5.74289 MINI EXTERN> -53.43065 9.51784 0.00000 0.00000 0.00000 MINI CONSTR> 71.27065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 116.87104 -19.47280 15.40182 0.00864 MINI INTERN> 27.65357 27.29027 0.00000 30.90323 5.10866 MINI EXTERN> -61.59761 12.21011 0.00000 0.00000 0.00000 MINI CONSTR> 75.30280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11253 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 98.70754 18.16350 6.60086 0.00373 MINI INTERN> 7.67093 31.79980 0.00000 29.83519 6.11006 MINI EXTERN> -62.65114 10.12871 0.00000 0.00000 0.00000 MINI CONSTR> 75.81399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 95.20039 3.50715 2.75647 0.00161 MINI INTERN> 6.61923 28.73632 0.00000 30.30636 5.61777 MINI EXTERN> -63.07960 11.15439 0.00000 0.00000 0.00000 MINI CONSTR> 75.84592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 94.32370 0.87669 0.31657 0.00029 MINI INTERN> 5.56713 29.24341 0.00000 30.14408 5.72551 MINI EXTERN> -63.24341 10.86452 0.00000 0.00000 0.00000 MINI CONSTR> 76.02246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 94.23216 0.09154 1.09821 0.00072 MINI INTERN> 5.72784 29.30330 0.00000 30.02717 5.78119 MINI EXTERN> -63.57590 10.77042 0.00000 0.00000 0.00000 MINI CONSTR> 76.19814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11247 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 94.04832 0.18384 1.11491 0.00075 MINI INTERN> 6.08617 28.92463 0.00000 29.99254 5.76058 MINI EXTERN> -63.92062 10.85921 0.00000 0.00000 0.00000 MINI CONSTR> 76.34582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 93.75672 0.29161 0.34317 0.00032 MINI INTERN> 5.49062 29.01289 0.00000 30.05817 5.66859 MINI EXTERN> -63.81075 10.86153 0.00000 0.00000 0.00000 MINI CONSTR> 76.47566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11244 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 93.60455 0.15217 0.26711 0.00034 MINI INTERN> 5.51166 28.94194 0.00000 30.01637 5.66495 MINI EXTERN> -63.98379 10.86151 0.00000 0.00000 0.00000 MINI CONSTR> 76.59192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 93.43334 0.17121 0.26021 0.00035 MINI INTERN> 5.50317 28.86231 0.00000 29.97582 5.65070 MINI EXTERN> -64.14893 10.86658 0.00000 0.00000 0.00000 MINI CONSTR> 76.72369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11243 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 93.26714 0.16620 0.26046 0.00036 MINI INTERN> 5.48948 28.78646 0.00000 29.93387 5.63574 MINI EXTERN> -64.30036 10.87199 0.00000 0.00000 0.00000 MINI CONSTR> 76.84996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 93.11612 0.15102 0.51978 0.00037 MINI INTERN> 5.43569 28.70098 0.00000 29.90734 5.59956 MINI EXTERN> -64.39233 10.88913 0.00000 0.00000 0.00000 MINI CONSTR> 76.97576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11239 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 92.96635 0.14977 0.33718 0.00039 MINI INTERN> 5.46154 28.63676 0.00000 29.85300 5.60193 MINI EXTERN> -64.55068 10.88748 0.00000 0.00000 0.00000 MINI CONSTR> 77.07631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 92.83895 0.12741 0.46092 0.00040 MINI INTERN> 5.42717 28.57775 0.00000 29.81839 5.58060 MINI EXTERN> -64.63717 10.89651 0.00000 0.00000 0.00000 MINI CONSTR> 77.17570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11237 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 92.73025 0.10870 0.59552 0.00042 MINI INTERN> 5.39867 28.52812 0.00000 29.78737 5.56163 MINI EXTERN> -64.71333 10.90397 0.00000 0.00000 0.00000 MINI CONSTR> 77.26383 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 92.61688 0.11338 0.69853 0.00043 MINI INTERN> 5.41453 28.46413 0.00000 29.73815 5.55116 MINI EXTERN> -64.81161 10.90704 0.00000 0.00000 0.00000 MINI CONSTR> 77.35348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11237 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 92.50429 0.11258 0.63123 0.00045 MINI INTERN> 5.36641 28.43555 0.00000 29.70761 5.53929 MINI EXTERN> -64.88428 10.91094 0.00000 0.00000 0.00000 MINI CONSTR> 77.42877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 92.39530 0.10900 0.74103 0.00046 MINI INTERN> 5.41146 28.34763 0.00000 29.65629 5.52566 MINI EXTERN> -64.97511 10.91337 0.00000 0.00000 0.00000 MINI CONSTR> 77.51599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11235 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 92.29123 0.10406 0.69046 0.00048 MINI INTERN> 5.36243 28.32658 0.00000 29.62241 5.51811 MINI EXTERN> -65.04550 10.92181 0.00000 0.00000 0.00000 MINI CONSTR> 77.58539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 92.14833 0.14290 0.22234 0.00021 MINI INTERN> 5.41500 28.31116 0.00000 29.54345 5.54970 MINI EXTERN> -65.22795 10.89578 0.00000 0.00000 0.00000 MINI CONSTR> 77.66119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11233 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 92.09928 0.04905 0.75292 0.00052 MINI INTERN> 5.35649 28.23064 0.00000 29.53881 5.49999 MINI EXTERN> -65.18687 10.93311 0.00000 0.00000 0.00000 MINI CONSTR> 77.72712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 92.02151 0.07776 0.91223 0.00054 MINI INTERN> 5.46199 28.18462 0.00000 29.47682 5.50310 MINI EXTERN> -65.28806 10.88835 0.00000 0.00000 0.00000 MINI CONSTR> 77.79470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11233 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 91.87016 0.15136 0.25438 0.00023 MINI INTERN> 5.40548 28.19082 0.00000 29.41864 5.52829 MINI EXTERN> -65.43018 10.89762 0.00000 0.00000 0.00000 MINI CONSTR> 77.85949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 91.79130 0.07886 0.19856 0.00024 MINI INTERN> 5.39067 28.14674 0.00000 29.38788 5.51633 MINI EXTERN> -65.46747 10.90437 0.00000 0.00000 0.00000 MINI CONSTR> 77.91277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11230 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 91.70920 0.08209 0.20740 0.00025 MINI INTERN> 5.39147 28.10938 0.00000 29.34748 5.51035 MINI EXTERN> -65.52577 10.90452 0.00000 0.00000 0.00000 MINI CONSTR> 77.97176 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 91.62897 0.08023 0.34147 0.00026 MINI INTERN> 5.41899 28.07836 0.00000 29.29605 5.51174 MINI EXTERN> -65.60876 10.89643 0.00000 0.00000 0.00000 MINI CONSTR> 78.03616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11228 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 91.54949 0.07948 0.25606 0.00027 MINI INTERN> 5.38490 28.04248 0.00000 29.26617 5.49891 MINI EXTERN> -65.63763 10.90595 0.00000 0.00000 0.00000 MINI CONSTR> 78.08871 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 91.47800 0.07149 0.30234 0.00028 MINI INTERN> 5.40178 28.00570 0.00000 29.22410 5.49578 MINI EXTERN> -65.69583 10.90334 0.00000 0.00000 0.00000 MINI CONSTR> 78.14313 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11226 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 91.41453 0.06347 0.42110 0.00029 MINI INTERN> 5.43583 27.97349 0.00000 29.17961 5.49478 MINI EXTERN> -65.75800 10.89220 0.00000 0.00000 0.00000 MINI CONSTR> 78.19662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 91.34904 0.06549 0.46258 0.00030 MINI INTERN> 5.41680 27.94241 0.00000 29.14535 5.48883 MINI EXTERN> -65.79989 10.90780 0.00000 0.00000 0.00000 MINI CONSTR> 78.24774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11226 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 91.28628 0.06276 0.46820 0.00031 MINI INTERN> 5.44936 27.90155 0.00000 29.10474 5.48588 MINI EXTERN> -65.85049 10.89946 0.00000 0.00000 0.00000 MINI CONSTR> 78.29576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 91.22313 0.06315 0.50695 0.00032 MINI INTERN> 5.45950 27.87383 0.00000 29.06690 5.47939 MINI EXTERN> -65.88983 10.88787 0.00000 0.00000 0.00000 MINI CONSTR> 78.34547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11224 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 91.16243 0.06070 0.47686 0.00033 MINI INTERN> 5.44123 27.84253 0.00000 29.03611 5.47376 MINI EXTERN> -65.92326 10.90220 0.00000 0.00000 0.00000 MINI CONSTR> 78.38986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 91.10510 0.05733 0.52981 0.00034 MINI INTERN> 5.44869 27.81967 0.00000 29.00345 5.46314 MINI EXTERN> -65.94498 10.88013 0.00000 0.00000 0.00000 MINI CONSTR> 78.43499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11224 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 91.03165 0.07345 0.16436 0.00015 MINI INTERN> 5.32875 27.80529 0.00000 28.99657 5.44052 MINI EXTERN> -65.91487 10.90416 0.00000 0.00000 0.00000 MINI CONSTR> 78.47123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 91.00101 0.03063 0.55912 0.00037 MINI INTERN> 5.45223 27.75462 0.00000 28.93479 5.45947 MINI EXTERN> -66.02846 10.90650 0.00000 0.00000 0.00000 MINI CONSTR> 78.52187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11222 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 90.95454 0.04647 0.64112 0.00038 MINI INTERN> 5.47562 27.73465 0.00000 28.90435 5.44804 MINI EXTERN> -66.04159 10.87141 0.00000 0.00000 0.00000 MINI CONSTR> 78.56206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 90.90343 0.05112 0.61425 0.00040 MINI INTERN> 5.50911 27.69270 0.00000 28.86364 5.45109 MINI EXTERN> -66.09711 10.87919 0.00000 0.00000 0.00000 MINI CONSTR> 78.60481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11221 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 90.82185 0.08157 0.18927 0.00017 MINI INTERN> 5.29872 27.71730 0.00000 28.87211 5.41765 MINI EXTERN> -66.02471 10.90101 0.00000 0.00000 0.00000 MINI CONSTR> 78.63977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 90.77751 0.04434 0.14837 0.00018 MINI INTERN> 5.31284 27.69407 0.00000 28.84080 5.41674 MINI EXTERN> -66.05978 10.89699 0.00000 0.00000 0.00000 MINI CONSTR> 78.67584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11221 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 90.73059 0.04692 0.15465 0.00019 MINI INTERN> 5.30331 27.67527 0.00000 28.81180 5.41109 MINI EXTERN> -66.08227 10.89608 0.00000 0.00000 0.00000 MINI CONSTR> 78.71532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 90.68392 0.04667 0.24974 0.00019 MINI INTERN> 5.26971 27.66170 0.00000 28.78585 5.40042 MINI EXTERN> -66.09039 10.89891 0.00000 0.00000 0.00000 MINI CONSTR> 78.75773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11221 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 90.63999 0.04393 0.20091 0.00020 MINI INTERN> 5.28772 27.63766 0.00000 28.75369 5.39914 MINI EXTERN> -66.12373 10.89137 0.00000 0.00000 0.00000 MINI CONSTR> 78.79415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 90.59950 0.04049 0.22567 0.00021 MINI INTERN> 5.26963 27.62500 0.00000 28.72855 5.39291 MINI EXTERN> -66.13898 10.89181 0.00000 0.00000 0.00000 MINI CONSTR> 78.83057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 90.55876 0.04074 0.23469 0.00021 MINI INTERN> 5.25946 27.60780 0.00000 28.70112 5.38859 MINI EXTERN> -66.16023 10.89452 0.00000 0.00000 0.00000 MINI CONSTR> 78.86749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 90.52448 0.03427 0.32005 0.00022 MINI INTERN> 5.23943 27.60066 0.00000 28.67902 5.37997 MINI EXTERN> -66.16579 10.88895 0.00000 0.00000 0.00000 MINI CONSTR> 78.90225 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 90.48662 0.03787 0.35793 0.00023 MINI INTERN> 5.23175 27.57931 0.00000 28.65037 5.37700 MINI EXTERN> -66.18997 10.89850 0.00000 0.00000 0.00000 MINI CONSTR> 78.93965 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 90.45217 0.03445 0.36835 0.00024 MINI INTERN> 5.21620 27.57214 0.00000 28.62807 5.37033 MINI EXTERN> -66.19930 10.89207 0.00000 0.00000 0.00000 MINI CONSTR> 78.97267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 90.41705 0.03512 0.35419 0.00025 MINI INTERN> 5.22876 27.55431 0.00000 28.60095 5.36734 MINI EXTERN> -66.22082 10.88156 0.00000 0.00000 0.00000 MINI CONSTR> 79.00496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 90.38421 0.03284 0.39304 0.00026 MINI INTERN> 5.22012 27.53428 0.00000 28.57386 5.36638 MINI EXTERN> -66.24690 10.89681 0.00000 0.00000 0.00000 MINI CONSTR> 79.03966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 90.35123 0.03298 0.37157 0.00027 MINI INTERN> 5.20383 27.52878 0.00000 28.55307 5.35963 MINI EXTERN> -66.25344 10.88848 0.00000 0.00000 0.00000 MINI CONSTR> 79.07088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 90.30961 0.04162 0.12524 0.00011 MINI INTERN> 5.30433 27.47278 0.00000 28.50757 5.37245 MINI EXTERN> -66.32755 10.87737 0.00000 0.00000 0.00000 MINI CONSTR> 79.10265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 90.29306 0.01654 0.41925 0.00029 MINI INTERN> 5.18448 27.50839 0.00000 28.50841 5.35053 MINI EXTERN> -66.27810 10.88601 0.00000 0.00000 0.00000 MINI CONSTR> 79.13335 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 90.26628 0.02678 0.49016 0.00030 MINI INTERN> 5.25253 27.47633 0.00000 28.47404 5.35091 MINI EXTERN> -66.31202 10.85916 0.00000 0.00000 0.00000 MINI CONSTR> 79.16533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 90.21858 0.04770 0.13507 0.00013 MINI INTERN> 5.30612 27.42638 0.00000 28.43344 5.36321 MINI EXTERN> -66.38001 10.87187 0.00000 0.00000 0.00000 MINI CONSTR> 79.19759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 90.19251 0.02607 0.11309 0.00013 MINI INTERN> 5.29192 27.41768 0.00000 28.41491 5.35856 MINI EXTERN> -66.38726 10.87198 0.00000 0.00000 0.00000 MINI CONSTR> 79.22472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 90.16527 0.02724 0.11642 0.00014 MINI INTERN> 5.29515 27.40249 0.00000 28.39120 5.35597 MINI EXTERN> -66.40401 10.86981 0.00000 0.00000 0.00000 MINI CONSTR> 79.25467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 90.13869 0.02658 0.11311 0.00014 MINI INTERN> 5.29304 27.38982 0.00000 28.36897 5.35259 MINI EXTERN> -66.41734 10.86752 0.00000 0.00000 0.00000 MINI CONSTR> 79.28409 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 90.11230 0.02639 0.19936 0.00015 MINI INTERN> 5.32267 27.36460 0.00000 28.33754 5.35395 MINI EXTERN> -66.45031 10.86581 0.00000 0.00000 0.00000 MINI CONSTR> 79.31805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 90.08650 0.02580 0.14347 0.00015 MINI INTERN> 5.30301 27.35985 0.00000 28.32065 5.34784 MINI EXTERN> -66.45174 10.86201 0.00000 0.00000 0.00000 MINI CONSTR> 79.34489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 90.06327 0.02323 0.17301 0.00016 MINI INTERN> 5.31410 27.34246 0.00000 28.29648 5.34685 MINI EXTERN> -66.47171 10.86132 0.00000 0.00000 0.00000 MINI CONSTR> 79.37376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 90.04259 0.02068 0.24021 0.00016 MINI INTERN> 5.32964 27.32444 0.00000 28.27176 5.34682 MINI EXTERN> -66.49444 10.86182 0.00000 0.00000 0.00000 MINI CONSTR> 79.40254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 90.02052 0.02207 0.26303 0.00017 MINI INTERN> 5.33505 27.31430 0.00000 28.25079 5.34298 MINI EXTERN> -66.50461 10.85187 0.00000 0.00000 0.00000 MINI CONSTR> 79.43014 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 90.00021 0.02031 0.26967 0.00018 MINI INTERN> 5.34279 27.29759 0.00000 28.22883 5.34237 MINI EXTERN> -66.52265 10.85459 0.00000 0.00000 0.00000 MINI CONSTR> 79.45669 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 89.97988 0.02033 0.29227 0.00018 MINI INTERN> 5.33305 27.28751 0.00000 28.20934 5.33991 MINI EXTERN> -66.53429 10.86024 0.00000 0.00000 0.00000 MINI CONSTR> 79.48411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 89.96001 0.01986 0.27214 0.00019 MINI INTERN> 5.34270 27.27536 0.00000 28.19012 5.33713 MINI EXTERN> -66.54446 10.85108 0.00000 0.00000 0.00000 MINI CONSTR> 79.50808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 89.94093 0.01908 0.30383 0.00020 MINI INTERN> 5.31234 27.27214 0.00000 28.17455 5.33301 MINI EXTERN> -66.54831 10.86241 0.00000 0.00000 0.00000 MINI CONSTR> 79.53479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 89.91650 0.02443 0.09313 0.00009 MINI INTERN> 5.26064 27.28120 0.00000 28.16882 5.32168 MINI EXTERN> -66.52508 10.85428 0.00000 0.00000 0.00000 MINI CONSTR> 79.55496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 89.90603 0.01047 0.31642 0.00021 MINI INTERN> 5.35247 27.24220 0.00000 28.13248 5.33032 MINI EXTERN> -66.57834 10.84348 0.00000 0.00000 0.00000 MINI CONSTR> 79.58343 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 89.89054 0.01549 0.36566 0.00022 MINI INTERN> 5.30745 27.24254 0.00000 28.12077 5.32573 MINI EXTERN> -66.57684 10.86283 0.00000 0.00000 0.00000 MINI CONSTR> 79.60806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 89.87351 0.01703 0.34803 0.00023 MINI INTERN> 5.34429 27.22034 0.00000 28.09655 5.32711 MINI EXTERN> -66.60084 10.85369 0.00000 0.00000 0.00000 MINI CONSTR> 79.63236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 89.84670 0.02681 0.10888 0.00010 MINI INTERN> 5.24847 27.24582 0.00000 28.09846 5.31054 MINI EXTERN> -66.55804 10.84899 0.00000 0.00000 0.00000 MINI CONSTR> 79.65246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 89.83199 0.01471 0.08496 0.00010 MINI INTERN> 5.25655 27.23413 0.00000 28.08119 5.31012 MINI EXTERN> -66.57174 10.84821 0.00000 0.00000 0.00000 MINI CONSTR> 79.67353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 89.81627 0.01572 0.08842 0.00011 MINI INTERN> 5.25267 27.22642 0.00000 28.06473 5.30731 MINI EXTERN> -66.57858 10.84687 0.00000 0.00000 0.00000 MINI CONSTR> 79.69685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11218 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 89.80116 0.01511 0.08731 0.00011 MINI INTERN> 5.25281 27.21762 0.00000 28.04800 5.30507 MINI EXTERN> -66.58698 10.84501 0.00000 0.00000 0.00000 MINI CONSTR> 79.71964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 89.78639 0.01477 0.15548 0.00011 MINI INTERN> 5.23003 27.21625 0.00000 28.03416 5.29931 MINI EXTERN> -66.58366 10.84583 0.00000 0.00000 0.00000 MINI CONSTR> 79.74447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11216 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 89.77146 0.01492 0.10996 0.00012 MINI INTERN> 5.24662 27.20199 0.00000 28.01520 5.29940 MINI EXTERN> -66.59970 10.84172 0.00000 0.00000 0.00000 MINI CONSTR> 79.76622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 89.75826 0.01320 0.13630 0.00012 MINI INTERN> 5.23521 27.19788 0.00000 28.00130 5.29579 MINI EXTERN> -66.60192 10.84179 0.00000 0.00000 0.00000 MINI CONSTR> 79.78820 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11216 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 89.74654 0.01172 0.18476 0.00013 MINI INTERN> 5.22023 27.19481 0.00000 27.98844 5.29198 MINI EXTERN> -66.60248 10.84393 0.00000 0.00000 0.00000 MINI CONSTR> 79.80964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 89.73414 0.01240 0.20684 0.00013 MINI INTERN> 5.23207 27.18477 0.00000 27.97152 5.28995 MINI EXTERN> -66.61115 10.83584 0.00000 0.00000 0.00000 MINI CONSTR> 79.83115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11215 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 89.72258 0.01156 0.21114 0.00014 MINI INTERN> 5.21914 27.18198 0.00000 27.95924 5.28687 MINI EXTERN> -66.61334 10.83754 0.00000 0.00000 0.00000 MINI CONSTR> 79.85115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 89.71117 0.01142 0.22202 0.00014 MINI INTERN> 5.20764 27.17686 0.00000 27.94594 5.28472 MINI EXTERN> -66.61838 10.84266 0.00000 0.00000 0.00000 MINI CONSTR> 79.87173 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11215 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 89.69976 0.01141 0.21084 0.00015 MINI INTERN> 5.21558 27.16923 0.00000 27.93141 5.28290 MINI EXTERN> -66.62571 10.83566 0.00000 0.00000 0.00000 MINI CONSTR> 79.89069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 89.68886 0.01090 0.23166 0.00015 MINI INTERN> 5.21179 27.15892 0.00000 27.91596 5.28277 MINI EXTERN> -66.63706 10.84483 0.00000 0.00000 0.00000 MINI CONSTR> 79.91166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11214 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 89.67495 0.01391 0.07182 0.00007 MINI INTERN> 5.25915 27.13599 0.00000 27.89448 5.28714 MINI EXTERN> -66.66595 10.83461 0.00000 0.00000 0.00000 MINI CONSTR> 79.92952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 89.66925 0.00570 0.24438 0.00016 MINI INTERN> 5.21058 27.15237 0.00000 27.89154 5.27641 MINI EXTERN> -66.64092 10.83093 0.00000 0.00000 0.00000 MINI CONSTR> 79.94833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11214 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 89.66044 0.00881 0.28346 0.00017 MINI INTERN> 5.20474 27.14150 0.00000 27.87681 5.27724 MINI EXTERN> -66.65367 10.84549 0.00000 0.00000 0.00000 MINI CONSTR> 79.96833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 89.65082 0.00962 0.27445 0.00018 MINI INTERN> 5.18995 27.14325 0.00000 27.86731 5.27269 MINI EXTERN> -66.64988 10.84123 0.00000 0.00000 0.00000 MINI CONSTR> 79.98626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11214 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 89.63502 0.01579 0.08257 0.00008 MINI INTERN> 5.26374 27.10714 0.00000 27.83964 5.28086 MINI EXTERN> -66.69242 10.83059 0.00000 0.00000 0.00000 MINI CONSTR> 80.00549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 89.62654 0.00849 0.06521 0.00008 MINI INTERN> 5.25454 27.10448 0.00000 27.82986 5.27824 MINI EXTERN> -66.69307 10.83094 0.00000 0.00000 0.00000 MINI CONSTR> 80.02155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11212 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 89.61757 0.00897 0.06820 0.00008 MINI INTERN> 5.25682 27.09723 0.00000 27.81663 5.27691 MINI EXTERN> -66.69972 10.82998 0.00000 0.00000 0.00000 MINI CONSTR> 80.03972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 89.60866 0.00891 0.11099 0.00008 MINI INTERN> 5.27258 27.08502 0.00000 27.79973 5.27709 MINI EXTERN> -66.71313 10.82744 0.00000 0.00000 0.00000 MINI CONSTR> 80.05993 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11212 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 89.60015 0.00851 0.08782 0.00009 MINI INTERN> 5.26062 27.08277 0.00000 27.78996 5.27443 MINI EXTERN> -66.71350 10.82933 0.00000 0.00000 0.00000 MINI CONSTR> 80.07654 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 89.59232 0.00783 0.09959 0.00009 MINI INTERN> 5.26709 27.07448 0.00000 27.77679 5.27361 MINI EXTERN> -66.72122 10.82779 0.00000 0.00000 0.00000 MINI CONSTR> 80.09378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11212 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 89.58446 0.00786 0.10404 0.00009 MINI INTERN> 5.27027 27.06814 0.00000 27.76445 5.27209 MINI EXTERN> -66.72655 10.82515 0.00000 0.00000 0.00000 MINI CONSTR> 80.11091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 89.57781 0.00665 0.14121 0.00010 MINI INTERN> 5.27902 27.05826 0.00000 27.75080 5.27222 MINI EXTERN> -66.73684 10.82635 0.00000 0.00000 0.00000 MINI CONSTR> 80.12799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11211 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 89.57045 0.00736 0.15781 0.00010 MINI INTERN> 5.28274 27.05359 0.00000 27.73883 5.27012 MINI EXTERN> -66.74068 10.82072 0.00000 0.00000 0.00000 MINI CONSTR> 80.14514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 89.56374 0.00671 0.16229 0.00011 MINI INTERN> 5.28733 27.04506 0.00000 27.72653 5.26979 MINI EXTERN> -66.74853 10.82230 0.00000 0.00000 0.00000 MINI CONSTR> 80.16127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11211 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 89.55688 0.00685 0.15594 0.00011 MINI INTERN> 5.27977 27.04121 0.00000 27.71677 5.26819 MINI EXTERN> -66.75129 10.82552 0.00000 0.00000 0.00000 MINI CONSTR> 80.17672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 89.55046 0.00643 0.17349 0.00011 MINI INTERN> 5.28374 27.03793 0.00000 27.70615 5.26562 MINI EXTERN> -66.75290 10.81754 0.00000 0.00000 0.00000 MINI CONSTR> 80.19238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11211 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 89.54397 0.00649 0.16308 0.00012 MINI INTERN> 5.28737 27.02939 0.00000 27.69429 5.26551 MINI EXTERN> -66.76081 10.82027 0.00000 0.00000 0.00000 MINI CONSTR> 80.20793 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 89.54397 0.00649 0.16308 0.00014 STPD INTERN> 5.28737 27.02939 0.00000 27.69429 5.26551 STPD EXTERN> -66.76081 10.82027 0.00000 0.00000 0.00000 STPD CONSTR> 80.20793 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 11211 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11211 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 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 89.54397 0.00649 0.16308 0.00000 MINI INTERN> 5.28737 27.02939 0.00000 27.69429 5.26551 MINI EXTERN> -66.76081 10.82027 0.00000 0.00000 0.00000 MINI CONSTR> 80.20793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 89.34209 0.20188 0.01135 0.01141 MINI INTERN> 5.22488 26.73927 0.00000 27.05060 5.17447 MINI EXTERN> -67.01704 10.80019 0.00000 0.00000 0.00000 MINI CONSTR> 81.36972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 89.34091 0.00118 0.03169 0.00318 MINI INTERN> 5.21632 26.75239 0.00000 27.03718 5.15551 MINI EXTERN> -66.86027 10.78104 0.00000 0.00000 0.00000 MINI CONSTR> 81.25875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 89.33973 0.00118 0.01879 0.00330 MINI INTERN> 5.22087 26.76083 0.00000 27.02908 5.17190 MINI EXTERN> -66.83640 10.82749 0.00000 0.00000 0.00000 MINI CONSTR> 81.16595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 89.33938 0.00036 0.01098 0.00078 MINI INTERN> 5.22959 26.77617 0.00000 27.03325 5.16727 MINI EXTERN> -66.86912 10.83527 0.00000 0.00000 0.00000 MINI CONSTR> 81.16695 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> 23 89.33927 0.00011 0.00837 0.02000 CONJ INTERN> 5.23242 26.77678 0.00000 27.03770 5.16672 CONJ EXTERN> -66.89513 10.84202 0.00000 0.00000 0.00000 CONJ CONSTR> 81.17875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "7200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 1.1376 ( PROT LYS 1 HT2 ) 1.1376 ( PROT LYS 1 N ) 1.4220 ( PROT LYS 1 HT3 ) 1.1376 ( PROT LYS 1 CA ) 1.4220 ( PROT LYS 1 CB ) 1.1376 ( PROT LYS 1 CG ) 1.1376 ( PROT LYS 1 CD ) 1.1376 ( PROT LYS 1 CE ) 1.1376 ( PROT LYS 1 NZ ) 1.1376 ( PROT LYS 1 HZ1 ) 1.1376 ( PROT LYS 1 HZ2 ) 1.1376 ( PROT LYS 1 HZ3 ) 1.1376 ( PROT LYS 1 C ) 1.4220 ( PROT LYS 1 O ) 1.4220 ( PROT MET 2 N ) 1.4220 ( PROT MET 2 H ) 1.1376 ( PROT MET 2 CA ) 1.4220 ( PROT MET 2 CB ) 1.1376 ( PROT MET 2 CG ) 1.1376 ( PROT MET 2 SD ) 1.1376 ( PROT MET 2 CE ) 1.1376 ( PROT MET 2 C ) 1.4220 ( PROT MET 2 O ) 1.4220 ( PROT LYS 3 N ) 1.4220 ( PROT LYS 3 H ) 1.1376 ( PROT LYS 3 CA ) 1.4220 ( PROT LYS 3 CB ) 1.1376 ( PROT LYS 3 CG ) 1.1376 ( PROT LYS 3 CD ) 1.1376 ( PROT LYS 3 CE ) 1.1376 ( PROT LYS 3 NZ ) 1.1376 ( PROT LYS 3 HZ1 ) 1.1376 ( PROT LYS 3 HZ2 ) 1.1376 ( PROT LYS 3 HZ3 ) 1.1376 ( PROT LYS 3 C ) 1.4220 ( PROT LYS 3 O ) 1.4220 ( PROT ALA 4 N ) 1.4220 ( PROT ALA 4 H ) 1.1376 ( PROT ALA 4 CA ) 1.4220 ( PROT ALA 4 CB ) 1.1376 ( PROT ALA 4 C ) 1.4220 ( PROT ALA 4 O ) 1.4220 ( PROT VAL 5 N ) 1.4220 ( PROT VAL 5 H ) 1.1376 ( PROT VAL 5 CA ) 1.4220 ( PROT VAL 5 CB ) 1.1376 ( PROT VAL 5 CG1 ) 1.1376 ( PROT VAL 5 CG2 ) 1.1376 ( PROT VAL 5 C ) 1.4220 ( PROT VAL 5 O ) 1.4220 ( PROT MET 6 N ) 1.4220 ( PROT MET 6 H ) 1.1376 ( PROT MET 6 CA ) 1.4220 ( PROT MET 6 CB ) 1.1376 ( PROT MET 6 CG ) 1.1376 ( PROT MET 6 SD ) 1.1376 ( PROT MET 6 CE ) 1.1376 ( PROT MET 6 C ) 1.4220 ( PROT MET 6 O ) 1.4220 ( PROT ILE 7 N ) 1.4220 ( PROT ILE 7 H ) 1.1376 ( PROT ILE 7 CA ) 1.4220 ( PROT ILE 7 CB ) 1.1376 ( PROT ILE 7 CG2 ) 1.1376 ( PROT ILE 7 CG1 ) 1.1376 ( PROT ILE 7 CD ) 1.1376 ( PROT ILE 7 C ) 1.4220 ( PROT ILE 7 O ) 1.4220 ( PROT GLY 8 N ) 1.4220 ( PROT GLY 8 H ) 1.1376 ( PROT GLY 8 CA ) 1.4220 ( PROT GLY 8 C ) 1.4220 ( PROT GLY 8 O ) 1.4220 ( PROT ALA 9 N ) 1.4220 ( PROT ALA 9 H ) 1.1376 ( PROT ALA 9 CA ) 1.4220 ( PROT ALA 9 CB ) 1.1376 ( PROT ALA 9 C ) 1.4220 ( PROT ALA 9 O ) 1.4220 ( PROT CYS 10 N ) 1.4220 ( PROT CYS 10 H ) 1.1376 ( PROT CYS 10 CA ) 1.4220 ( PROT CYS 10 CB ) 1.1376 ( PROT CYS 10 SG ) 1.1376 ( PROT CYS 10 C ) 1.4220 ( PROT CYS 10 O ) 1.4220 ( PROT PHE 11 N ) 1.4220 ( PROT PHE 11 H ) 1.1376 ( PROT PHE 11 CA ) 1.4220 ( PROT PHE 11 CB ) 1.1376 ( PROT PHE 11 CG ) 1.1376 ( PROT PHE 11 CD1 ) 1.1376 ( PROT PHE 11 CD2 ) 1.1376 ( PROT PHE 11 CE1 ) 1.1376 ( PROT PHE 11 CE2 ) 1.1376 ( PROT PHE 11 CZ ) 1.1376 ( PROT PHE 11 C ) 1.4220 ( PROT PHE 11 O ) 1.4220 ( PROT LEU 12 N ) 1.4220 ( PROT LEU 12 H ) 1.1376 ( PROT LEU 12 CA ) 1.4220 ( PROT LEU 12 CB ) 1.1376 ( PROT LEU 12 CG ) 1.1376 ( PROT LEU 12 CD1 ) 1.1376 ( PROT LEU 12 CD2 ) 1.1376 ( PROT LEU 12 C ) 1.4220 ( PROT LEU 12 O ) 1.4220 ( PROT ILE 13 N ) 1.4220 ( PROT ILE 13 H ) 1.1376 ( PROT ILE 13 CA ) 1.4220 ( PROT ILE 13 CB ) 1.1376 ( PROT ILE 13 CG2 ) 1.1376 ( PROT ILE 13 CG1 ) 1.1376 ( PROT ILE 13 CD ) 1.1376 ( PROT ILE 13 C ) 1.4220 ( PROT ILE 13 O ) 1.4220 ( PROT ASH 14 N ) 1.4220 ( PROT ASH 14 H ) 1.1376 ( PROT ASH 14 CA ) 1.4220 ( PROT ASH 14 CB ) 1.1376 ( PROT ASH 14 CG ) 1.1376 ( PROT ASH 14 OD1 ) 1.1376 ( PROT ASH 14 OD2 ) 1.1376 ( PROT ASH 14 HD2 ) 1.1376 ( PROT ASH 14 C ) 1.4220 ( PROT ASH 14 O ) 1.4220 ( PROT PHE 15 N ) 1.4220 ( PROT PHE 15 H ) 1.1376 ( PROT PHE 15 CA ) 1.4220 ( PROT PHE 15 CB ) 1.1376 ( PROT PHE 15 CG ) 1.1376 ( PROT PHE 15 CD1 ) 1.1376 ( PROT PHE 15 CD2 ) 1.1376 ( PROT PHE 15 CE1 ) 1.1376 ( PROT PHE 15 CE2 ) 1.1376 ( PROT PHE 15 CZ ) 1.1376 ( PROT PHE 15 C ) 1.4220 ( PROT PHE 15 O ) 1.4220 ( PROT MET 16 N ) 1.4220 ( PROT MET 16 H ) 1.1376 ( PROT MET 16 CA ) 1.4220 ( PROT MET 16 CB ) 1.1376 ( PROT MET 16 CG ) 1.1376 ( PROT MET 16 SD ) 1.1376 ( PROT MET 16 CE ) 1.1376 ( PROT MET 16 C ) 1.4220 ( PROT MET 16 O ) 1.4220 ( PROT PHE 17 N ) 1.4220 ( PROT PHE 17 H ) 1.1376 ( PROT PHE 17 CA ) 1.4220 ( PROT PHE 17 CB ) 1.1376 ( PROT PHE 17 CG ) 1.1376 ( PROT PHE 17 CD1 ) 1.1376 ( PROT PHE 17 CD2 ) 1.1376 ( PROT PHE 17 CE1 ) 1.1376 ( PROT PHE 17 CE2 ) 1.1376 ( PROT PHE 17 CZ ) 1.1376 ( PROT PHE 17 C ) 1.4220 ( PROT PHE 17 O ) 1.4220 ( PROT PHE 18 N ) 1.4220 ( PROT PHE 18 H ) 1.1376 ( PROT PHE 18 CA ) 1.4220 ( PROT PHE 18 CB ) 1.1376 ( PROT PHE 18 CG ) 1.1376 ( PROT PHE 18 CD1 ) 1.1376 ( PROT PHE 18 CD2 ) 1.1376 ( PROT PHE 18 CE1 ) 1.1376 ( PROT PHE 18 CE2 ) 1.1376 ( PROT PHE 18 CZ ) 1.1376 ( PROT PHE 18 C ) 1.4220 ( PROT PHE 18 O ) 1.4220 ( PROT GLU 19 N ) 1.4220 ( PROT GLU 19 H ) 1.1376 ( PROT GLU 19 CA ) 1.4220 ( PROT GLU 19 CB ) 1.1376 ( PROT GLU 19 CG ) 1.1376 ( PROT GLU 19 CD ) 1.1376 ( PROT GLU 19 OE1 ) 1.1376 ( PROT GLU 19 OE2 ) 1.1376 ( PROT GLU 19 C ) 1.4220 ( PROT GLU 19 OT1 ) 1.1376 ( PROT GLU 19 OT2 ) 1.1376 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40351 5.29331 -8.69146 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00103 -0.00089 -0.00176 ROTATION MATRIX 1.000000 -0.000173 0.000057 0.000173 1.000000 0.000246 -0.000057 -0.000246 1.000000 AXIS OF ROTATION IS 0.802897 -0.185988 -0.566361 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 42.5257 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.482059 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4821" Parameter: A <- "0.4821" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70720 5.22114 -8.78297 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00764 0.04328 -0.01140 ROTATION MATRIX 0.999756 0.017863 0.013016 -0.017650 0.999712 -0.016265 -0.013303 0.016032 0.999783 AXIS OF ROTATION IS -0.589963 -0.480764 0.648699 ANGLE IS 1.57 CENTER OF ROTATION 8.885645 5.178167 -9.587194 SHIFT IS -0.032714 TOTAL SQUARE DIFF IS 1.8550 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.312459 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4821" RDCMND substituted energy or value "?RMS" to " 0.3125" Parameter: A <- "0.4821 0.3125" 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 0.4821 0.3125 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 " 81.18" Parameter: H <- "81.18" 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 8.16052 81.17875 1.06971 ENER INTERN> 5.23242 26.77678 0.00000 27.03770 5.16672 ENER EXTERN> -66.89513 10.84202 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 " 8.16" Parameter: B <- "8.16" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 10.84" Parameter: C <- "10.84" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -66.90" Parameter: C <- " -56.06" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -56.06" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.23" Parameter: D <- "5.23" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 26.78" Parameter: D <- " 32.01" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 27.04" Parameter: D <- " 59.05" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.17" Parameter: D <- " 64.22" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 64.22" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 7200 ENER= 8.16 GRMS= 1.07 ELEC= 10.84 VDW= -66.90 RDTITL> *EXTERNAL= -56.06 INTERNAL= 64.22 USER= 0.00 HARM= 81.18 RDTITL> *BOND= 5.23 ANGL= 26.78 DIHE= 27.04 IMPR= 5.17 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= 8.16 GRMS= 1.07 ELEC= 10.84 VDW= -66.90 RDTITL> *EXTERNAL= -56.06 INTERNAL= 64.22 USER= 0.00 HARM= 81.18 RDTITL> *BOND= 5.23 ANGL= 26.78 DIHE= 27.04 IMPR= 5.17 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= 8.16 GRMS= 1.07 ELEC= 10.84 VDW= -66.90 RDTITL> *EXTERNAL= -56.06 INTERNAL= 64.22 USER= 0.00 HARM= 81.18 RDTITL> *BOND= 5.23 ANGL= 26.78 DIHE= 27.04 IMPR= 5.17 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 7200 0.4821 0.3125 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11211 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11209 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 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 64.04490 -55.88438 0.40935 0.02000 MINI INTERN> 5.23242 26.77678 0.00000 27.03770 5.16672 MINI EXTERN> -66.89513 10.84202 0.00000 0.00000 0.00000 MINI CONSTR> 55.88438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 85.95786 -21.91296 16.03705 0.00864 MINI INTERN> 29.09012 24.83183 0.00000 28.63809 4.70662 MINI EXTERN> -73.40510 13.27361 0.00000 0.00000 0.00000 MINI CONSTR> 58.82268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11203 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 62.29455 23.66331 0.40988 0.00156 MINI INTERN> 5.29885 26.50147 0.00000 28.03912 5.23132 MINI EXTERN> -73.85275 12.01951 0.00000 0.00000 0.00000 MINI CONSTR> 59.05701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 62.14328 0.15127 0.94024 0.00067 MINI INTERN> 5.43654 26.58866 0.00000 27.89177 5.23682 MINI EXTERN> -74.21494 11.94255 0.00000 0.00000 0.00000 MINI CONSTR> 59.26187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11198 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 61.93475 0.20853 0.29948 0.00029 MINI INTERN> 5.33405 26.38750 0.00000 27.88302 5.18810 MINI EXTERN> -74.16765 11.94348 0.00000 0.00000 0.00000 MINI CONSTR> 59.36625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 61.82728 0.10748 0.28513 0.00030 MINI INTERN> 5.32095 26.33572 0.00000 27.84243 5.17571 MINI EXTERN> -74.24476 11.92824 0.00000 0.00000 0.00000 MINI CONSTR> 59.46900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11198 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 61.72502 0.10225 0.38956 0.00031 MINI INTERN> 5.33432 26.25144 0.00000 27.80135 5.16028 MINI EXTERN> -74.32120 11.92164 0.00000 0.00000 0.00000 MINI CONSTR> 59.57721 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 61.62681 0.09821 0.34408 0.00032 MINI INTERN> 5.29961 26.22547 0.00000 27.76416 5.14993 MINI EXTERN> -74.39845 11.91283 0.00000 0.00000 0.00000 MINI CONSTR> 59.67327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11195 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 61.53953 0.08728 0.47735 0.00034 MINI INTERN> 5.29708 26.14576 0.00000 27.72871 5.13387 MINI EXTERN> -74.47324 11.93330 0.00000 0.00000 0.00000 MINI CONSTR> 59.77404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 61.44971 0.08982 0.50064 0.00035 MINI INTERN> 5.30703 26.09583 0.00000 27.69151 5.12086 MINI EXTERN> -74.55129 11.91671 0.00000 0.00000 0.00000 MINI CONSTR> 59.86906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11194 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 61.36445 0.08526 0.55226 0.00036 MINI INTERN> 5.26945 26.05695 0.00000 27.65528 5.11132 MINI EXTERN> -74.62820 11.93609 0.00000 0.00000 0.00000 MINI CONSTR> 59.96358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 61.28120 0.08326 0.55624 0.00037 MINI INTERN> 5.24694 26.02614 0.00000 27.62231 5.09825 MINI EXTERN> -74.69214 11.92765 0.00000 0.00000 0.00000 MINI CONSTR> 60.05205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 61.19921 0.08199 0.61497 0.00039 MINI INTERN> 5.27367 25.97555 0.00000 27.57981 5.08909 MINI EXTERN> -74.77432 11.91118 0.00000 0.00000 0.00000 MINI CONSTR> 60.14424 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 61.11766 0.08155 0.57102 0.00040 MINI INTERN> 5.21243 25.95875 0.00000 27.54677 5.08215 MINI EXTERN> -74.83738 11.92873 0.00000 0.00000 0.00000 MINI CONSTR> 60.22622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 61.01480 0.10287 0.19617 0.00017 MINI INTERN> 5.20291 25.98570 0.00000 27.48748 5.10459 MINI EXTERN> -74.96719 11.89437 0.00000 0.00000 0.00000 MINI CONSTR> 60.30694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 60.96842 0.04638 0.61263 0.00043 MINI INTERN> 5.19986 25.88599 0.00000 27.47330 5.06334 MINI EXTERN> -74.96586 11.92174 0.00000 0.00000 0.00000 MINI CONSTR> 60.39005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11192 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 60.85554 0.11288 0.18478 0.00019 MINI INTERN> 5.18431 25.90777 0.00000 27.40824 5.08795 MINI EXTERN> -75.10345 11.89491 0.00000 0.00000 0.00000 MINI CONSTR> 60.47580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 60.82130 0.03424 0.70517 0.00046 MINI INTERN> 5.27032 25.76733 0.00000 27.38341 5.05130 MINI EXTERN> -75.12191 11.91364 0.00000 0.00000 0.00000 MINI CONSTR> 60.55722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11190 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 60.71069 0.11061 0.21780 0.00020 MINI INTERN> 5.16527 25.84980 0.00000 27.32903 5.07653 MINI EXTERN> -75.23350 11.89119 0.00000 0.00000 0.00000 MINI CONSTR> 60.63237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 60.64788 0.06281 0.17875 0.00021 MINI INTERN> 5.17149 25.80187 0.00000 27.29661 5.06702 MINI EXTERN> -75.27995 11.89348 0.00000 0.00000 0.00000 MINI CONSTR> 60.69736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11189 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 60.58366 0.06422 0.18236 0.00022 MINI INTERN> 5.16899 25.76966 0.00000 27.25973 5.06118 MINI EXTERN> -75.33500 11.89261 0.00000 0.00000 0.00000 MINI CONSTR> 60.76648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 60.51767 0.06599 0.28079 0.00022 MINI INTERN> 5.15744 25.75833 0.00000 27.21535 5.06069 MINI EXTERN> -75.40494 11.88732 0.00000 0.00000 0.00000 MINI CONSTR> 60.84348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11188 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 60.46038 0.05729 0.17696 0.00023 MINI INTERN> 5.16293 25.70522 0.00000 27.18822 5.04837 MINI EXTERN> -75.43485 11.89160 0.00000 0.00000 0.00000 MINI CONSTR> 60.89888 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 60.39992 0.06046 0.33100 0.00024 MINI INTERN> 5.16724 25.69463 0.00000 27.14090 5.05086 MINI EXTERN> -75.51018 11.88221 0.00000 0.00000 0.00000 MINI CONSTR> 60.97426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11187 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 60.33613 0.06379 0.23238 0.00025 MINI INTERN> 5.14641 25.65474 0.00000 27.11018 5.03861 MINI EXTERN> -75.54005 11.88995 0.00000 0.00000 0.00000 MINI CONSTR> 61.03630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 60.28461 0.05152 0.37027 0.00026 MINI INTERN> 5.16027 25.64157 0.00000 27.06845 5.03946 MINI EXTERN> -75.60437 11.87670 0.00000 0.00000 0.00000 MINI CONSTR> 61.10254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11184 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 60.23079 0.05383 0.41424 0.00027 MINI INTERN> 5.13970 25.61584 0.00000 27.03321 5.03298 MINI EXTERN> -75.64255 11.88714 0.00000 0.00000 0.00000 MINI CONSTR> 61.16446 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 60.17966 0.05113 0.42368 0.00028 MINI INTERN> 5.15879 25.58192 0.00000 26.99622 5.02972 MINI EXTERN> -75.69102 11.88181 0.00000 0.00000 0.00000 MINI CONSTR> 61.22221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11180 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 60.12910 0.05056 0.43887 0.00029 MINI INTERN> 5.18188 25.54725 0.00000 26.96056 5.02507 MINI EXTERN> -75.73682 11.87172 0.00000 0.00000 0.00000 MINI CONSTR> 61.27943 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 60.07812 0.05098 0.42788 0.00030 MINI INTERN> 5.16338 25.52046 0.00000 26.92832 5.01863 MINI EXTERN> -75.76835 11.88129 0.00000 0.00000 0.00000 MINI CONSTR> 61.33439 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11180 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 60.03055 0.04757 0.46820 0.00031 MINI INTERN> 5.18772 25.48689 0.00000 26.89669 5.01025 MINI EXTERN> -75.80335 11.86337 0.00000 0.00000 0.00000 MINI CONSTR> 61.38898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 59.98229 0.04826 0.44593 0.00032 MINI INTERN> 5.19282 25.45730 0.00000 26.86002 5.00858 MINI EXTERN> -75.84678 11.86771 0.00000 0.00000 0.00000 MINI CONSTR> 61.44265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11180 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 59.92082 0.06148 0.15200 0.00014 MINI INTERN> 5.11907 25.42390 0.00000 26.84640 4.98538 MINI EXTERN> -75.82698 11.88371 0.00000 0.00000 0.00000 MINI CONSTR> 61.48933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 59.89529 0.02553 0.50662 0.00034 MINI INTERN> 5.20996 25.40375 0.00000 26.79267 5.00001 MINI EXTERN> -75.91941 11.86139 0.00000 0.00000 0.00000 MINI CONSTR> 61.54692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11178 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 59.85591 0.03938 0.59746 0.00036 MINI INTERN> 5.14816 25.39201 0.00000 26.76656 4.99034 MINI EXTERN> -75.92983 11.88975 0.00000 0.00000 0.00000 MINI CONSTR> 61.59893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 59.81296 0.04295 0.58337 0.00037 MINI INTERN> 5.18560 25.35905 0.00000 26.72816 4.99069 MINI EXTERN> -75.97830 11.87869 0.00000 0.00000 0.00000 MINI CONSTR> 61.64908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11178 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 59.74190 0.07106 0.17027 0.00016 MINI INTERN> 5.10026 25.33630 0.00000 26.72002 4.96388 MINI EXTERN> -75.94734 11.87582 0.00000 0.00000 0.00000 MINI CONSTR> 61.69295 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 59.70321 0.03869 0.14041 0.00017 MINI INTERN> 5.09968 25.31932 0.00000 26.69043 4.96182 MINI EXTERN> -75.97867 11.87392 0.00000 0.00000 0.00000 MINI CONSTR> 61.73671 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11178 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 59.66274 0.04047 0.14544 0.00017 MINI INTERN> 5.09359 25.30020 0.00000 26.66093 4.95654 MINI EXTERN> -76.00414 11.87188 0.00000 0.00000 0.00000 MINI CONSTR> 61.78373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 59.62329 0.03945 0.14574 0.00018 MINI INTERN> 5.09061 25.28112 0.00000 26.63141 4.95182 MINI EXTERN> -76.03023 11.86882 0.00000 0.00000 0.00000 MINI CONSTR> 61.82974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11176 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 59.58307 0.04022 0.24476 0.00019 MINI INTERN> 5.06868 25.26226 0.00000 26.60266 4.94196 MINI EXTERN> -76.04485 11.87116 0.00000 0.00000 0.00000 MINI CONSTR> 61.88121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 59.54391 0.03916 0.19200 0.00019 MINI INTERN> 5.08213 25.24086 0.00000 26.57104 4.94032 MINI EXTERN> -76.07829 11.86299 0.00000 0.00000 0.00000 MINI CONSTR> 61.92486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11175 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 59.50846 0.03545 0.22407 0.00020 MINI INTERN> 5.06834 25.22682 0.00000 26.54463 4.93417 MINI EXTERN> -76.09642 11.86228 0.00000 0.00000 0.00000 MINI CONSTR> 61.96864 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 59.47618 0.03228 0.30061 0.00021 MINI INTERN> 5.04538 25.21469 0.00000 26.51951 4.92719 MINI EXTERN> -76.11002 11.86724 0.00000 0.00000 0.00000 MINI CONSTR> 62.01219 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11174 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 59.44206 0.03412 0.33136 0.00021 MINI INTERN> 5.06178 25.19384 0.00000 26.49002 4.92269 MINI EXTERN> -76.13532 11.85396 0.00000 0.00000 0.00000 MINI CONSTR> 62.05509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 59.40924 0.03282 0.33539 0.00022 MINI INTERN> 5.03842 25.18471 0.00000 26.46597 4.91699 MINI EXTERN> -76.15003 11.85720 0.00000 0.00000 0.00000 MINI CONSTR> 62.09599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11174 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 59.37640 0.03284 0.36437 0.00023 MINI INTERN> 5.02381 25.16940 0.00000 26.43785 4.91331 MINI EXTERN> -76.17109 11.86431 0.00000 0.00000 0.00000 MINI CONSTR> 62.13882 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 59.34388 0.03251 0.33999 0.00024 MINI INTERN> 5.03293 25.15332 0.00000 26.41205 4.90900 MINI EXTERN> -76.19199 11.85166 0.00000 0.00000 0.00000 MINI CONSTR> 62.17692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11173 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 59.31296 0.03092 0.38344 0.00025 MINI INTERN> 5.02298 25.13493 0.00000 26.38230 4.90793 MINI EXTERN> -76.21842 11.86437 0.00000 0.00000 0.00000 MINI CONSTR> 62.21887 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 59.28136 0.03160 0.35894 0.00026 MINI INTERN> 5.01189 25.12545 0.00000 26.35938 4.90130 MINI EXTERN> -76.23030 11.85652 0.00000 0.00000 0.00000 MINI CONSTR> 62.25713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11173 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 59.24195 0.03941 0.12181 0.00011 MINI INTERN> 5.08077 25.08470 0.00000 26.31935 4.91039 MINI EXTERN> -76.29058 11.84345 0.00000 0.00000 0.00000 MINI CONSTR> 62.29387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 59.22536 0.01659 0.40644 0.00028 MINI INTERN> 4.99652 25.10116 0.00000 26.31064 4.89231 MINI EXTERN> -76.26247 11.85419 0.00000 0.00000 0.00000 MINI CONSTR> 62.33302 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11173 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 59.19966 0.02569 0.47574 0.00029 MINI INTERN> 5.05862 25.07075 0.00000 26.27779 4.89126 MINI EXTERN> -76.29628 11.82662 0.00000 0.00000 0.00000 MINI CONSTR> 62.37090 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 59.17140 0.02827 0.45840 0.00030 MINI INTERN> 5.01550 25.07037 0.00000 26.25965 4.88339 MINI EXTERN> -76.29825 11.83311 0.00000 0.00000 0.00000 MINI CONSTR> 62.40762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11173 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 59.12597 0.04543 0.13907 0.00013 MINI INTERN> 5.08027 25.02116 0.00000 26.21532 4.89681 MINI EXTERN> -76.36805 11.83545 0.00000 0.00000 0.00000 MINI CONSTR> 62.44500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 59.10086 0.02510 0.11250 0.00013 MINI INTERN> 5.07028 25.01082 0.00000 26.19526 4.89186 MINI EXTERN> -76.37776 11.83332 0.00000 0.00000 0.00000 MINI CONSTR> 62.47708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11173 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 59.07434 0.02652 0.11650 0.00014 MINI INTERN> 5.07161 24.99540 0.00000 26.17031 4.88887 MINI EXTERN> -76.39600 11.83144 0.00000 0.00000 0.00000 MINI CONSTR> 62.51271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 59.04845 0.02589 0.11710 0.00014 MINI INTERN> 5.06975 24.98123 0.00000 26.14629 4.88562 MINI EXTERN> -76.41250 11.83039 0.00000 0.00000 0.00000 MINI CONSTR> 62.54768 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11169 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 59.02214 0.02631 0.19504 0.00015 MINI INTERN> 5.09407 24.95818 0.00000 26.11473 4.88523 MINI EXTERN> -76.44248 11.82508 0.00000 0.00000 0.00000 MINI CONSTR> 62.58732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 58.99662 0.02552 0.15301 0.00015 MINI INTERN> 5.07312 24.95043 0.00000 26.09517 4.88010 MINI EXTERN> -76.45008 11.82778 0.00000 0.00000 0.00000 MINI CONSTR> 62.62011 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 58.97322 0.02340 0.17577 0.00016 MINI INTERN> 5.08300 24.93319 0.00000 26.07010 4.87813 MINI EXTERN> -76.46970 11.82468 0.00000 0.00000 0.00000 MINI CONSTR> 62.65382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 58.94978 0.02344 0.18624 0.00016 MINI INTERN> 5.08994 24.91795 0.00000 26.04621 4.87516 MINI EXTERN> -76.48627 11.81965 0.00000 0.00000 0.00000 MINI CONSTR> 62.68714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 58.92918 0.02061 0.24777 0.00017 MINI INTERN> 5.10078 24.90012 0.00000 26.02067 4.87446 MINI EXTERN> -76.50824 11.82082 0.00000 0.00000 0.00000 MINI CONSTR> 62.72056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 58.90706 0.02212 0.27945 0.00018 MINI INTERN> 5.10995 24.88728 0.00000 25.99755 4.87027 MINI EXTERN> -76.52199 11.81027 0.00000 0.00000 0.00000 MINI CONSTR> 62.75373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 58.88617 0.02089 0.28503 0.00018 MINI INTERN> 5.11701 24.87030 0.00000 25.97411 4.86892 MINI EXTERN> -76.54011 11.81098 0.00000 0.00000 0.00000 MINI CONSTR> 62.78495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 58.86480 0.02137 0.27477 0.00019 MINI INTERN> 5.10070 24.86101 0.00000 25.95465 4.86594 MINI EXTERN> -76.55068 11.81787 0.00000 0.00000 0.00000 MINI CONSTR> 62.81531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 58.84461 0.02019 0.30159 0.00020 MINI INTERN> 5.11188 24.84967 0.00000 25.93344 4.86113 MINI EXTERN> -76.56117 11.80371 0.00000 0.00000 0.00000 MINI CONSTR> 62.84596 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 58.82386 0.02075 0.28427 0.00020 MINI INTERN> 5.11642 24.83232 0.00000 25.91012 4.86058 MINI EXTERN> -76.58007 11.80789 0.00000 0.00000 0.00000 MINI CONSTR> 62.87660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11167 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 58.79735 0.02651 0.09755 0.00009 MINI INTERN> 5.03461 24.85008 0.00000 25.90514 4.84743 MINI EXTERN> -76.55657 11.81256 0.00000 0.00000 0.00000 MINI CONSTR> 62.90410 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 58.78619 0.01116 0.33396 0.00022 MINI INTERN> 5.12448 24.80863 0.00000 25.86771 4.85448 MINI EXTERN> -76.60575 11.79948 0.00000 0.00000 0.00000 MINI CONSTR> 62.93716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 58.76895 0.01724 0.37504 0.00023 MINI INTERN> 5.08430 24.80653 0.00000 25.85181 4.85096 MINI EXTERN> -76.61031 11.81871 0.00000 0.00000 0.00000 MINI CONSTR> 62.96694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 58.74963 0.01932 0.35045 0.00024 MINI INTERN> 5.12441 24.78111 0.00000 25.82502 4.85152 MINI EXTERN> -76.63555 11.80682 0.00000 0.00000 0.00000 MINI CONSTR> 62.99630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 58.71972 0.02991 0.10910 0.00010 MINI INTERN> 5.02458 24.80775 0.00000 25.82414 4.83474 MINI EXTERN> -76.60114 11.80629 0.00000 0.00000 0.00000 MINI CONSTR> 63.02337 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 58.70306 0.01666 0.09270 0.00011 MINI INTERN> 5.02813 24.79608 0.00000 25.80528 4.83327 MINI EXTERN> -76.61449 11.80562 0.00000 0.00000 0.00000 MINI CONSTR> 63.04917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11166 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 58.68557 0.01749 0.09455 0.00011 MINI INTERN> 5.02539 24.78674 0.00000 25.78655 4.83021 MINI EXTERN> -76.62425 11.80399 0.00000 0.00000 0.00000 MINI CONSTR> 63.07693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 58.66800 0.01757 0.09048 0.00011 MINI INTERN> 5.02685 24.77548 0.00000 25.76682 4.82773 MINI EXTERN> -76.63600 11.80213 0.00000 0.00000 0.00000 MINI CONSTR> 63.10499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11166 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 58.64960 0.01839 0.15310 0.00012 MINI INTERN> 5.00598 24.77132 0.00000 25.74855 4.82175 MINI EXTERN> -76.63826 11.80324 0.00000 0.00000 0.00000 MINI CONSTR> 63.13702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 58.63291 0.01670 0.12435 0.00012 MINI INTERN> 5.01696 24.75792 0.00000 25.72869 4.82035 MINI EXTERN> -76.65268 11.79861 0.00000 0.00000 0.00000 MINI CONSTR> 63.16306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11166 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 58.61720 0.01571 0.13712 0.00013 MINI INTERN> 5.00821 24.75139 0.00000 25.71182 4.81691 MINI EXTERN> -76.65953 11.79880 0.00000 0.00000 0.00000 MINI CONSTR> 63.18959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 58.60090 0.01630 0.13619 0.00013 MINI INTERN> 5.00553 24.74127 0.00000 25.69304 4.81459 MINI EXTERN> -76.67009 11.79972 0.00000 0.00000 0.00000 MINI CONSTR> 63.21685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11166 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 58.58722 0.01368 0.19715 0.00014 MINI INTERN> 4.99452 24.73799 0.00000 25.67776 4.80943 MINI EXTERN> -76.67198 11.79638 0.00000 0.00000 0.00000 MINI CONSTR> 63.24312 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 58.57207 0.01515 0.21743 0.00014 MINI INTERN> 4.98874 24.72754 0.00000 25.65905 4.80767 MINI EXTERN> -76.68290 11.80162 0.00000 0.00000 0.00000 MINI CONSTR> 63.27035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11166 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 58.55797 0.01410 0.22299 0.00015 MINI INTERN> 4.98255 24.72270 0.00000 25.64359 4.80366 MINI EXTERN> -76.68757 11.79784 0.00000 0.00000 0.00000 MINI CONSTR> 63.29521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 58.54384 0.01413 0.24149 0.00015 MINI INTERN> 4.99061 24.71241 0.00000 25.62534 4.80070 MINI EXTERN> -76.69692 11.79076 0.00000 0.00000 0.00000 MINI CONSTR> 63.32093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11165 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 58.52977 0.01407 0.22489 0.00016 MINI INTERN> 4.97921 24.70593 0.00000 25.60994 4.79874 MINI EXTERN> -76.70485 11.79609 0.00000 0.00000 0.00000 MINI CONSTR> 63.34472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 58.51625 0.01352 0.25324 0.00016 MINI INTERN> 5.00187 24.69090 0.00000 25.58961 4.79691 MINI EXTERN> -76.71841 11.78518 0.00000 0.00000 0.00000 MINI CONSTR> 63.37020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11164 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 58.50240 0.01385 0.23462 0.00017 MINI INTERN> 4.98169 24.68863 0.00000 25.57595 4.79329 MINI EXTERN> -76.72134 11.78987 0.00000 0.00000 0.00000 MINI CONSTR> 63.39429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 58.48497 0.01743 0.08041 0.00007 MINI INTERN> 5.02679 24.65878 0.00000 25.54985 4.79910 MINI EXTERN> -76.75577 11.78825 0.00000 0.00000 0.00000 MINI CONSTR> 63.41797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11164 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 58.47778 0.00719 0.26833 0.00018 MINI INTERN> 4.97867 24.67396 0.00000 25.54412 4.78774 MINI EXTERN> -76.73525 11.78645 0.00000 0.00000 0.00000 MINI CONSTR> 63.44207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 58.46648 0.01129 0.31341 0.00019 MINI INTERN> 4.97476 24.66117 0.00000 25.52576 4.78862 MINI EXTERN> -76.75037 11.79965 0.00000 0.00000 0.00000 MINI CONSTR> 63.46689 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11163 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 58.45401 0.01247 0.29913 0.00020 MINI INTERN> 4.96033 24.66139 0.00000 25.51362 4.78309 MINI EXTERN> -76.74862 11.79451 0.00000 0.00000 0.00000 MINI CONSTR> 63.48970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 58.43421 0.01981 0.09307 0.00008 MINI INTERN> 5.02943 24.62360 0.00000 25.48397 4.79062 MINI EXTERN> -76.79049 11.78402 0.00000 0.00000 0.00000 MINI CONSTR> 63.51305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11162 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 58.42321 0.01100 0.07370 0.00009 MINI INTERN> 5.02017 24.61943 0.00000 25.47166 4.78755 MINI EXTERN> -76.79332 11.78441 0.00000 0.00000 0.00000 MINI CONSTR> 63.53331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 58.41140 0.01181 0.07658 0.00009 MINI INTERN> 5.02194 24.61059 0.00000 25.45561 4.78564 MINI EXTERN> -76.80193 11.78328 0.00000 0.00000 0.00000 MINI CONSTR> 63.55626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11161 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 58.39984 0.01155 0.07582 0.00009 MINI INTERN> 5.02169 24.60285 0.00000 25.44031 4.78338 MINI EXTERN> -76.80915 11.78199 0.00000 0.00000 0.00000 MINI CONSTR> 63.57877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 58.38830 0.01154 0.13081 0.00010 MINI INTERN> 5.03571 24.58873 0.00000 25.42028 4.78329 MINI EXTERN> -76.82507 11.78113 0.00000 0.00000 0.00000 MINI CONSTR> 63.60424 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11161 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 58.37685 0.01145 0.09540 0.00010 MINI INTERN> 5.02658 24.58524 0.00000 25.40785 4.77958 MINI EXTERN> -76.82669 11.77915 0.00000 0.00000 0.00000 MINI CONSTR> 63.62514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 58.36633 0.01052 0.11232 0.00011 MINI INTERN> 5.03119 24.57540 0.00000 25.39179 4.77839 MINI EXTERN> -76.83664 11.77892 0.00000 0.00000 0.00000 MINI CONSTR> 63.64728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11161 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 58.35560 0.01074 0.11483 0.00011 MINI INTERN> 5.02765 24.56849 0.00000 25.37716 4.77632 MINI EXTERN> -76.84335 11.77998 0.00000 0.00000 0.00000 MINI CONSTR> 63.66933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 58.34663 0.00897 0.16240 0.00011 MINI INTERN> 5.04265 24.55654 0.00000 25.36023 4.77581 MINI EXTERN> -76.85584 11.77643 0.00000 0.00000 0.00000 MINI CONSTR> 63.69080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11160 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 58.33649 0.01014 0.17947 0.00012 MINI INTERN> 5.03198 24.55181 0.00000 25.34650 4.77357 MINI EXTERN> -76.86121 11.78081 0.00000 0.00000 0.00000 MINI CONSTR> 63.71302 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 58.33649 0.01014 0.17947 0.00014 STPD INTERN> 5.03198 24.55181 0.00000 25.34650 4.77357 STPD EXTERN> -76.86121 11.78081 0.00000 0.00000 0.00000 STPD CONSTR> 63.71302 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 11160 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11160 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 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 58.33649 0.01014 0.17947 0.00000 MINI INTERN> 5.03198 24.55181 0.00000 25.34650 4.77357 MINI EXTERN> -76.86121 11.78081 0.00000 0.00000 0.00000 MINI CONSTR> 63.71302 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 57.87407 0.46242 0.02800 0.01882 MINI INTERN> 4.96400 23.92195 0.00000 24.09320 4.59399 MINI EXTERN> -77.53200 11.76244 0.00000 0.00000 0.00000 MINI CONSTR> 66.07049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 57.87140 0.00267 0.04974 0.00375 MINI INTERN> 4.94333 23.93522 0.00000 24.07554 4.56114 MINI EXTERN> -77.31677 11.71356 0.00000 0.00000 0.00000 MINI CONSTR> 65.95938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 57.86659 0.00481 0.04785 0.00804 MINI INTERN> 4.92527 23.93615 0.00000 24.05265 4.58461 MINI EXTERN> -77.13005 11.76734 0.00000 0.00000 0.00000 MINI CONSTR> 65.73062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 57.86423 0.00236 0.02699 0.00295 MINI INTERN> 4.95827 23.98068 0.00000 24.06311 4.57488 MINI EXTERN> -77.15818 11.79244 0.00000 0.00000 0.00000 MINI CONSTR> 65.65303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 57.86330 0.00093 0.01975 0.00165 MINI INTERN> 4.96871 23.99372 0.00000 24.08522 4.57830 MINI EXTERN> -77.23348 11.81845 0.00000 0.00000 0.00000 MINI CONSTR> 65.65238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 57.86281 0.00049 0.01437 0.00138 MINI INTERN> 4.97317 23.98764 0.00000 24.09825 4.58493 MINI EXTERN> -77.26486 11.81913 0.00000 0.00000 0.00000 MINI CONSTR> 65.66454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 57.86247 0.00035 0.01289 0.00156 MINI INTERN> 4.96246 23.98646 0.00000 24.10182 4.58875 MINI EXTERN> -77.27577 11.82380 0.00000 0.00000 0.00000 MINI CONSTR> 65.67496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 57.86218 0.00028 0.01117 0.00140 MINI INTERN> 4.96069 23.97848 0.00000 24.09896 4.58702 MINI EXTERN> -77.26856 11.82114 0.00000 0.00000 0.00000 MINI CONSTR> 65.68446 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 57.86199 0.00020 0.00966 0.00107 MINI INTERN> 4.96432 23.97491 0.00000 24.08435 4.58276 MINI EXTERN> -77.26469 11.82759 0.00000 0.00000 0.00000 MINI CONSTR> 65.69274 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> 45 57.86199 0.00020 0.00966 0.02000 CONJ INTERN> 4.96432 23.97491 0.00000 24.08435 4.58276 CONJ EXTERN> -77.26469 11.82759 0.00000 0.00000 0.00000 CONJ CONSTR> 65.69274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "7800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.73944 ( PROT LYS 1 HT2 ) 0.73944 ( PROT LYS 1 N ) 0.92430 ( PROT LYS 1 HT3 ) 0.73944 ( PROT LYS 1 CA ) 0.92430 ( PROT LYS 1 CB ) 0.73944 ( PROT LYS 1 CG ) 0.73944 ( PROT LYS 1 CD ) 0.73944 ( PROT LYS 1 CE ) 0.73944 ( PROT LYS 1 NZ ) 0.73944 ( PROT LYS 1 HZ1 ) 0.73944 ( PROT LYS 1 HZ2 ) 0.73944 ( PROT LYS 1 HZ3 ) 0.73944 ( PROT LYS 1 C ) 0.92430 ( PROT LYS 1 O ) 0.92430 ( PROT MET 2 N ) 0.92430 ( PROT MET 2 H ) 0.73944 ( PROT MET 2 CA ) 0.92430 ( PROT MET 2 CB ) 0.73944 ( PROT MET 2 CG ) 0.73944 ( PROT MET 2 SD ) 0.73944 ( PROT MET 2 CE ) 0.73944 ( PROT MET 2 C ) 0.92430 ( PROT MET 2 O ) 0.92430 ( PROT LYS 3 N ) 0.92430 ( PROT LYS 3 H ) 0.73944 ( PROT LYS 3 CA ) 0.92430 ( PROT LYS 3 CB ) 0.73944 ( PROT LYS 3 CG ) 0.73944 ( PROT LYS 3 CD ) 0.73944 ( PROT LYS 3 CE ) 0.73944 ( PROT LYS 3 NZ ) 0.73944 ( PROT LYS 3 HZ1 ) 0.73944 ( PROT LYS 3 HZ2 ) 0.73944 ( PROT LYS 3 HZ3 ) 0.73944 ( PROT LYS 3 C ) 0.92430 ( PROT LYS 3 O ) 0.92430 ( PROT ALA 4 N ) 0.92430 ( PROT ALA 4 H ) 0.73944 ( PROT ALA 4 CA ) 0.92430 ( PROT ALA 4 CB ) 0.73944 ( PROT ALA 4 C ) 0.92430 ( PROT ALA 4 O ) 0.92430 ( PROT VAL 5 N ) 0.92430 ( PROT VAL 5 H ) 0.73944 ( PROT VAL 5 CA ) 0.92430 ( PROT VAL 5 CB ) 0.73944 ( PROT VAL 5 CG1 ) 0.73944 ( PROT VAL 5 CG2 ) 0.73944 ( PROT VAL 5 C ) 0.92430 ( PROT VAL 5 O ) 0.92430 ( PROT MET 6 N ) 0.92430 ( PROT MET 6 H ) 0.73944 ( PROT MET 6 CA ) 0.92430 ( PROT MET 6 CB ) 0.73944 ( PROT MET 6 CG ) 0.73944 ( PROT MET 6 SD ) 0.73944 ( PROT MET 6 CE ) 0.73944 ( PROT MET 6 C ) 0.92430 ( PROT MET 6 O ) 0.92430 ( PROT ILE 7 N ) 0.92430 ( PROT ILE 7 H ) 0.73944 ( PROT ILE 7 CA ) 0.92430 ( PROT ILE 7 CB ) 0.73944 ( PROT ILE 7 CG2 ) 0.73944 ( PROT ILE 7 CG1 ) 0.73944 ( PROT ILE 7 CD ) 0.73944 ( PROT ILE 7 C ) 0.92430 ( PROT ILE 7 O ) 0.92430 ( PROT GLY 8 N ) 0.92430 ( PROT GLY 8 H ) 0.73944 ( PROT GLY 8 CA ) 0.92430 ( PROT GLY 8 C ) 0.92430 ( PROT GLY 8 O ) 0.92430 ( PROT ALA 9 N ) 0.92430 ( PROT ALA 9 H ) 0.73944 ( PROT ALA 9 CA ) 0.92430 ( PROT ALA 9 CB ) 0.73944 ( PROT ALA 9 C ) 0.92430 ( PROT ALA 9 O ) 0.92430 ( PROT CYS 10 N ) 0.92430 ( PROT CYS 10 H ) 0.73944 ( PROT CYS 10 CA ) 0.92430 ( PROT CYS 10 CB ) 0.73944 ( PROT CYS 10 SG ) 0.73944 ( PROT CYS 10 C ) 0.92430 ( PROT CYS 10 O ) 0.92430 ( PROT PHE 11 N ) 0.92430 ( PROT PHE 11 H ) 0.73944 ( PROT PHE 11 CA ) 0.92430 ( PROT PHE 11 CB ) 0.73944 ( PROT PHE 11 CG ) 0.73944 ( PROT PHE 11 CD1 ) 0.73944 ( PROT PHE 11 CD2 ) 0.73944 ( PROT PHE 11 CE1 ) 0.73944 ( PROT PHE 11 CE2 ) 0.73944 ( PROT PHE 11 CZ ) 0.73944 ( PROT PHE 11 C ) 0.92430 ( PROT PHE 11 O ) 0.92430 ( PROT LEU 12 N ) 0.92430 ( PROT LEU 12 H ) 0.73944 ( PROT LEU 12 CA ) 0.92430 ( PROT LEU 12 CB ) 0.73944 ( PROT LEU 12 CG ) 0.73944 ( PROT LEU 12 CD1 ) 0.73944 ( PROT LEU 12 CD2 ) 0.73944 ( PROT LEU 12 C ) 0.92430 ( PROT LEU 12 O ) 0.92430 ( PROT ILE 13 N ) 0.92430 ( PROT ILE 13 H ) 0.73944 ( PROT ILE 13 CA ) 0.92430 ( PROT ILE 13 CB ) 0.73944 ( PROT ILE 13 CG2 ) 0.73944 ( PROT ILE 13 CG1 ) 0.73944 ( PROT ILE 13 CD ) 0.73944 ( PROT ILE 13 C ) 0.92430 ( PROT ILE 13 O ) 0.92430 ( PROT ASH 14 N ) 0.92430 ( PROT ASH 14 H ) 0.73944 ( PROT ASH 14 CA ) 0.92430 ( PROT ASH 14 CB ) 0.73944 ( PROT ASH 14 CG ) 0.73944 ( PROT ASH 14 OD1 ) 0.73944 ( PROT ASH 14 OD2 ) 0.73944 ( PROT ASH 14 HD2 ) 0.73944 ( PROT ASH 14 C ) 0.92430 ( PROT ASH 14 O ) 0.92430 ( PROT PHE 15 N ) 0.92430 ( PROT PHE 15 H ) 0.73944 ( PROT PHE 15 CA ) 0.92430 ( PROT PHE 15 CB ) 0.73944 ( PROT PHE 15 CG ) 0.73944 ( PROT PHE 15 CD1 ) 0.73944 ( PROT PHE 15 CD2 ) 0.73944 ( PROT PHE 15 CE1 ) 0.73944 ( PROT PHE 15 CE2 ) 0.73944 ( PROT PHE 15 CZ ) 0.73944 ( PROT PHE 15 C ) 0.92430 ( PROT PHE 15 O ) 0.92430 ( PROT MET 16 N ) 0.92430 ( PROT MET 16 H ) 0.73944 ( PROT MET 16 CA ) 0.92430 ( PROT MET 16 CB ) 0.73944 ( PROT MET 16 CG ) 0.73944 ( PROT MET 16 SD ) 0.73944 ( PROT MET 16 CE ) 0.73944 ( PROT MET 16 C ) 0.92430 ( PROT MET 16 O ) 0.92430 ( PROT PHE 17 N ) 0.92430 ( PROT PHE 17 H ) 0.73944 ( PROT PHE 17 CA ) 0.92430 ( PROT PHE 17 CB ) 0.73944 ( PROT PHE 17 CG ) 0.73944 ( PROT PHE 17 CD1 ) 0.73944 ( PROT PHE 17 CD2 ) 0.73944 ( PROT PHE 17 CE1 ) 0.73944 ( PROT PHE 17 CE2 ) 0.73944 ( PROT PHE 17 CZ ) 0.73944 ( PROT PHE 17 C ) 0.92430 ( PROT PHE 17 O ) 0.92430 ( PROT PHE 18 N ) 0.92430 ( PROT PHE 18 H ) 0.73944 ( PROT PHE 18 CA ) 0.92430 ( PROT PHE 18 CB ) 0.73944 ( PROT PHE 18 CG ) 0.73944 ( PROT PHE 18 CD1 ) 0.73944 ( PROT PHE 18 CD2 ) 0.73944 ( PROT PHE 18 CE1 ) 0.73944 ( PROT PHE 18 CE2 ) 0.73944 ( PROT PHE 18 CZ ) 0.73944 ( PROT PHE 18 C ) 0.92430 ( PROT PHE 18 O ) 0.92430 ( PROT GLU 19 N ) 0.92430 ( PROT GLU 19 H ) 0.73944 ( PROT GLU 19 CA ) 0.92430 ( PROT GLU 19 CB ) 0.73944 ( PROT GLU 19 CG ) 0.73944 ( PROT GLU 19 CD ) 0.73944 ( PROT GLU 19 OE1 ) 0.73944 ( PROT GLU 19 OE2 ) 0.73944 ( PROT GLU 19 C ) 0.92430 ( PROT GLU 19 OT1 ) 0.73944 ( PROT GLU 19 OT2 ) 0.73944 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40326 5.29263 -8.69093 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00128 -0.00022 -0.00228 ROTATION MATRIX 1.000000 -0.000151 0.000078 0.000151 1.000000 0.000262 -0.000078 -0.000262 1.000000 AXIS OF ROTATION IS 0.838096 -0.251143 -0.484275 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 53.0823 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.538579 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.5386" Parameter: A <- "0.5386" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.70881 5.22463 -8.78606 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00603 0.03979 -0.00831 ROTATION MATRIX 0.999757 0.017993 0.012769 -0.017780 0.999705 -0.016573 -0.013063 0.016342 0.999781 AXIS OF ROTATION IS -0.597922 -0.469257 0.649836 ANGLE IS 1.58 CENTER OF ROTATION 8.914050 5.206564 -9.551670 SHIFT IS -0.027678 TOTAL SQUARE DIFF IS 2.6146 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.370959 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.5386" RDCMND substituted energy or value "?RMS" to " 0.3710" Parameter: A <- "0.5386 0.3710" 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 0.5386 0.3710 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 " 65.69" Parameter: H <- "65.69" 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 -7.83075 65.69274 0.77414 ENER INTERN> 4.96432 23.97491 0.00000 24.08435 4.58276 ENER EXTERN> -77.26469 11.82759 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 " -7.83" Parameter: B <- "-7.83" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 11.83" Parameter: C <- "11.83" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -77.26" Parameter: C <- " -65.43" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -65.43" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.96" Parameter: D <- "4.96" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 23.97" Parameter: D <- " 28.93" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 24.08" Parameter: D <- " 53.01" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.58" Parameter: D <- " 57.59" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 57.59" 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= -7.83 GRMS= 0.77 ELEC= 11.83 VDW= -77.26 RDTITL> *EXTERNAL= -65.43 INTERNAL= 57.59 USER= 0.00 HARM= 65.69 RDTITL> *BOND= 4.96 ANGL= 23.97 DIHE= 24.08 IMPR= 4.58 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11160 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11144 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 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 36.88851 -44.71926 0.29118 0.02000 MINI INTERN> 4.96432 23.97491 0.00000 24.08435 4.58276 MINI EXTERN> -77.26469 11.82759 0.00000 0.00000 0.00000 MINI CONSTR> 44.71926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 59.99282 -23.10431 16.34512 0.00864 MINI INTERN> 29.03370 23.11406 0.00000 25.32086 4.14729 MINI EXTERN> -82.13015 13.58473 0.00000 0.00000 0.00000 MINI CONSTR> 46.92234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11139 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 35.72202 24.27080 0.48060 0.00156 MINI INTERN> 5.13927 23.77861 0.00000 24.80302 4.64276 MINI EXTERN> -82.58864 12.88122 0.00000 0.00000 0.00000 MINI CONSTR> 47.06578 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 35.62241 0.09961 0.51441 0.00067 MINI INTERN> 5.12941 23.92817 0.00000 24.66958 4.66206 MINI EXTERN> -82.72324 12.79957 0.00000 0.00000 0.00000 MINI CONSTR> 47.15686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11137 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 35.53797 0.08444 0.34953 0.00029 MINI INTERN> 5.08021 23.78669 0.00000 24.66370 4.61323 MINI EXTERN> -82.60782 12.78194 0.00000 0.00000 0.00000 MINI CONSTR> 47.22001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 35.47657 0.06140 0.43139 0.00030 MINI INTERN> 5.06336 23.74318 0.00000 24.62072 4.59895 MINI EXTERN> -82.59164 12.74989 0.00000 0.00000 0.00000 MINI CONSTR> 47.29212 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11136 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 35.40919 0.06738 0.44867 0.00031 MINI INTERN> 5.08217 23.68055 0.00000 24.57244 4.58850 MINI EXTERN> -82.60904 12.72407 0.00000 0.00000 0.00000 MINI CONSTR> 47.37050 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 35.35140 0.05779 0.52413 0.00032 MINI INTERN> 5.05567 23.64918 0.00000 24.53011 4.58185 MINI EXTERN> -82.63135 12.71817 0.00000 0.00000 0.00000 MINI CONSTR> 47.44777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11136 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 35.29202 0.05937 0.47031 0.00034 MINI INTERN> 5.03743 23.63007 0.00000 24.49671 4.57270 MINI EXTERN> -82.65417 12.69343 0.00000 0.00000 0.00000 MINI CONSTR> 47.51585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 35.23145 0.06058 0.50212 0.00035 MINI INTERN> 5.07022 23.55475 0.00000 24.45277 4.56521 MINI EXTERN> -82.70521 12.69673 0.00000 0.00000 0.00000 MINI CONSTR> 47.59697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11135 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 35.15737 0.07408 0.16937 0.00015 MINI INTERN> 5.00848 23.61584 0.00000 24.40278 4.58896 MINI EXTERN> -82.77947 12.65528 0.00000 0.00000 0.00000 MINI CONSTR> 47.66550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 35.13117 0.02620 0.58499 0.00037 MINI INTERN> 5.05287 23.53129 0.00000 24.38069 4.55557 MINI EXTERN> -82.77877 12.65197 0.00000 0.00000 0.00000 MINI CONSTR> 47.73754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11132 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 35.08241 0.04876 0.61444 0.00039 MINI INTERN> 4.99553 23.51099 0.00000 24.35396 4.54984 MINI EXTERN> -82.81752 12.68117 0.00000 0.00000 0.00000 MINI CONSTR> 47.80844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 35.03282 0.04959 0.61301 0.00040 MINI INTERN> 5.00636 23.48519 0.00000 24.32387 4.53754 MINI EXTERN> -82.85041 12.65344 0.00000 0.00000 0.00000 MINI CONSTR> 47.87683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11132 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 34.95088 0.08194 0.18920 0.00017 MINI INTERN> 4.99503 23.49471 0.00000 24.26589 4.56865 MINI EXTERN> -82.95586 12.63683 0.00000 0.00000 0.00000 MINI CONSTR> 47.94563 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 34.90594 0.04494 0.15177 0.00018 MINI INTERN> 4.99465 23.45950 0.00000 24.23917 4.55972 MINI EXTERN> -82.98930 12.63653 0.00000 0.00000 0.00000 MINI CONSTR> 48.00566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11132 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 34.85895 0.04699 0.15718 0.00019 MINI INTERN> 4.99472 23.43093 0.00000 24.20663 4.55533 MINI EXTERN> -83.03419 12.63407 0.00000 0.00000 0.00000 MINI CONSTR> 48.07146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 34.81107 0.04788 0.24900 0.00019 MINI INTERN> 5.00067 23.40799 0.00000 24.16616 4.55673 MINI EXTERN> -83.09432 12.62920 0.00000 0.00000 0.00000 MINI CONSTR> 48.14464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11128 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 34.76527 0.04580 0.20125 0.00020 MINI INTERN> 4.99690 23.37745 0.00000 24.13899 4.54753 MINI EXTERN> -83.12758 12.62636 0.00000 0.00000 0.00000 MINI CONSTR> 48.20562 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 34.72213 0.04314 0.22093 0.00021 MINI INTERN> 5.00394 23.34729 0.00000 24.10598 4.54451 MINI EXTERN> -83.17333 12.62543 0.00000 0.00000 0.00000 MINI CONSTR> 48.26829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11126 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 34.67799 0.04413 0.22669 0.00022 MINI INTERN> 4.99673 23.32167 0.00000 24.07521 4.53955 MINI EXTERN> -83.21410 12.62737 0.00000 0.00000 0.00000 MINI CONSTR> 48.33157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 34.64038 0.03761 0.32369 0.00022 MINI INTERN> 5.02788 23.29027 0.00000 24.03770 4.53991 MINI EXTERN> -83.26705 12.61809 0.00000 0.00000 0.00000 MINI CONSTR> 48.39358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11124 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 34.59889 0.04149 0.35382 0.00023 MINI INTERN> 5.00650 23.27053 0.00000 24.00912 4.53460 MINI EXTERN> -83.30353 12.62605 0.00000 0.00000 0.00000 MINI CONSTR> 48.45562 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 34.56011 0.03878 0.36315 0.00024 MINI INTERN> 5.03443 23.23494 0.00000 23.97493 4.53227 MINI EXTERN> -83.34865 12.61874 0.00000 0.00000 0.00000 MINI CONSTR> 48.51345 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11124 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 34.52048 0.03963 0.39199 0.00025 MINI INTERN> 5.04387 23.21010 0.00000 23.94345 4.52685 MINI EXTERN> -83.38674 12.60953 0.00000 0.00000 0.00000 MINI CONSTR> 48.57342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 34.48197 0.03852 0.37109 0.00026 MINI INTERN> 5.03031 23.18607 0.00000 23.91674 4.52245 MINI EXTERN> -83.41941 12.61835 0.00000 0.00000 0.00000 MINI CONSTR> 48.62745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 34.44517 0.03679 0.41229 0.00027 MINI INTERN> 5.03922 23.16485 0.00000 23.88863 4.51423 MINI EXTERN> -83.44896 12.60348 0.00000 0.00000 0.00000 MINI CONSTR> 48.68373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 34.40744 0.03773 0.38695 0.00028 MINI INTERN> 5.05014 23.13243 0.00000 23.85618 4.51345 MINI EXTERN> -83.49092 12.60801 0.00000 0.00000 0.00000 MINI CONSTR> 48.73814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11122 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 34.35956 0.04788 0.13254 0.00012 MINI INTERN> 4.93625 23.14653 0.00000 23.85335 4.49044 MINI EXTERN> -83.47336 12.61897 0.00000 0.00000 0.00000 MINI CONSTR> 48.78738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 34.33919 0.02038 0.44322 0.00030 MINI INTERN> 5.06618 23.08353 0.00000 23.79695 4.50558 MINI EXTERN> -83.55938 12.60113 0.00000 0.00000 0.00000 MINI CONSTR> 48.84519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11121 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 34.30736 0.03183 0.50837 0.00031 MINI INTERN> 5.00955 23.07945 0.00000 23.77709 4.49823 MINI EXTERN> -83.57765 12.62223 0.00000 0.00000 0.00000 MINI CONSTR> 48.89846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 34.27212 0.03524 0.47777 0.00032 MINI INTERN> 5.06944 23.03473 0.00000 23.73813 4.49975 MINI EXTERN> -83.62729 12.60696 0.00000 0.00000 0.00000 MINI CONSTR> 48.95040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11120 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 34.21713 0.05498 0.14866 0.00014 MINI INTERN> 4.91639 23.06985 0.00000 23.74199 4.47104 MINI EXTERN> -83.59252 12.61122 0.00000 0.00000 0.00000 MINI CONSTR> 48.99916 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 34.18644 0.03069 0.12457 0.00014 MINI INTERN> 4.92138 23.05010 0.00000 23.71518 4.46945 MINI EXTERN> -83.62324 12.60930 0.00000 0.00000 0.00000 MINI CONSTR> 49.04427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11120 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 34.15388 0.03256 0.12782 0.00015 MINI INTERN> 4.91540 23.03356 0.00000 23.68910 4.46470 MINI EXTERN> -83.64918 12.60703 0.00000 0.00000 0.00000 MINI CONSTR> 49.09327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 34.12132 0.03256 0.12340 0.00015 MINI INTERN> 4.91579 23.01411 0.00000 23.66153 4.46090 MINI EXTERN> -83.67750 12.60426 0.00000 0.00000 0.00000 MINI CONSTR> 49.14223 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11120 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 34.08727 0.03405 0.20793 0.00016 MINI INTERN> 4.88414 23.00526 0.00000 23.63735 4.45100 MINI EXTERN> -83.69418 12.60584 0.00000 0.00000 0.00000 MINI CONSTR> 49.19786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 34.05593 0.03134 0.16462 0.00017 MINI INTERN> 4.89935 22.98195 0.00000 23.60846 4.44956 MINI EXTERN> -83.72587 12.59942 0.00000 0.00000 0.00000 MINI CONSTR> 49.24307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11119 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 34.02628 0.02965 0.18289 0.00017 MINI INTERN> 4.88430 22.97066 0.00000 23.58487 4.44421 MINI EXTERN> -83.74638 12.59923 0.00000 0.00000 0.00000 MINI CONSTR> 49.28938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 33.99522 0.03106 0.17582 0.00018 MINI INTERN> 4.88276 22.95173 0.00000 23.55761 4.44086 MINI EXTERN> -83.77309 12.59863 0.00000 0.00000 0.00000 MINI CONSTR> 49.33672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11118 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 33.96898 0.02623 0.27149 0.00019 MINI INTERN> 4.86213 22.94610 0.00000 23.53645 4.43214 MINI EXTERN> -83.78582 12.59453 0.00000 0.00000 0.00000 MINI CONSTR> 49.38346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 33.94081 0.02817 0.29519 0.00019 MINI INTERN> 4.85118 22.93055 0.00000 23.51105 4.42921 MINI EXTERN> -83.81010 12.59992 0.00000 0.00000 0.00000 MINI CONSTR> 49.42900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11118 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 33.91380 0.02701 0.30036 0.00020 MINI INTERN> 4.84040 22.92217 0.00000 23.48904 4.42323 MINI EXTERN> -83.82673 12.59386 0.00000 0.00000 0.00000 MINI CONSTR> 49.47183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 33.88533 0.02847 0.31685 0.00021 MINI INTERN> 4.84540 22.90369 0.00000 23.46216 4.41877 MINI EXTERN> -83.85009 12.58775 0.00000 0.00000 0.00000 MINI CONSTR> 49.51764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11118 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 33.85921 0.02612 0.33905 0.00021 MINI INTERN> 4.82804 22.89300 0.00000 23.43912 4.41499 MINI EXTERN> -83.86981 12.59283 0.00000 0.00000 0.00000 MINI CONSTR> 49.56103 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 33.83264 0.02656 0.31760 0.00022 MINI INTERN> 4.83406 22.87783 0.00000 23.41526 4.41128 MINI EXTERN> -83.89066 12.58414 0.00000 0.00000 0.00000 MINI CONSTR> 49.60072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11118 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 33.80642 0.02622 0.35144 0.00023 MINI INTERN> 4.83103 22.85769 0.00000 23.38814 4.40993 MINI EXTERN> -83.91717 12.59167 0.00000 0.00000 0.00000 MINI CONSTR> 49.64513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 33.77995 0.02646 0.32699 0.00024 MINI INTERN> 4.82272 22.85013 0.00000 23.36699 4.40351 MINI EXTERN> -83.93100 12.58207 0.00000 0.00000 0.00000 MINI CONSTR> 49.68554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11118 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 33.74569 0.03426 0.10987 0.00010 MINI INTERN> 4.90577 22.79140 0.00000 23.32458 4.41357 MINI EXTERN> -83.99000 12.57465 0.00000 0.00000 0.00000 MINI CONSTR> 49.72572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 33.73169 0.01400 0.37102 0.00026 MINI INTERN> 4.81060 22.82575 0.00000 23.32093 4.39462 MINI EXTERN> -83.96640 12.57827 0.00000 0.00000 0.00000 MINI CONSTR> 49.76792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11118 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 33.70526 0.02643 0.37709 0.00027 MINI INTERN> 4.81331 22.80596 0.00000 23.29436 4.39104 MINI EXTERN> -83.98794 12.57707 0.00000 0.00000 0.00000 MINI CONSTR> 49.81146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 33.66752 0.03774 0.11848 0.00011 MINI INTERN> 4.90347 22.74475 0.00000 23.24932 4.40293 MINI EXTERN> -84.05292 12.56748 0.00000 0.00000 0.00000 MINI CONSTR> 49.85249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11117 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 33.65871 0.00881 0.40835 0.00029 MINI INTERN> 4.80608 22.78053 0.00000 23.24836 4.38293 MINI EXTERN> -84.02313 12.57256 0.00000 0.00000 0.00000 MINI CONSTR> 49.89138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 33.61670 0.04201 0.11921 0.00012 MINI INTERN> 4.89752 22.71663 0.00000 23.20034 4.39537 MINI EXTERN> -84.09183 12.56286 0.00000 0.00000 0.00000 MINI CONSTR> 49.93581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11117 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 33.59480 0.02190 0.10175 0.00013 MINI INTERN> 4.88965 22.70576 0.00000 23.18064 4.39098 MINI EXTERN> -84.10503 12.56156 0.00000 0.00000 0.00000 MINI CONSTR> 49.97123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 33.57083 0.02397 0.10606 0.00013 MINI INTERN> 4.88941 22.69119 0.00000 23.15636 4.38772 MINI EXTERN> -84.12434 12.55926 0.00000 0.00000 0.00000 MINI CONSTR> 50.01123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11116 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 33.54800 0.02283 0.18355 0.00014 MINI INTERN> 4.90688 22.67132 0.00000 23.12763 4.38724 MINI EXTERN> -84.15353 12.55489 0.00000 0.00000 0.00000 MINI CONSTR> 50.05358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 33.52735 0.02065 0.10071 0.00014 MINI INTERN> 4.88443 22.66590 0.00000 23.11337 4.38076 MINI EXTERN> -84.15640 12.55548 0.00000 0.00000 0.00000 MINI CONSTR> 50.08381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11115 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 33.50550 0.02185 0.21186 0.00015 MINI INTERN> 4.90799 22.64459 0.00000 23.08250 4.38124 MINI EXTERN> -84.18863 12.55063 0.00000 0.00000 0.00000 MINI CONSTR> 50.12717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 33.48318 0.02232 0.15967 0.00015 MINI INTERN> 4.89608 22.63407 0.00000 23.06459 4.37606 MINI EXTERN> -84.19879 12.54975 0.00000 0.00000 0.00000 MINI CONSTR> 50.16142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11115 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 33.46524 0.01794 0.22659 0.00016 MINI INTERN> 4.91232 22.61652 0.00000 23.03983 4.37547 MINI EXTERN> -84.22231 12.54642 0.00000 0.00000 0.00000 MINI CONSTR> 50.19699 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 33.44150 0.02375 0.15017 0.00016 MINI INTERN> 4.88924 22.61090 0.00000 23.02184 4.36926 MINI EXTERN> -84.22846 12.54639 0.00000 0.00000 0.00000 MINI CONSTR> 50.23233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11114 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 33.42466 0.01683 0.24081 0.00017 MINI INTERN> 4.90958 22.59238 0.00000 22.99671 4.36914 MINI EXTERN> -84.25392 12.54264 0.00000 0.00000 0.00000 MINI CONSTR> 50.26813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 33.40456 0.02010 0.27589 0.00018 MINI INTERN> 4.90801 22.58107 0.00000 22.97564 4.36526 MINI EXTERN> -84.27048 12.53931 0.00000 0.00000 0.00000 MINI CONSTR> 50.30574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11114 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 33.38622 0.01834 0.28261 0.00018 MINI INTERN> 4.91445 22.56636 0.00000 22.95336 4.36343 MINI EXTERN> -84.28809 12.53755 0.00000 0.00000 0.00000 MINI CONSTR> 50.33915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 33.36712 0.01910 0.27017 0.00019 MINI INTERN> 4.90877 22.55615 0.00000 22.93369 4.36009 MINI EXTERN> -84.29994 12.53692 0.00000 0.00000 0.00000 MINI CONSTR> 50.37143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11114 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 33.34847 0.01865 0.29803 0.00020 MINI INTERN> 4.90509 22.54534 0.00000 22.91548 4.35551 MINI EXTERN> -84.31280 12.53383 0.00000 0.00000 0.00000 MINI CONSTR> 50.40603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 33.32452 0.02395 0.09240 0.00009 MINI INTERN> 4.86165 22.54455 0.00000 22.90372 4.34673 MINI EXTERN> -84.30406 12.53749 0.00000 0.00000 0.00000 MINI CONSTR> 50.43444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11113 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 33.31382 0.01070 0.31165 0.00021 MINI INTERN> 4.90996 22.52111 0.00000 22.87262 4.35157 MINI EXTERN> -84.34369 12.53174 0.00000 0.00000 0.00000 MINI CONSTR> 50.47052 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 33.29760 0.01622 0.35811 0.00022 MINI INTERN> 4.90657 22.51047 0.00000 22.85711 4.34623 MINI EXTERN> -84.35368 12.52796 0.00000 0.00000 0.00000 MINI CONSTR> 50.50294 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11113 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 33.27953 0.01807 0.33400 0.00023 MINI INTERN> 4.91838 22.49504 0.00000 22.83278 4.34629 MINI EXTERN> -84.37482 12.52636 0.00000 0.00000 0.00000 MINI CONSTR> 50.53549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 33.26269 0.01684 0.36271 0.00024 MINI INTERN> 4.90657 22.48960 0.00000 22.81259 4.34262 MINI EXTERN> -84.38473 12.52710 0.00000 0.00000 0.00000 MINI CONSTR> 50.56895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 33.23447 0.02822 0.11207 0.00010 MINI INTERN> 4.85129 22.48896 0.00000 22.80501 4.33057 MINI EXTERN> -84.36887 12.52938 0.00000 0.00000 0.00000 MINI CONSTR> 50.59811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 33.21899 0.01548 0.08718 0.00011 MINI INTERN> 4.85465 22.47855 0.00000 22.78702 4.32910 MINI EXTERN> -84.38351 12.52736 0.00000 0.00000 0.00000 MINI CONSTR> 50.62581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 33.20216 0.01683 0.09138 0.00011 MINI INTERN> 4.85190 22.46829 0.00000 22.76828 4.32584 MINI EXTERN> -84.39515 12.52588 0.00000 0.00000 0.00000 MINI CONSTR> 50.65712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 33.18573 0.01644 0.09053 0.00011 MINI INTERN> 4.85123 22.45766 0.00000 22.74961 4.32300 MINI EXTERN> -84.40767 12.52414 0.00000 0.00000 0.00000 MINI CONSTR> 50.68775 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 33.16922 0.01651 0.15767 0.00012 MINI INTERN> 4.84052 22.44868 0.00000 22.73068 4.31773 MINI EXTERN> -84.41419 12.52400 0.00000 0.00000 0.00000 MINI CONSTR> 50.72180 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 33.15266 0.01655 0.11390 0.00012 MINI INTERN> 4.84707 22.43623 0.00000 22.71172 4.31639 MINI EXTERN> -84.43075 12.52117 0.00000 0.00000 0.00000 MINI CONSTR> 50.75083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 33.13738 0.01528 0.13452 0.00013 MINI INTERN> 4.84141 22.42764 0.00000 22.69408 4.31278 MINI EXTERN> -84.43976 12.52036 0.00000 0.00000 0.00000 MINI CONSTR> 50.78087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 33.12159 0.01579 0.13476 0.00013 MINI INTERN> 4.84014 22.41744 0.00000 22.67525 4.31009 MINI EXTERN> -84.45162 12.51919 0.00000 0.00000 0.00000 MINI CONSTR> 50.81110 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 33.10838 0.01322 0.19543 0.00014 MINI INTERN> 4.83466 22.40885 0.00000 22.65904 4.30577 MINI EXTERN> -84.45846 12.51812 0.00000 0.00000 0.00000 MINI CONSTR> 50.84039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 33.09360 0.01478 0.21696 0.00014 MINI INTERN> 4.83343 22.39898 0.00000 22.63950 4.30339 MINI EXTERN> -84.47003 12.51787 0.00000 0.00000 0.00000 MINI CONSTR> 50.87046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 33.07979 0.01381 0.22240 0.00015 MINI INTERN> 4.82901 22.39094 0.00000 22.62381 4.29987 MINI EXTERN> -84.47836 12.51634 0.00000 0.00000 0.00000 MINI CONSTR> 50.89818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 33.06591 0.01388 0.23928 0.00015 MINI INTERN> 4.83173 22.37995 0.00000 22.60695 4.29701 MINI EXTERN> -84.49015 12.51369 0.00000 0.00000 0.00000 MINI CONSTR> 50.92674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 33.05193 0.01398 0.22361 0.00016 MINI INTERN> 4.82601 22.37333 0.00000 22.59032 4.29463 MINI EXTERN> -84.49916 12.51369 0.00000 0.00000 0.00000 MINI CONSTR> 50.95311 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 33.03848 0.01345 0.25184 0.00016 MINI INTERN> 4.83660 22.35954 0.00000 22.57278 4.29263 MINI EXTERN> -84.51452 12.50982 0.00000 0.00000 0.00000 MINI CONSTR> 50.98163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 33.02464 0.01384 0.23505 0.00017 MINI INTERN> 4.82658 22.35386 0.00000 22.55704 4.28916 MINI EXTERN> -84.52054 12.51005 0.00000 0.00000 0.00000 MINI CONSTR> 51.00849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 33.00728 0.01736 0.08064 0.00007 MINI INTERN> 4.84468 22.34049 0.00000 22.53662 4.29171 MINI EXTERN> -84.54635 12.50617 0.00000 0.00000 0.00000 MINI CONSTR> 51.03395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11112 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 32.99975 0.00753 0.26639 0.00018 MINI INTERN> 4.82329 22.33709 0.00000 22.52509 4.28352 MINI EXTERN> -84.53873 12.50765 0.00000 0.00000 0.00000 MINI CONSTR> 51.06185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 32.98105 0.01870 0.08589 0.00008 MINI INTERN> 4.84429 22.32246 0.00000 22.50373 4.28684 MINI EXTERN> -84.56713 12.50344 0.00000 0.00000 0.00000 MINI CONSTR> 51.08743 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11111 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 32.97602 0.00503 0.30166 0.00020 MINI INTERN> 4.81660 22.32366 0.00000 22.49212 4.27905 MINI EXTERN> -84.55669 12.50763 0.00000 0.00000 0.00000 MINI CONSTR> 51.11365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 32.95592 0.02010 0.09241 0.00008 MINI INTERN> 4.84397 22.30496 0.00000 22.47165 4.28213 MINI EXTERN> -84.58713 12.50091 0.00000 0.00000 0.00000 MINI CONSTR> 51.13942 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11110 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 32.95216 0.00375 0.31021 0.00021 MINI INTERN> 4.80996 22.30891 0.00000 22.46240 4.27303 MINI EXTERN> -84.57216 12.50527 0.00000 0.00000 0.00000 MINI CONSTR> 51.16476 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 32.93142 0.02074 0.10944 0.00009 MINI INTERN> 4.84421 22.28775 0.00000 22.43944 4.27764 MINI EXTERN> -84.60736 12.49848 0.00000 0.00000 0.00000 MINI CONSTR> 51.19126 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11109 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 32.92059 0.01083 0.07714 0.00009 MINI INTERN> 4.83911 22.28101 0.00000 22.42730 4.27465 MINI EXTERN> -84.61202 12.49794 0.00000 0.00000 0.00000 MINI CONSTR> 51.21260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 32.90806 0.01254 0.12560 0.00010 MINI INTERN> 4.84546 22.27058 0.00000 22.40829 4.27328 MINI EXTERN> -84.62696 12.49596 0.00000 0.00000 0.00000 MINI CONSTR> 51.24147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11109 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 32.89723 0.01082 0.07642 0.00010 MINI INTERN> 4.83748 22.26473 0.00000 22.39703 4.26989 MINI EXTERN> -84.62978 12.49573 0.00000 0.00000 0.00000 MINI CONSTR> 51.26215 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 32.88569 0.01154 0.14730 0.00011 MINI INTERN> 4.84859 22.25307 0.00000 22.37780 4.26908 MINI EXTERN> -84.64664 12.49313 0.00000 0.00000 0.00000 MINI CONSTR> 51.29066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11108 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 32.87362 0.01207 0.10861 0.00011 MINI INTERN> 4.83920 22.24752 0.00000 22.36418 4.26575 MINI EXTERN> -84.65074 12.49338 0.00000 0.00000 0.00000 MINI CONSTR> 51.31433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 32.86366 0.00995 0.16092 0.00011 MINI INTERN> 4.84851 22.23715 0.00000 22.34762 4.26476 MINI EXTERN> -84.66482 12.49106 0.00000 0.00000 0.00000 MINI CONSTR> 51.33939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11108 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 32.85071 0.01295 0.09595 0.00012 MINI INTERN> 4.83699 22.23169 0.00000 22.33454 4.26077 MINI EXTERN> -84.66788 12.49087 0.00000 0.00000 0.00000 MINI CONSTR> 51.36372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 32.85071 0.01295 0.09595 0.00014 STPD INTERN> 4.83699 22.23169 0.00000 22.33454 4.26077 STPD EXTERN> -84.66788 12.49087 0.00000 0.00000 0.00000 STPD CONSTR> 51.36372 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 11108 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11108 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 32.85071 0.01295 0.09595 0.00000 MINI INTERN> 4.83699 22.23169 0.00000 22.33454 4.26077 MINI EXTERN> -84.66788 12.49087 0.00000 0.00000 0.00000 MINI CONSTR> 51.36372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 32.12657 0.72414 0.06168 0.01264 MINI INTERN> 4.76359 21.22340 0.00000 20.50647 3.98284 MINI EXTERN> -85.99624 12.48110 0.00000 0.00000 0.00000 MINI CONSTR> 55.16541 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 32.12048 0.00609 0.07366 0.00498 MINI INTERN> 4.72483 21.23069 0.00000 20.47707 3.93684 MINI EXTERN> -85.74796 12.40051 0.00000 0.00000 0.00000 MINI CONSTR> 55.09850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 32.10906 0.01142 0.09007 0.01214 MINI INTERN> 4.68609 21.20278 0.00000 20.40969 3.95377 MINI EXTERN> -85.39703 12.38422 0.00000 0.00000 0.00000 MINI CONSTR> 54.86954 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 32.09887 0.01019 0.06850 0.00691 MINI INTERN> 4.74644 21.27797 0.00000 20.39262 3.92030 MINI EXTERN> -85.30063 12.38536 0.00000 0.00000 0.00000 MINI CONSTR> 54.67680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 32.09332 0.00555 0.05540 0.00568 MINI INTERN> 4.75884 21.34414 0.00000 20.41785 3.91620 MINI EXTERN> -85.37471 12.42705 0.00000 0.00000 0.00000 MINI CONSTR> 54.60395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 32.08976 0.00356 0.04519 0.00442 MINI INTERN> 4.78246 21.33635 0.00000 20.44916 3.93137 MINI EXTERN> -85.43001 12.44413 0.00000 0.00000 0.00000 MINI CONSTR> 54.57629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 32.08746 0.00229 0.03331 0.00274 MINI INTERN> 4.76688 21.33500 0.00000 20.47419 3.94055 MINI EXTERN> -85.45500 12.45719 0.00000 0.00000 0.00000 MINI CONSTR> 54.56866 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 32.08577 0.00169 0.03253 0.00374 MINI INTERN> 4.75883 21.32598 0.00000 20.49641 3.94212 MINI EXTERN> -85.46631 12.45512 0.00000 0.00000 0.00000 MINI CONSTR> 54.57361 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 32.08429 0.00148 0.03123 0.00350 MINI INTERN> 4.76384 21.31568 0.00000 20.48290 3.93677 MINI EXTERN> -85.45005 12.44754 0.00000 0.00000 0.00000 MINI CONSTR> 54.58763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 32.08301 0.00128 0.02730 0.00338 MINI INTERN> 4.75764 21.31495 0.00000 20.47413 3.93723 MINI EXTERN> -85.49008 12.48551 0.00000 0.00000 0.00000 MINI CONSTR> 54.60363 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 32.08204 0.00097 0.02312 0.00324 MINI INTERN> 4.75750 21.29258 0.00000 20.46100 3.93889 MINI EXTERN> -85.45921 12.48001 0.00000 0.00000 0.00000 MINI CONSTR> 54.61128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 32.08107 0.00097 0.02519 0.00372 MINI INTERN> 4.76319 21.28101 0.00000 20.44463 3.93268 MINI EXTERN> -85.42519 12.46669 0.00000 0.00000 0.00000 MINI CONSTR> 54.61805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 32.07986 0.00120 0.02911 0.00506 MINI INTERN> 4.75779 21.28651 0.00000 20.41370 3.92127 MINI EXTERN> -85.43958 12.50664 0.00000 0.00000 0.00000 MINI CONSTR> 54.63353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 32.07769 0.00217 0.04877 0.00926 MINI INTERN> 4.75811 21.29569 0.00000 20.39051 3.90455 MINI EXTERN> -85.43685 12.48967 0.00000 0.00000 0.00000 MINI CONSTR> 54.67600 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 32.06015 0.01754 0.22366 0.12929 MINI INTERN> 4.78209 21.24766 0.00000 20.22733 3.89880 MINI EXTERN> -85.93603 12.75723 0.00000 0.00000 0.00000 MINI CONSTR> 55.08308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 32.05281 0.00734 0.22650 0.02343 MINI INTERN> 4.75810 21.16753 0.00000 20.20520 3.91050 MINI EXTERN> -86.33312 13.02713 0.00000 0.00000 0.00000 MINI CONSTR> 55.31747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 32.04838 0.00443 0.21323 0.01633 MINI INTERN> 4.73331 21.09730 0.00000 20.20179 3.92384 MINI EXTERN> -86.58856 13.21125 0.00000 0.00000 0.00000 MINI CONSTR> 55.46945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 32.04512 0.00326 0.21084 0.01272 MINI INTERN> 4.70371 21.04583 0.00000 20.19626 3.94346 MINI EXTERN> -86.75283 13.32730 0.00000 0.00000 0.00000 MINI CONSTR> 55.58140 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 32.04234 0.00278 0.20451 0.01089 MINI INTERN> 4.68473 20.98269 0.00000 20.19101 3.96444 MINI EXTERN> -86.87182 13.41652 0.00000 0.00000 0.00000 MINI CONSTR> 55.67479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 32.03994 0.00240 0.19755 0.00946 MINI INTERN> 4.67214 20.90359 0.00000 20.18455 3.97981 MINI EXTERN> -86.94853 13.49618 0.00000 0.00000 0.00000 MINI CONSTR> 55.75220 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 32.03994 0.00240 0.19755 0.02000 CONJ INTERN> 4.67214 20.90359 0.00000 20.18455 3.97981 CONJ EXTERN> -86.94853 13.49618 0.00000 0.00000 0.00000 CONJ CONSTR> 55.75220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "8400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.48064 ( PROT LYS 1 HT2 ) 0.48064 ( PROT LYS 1 N ) 0.60080 ( PROT LYS 1 HT3 ) 0.48064 ( PROT LYS 1 CA ) 0.60080 ( PROT LYS 1 CB ) 0.48064 ( PROT LYS 1 CG ) 0.48064 ( PROT LYS 1 CD ) 0.48064 ( PROT LYS 1 CE ) 0.48064 ( PROT LYS 1 NZ ) 0.48064 ( PROT LYS 1 HZ1 ) 0.48064 ( PROT LYS 1 HZ2 ) 0.48064 ( PROT LYS 1 HZ3 ) 0.48064 ( PROT LYS 1 C ) 0.60080 ( PROT LYS 1 O ) 0.60080 ( PROT MET 2 N ) 0.60080 ( PROT MET 2 H ) 0.48064 ( PROT MET 2 CA ) 0.60080 ( PROT MET 2 CB ) 0.48064 ( PROT MET 2 CG ) 0.48064 ( PROT MET 2 SD ) 0.48064 ( PROT MET 2 CE ) 0.48064 ( PROT MET 2 C ) 0.60080 ( PROT MET 2 O ) 0.60080 ( PROT LYS 3 N ) 0.60080 ( PROT LYS 3 H ) 0.48064 ( PROT LYS 3 CA ) 0.60080 ( PROT LYS 3 CB ) 0.48064 ( PROT LYS 3 CG ) 0.48064 ( PROT LYS 3 CD ) 0.48064 ( PROT LYS 3 CE ) 0.48064 ( PROT LYS 3 NZ ) 0.48064 ( PROT LYS 3 HZ1 ) 0.48064 ( PROT LYS 3 HZ2 ) 0.48064 ( PROT LYS 3 HZ3 ) 0.48064 ( PROT LYS 3 C ) 0.60080 ( PROT LYS 3 O ) 0.60080 ( PROT ALA 4 N ) 0.60080 ( PROT ALA 4 H ) 0.48064 ( PROT ALA 4 CA ) 0.60080 ( PROT ALA 4 CB ) 0.48064 ( PROT ALA 4 C ) 0.60080 ( PROT ALA 4 O ) 0.60080 ( PROT VAL 5 N ) 0.60080 ( PROT VAL 5 H ) 0.48064 ( PROT VAL 5 CA ) 0.60080 ( PROT VAL 5 CB ) 0.48064 ( PROT VAL 5 CG1 ) 0.48064 ( PROT VAL 5 CG2 ) 0.48064 ( PROT VAL 5 C ) 0.60080 ( PROT VAL 5 O ) 0.60080 ( PROT MET 6 N ) 0.60080 ( PROT MET 6 H ) 0.48064 ( PROT MET 6 CA ) 0.60080 ( PROT MET 6 CB ) 0.48064 ( PROT MET 6 CG ) 0.48064 ( PROT MET 6 SD ) 0.48064 ( PROT MET 6 CE ) 0.48064 ( PROT MET 6 C ) 0.60080 ( PROT MET 6 O ) 0.60080 ( PROT ILE 7 N ) 0.60080 ( PROT ILE 7 H ) 0.48064 ( PROT ILE 7 CA ) 0.60080 ( PROT ILE 7 CB ) 0.48064 ( PROT ILE 7 CG2 ) 0.48064 ( PROT ILE 7 CG1 ) 0.48064 ( PROT ILE 7 CD ) 0.48064 ( PROT ILE 7 C ) 0.60080 ( PROT ILE 7 O ) 0.60080 ( PROT GLY 8 N ) 0.60080 ( PROT GLY 8 H ) 0.48064 ( PROT GLY 8 CA ) 0.60080 ( PROT GLY 8 C ) 0.60080 ( PROT GLY 8 O ) 0.60080 ( PROT ALA 9 N ) 0.60080 ( PROT ALA 9 H ) 0.48064 ( PROT ALA 9 CA ) 0.60080 ( PROT ALA 9 CB ) 0.48064 ( PROT ALA 9 C ) 0.60080 ( PROT ALA 9 O ) 0.60080 ( PROT CYS 10 N ) 0.60080 ( PROT CYS 10 H ) 0.48064 ( PROT CYS 10 CA ) 0.60080 ( PROT CYS 10 CB ) 0.48064 ( PROT CYS 10 SG ) 0.48064 ( PROT CYS 10 C ) 0.60080 ( PROT CYS 10 O ) 0.60080 ( PROT PHE 11 N ) 0.60080 ( PROT PHE 11 H ) 0.48064 ( PROT PHE 11 CA ) 0.60080 ( PROT PHE 11 CB ) 0.48064 ( PROT PHE 11 CG ) 0.48064 ( PROT PHE 11 CD1 ) 0.48064 ( PROT PHE 11 CD2 ) 0.48064 ( PROT PHE 11 CE1 ) 0.48064 ( PROT PHE 11 CE2 ) 0.48064 ( PROT PHE 11 CZ ) 0.48064 ( PROT PHE 11 C ) 0.60080 ( PROT PHE 11 O ) 0.60080 ( PROT LEU 12 N ) 0.60080 ( PROT LEU 12 H ) 0.48064 ( PROT LEU 12 CA ) 0.60080 ( PROT LEU 12 CB ) 0.48064 ( PROT LEU 12 CG ) 0.48064 ( PROT LEU 12 CD1 ) 0.48064 ( PROT LEU 12 CD2 ) 0.48064 ( PROT LEU 12 C ) 0.60080 ( PROT LEU 12 O ) 0.60080 ( PROT ILE 13 N ) 0.60080 ( PROT ILE 13 H ) 0.48064 ( PROT ILE 13 CA ) 0.60080 ( PROT ILE 13 CB ) 0.48064 ( PROT ILE 13 CG2 ) 0.48064 ( PROT ILE 13 CG1 ) 0.48064 ( PROT ILE 13 CD ) 0.48064 ( PROT ILE 13 C ) 0.60080 ( PROT ILE 13 O ) 0.60080 ( PROT ASH 14 N ) 0.60080 ( PROT ASH 14 H ) 0.48064 ( PROT ASH 14 CA ) 0.60080 ( PROT ASH 14 CB ) 0.48064 ( PROT ASH 14 CG ) 0.48064 ( PROT ASH 14 OD1 ) 0.48064 ( PROT ASH 14 OD2 ) 0.48064 ( PROT ASH 14 HD2 ) 0.48064 ( PROT ASH 14 C ) 0.60080 ( PROT ASH 14 O ) 0.60080 ( PROT PHE 15 N ) 0.60080 ( PROT PHE 15 H ) 0.48064 ( PROT PHE 15 CA ) 0.60080 ( PROT PHE 15 CB ) 0.48064 ( PROT PHE 15 CG ) 0.48064 ( PROT PHE 15 CD1 ) 0.48064 ( PROT PHE 15 CD2 ) 0.48064 ( PROT PHE 15 CE1 ) 0.48064 ( PROT PHE 15 CE2 ) 0.48064 ( PROT PHE 15 CZ ) 0.48064 ( PROT PHE 15 C ) 0.60080 ( PROT PHE 15 O ) 0.60080 ( PROT MET 16 N ) 0.60080 ( PROT MET 16 H ) 0.48064 ( PROT MET 16 CA ) 0.60080 ( PROT MET 16 CB ) 0.48064 ( PROT MET 16 CG ) 0.48064 ( PROT MET 16 SD ) 0.48064 ( PROT MET 16 CE ) 0.48064 ( PROT MET 16 C ) 0.60080 ( PROT MET 16 O ) 0.60080 ( PROT PHE 17 N ) 0.60080 ( PROT PHE 17 H ) 0.48064 ( PROT PHE 17 CA ) 0.60080 ( PROT PHE 17 CB ) 0.48064 ( PROT PHE 17 CG ) 0.48064 ( PROT PHE 17 CD1 ) 0.48064 ( PROT PHE 17 CD2 ) 0.48064 ( PROT PHE 17 CE1 ) 0.48064 ( PROT PHE 17 CE2 ) 0.48064 ( PROT PHE 17 CZ ) 0.48064 ( PROT PHE 17 C ) 0.60080 ( PROT PHE 17 O ) 0.60080 ( PROT PHE 18 N ) 0.60080 ( PROT PHE 18 H ) 0.48064 ( PROT PHE 18 CA ) 0.60080 ( PROT PHE 18 CB ) 0.48064 ( PROT PHE 18 CG ) 0.48064 ( PROT PHE 18 CD1 ) 0.48064 ( PROT PHE 18 CD2 ) 0.48064 ( PROT PHE 18 CE1 ) 0.48064 ( PROT PHE 18 CE2 ) 0.48064 ( PROT PHE 18 CZ ) 0.48064 ( PROT PHE 18 C ) 0.60080 ( PROT PHE 18 O ) 0.60080 ( PROT GLU 19 N ) 0.60080 ( PROT GLU 19 H ) 0.48064 ( PROT GLU 19 CA ) 0.60080 ( PROT GLU 19 CB ) 0.48064 ( PROT GLU 19 CG ) 0.48064 ( PROT GLU 19 CD ) 0.48064 ( PROT GLU 19 OE1 ) 0.48064 ( PROT GLU 19 OE2 ) 0.48064 ( PROT GLU 19 C ) 0.60080 ( PROT GLU 19 OT1 ) 0.48064 ( PROT GLU 19 OT2 ) 0.48064 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40345 5.29278 -8.69112 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00109 -0.00036 -0.00209 ROTATION MATRIX 1.000000 0.000518 0.000724 -0.000518 1.000000 -0.000285 -0.000724 0.000285 1.000000 AXIS OF ROTATION IS -0.305208 -0.774362 0.554266 ANGLE IS 0.05 TOTAL SQUARE DIFF IS 69.5209 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.616357 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.6164" Parameter: A <- "0.6164" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.71126 5.23391 -8.78936 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00359 0.03051 -0.00501 ROTATION MATRIX 0.999765 0.017922 0.012176 -0.017722 0.999709 -0.016336 -0.012466 0.016117 0.999792 AXIS OF ROTATION IS -0.599456 -0.455176 0.658383 ANGLE IS 1.55 CENTER OF ROTATION 9.055356 5.225408 -9.407115 SHIFT IS -0.019338 TOTAL SQUARE DIFF IS 3.8015 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.447304 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.6164" RDCMND substituted energy or value "?RMS" to " 0.4473" Parameter: A <- "0.6164 0.4473" 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 0.6164 0.4473 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 " 55.75" Parameter: H <- "55.75" 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 -23.71225 55.75220 0.58487 ENER INTERN> 4.67214 20.90359 0.00000 20.18455 3.97981 ENER EXTERN> -86.94853 13.49618 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 " -23.71" Parameter: B <- "-23.71" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 13.50" Parameter: C <- "13.50" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -86.95" Parameter: C <- " -73.45" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -73.45" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.67" Parameter: D <- "4.67" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 20.90" Parameter: D <- " 25.57" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 20.18" Parameter: D <- " 45.75" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.98" Parameter: D <- " 49.73" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 49.73" 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= -23.71 GRMS= 0.58 ELEC= 13.50 VDW= -86.95 RDTITL> *EXTERNAL= -73.45 INTERNAL= 49.73 USER= 0.00 HARM= 55.75 RDTITL> *BOND= 4.67 ANGL= 20.90 DIHE= 20.18 IMPR= 3.98 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= -23.71 GRMS= 0.58 ELEC= 13.50 VDW= -86.95 RDTITL> *EXTERNAL= -73.45 INTERNAL= 49.73 USER= 0.00 HARM= 55.75 RDTITL> *BOND= 4.67 ANGL= 20.90 DIHE= 20.18 IMPR= 3.98 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= -23.71 GRMS= 0.58 ELEC= 13.50 VDW= -86.95 RDTITL> *EXTERNAL= -73.45 INTERNAL= 49.73 USER= 0.00 HARM= 55.75 RDTITL> *BOND= 4.67 ANGL= 20.90 DIHE= 20.18 IMPR= 3.98 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 8400 0.6164 0.4473 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11108 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11094 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 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 13.76046 -37.47271 0.27328 0.02000 MINI INTERN> 4.67214 20.90359 0.00000 20.18455 3.97981 MINI EXTERN> -86.94853 13.49618 0.00000 0.00000 0.00000 MINI CONSTR> 37.47271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 13.30934 0.45111 1.53370 0.00150 MINI INTERN> 5.31995 20.75367 0.00000 20.42011 3.96775 MINI EXTERN> -89.87616 14.01453 0.00000 0.00000 0.00000 MINI CONSTR> 38.70949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11088 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 12.97223 0.33711 0.81806 0.00065 MINI INTERN> 4.83861 20.87111 0.00000 20.39894 3.95574 MINI EXTERN> -89.77980 13.92049 0.00000 0.00000 0.00000 MINI CONSTR> 38.76715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 12.82390 0.14833 0.36275 0.00028 MINI INTERN> 4.78983 20.75974 0.00000 20.35700 3.93974 MINI EXTERN> -89.72920 13.87395 0.00000 0.00000 0.00000 MINI CONSTR> 38.83284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11086 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 12.78152 0.04238 0.50286 0.00029 MINI INTERN> 4.78973 20.72430 0.00000 20.32978 3.93246 MINI EXTERN> -89.73029 13.84759 0.00000 0.00000 0.00000 MINI CONSTR> 38.88794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 12.71929 0.06223 0.15248 0.00013 MINI INTERN> 4.73960 20.70625 0.00000 20.30483 3.92894 MINI EXTERN> -89.73922 13.83977 0.00000 0.00000 0.00000 MINI CONSTR> 38.93913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11085 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 12.70004 0.01925 0.54980 0.00031 MINI INTERN> 4.77562 20.67147 0.00000 20.28407 3.92298 MINI EXTERN> -89.76730 13.81949 0.00000 0.00000 0.00000 MINI CONSTR> 38.99371 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 12.66091 0.03913 0.57579 0.00032 MINI INTERN> 4.77129 20.64708 0.00000 20.26210 3.91868 MINI EXTERN> -89.79773 13.81037 0.00000 0.00000 0.00000 MINI CONSTR> 39.04913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11085 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 12.59740 0.06351 0.18641 0.00014 MINI INTERN> 4.71454 20.63626 0.00000 20.23927 3.91632 MINI EXTERN> -89.82473 13.81375 0.00000 0.00000 0.00000 MINI CONSTR> 39.10198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 12.56477 0.03262 0.13668 0.00014 MINI INTERN> 4.71238 20.61674 0.00000 20.22301 3.91325 MINI EXTERN> -89.85525 13.80892 0.00000 0.00000 0.00000 MINI CONSTR> 39.14573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11085 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 12.52645 0.03833 0.13503 0.00015 MINI INTERN> 4.70680 20.59550 0.00000 20.20259 3.90985 MINI EXTERN> -89.89424 13.80571 0.00000 0.00000 0.00000 MINI CONSTR> 39.20024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 12.48862 0.03783 0.13651 0.00016 MINI INTERN> 4.70130 20.57477 0.00000 20.18226 3.90660 MINI EXTERN> -89.93503 13.80375 0.00000 0.00000 0.00000 MINI CONSTR> 39.25496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11083 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 12.45330 0.03532 0.27510 0.00016 MINI INTERN> 4.69205 20.55754 0.00000 20.15977 3.90365 MINI EXTERN> -89.97852 13.80497 0.00000 0.00000 0.00000 MINI CONSTR> 39.31384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 12.41779 0.03551 0.16991 0.00017 MINI INTERN> 4.69025 20.53668 0.00000 20.14312 3.90075 MINI EXTERN> -90.01627 13.80286 0.00000 0.00000 0.00000 MINI CONSTR> 39.36039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11082 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 12.38260 0.03519 0.17641 0.00017 MINI INTERN> 4.68572 20.51739 0.00000 20.12361 3.89788 MINI EXTERN> -90.05801 13.80287 0.00000 0.00000 0.00000 MINI CONSTR> 39.41313 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 12.34886 0.03374 0.20545 0.00018 MINI INTERN> 4.68084 20.49920 0.00000 20.10414 3.89517 MINI EXTERN> -90.09929 13.80356 0.00000 0.00000 0.00000 MINI CONSTR> 39.46523 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11081 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 12.32309 0.02576 0.32331 0.00019 MINI INTERN> 4.67630 20.48559 0.00000 20.08610 3.89297 MINI EXTERN> -90.13572 13.80563 0.00000 0.00000 0.00000 MINI CONSTR> 39.51221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 12.29089 0.03220 0.33482 0.00019 MINI INTERN> 4.67236 20.46803 0.00000 20.06730 3.89040 MINI EXTERN> -90.17563 13.80630 0.00000 0.00000 0.00000 MINI CONSTR> 39.56213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11080 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 12.25984 0.03105 0.36095 0.00020 MINI INTERN> 4.66846 20.45121 0.00000 20.04831 3.88790 MINI EXTERN> -90.21521 13.80722 0.00000 0.00000 0.00000 MINI CONSTR> 39.61194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 12.23119 0.02864 0.39837 0.00021 MINI INTERN> 4.66519 20.43543 0.00000 20.02995 3.88554 MINI EXTERN> -90.25289 13.80835 0.00000 0.00000 0.00000 MINI CONSTR> 39.65963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11080 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 12.20361 0.02759 0.37546 0.00022 MINI INTERN> 4.66293 20.41933 0.00000 20.01475 3.88330 MINI EXTERN> -90.28526 13.80879 0.00000 0.00000 0.00000 MINI CONSTR> 39.69978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 12.17415 0.02945 0.39057 0.00022 MINI INTERN> 4.65936 20.40324 0.00000 19.99639 3.88094 MINI EXTERN> -90.32226 13.80962 0.00000 0.00000 0.00000 MINI CONSTR> 39.74687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11080 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 12.14442 0.02973 0.39607 0.00023 MINI INTERN> 4.65565 20.38708 0.00000 19.97804 3.87858 MINI EXTERN> -90.35882 13.81030 0.00000 0.00000 0.00000 MINI CONSTR> 39.79360 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 12.10633 0.03810 0.12642 0.00010 MINI INTERN> 4.66558 20.35659 0.00000 19.96459 3.87489 MINI EXTERN> -90.39565 13.80629 0.00000 0.00000 0.00000 MINI CONSTR> 39.83403 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11079 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 12.09374 0.01259 0.43581 0.00025 MINI INTERN> 4.65100 20.35801 0.00000 19.94488 3.87428 MINI EXTERN> -90.42348 13.81199 0.00000 0.00000 0.00000 MINI CONSTR> 39.87706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 12.06655 0.02719 0.45050 0.00026 MINI INTERN> 4.64743 20.34342 0.00000 19.92691 3.87208 MINI EXTERN> -90.45732 13.81258 0.00000 0.00000 0.00000 MINI CONSTR> 39.92144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11080 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 12.04010 0.02645 0.47302 0.00027 MINI INTERN> 4.64366 20.32955 0.00000 19.90867 3.86994 MINI EXTERN> -90.49072 13.81314 0.00000 0.00000 0.00000 MINI CONSTR> 39.96584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 11.99678 0.04331 0.15275 0.00012 MINI INTERN> 4.65984 20.29025 0.00000 19.89566 3.86529 MINI EXTERN> -90.52934 13.80819 0.00000 0.00000 0.00000 MINI CONSTR> 40.00689 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11080 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 11.97441 0.02238 0.11324 0.00012 MINI INTERN> 4.65204 20.28121 0.00000 19.88118 3.86382 MINI EXTERN> -90.55385 13.80914 0.00000 0.00000 0.00000 MINI CONSTR> 40.04088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 11.94793 0.02647 0.11223 0.00012 MINI INTERN> 4.64973 20.26571 0.00000 19.86389 3.86151 MINI EXTERN> -90.58522 13.80951 0.00000 0.00000 0.00000 MINI CONSTR> 40.08280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11079 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 11.92145 0.02648 0.11307 0.00013 MINI INTERN> 4.64793 20.24983 0.00000 19.84643 3.85914 MINI EXTERN> -90.61656 13.80978 0.00000 0.00000 0.00000 MINI CONSTR> 40.12490 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 11.89544 0.02601 0.21710 0.00013 MINI INTERN> 4.66023 20.22413 0.00000 19.82852 3.85557 MINI EXTERN> -90.65308 13.80912 0.00000 0.00000 0.00000 MINI CONSTR> 40.17095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11078 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 11.87074 0.02470 0.14300 0.00014 MINI INTERN> 4.64915 20.21587 0.00000 19.81252 3.85413 MINI EXTERN> -90.67762 13.80985 0.00000 0.00000 0.00000 MINI CONSTR> 40.20683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 11.84568 0.02505 0.14284 0.00014 MINI INTERN> 4.64762 20.20049 0.00000 19.79550 3.85180 MINI EXTERN> -90.70673 13.81006 0.00000 0.00000 0.00000 MINI CONSTR> 40.24696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11077 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 11.82076 0.02492 0.15277 0.00015 MINI INTERN> 4.64762 20.18398 0.00000 19.77836 3.84932 MINI EXTERN> -90.73610 13.81017 0.00000 0.00000 0.00000 MINI CONSTR> 40.28741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 11.80047 0.02029 0.26935 0.00015 MINI INTERN> 4.66283 20.15911 0.00000 19.76290 3.84586 MINI EXTERN> -90.76703 13.80994 0.00000 0.00000 0.00000 MINI CONSTR> 40.32685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11077 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 11.77711 0.02336 0.26922 0.00016 MINI INTERN> 4.66183 20.14416 0.00000 19.74660 3.84356 MINI EXTERN> -90.79380 13.81015 0.00000 0.00000 0.00000 MINI CONSTR> 40.36461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 11.75356 0.02355 0.27622 0.00017 MINI INTERN> 4.66227 20.12780 0.00000 19.72989 3.84106 MINI EXTERN> -90.82128 13.81050 0.00000 0.00000 0.00000 MINI CONSTR> 40.40333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11077 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 11.73040 0.02316 0.29284 0.00017 MINI INTERN> 4.66414 20.11047 0.00000 19.71304 3.83844 MINI EXTERN> -90.84895 13.81092 0.00000 0.00000 0.00000 MINI CONSTR> 40.44233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 11.70858 0.02182 0.32191 0.00018 MINI INTERN> 4.66773 20.09281 0.00000 19.69658 3.83578 MINI EXTERN> -90.87600 13.81125 0.00000 0.00000 0.00000 MINI CONSTR> 40.48044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11075 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 11.68783 0.02076 0.30772 0.00019 MINI INTERN> 4.66353 20.08233 0.00000 19.68180 3.83401 MINI EXTERN> -90.89776 13.81084 0.00000 0.00000 0.00000 MINI CONSTR> 40.51308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 11.66624 0.02158 0.32292 0.00019 MINI INTERN> 4.66495 20.06650 0.00000 19.66552 3.83158 MINI EXTERN> -90.92315 13.81102 0.00000 0.00000 0.00000 MINI CONSTR> 40.54982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11074 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 11.64421 0.02203 0.33300 0.00020 MINI INTERN> 4.66564 20.05092 0.00000 19.64885 3.82917 MINI EXTERN> -90.94854 13.81118 0.00000 0.00000 0.00000 MINI CONSTR> 40.58699 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 11.61515 0.02906 0.10215 0.00009 MINI INTERN> 4.61373 20.07497 0.00000 19.62887 3.83116 MINI EXTERN> -90.96135 13.80713 0.00000 0.00000 0.00000 MINI CONSTR> 40.62064 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11073 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 11.60418 0.01097 0.36326 0.00021 MINI INTERN> 4.66851 20.02159 0.00000 19.61777 3.82459 MINI EXTERN> -90.99537 13.81100 0.00000 0.00000 0.00000 MINI CONSTR> 40.65610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 11.58387 0.02032 0.37234 0.00022 MINI INTERN> 4.66904 20.00743 0.00000 19.60198 3.82233 MINI EXTERN> -91.01845 13.81079 0.00000 0.00000 0.00000 MINI CONSTR> 40.69075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11072 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 11.56352 0.02035 0.38600 0.00023 MINI INTERN> 4.67080 19.99222 0.00000 19.58584 3.81995 MINI EXTERN> -91.04206 13.81067 0.00000 0.00000 0.00000 MINI CONSTR> 40.72609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 11.54387 0.01966 0.40694 0.00024 MINI INTERN> 4.67417 19.97620 0.00000 19.56977 3.81748 MINI EXTERN> -91.06568 13.81060 0.00000 0.00000 0.00000 MINI CONSTR> 40.76132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11071 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 11.51129 0.03258 0.13382 0.00010 MINI INTERN> 4.59686 20.01985 0.00000 19.54793 3.82127 MINI EXTERN> -91.07194 13.80278 0.00000 0.00000 0.00000 MINI CONSTR> 40.79453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 11.49446 0.01682 0.09634 0.00011 MINI INTERN> 4.60415 20.00185 0.00000 19.53626 3.81874 MINI EXTERN> -91.09116 13.80323 0.00000 0.00000 0.00000 MINI CONSTR> 40.82139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11071 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 11.47437 0.02010 0.09562 0.00011 MINI INTERN> 4.60243 19.98971 0.00000 19.52042 3.81662 MINI EXTERN> -91.11242 13.80242 0.00000 0.00000 0.00000 MINI CONSTR> 40.85519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 11.45425 0.02011 0.09650 0.00011 MINI INTERN> 4.60001 19.97816 0.00000 19.50436 3.81453 MINI EXTERN> -91.13347 13.80147 0.00000 0.00000 0.00000 MINI CONSTR> 40.88919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11070 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 11.43458 0.01968 0.18754 0.00012 MINI INTERN> 4.58103 19.98186 0.00000 19.48513 3.81378 MINI EXTERN> -91.15200 13.79817 0.00000 0.00000 0.00000 MINI CONSTR> 40.92661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 11.41577 0.01881 0.12226 0.00012 MINI INTERN> 4.58972 19.96104 0.00000 19.47241 3.81094 MINI EXTERN> -91.17255 13.79878 0.00000 0.00000 0.00000 MINI CONSTR> 40.95543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11068 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 11.39671 0.01906 0.12254 0.00013 MINI INTERN> 4.58789 19.94958 0.00000 19.45694 3.80886 MINI EXTERN> -91.19236 13.79784 0.00000 0.00000 0.00000 MINI CONSTR> 40.98797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 11.37776 0.01895 0.13198 0.00013 MINI INTERN> 4.58441 19.93963 0.00000 19.44116 3.80689 MINI EXTERN> -91.21177 13.79664 0.00000 0.00000 0.00000 MINI CONSTR> 41.02079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11067 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 11.36248 0.01528 0.23195 0.00014 MINI INTERN> 4.56828 19.94375 0.00000 19.42466 3.80620 MINI EXTERN> -91.22674 13.79355 0.00000 0.00000 0.00000 MINI CONSTR> 41.05279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 11.34470 0.01778 0.23302 0.00014 MINI INTERN> 4.56661 19.93286 0.00000 19.40999 3.80415 MINI EXTERN> -91.24507 13.79262 0.00000 0.00000 0.00000 MINI CONSTR> 41.08355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11067 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 11.32683 0.01787 0.24045 0.00015 MINI INTERN> 4.56450 19.92216 0.00000 19.39496 3.80206 MINI EXTERN> -91.26356 13.79166 0.00000 0.00000 0.00000 MINI CONSTR> 41.11505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 11.30937 0.01745 0.25675 0.00015 MINI INTERN> 4.56203 19.91196 0.00000 19.37987 3.79997 MINI EXTERN> -91.28182 13.79068 0.00000 0.00000 0.00000 MINI CONSTR> 41.14669 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11067 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 11.29299 0.01638 0.28154 0.00016 MINI INTERN> 4.55903 19.90304 0.00000 19.36509 3.79802 MINI EXTERN> -91.29920 13.78961 0.00000 0.00000 0.00000 MINI CONSTR> 41.17741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 11.27721 0.01579 0.26726 0.00016 MINI INTERN> 4.55879 19.89242 0.00000 19.35226 3.79618 MINI EXTERN> -91.31501 13.78881 0.00000 0.00000 0.00000 MINI CONSTR> 41.20376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11067 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 11.26058 0.01662 0.27880 0.00017 MINI INTERN> 4.55853 19.88064 0.00000 19.33792 3.79397 MINI EXTERN> -91.33271 13.78824 0.00000 0.00000 0.00000 MINI CONSTR> 41.23400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 11.24358 0.01700 0.28555 0.00018 MINI INTERN> 4.56084 19.86611 0.00000 19.32359 3.79148 MINI EXTERN> -91.35124 13.78817 0.00000 0.00000 0.00000 MINI CONSTR> 41.26462 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11067 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 11.22648 0.01710 0.28609 0.00018 MINI INTERN> 4.56451 19.85038 0.00000 19.30936 3.78892 MINI EXTERN> -91.36990 13.78826 0.00000 0.00000 0.00000 MINI CONSTR> 41.29495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 11.20478 0.02170 0.09269 0.00008 MINI INTERN> 4.58745 19.81832 0.00000 19.29588 3.78582 MINI EXTERN> -91.39243 13.78849 0.00000 0.00000 0.00000 MINI CONSTR> 41.32126 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11067 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 11.19734 0.00745 0.31709 0.00020 MINI INTERN> 4.56356 19.83041 0.00000 19.28272 3.78504 MINI EXTERN> -91.40121 13.78691 0.00000 0.00000 0.00000 MINI CONSTR> 41.34992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 11.18134 0.01599 0.32606 0.00020 MINI INTERN> 4.56862 19.81422 0.00000 19.26874 3.78249 MINI EXTERN> -91.41942 13.78721 0.00000 0.00000 0.00000 MINI CONSTR> 41.37950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11065 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 11.16553 0.01582 0.33982 0.00021 MINI INTERN> 4.57356 19.79839 0.00000 19.25443 3.77997 MINI EXTERN> -91.43761 13.78733 0.00000 0.00000 0.00000 MINI CONSTR> 41.40945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 11.13991 0.02561 0.10392 0.00009 MINI INTERN> 4.58140 19.77877 0.00000 19.23782 3.77805 MINI EXTERN> -91.45790 13.78378 0.00000 0.00000 0.00000 MINI CONSTR> 41.43799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11065 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 11.12645 0.01346 0.08388 0.00010 MINI INTERN> 4.57894 19.77070 0.00000 19.22626 3.77638 MINI EXTERN> -91.47078 13.78321 0.00000 0.00000 0.00000 MINI CONSTR> 41.46174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 11.11090 0.01555 0.08286 0.00010 MINI INTERN> 4.57759 19.76089 0.00000 19.21218 3.77444 MINI EXTERN> -91.48637 13.78217 0.00000 0.00000 0.00000 MINI CONSTR> 41.48999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11065 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 11.09516 0.01574 0.08285 0.00010 MINI INTERN> 4.57635 19.75089 0.00000 19.19781 3.77247 MINI EXTERN> -91.50217 13.78109 0.00000 0.00000 0.00000 MINI CONSTR> 41.51873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 11.07964 0.01552 0.08500 0.00011 MINI INTERN> 4.57527 19.74098 0.00000 19.18347 3.77051 MINI EXTERN> -91.51782 13.77997 0.00000 0.00000 0.00000 MINI CONSTR> 41.54725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11064 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 11.06525 0.01439 0.17096 0.00011 MINI INTERN> 4.57747 19.73106 0.00000 19.16745 3.76863 MINI EXTERN> -91.53494 13.77804 0.00000 0.00000 0.00000 MINI CONSTR> 41.57754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 11.05025 0.01500 0.10455 0.00011 MINI INTERN> 4.57360 19.72217 0.00000 19.15568 3.76678 MINI EXTERN> -91.54777 13.77768 0.00000 0.00000 0.00000 MINI CONSTR> 41.60212 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11064 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 11.03523 0.01502 0.10719 0.00012 MINI INTERN> 4.57232 19.71260 0.00000 19.14157 3.76484 MINI EXTERN> -91.56286 13.77665 0.00000 0.00000 0.00000 MINI CONSTR> 41.63012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 11.02054 0.01470 0.12084 0.00012 MINI INTERN> 4.57139 19.70315 0.00000 19.12737 3.76292 MINI EXTERN> -91.57792 13.77555 0.00000 0.00000 0.00000 MINI CONSTR> 41.65808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11063 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 11.00911 0.01142 0.20116 0.00013 MINI INTERN> 4.57292 19.69519 0.00000 19.11369 3.76128 MINI EXTERN> -91.59214 13.77414 0.00000 0.00000 0.00000 MINI CONSTR> 41.68402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 10.99512 0.01399 0.20535 0.00013 MINI INTERN> 4.57184 19.68603 0.00000 19.10021 3.75943 MINI EXTERN> -91.60635 13.77330 0.00000 0.00000 0.00000 MINI CONSTR> 41.71066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11062 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 10.98126 0.01386 0.21637 0.00014 MINI INTERN> 4.57098 19.67686 0.00000 19.08647 3.75756 MINI EXTERN> -91.62076 13.77245 0.00000 0.00000 0.00000 MINI CONSTR> 41.73769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 10.96810 0.01316 0.23717 0.00014 MINI INTERN> 4.57059 19.66795 0.00000 19.07282 3.75574 MINI EXTERN> -91.63497 13.77159 0.00000 0.00000 0.00000 MINI CONSTR> 41.76436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11061 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 10.95564 0.01245 0.22820 0.00015 MINI INTERN> 4.56930 19.65988 0.00000 19.06119 3.75410 MINI EXTERN> -91.64695 13.77076 0.00000 0.00000 0.00000 MINI CONSTR> 41.78737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 10.94285 0.01279 0.24042 0.00015 MINI INTERN> 4.56842 19.65143 0.00000 19.04816 3.75234 MINI EXTERN> -91.66032 13.76992 0.00000 0.00000 0.00000 MINI CONSTR> 41.81290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11061 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 10.92975 0.01310 0.24880 0.00016 MINI INTERN> 4.56734 19.64280 0.00000 19.03492 3.75055 MINI EXTERN> -91.67386 13.76914 0.00000 0.00000 0.00000 MINI CONSTR> 41.83885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 10.91653 0.01322 0.25084 0.00016 MINI INTERN> 4.56608 19.63414 0.00000 19.02182 3.74876 MINI EXTERN> -91.68721 13.76835 0.00000 0.00000 0.00000 MINI CONSTR> 41.86459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11060 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 10.89970 0.01683 0.08111 0.00007 MINI INTERN> 4.56123 19.62313 0.00000 19.01184 3.74647 MINI EXTERN> -91.69711 13.76713 0.00000 0.00000 0.00000 MINI CONSTR> 41.88700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 10.89412 0.00558 0.27794 0.00018 MINI INTERN> 4.56512 19.61882 0.00000 18.99808 3.74554 MINI EXTERN> -91.71099 13.76675 0.00000 0.00000 0.00000 MINI CONSTR> 41.91079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11059 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 10.88184 0.01228 0.28715 0.00018 MINI INTERN> 4.56451 19.61034 0.00000 18.98524 3.74383 MINI EXTERN> -91.72397 13.76607 0.00000 0.00000 0.00000 MINI CONSTR> 41.93580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 10.86980 0.01204 0.30099 0.00019 MINI INTERN> 4.56410 19.60194 0.00000 18.97227 3.74215 MINI EXTERN> -91.73705 13.76540 0.00000 0.00000 0.00000 MINI CONSTR> 41.96099 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11059 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 10.85013 0.01967 0.09591 0.00008 MINI INTERN> 4.55769 19.58963 0.00000 18.96191 3.73936 MINI EXTERN> -91.74649 13.76329 0.00000 0.00000 0.00000 MINI CONSTR> 41.98475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 10.83990 0.01023 0.07287 0.00008 MINI INTERN> 4.55659 19.58329 0.00000 18.95163 3.73811 MINI EXTERN> -91.75675 13.76274 0.00000 0.00000 0.00000 MINI CONSTR> 42.00430 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11059 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 10.82784 0.01207 0.07217 0.00009 MINI INTERN> 4.55569 19.57512 0.00000 18.93927 3.73638 MINI EXTERN> -91.76879 13.76185 0.00000 0.00000 0.00000 MINI CONSTR> 42.02831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 10.81567 0.01217 0.07241 0.00009 MINI INTERN> 4.55479 19.56682 0.00000 18.92674 3.73461 MINI EXTERN> -91.78093 13.76095 0.00000 0.00000 0.00000 MINI CONSTR> 42.05268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11058 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 10.80324 0.01242 0.13331 0.00009 MINI INTERN> 4.55507 19.55675 0.00000 18.91311 3.73218 MINI EXTERN> -91.79347 13.75955 0.00000 0.00000 0.00000 MINI CONSTR> 42.08006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 10.79202 0.01122 0.09332 0.00010 MINI INTERN> 4.55335 19.55010 0.00000 18.90205 3.73089 MINI EXTERN> -91.80439 13.75902 0.00000 0.00000 0.00000 MINI CONSTR> 42.10101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11057 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 10.78052 0.01150 0.09189 0.00010 MINI INTERN> 4.55237 19.54225 0.00000 18.89002 3.72918 MINI EXTERN> -91.81582 13.75821 0.00000 0.00000 0.00000 MINI CONSTR> 42.12431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 10.76895 0.01157 0.09581 0.00011 MINI INTERN> 4.55145 19.53419 0.00000 18.87779 3.72739 MINI EXTERN> -91.82729 13.75738 0.00000 0.00000 0.00000 MINI CONSTR> 42.14804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11057 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 10.75775 0.01120 0.11060 0.00011 MINI INTERN> 4.55070 19.52612 0.00000 18.86573 3.72553 MINI EXTERN> -91.83843 13.75651 0.00000 0.00000 0.00000 MINI CONSTR> 42.17160 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 10.74903 0.00872 0.17561 0.00011 MINI INTERN> 4.55128 19.51849 0.00000 18.85497 3.72347 MINI EXTERN> -91.84779 13.75543 0.00000 0.00000 0.00000 MINI CONSTR> 42.19318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11056 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 10.73816 0.01087 0.17947 0.00012 MINI INTERN> 4.55040 19.51070 0.00000 18.84321 3.72169 MINI EXTERN> -91.85855 13.75476 0.00000 0.00000 0.00000 MINI CONSTR> 42.21594 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 10.73816 0.01087 0.17947 0.00014 STPD INTERN> 4.55040 19.51070 0.00000 18.84321 3.72169 STPD EXTERN> -91.85855 13.75476 0.00000 0.00000 0.00000 STPD CONSTR> 42.21594 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 11056 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11056 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 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 10.73816 0.01087 0.17947 0.00000 MINI INTERN> 4.55040 19.51070 0.00000 18.84321 3.72169 MINI EXTERN> -91.85855 13.75476 0.00000 0.00000 0.00000 MINI CONSTR> 42.21594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 9.90152 0.83665 0.09296 0.02325 MINI INTERN> 4.50054 18.43274 0.00000 17.21994 3.51556 MINI EXTERN> -93.77269 13.83014 0.00000 0.00000 0.00000 MINI CONSTR> 46.17529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 9.88723 0.01429 0.11727 0.00765 MINI INTERN> 4.41997 18.42155 0.00000 17.16921 3.46050 MINI EXTERN> -93.46467 13.73482 0.00000 0.00000 0.00000 MINI CONSTR> 46.14584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 9.85762 0.02961 0.14622 0.02351 MINI INTERN> 4.32857 18.36467 0.00000 17.05439 3.49198 MINI EXTERN> -92.98759 13.63469 0.00000 0.00000 0.00000 MINI CONSTR> 45.97092 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 9.82447 0.03315 0.12356 0.01644 MINI INTERN> 4.44779 18.44159 0.00000 16.95475 3.45161 MINI EXTERN> -92.84167 13.58081 0.00000 0.00000 0.00000 MINI CONSTR> 45.78959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 9.80421 0.02026 0.09630 0.01264 MINI INTERN> 4.49235 18.48562 0.00000 16.93459 3.42286 MINI EXTERN> -93.01242 13.76560 0.00000 0.00000 0.00000 MINI CONSTR> 45.71560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 9.79114 0.01307 0.08662 0.01089 MINI INTERN> 4.51665 18.44337 0.00000 16.92741 3.45445 MINI EXTERN> -93.05544 13.82017 0.00000 0.00000 0.00000 MINI CONSTR> 45.68454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 9.78098 0.01016 0.07015 0.01046 MINI INTERN> 4.47152 18.41141 0.00000 16.92791 3.46545 MINI EXTERN> -93.02270 13.85624 0.00000 0.00000 0.00000 MINI CONSTR> 45.67116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 9.77285 0.00813 0.06685 0.00871 MINI INTERN> 4.44830 18.41002 0.00000 16.93391 3.48053 MINI EXTERN> -93.02920 13.85287 0.00000 0.00000 0.00000 MINI CONSTR> 45.67642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 9.76687 0.00598 0.05481 0.00672 MINI INTERN> 4.48518 18.38810 0.00000 16.91297 3.46858 MINI EXTERN> -92.98459 13.80179 0.00000 0.00000 0.00000 MINI CONSTR> 45.69483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 9.76277 0.00410 0.04554 0.00566 MINI INTERN> 4.46494 18.39485 0.00000 16.90382 3.46572 MINI EXTERN> -93.04243 13.86661 0.00000 0.00000 0.00000 MINI CONSTR> 45.70925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 9.76017 0.00260 0.03559 0.00429 MINI INTERN> 4.47577 18.36539 0.00000 16.89573 3.46183 MINI EXTERN> -92.98757 13.84331 0.00000 0.00000 0.00000 MINI CONSTR> 45.70570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 9.75800 0.00216 0.03523 0.00448 MINI INTERN> 4.48984 18.36320 0.00000 16.87010 3.46659 MINI EXTERN> -92.91242 13.79296 0.00000 0.00000 0.00000 MINI CONSTR> 45.68773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 9.75619 0.00181 0.03059 0.00424 MINI INTERN> 4.47004 18.37402 0.00000 16.85154 3.47004 MINI EXTERN> -92.88113 13.80121 0.00000 0.00000 0.00000 MINI CONSTR> 45.67046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 9.75446 0.00174 0.02967 0.00451 MINI INTERN> 4.46924 18.35819 0.00000 16.84864 3.46355 MINI EXTERN> -92.82748 13.78187 0.00000 0.00000 0.00000 MINI CONSTR> 45.66044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 9.75286 0.00159 0.03199 0.00382 MINI INTERN> 4.47815 18.35318 0.00000 16.85025 3.46400 MINI EXTERN> -92.84193 13.78905 0.00000 0.00000 0.00000 MINI CONSTR> 45.66016 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 9.75124 0.00162 0.02896 0.00555 MINI INTERN> 4.48362 18.34544 0.00000 16.84496 3.46087 MINI EXTERN> -92.84394 13.79559 0.00000 0.00000 0.00000 MINI CONSTR> 45.66470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 9.74992 0.00131 0.02952 0.00417 MINI INTERN> 4.48040 18.32910 0.00000 16.84105 3.46368 MINI EXTERN> -92.81202 13.77457 0.00000 0.00000 0.00000 MINI CONSTR> 45.67314 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 9.74857 0.00136 0.03157 0.00590 MINI INTERN> 4.48331 18.32456 0.00000 16.83187 3.46097 MINI EXTERN> -92.81611 13.77394 0.00000 0.00000 0.00000 MINI CONSTR> 45.69003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 9.74661 0.00195 0.03304 0.00720 MINI INTERN> 4.48232 18.30444 0.00000 16.82348 3.45261 MINI EXTERN> -92.85921 13.81930 0.00000 0.00000 0.00000 MINI CONSTR> 45.72367 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 9.74488 0.00174 0.03028 0.00661 MINI INTERN> 4.48395 18.27350 0.00000 16.80900 3.45568 MINI EXTERN> -92.85983 13.82648 0.00000 0.00000 0.00000 MINI CONSTR> 45.75610 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 9.74488 0.00174 0.03028 0.02000 CONJ INTERN> 4.48395 18.27350 0.00000 16.80900 3.45568 CONJ EXTERN> -92.85983 13.82648 0.00000 0.00000 0.00000 CONJ CONSTR> 45.75610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "9000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.31241 ( PROT LYS 1 HT2 ) 0.31241 ( PROT LYS 1 N ) 0.39052 ( PROT LYS 1 HT3 ) 0.31241 ( PROT LYS 1 CA ) 0.39052 ( PROT LYS 1 CB ) 0.31241 ( PROT LYS 1 CG ) 0.31241 ( PROT LYS 1 CD ) 0.31241 ( PROT LYS 1 CE ) 0.31241 ( PROT LYS 1 NZ ) 0.31241 ( PROT LYS 1 HZ1 ) 0.31241 ( PROT LYS 1 HZ2 ) 0.31241 ( PROT LYS 1 HZ3 ) 0.31241 ( PROT LYS 1 C ) 0.39052 ( PROT LYS 1 O ) 0.39052 ( PROT MET 2 N ) 0.39052 ( PROT MET 2 H ) 0.31241 ( PROT MET 2 CA ) 0.39052 ( PROT MET 2 CB ) 0.31241 ( PROT MET 2 CG ) 0.31241 ( PROT MET 2 SD ) 0.31241 ( PROT MET 2 CE ) 0.31241 ( PROT MET 2 C ) 0.39052 ( PROT MET 2 O ) 0.39052 ( PROT LYS 3 N ) 0.39052 ( PROT LYS 3 H ) 0.31241 ( PROT LYS 3 CA ) 0.39052 ( PROT LYS 3 CB ) 0.31241 ( PROT LYS 3 CG ) 0.31241 ( PROT LYS 3 CD ) 0.31241 ( PROT LYS 3 CE ) 0.31241 ( PROT LYS 3 NZ ) 0.31241 ( PROT LYS 3 HZ1 ) 0.31241 ( PROT LYS 3 HZ2 ) 0.31241 ( PROT LYS 3 HZ3 ) 0.31241 ( PROT LYS 3 C ) 0.39052 ( PROT LYS 3 O ) 0.39052 ( PROT ALA 4 N ) 0.39052 ( PROT ALA 4 H ) 0.31241 ( PROT ALA 4 CA ) 0.39052 ( PROT ALA 4 CB ) 0.31241 ( PROT ALA 4 C ) 0.39052 ( PROT ALA 4 O ) 0.39052 ( PROT VAL 5 N ) 0.39052 ( PROT VAL 5 H ) 0.31241 ( PROT VAL 5 CA ) 0.39052 ( PROT VAL 5 CB ) 0.31241 ( PROT VAL 5 CG1 ) 0.31241 ( PROT VAL 5 CG2 ) 0.31241 ( PROT VAL 5 C ) 0.39052 ( PROT VAL 5 O ) 0.39052 ( PROT MET 6 N ) 0.39052 ( PROT MET 6 H ) 0.31241 ( PROT MET 6 CA ) 0.39052 ( PROT MET 6 CB ) 0.31241 ( PROT MET 6 CG ) 0.31241 ( PROT MET 6 SD ) 0.31241 ( PROT MET 6 CE ) 0.31241 ( PROT MET 6 C ) 0.39052 ( PROT MET 6 O ) 0.39052 ( PROT ILE 7 N ) 0.39052 ( PROT ILE 7 H ) 0.31241 ( PROT ILE 7 CA ) 0.39052 ( PROT ILE 7 CB ) 0.31241 ( PROT ILE 7 CG2 ) 0.31241 ( PROT ILE 7 CG1 ) 0.31241 ( PROT ILE 7 CD ) 0.31241 ( PROT ILE 7 C ) 0.39052 ( PROT ILE 7 O ) 0.39052 ( PROT GLY 8 N ) 0.39052 ( PROT GLY 8 H ) 0.31241 ( PROT GLY 8 CA ) 0.39052 ( PROT GLY 8 C ) 0.39052 ( PROT GLY 8 O ) 0.39052 ( PROT ALA 9 N ) 0.39052 ( PROT ALA 9 H ) 0.31241 ( PROT ALA 9 CA ) 0.39052 ( PROT ALA 9 CB ) 0.31241 ( PROT ALA 9 C ) 0.39052 ( PROT ALA 9 O ) 0.39052 ( PROT CYS 10 N ) 0.39052 ( PROT CYS 10 H ) 0.31241 ( PROT CYS 10 CA ) 0.39052 ( PROT CYS 10 CB ) 0.31241 ( PROT CYS 10 SG ) 0.31241 ( PROT CYS 10 C ) 0.39052 ( PROT CYS 10 O ) 0.39052 ( PROT PHE 11 N ) 0.39052 ( PROT PHE 11 H ) 0.31241 ( PROT PHE 11 CA ) 0.39052 ( PROT PHE 11 CB ) 0.31241 ( PROT PHE 11 CG ) 0.31241 ( PROT PHE 11 CD1 ) 0.31241 ( PROT PHE 11 CD2 ) 0.31241 ( PROT PHE 11 CE1 ) 0.31241 ( PROT PHE 11 CE2 ) 0.31241 ( PROT PHE 11 CZ ) 0.31241 ( PROT PHE 11 C ) 0.39052 ( PROT PHE 11 O ) 0.39052 ( PROT LEU 12 N ) 0.39052 ( PROT LEU 12 H ) 0.31241 ( PROT LEU 12 CA ) 0.39052 ( PROT LEU 12 CB ) 0.31241 ( PROT LEU 12 CG ) 0.31241 ( PROT LEU 12 CD1 ) 0.31241 ( PROT LEU 12 CD2 ) 0.31241 ( PROT LEU 12 C ) 0.39052 ( PROT LEU 12 O ) 0.39052 ( PROT ILE 13 N ) 0.39052 ( PROT ILE 13 H ) 0.31241 ( PROT ILE 13 CA ) 0.39052 ( PROT ILE 13 CB ) 0.31241 ( PROT ILE 13 CG2 ) 0.31241 ( PROT ILE 13 CG1 ) 0.31241 ( PROT ILE 13 CD ) 0.31241 ( PROT ILE 13 C ) 0.39052 ( PROT ILE 13 O ) 0.39052 ( PROT ASH 14 N ) 0.39052 ( PROT ASH 14 H ) 0.31241 ( PROT ASH 14 CA ) 0.39052 ( PROT ASH 14 CB ) 0.31241 ( PROT ASH 14 CG ) 0.31241 ( PROT ASH 14 OD1 ) 0.31241 ( PROT ASH 14 OD2 ) 0.31241 ( PROT ASH 14 HD2 ) 0.31241 ( PROT ASH 14 C ) 0.39052 ( PROT ASH 14 O ) 0.39052 ( PROT PHE 15 N ) 0.39052 ( PROT PHE 15 H ) 0.31241 ( PROT PHE 15 CA ) 0.39052 ( PROT PHE 15 CB ) 0.31241 ( PROT PHE 15 CG ) 0.31241 ( PROT PHE 15 CD1 ) 0.31241 ( PROT PHE 15 CD2 ) 0.31241 ( PROT PHE 15 CE1 ) 0.31241 ( PROT PHE 15 CE2 ) 0.31241 ( PROT PHE 15 CZ ) 0.31241 ( PROT PHE 15 C ) 0.39052 ( PROT PHE 15 O ) 0.39052 ( PROT MET 16 N ) 0.39052 ( PROT MET 16 H ) 0.31241 ( PROT MET 16 CA ) 0.39052 ( PROT MET 16 CB ) 0.31241 ( PROT MET 16 CG ) 0.31241 ( PROT MET 16 SD ) 0.31241 ( PROT MET 16 CE ) 0.31241 ( PROT MET 16 C ) 0.39052 ( PROT MET 16 O ) 0.39052 ( PROT PHE 17 N ) 0.39052 ( PROT PHE 17 H ) 0.31241 ( PROT PHE 17 CA ) 0.39052 ( PROT PHE 17 CB ) 0.31241 ( PROT PHE 17 CG ) 0.31241 ( PROT PHE 17 CD1 ) 0.31241 ( PROT PHE 17 CD2 ) 0.31241 ( PROT PHE 17 CE1 ) 0.31241 ( PROT PHE 17 CE2 ) 0.31241 ( PROT PHE 17 CZ ) 0.31241 ( PROT PHE 17 C ) 0.39052 ( PROT PHE 17 O ) 0.39052 ( PROT PHE 18 N ) 0.39052 ( PROT PHE 18 H ) 0.31241 ( PROT PHE 18 CA ) 0.39052 ( PROT PHE 18 CB ) 0.31241 ( PROT PHE 18 CG ) 0.31241 ( PROT PHE 18 CD1 ) 0.31241 ( PROT PHE 18 CD2 ) 0.31241 ( PROT PHE 18 CE1 ) 0.31241 ( PROT PHE 18 CE2 ) 0.31241 ( PROT PHE 18 CZ ) 0.31241 ( PROT PHE 18 C ) 0.39052 ( PROT PHE 18 O ) 0.39052 ( PROT GLU 19 N ) 0.39052 ( PROT GLU 19 H ) 0.31241 ( PROT GLU 19 CA ) 0.39052 ( PROT GLU 19 CB ) 0.31241 ( PROT GLU 19 CG ) 0.31241 ( PROT GLU 19 CD ) 0.31241 ( PROT GLU 19 OE1 ) 0.31241 ( PROT GLU 19 OE2 ) 0.31241 ( PROT GLU 19 C ) 0.39052 ( PROT GLU 19 OT1 ) 0.31241 ( PROT GLU 19 OT2 ) 0.31241 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40286 5.28922 -8.68997 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00169 0.00319 -0.00325 ROTATION MATRIX 1.000000 0.000301 0.000447 -0.000301 1.000000 0.000013 -0.000447 -0.000013 1.000000 AXIS OF ROTATION IS 0.024284 -0.829126 0.558534 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 88.1673 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.694110 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.6941" Parameter: A <- "0.6941" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.71495 5.24338 -8.79104 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.00011 0.02104 -0.00332 ROTATION MATRIX 0.999799 0.017114 0.010416 -0.016942 0.999722 -0.016379 -0.010693 0.016199 0.999812 AXIS OF ROTATION IS -0.630861 -0.408762 0.659490 ANGLE IS 1.48 CENTER OF ROTATION 9.230255 5.169960 -9.308337 SHIFT IS -0.010724 TOTAL SQUARE DIFF IS 4.9889 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.512420 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.6941" RDCMND substituted energy or value "?RMS" to " 0.5124" Parameter: A <- "0.6941 0.5124" 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 0.6941 0.5124 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 " 45.76" Parameter: H <- "45.76" 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 -36.01122 45.75610 0.41894 ENER INTERN> 4.48395 18.27350 0.00000 16.80900 3.45568 ENER EXTERN> -92.85983 13.82648 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 " -36.01" Parameter: B <- "-36.01" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 13.83" Parameter: C <- "13.83" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -92.86" Parameter: C <- " -79.03" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -79.03" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.48" Parameter: D <- "4.48" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 18.27" Parameter: D <- " 22.75" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 16.81" Parameter: D <- " 39.56" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.46" Parameter: D <- " 43.02" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 43.02" 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= -36.01 GRMS= 0.42 ELEC= 13.83 VDW= -92.86 RDTITL> *EXTERNAL= -79.03 INTERNAL= 43.02 USER= 0.00 HARM= 45.76 RDTITL> *BOND= 4.48 ANGL= 18.27 DIHE= 16.81 IMPR= 3.46 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 11056 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11017 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 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 -5.51858 -30.49264 0.15488 0.02000 MINI INTERN> 4.48395 18.27350 0.00000 16.80900 3.45568 MINI EXTERN> -92.85983 13.82648 0.00000 0.00000 0.00000 MINI CONSTR> 30.49264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -5.66304 0.14445 1.76495 0.00150 MINI INTERN> 4.97482 18.98100 0.00000 17.12590 3.49112 MINI EXTERN> -97.25957 15.21220 0.00000 0.00000 0.00000 MINI CONSTR> 31.81150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11010 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -5.99450 0.33146 0.84947 0.00065 MINI INTERN> 4.79375 18.37891 0.00000 17.11401 3.48097 MINI EXTERN> -96.47775 14.90302 0.00000 0.00000 0.00000 MINI CONSTR> 31.81260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -6.10771 0.11322 0.45063 0.00028 MINI INTERN> 4.68829 18.36376 0.00000 17.03176 3.48151 MINI EXTERN> -96.18705 14.67407 0.00000 0.00000 0.00000 MINI CONSTR> 31.83995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11008 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -6.13745 0.02974 0.44939 0.00029 MINI INTERN> 4.67585 18.30844 0.00000 16.99476 3.48080 MINI EXTERN> -96.05568 14.59511 0.00000 0.00000 0.00000 MINI CONSTR> 31.86328 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -6.18280 0.04535 0.12976 0.00013 MINI INTERN> 4.60291 18.27123 0.00000 16.97117 3.48198 MINI EXTERN> -95.93075 14.52936 0.00000 0.00000 0.00000 MINI CONSTR> 31.89128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11008 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -6.20524 0.02244 0.10477 0.00013 MINI INTERN> 4.59804 18.24294 0.00000 16.94502 3.48031 MINI EXTERN> -95.87643 14.48732 0.00000 0.00000 0.00000 MINI CONSTR> 31.91756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -6.22943 0.02419 0.10463 0.00013 MINI INTERN> 4.58563 18.21800 0.00000 16.91813 3.47890 MINI EXTERN> -95.82764 14.44770 0.00000 0.00000 0.00000 MINI CONSTR> 31.94984 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11008 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -6.25173 0.02229 0.20465 0.00014 MINI INTERN> 4.55581 18.20517 0.00000 16.89418 3.47787 MINI EXTERN> -95.78087 14.40935 0.00000 0.00000 0.00000 MINI CONSTR> 31.98676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -6.27443 0.02270 0.12793 0.00014 MINI INTERN> 4.56134 18.17849 0.00000 16.87163 3.47581 MINI EXTERN> -95.77234 14.39247 0.00000 0.00000 0.00000 MINI CONSTR> 32.01816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11009 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -6.29664 0.02221 0.13559 0.00015 MINI INTERN> 4.55206 18.16032 0.00000 16.85009 3.47403 MINI EXTERN> -95.76091 14.37316 0.00000 0.00000 0.00000 MINI CONSTR> 32.05462 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -6.31457 0.01793 0.23676 0.00016 MINI INTERN> 4.52936 18.15367 0.00000 16.83255 3.47253 MINI EXTERN> -95.74689 14.35299 0.00000 0.00000 0.00000 MINI CONSTR> 32.09122 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11007 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -6.33512 0.02055 0.23771 0.00016 MINI INTERN> 4.52355 18.13755 0.00000 16.81404 3.47064 MINI EXTERN> -95.74962 14.34163 0.00000 0.00000 0.00000 MINI CONSTR> 32.12710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -6.35560 0.02048 0.24621 0.00017 MINI INTERN> 4.51532 18.12371 0.00000 16.79615 3.46878 MINI EXTERN> -95.75564 14.33169 0.00000 0.00000 0.00000 MINI CONSTR> 32.16438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11007 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -6.37533 0.01974 0.26540 0.00017 MINI INTERN> 4.50734 18.11135 0.00000 16.77916 3.46682 MINI EXTERN> -95.76413 14.32204 0.00000 0.00000 0.00000 MINI CONSTR> 32.20209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -6.39351 0.01818 0.29279 0.00018 MINI INTERN> 4.49672 18.10060 0.00000 16.76353 3.46528 MINI EXTERN> -95.77471 14.31649 0.00000 0.00000 0.00000 MINI CONSTR> 32.23857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11007 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -6.41122 0.01770 0.27502 0.00019 MINI INTERN> 4.50186 18.08228 0.00000 16.74888 3.46323 MINI EXTERN> -95.79128 14.31395 0.00000 0.00000 0.00000 MINI CONSTR> 32.26986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -6.43008 0.01886 0.28606 0.00019 MINI INTERN> 4.49523 18.07093 0.00000 16.73357 3.46139 MINI EXTERN> -95.80667 14.30863 0.00000 0.00000 0.00000 MINI CONSTR> 32.30683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11005 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -6.44918 0.01910 0.29113 0.00020 MINI INTERN> 4.48789 18.05979 0.00000 16.71835 3.45978 MINI EXTERN> -95.82437 14.30532 0.00000 0.00000 0.00000 MINI CONSTR> 32.34406 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -6.47379 0.02461 0.09231 0.00009 MINI INTERN> 4.54843 18.00470 0.00000 16.69448 3.45748 MINI EXTERN> -95.88286 14.32708 0.00000 0.00000 0.00000 MINI CONSTR> 32.37688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11002 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -6.48232 0.00853 0.31869 0.00022 MINI INTERN> 4.48047 18.03682 0.00000 16.69116 3.45630 MINI EXTERN> -95.85868 14.29991 0.00000 0.00000 0.00000 MINI CONSTR> 32.41169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -6.49976 0.01744 0.33150 0.00022 MINI INTERN> 4.48217 18.02405 0.00000 16.67674 3.45417 MINI EXTERN> -95.87888 14.29464 0.00000 0.00000 0.00000 MINI CONSTR> 32.44735 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11000 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -6.52673 0.02697 0.10276 0.00010 MINI INTERN> 4.54846 17.96268 0.00000 16.65049 3.45232 MINI EXTERN> -95.94792 14.32600 0.00000 0.00000 0.00000 MINI CONSTR> 32.48123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -6.54163 0.01490 0.08626 0.00010 MINI INTERN> 4.53901 17.95762 0.00000 16.63983 3.45103 MINI EXTERN> -95.96134 14.32200 0.00000 0.00000 0.00000 MINI CONSTR> 32.51022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10999 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -6.55790 0.01627 0.08822 0.00010 MINI INTERN> 4.53837 17.94542 0.00000 16.62632 3.44952 MINI EXTERN> -95.98276 14.32239 0.00000 0.00000 0.00000 MINI CONSTR> 32.54284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -6.57387 0.01597 0.08781 0.00011 MINI INTERN> 4.53732 17.93411 0.00000 16.61327 3.44793 MINI EXTERN> -96.00308 14.32165 0.00000 0.00000 0.00000 MINI CONSTR> 32.57493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10999 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -6.59025 0.01638 0.14780 0.00011 MINI INTERN> 4.55569 17.91011 0.00000 16.59552 3.44609 MINI EXTERN> -96.03780 14.32917 0.00000 0.00000 0.00000 MINI CONSTR> 32.61096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -6.60449 0.01424 0.08383 0.00012 MINI INTERN> 4.53269 17.91383 0.00000 16.58849 3.44496 MINI EXTERN> -96.04154 14.32032 0.00000 0.00000 0.00000 MINI CONSTR> 32.63676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10999 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -6.62049 0.01601 0.17248 0.00012 MINI INTERN> 4.56026 17.88511 0.00000 16.56881 3.44296 MINI EXTERN> -96.08222 14.33043 0.00000 0.00000 0.00000 MINI CONSTR> 32.67416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -6.63677 0.01628 0.11141 0.00012 MINI INTERN> 4.53895 17.88519 0.00000 16.55960 3.44180 MINI EXTERN> -96.09113 14.32493 0.00000 0.00000 0.00000 MINI CONSTR> 32.70388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10998 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -6.65156 0.01479 0.14127 0.00013 MINI INTERN> 4.54870 17.86901 0.00000 16.54500 3.44006 MINI EXTERN> -96.11744 14.32722 0.00000 0.00000 0.00000 MINI CONSTR> 32.73589 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -6.66430 0.01274 0.19609 0.00013 MINI INTERN> 4.56023 17.85238 0.00000 16.53052 3.43871 MINI EXTERN> -96.14513 14.33284 0.00000 0.00000 0.00000 MINI CONSTR> 32.76614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10998 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -6.67974 0.01543 0.19623 0.00014 MINI INTERN> 4.56104 17.84080 0.00000 16.51749 3.43681 MINI EXTERN> -96.16520 14.33124 0.00000 0.00000 0.00000 MINI CONSTR> 32.79808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -6.69508 0.01535 0.16235 0.00014 MINI INTERN> 4.54634 17.83719 0.00000 16.50705 3.43588 MINI EXTERN> -96.17911 14.33007 0.00000 0.00000 0.00000 MINI CONSTR> 32.82749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10997 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -6.70660 0.01152 0.21318 0.00015 MINI INTERN> 4.55933 17.82149 0.00000 16.49331 3.43447 MINI EXTERN> -96.20529 14.33441 0.00000 0.00000 0.00000 MINI CONSTR> 32.85567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -6.72051 0.01391 0.24799 0.00015 MINI INTERN> 4.56862 17.80688 0.00000 16.47930 3.43215 MINI EXTERN> -96.22771 14.33242 0.00000 0.00000 0.00000 MINI CONSTR> 32.88783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10995 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -6.73398 0.01347 0.23144 0.00016 MINI INTERN> 4.56139 17.79974 0.00000 16.46820 3.43153 MINI EXTERN> -96.24586 14.33607 0.00000 0.00000 0.00000 MINI CONSTR> 32.91494 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -6.74790 0.01392 0.24735 0.00017 MINI INTERN> 4.56616 17.78781 0.00000 16.45533 3.42935 MINI EXTERN> -96.26521 14.33305 0.00000 0.00000 0.00000 MINI CONSTR> 32.94562 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10995 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -6.76555 0.01766 0.08067 0.00007 MINI INTERN> 4.50779 17.80826 0.00000 16.45368 3.42868 MINI EXTERN> -96.25044 14.31496 0.00000 0.00000 0.00000 MINI CONSTR> 32.97152 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -6.77303 0.00747 0.26103 0.00018 MINI INTERN> 4.56552 17.76839 0.00000 16.43145 3.42718 MINI EXTERN> -96.30473 14.33831 0.00000 0.00000 0.00000 MINI CONSTR> 33.00086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10994 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -6.79265 0.01963 0.07848 0.00008 MINI INTERN> 4.50677 17.78864 0.00000 16.42954 3.42578 MINI EXTERN> -96.28789 14.31536 0.00000 0.00000 0.00000 MINI CONSTR> 33.02915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -6.79903 0.00637 0.28213 0.00019 MINI INTERN> 4.56511 17.74818 0.00000 16.40678 3.42436 MINI EXTERN> -96.34312 14.34078 0.00000 0.00000 0.00000 MINI CONSTR> 33.05889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10993 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -6.81135 0.01232 0.31038 0.00020 MINI INTERN> 4.57178 17.73756 0.00000 16.39496 3.42173 MINI EXTERN> -96.35868 14.33346 0.00000 0.00000 0.00000 MINI CONSTR> 33.08785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -6.83181 0.02046 0.09566 0.00009 MINI INTERN> 4.49824 17.76431 0.00000 16.39508 3.42154 MINI EXTERN> -96.33799 14.31309 0.00000 0.00000 0.00000 MINI CONSTR> 33.11390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10993 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -6.83504 0.00323 0.31273 0.00021 MINI INTERN> 4.57364 17.71761 0.00000 16.37129 3.41970 MINI EXTERN> -96.39801 14.34037 0.00000 0.00000 0.00000 MINI CONSTR> 33.14036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -6.85675 0.02172 0.11077 0.00009 MINI INTERN> 4.49370 17.74835 0.00000 16.37261 3.41872 MINI EXTERN> -96.37021 14.31148 0.00000 0.00000 0.00000 MINI CONSTR> 33.16859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10993 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -6.86776 0.01100 0.07342 0.00010 MINI INTERN> 4.50333 17.73409 0.00000 16.36095 3.41753 MINI EXTERN> -96.39159 14.31692 0.00000 0.00000 0.00000 MINI CONSTR> 33.19100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -6.88039 0.01264 0.07959 0.00010 MINI INTERN> 4.49992 17.72665 0.00000 16.34967 3.41608 MINI EXTERN> -96.40705 14.31557 0.00000 0.00000 0.00000 MINI CONSTR> 33.21877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10992 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -6.89242 0.01203 0.14060 0.00010 MINI INTERN> 4.48604 17.72579 0.00000 16.33986 3.41464 MINI EXTERN> -96.41610 14.30927 0.00000 0.00000 0.00000 MINI CONSTR> 33.24809 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -6.90492 0.01250 0.09180 0.00011 MINI INTERN> 4.49484 17.71112 0.00000 16.32710 3.41331 MINI EXTERN> -96.43866 14.31438 0.00000 0.00000 0.00000 MINI CONSTR> 33.27299 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10991 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -6.91607 0.01115 0.07404 0.00011 MINI INTERN> 4.50002 17.69966 0.00000 16.31572 3.41197 MINI EXTERN> -96.45711 14.31679 0.00000 0.00000 0.00000 MINI CONSTR> 33.29688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -6.92733 0.01126 0.16859 0.00011 MINI INTERN> 4.48123 17.70242 0.00000 16.30670 3.41047 MINI EXTERN> -96.46241 14.30735 0.00000 0.00000 0.00000 MINI CONSTR> 33.32691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10989 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -6.94008 0.01275 0.11391 0.00012 MINI INTERN> 4.48822 17.68776 0.00000 16.29377 3.40940 MINI EXTERN> -96.48543 14.31454 0.00000 0.00000 0.00000 MINI CONSTR> 33.35166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -6.94919 0.00911 0.17897 0.00012 MINI INTERN> 4.47642 17.68750 0.00000 16.28556 3.40820 MINI EXTERN> -96.49229 14.30920 0.00000 0.00000 0.00000 MINI CONSTR> 33.37622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10989 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -6.95951 0.01032 0.20679 0.00013 MINI INTERN> 4.48253 17.67795 0.00000 16.27459 3.40610 MINI EXTERN> -96.50697 14.30501 0.00000 0.00000 0.00000 MINI CONSTR> 33.40127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -6.97018 0.01067 0.18908 0.00013 MINI INTERN> 4.47471 17.67279 0.00000 16.26520 3.40543 MINI EXTERN> -96.51955 14.30725 0.00000 0.00000 0.00000 MINI CONSTR> 33.42399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10988 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -6.98148 0.01130 0.21090 0.00014 MINI INTERN> 4.47547 17.66463 0.00000 16.25349 3.40377 MINI EXTERN> -96.53531 14.30524 0.00000 0.00000 0.00000 MINI CONSTR> 33.45123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -6.99202 0.01054 0.20666 0.00014 MINI INTERN> 4.47118 17.65741 0.00000 16.24312 3.40308 MINI EXTERN> -96.55049 14.30918 0.00000 0.00000 0.00000 MINI CONSTR> 33.47451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10988 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -7.00233 0.01031 0.21859 0.00015 MINI INTERN> 4.48294 17.64506 0.00000 16.23165 3.40079 MINI EXTERN> -96.56706 14.30595 0.00000 0.00000 0.00000 MINI CONSTR> 33.49835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -7.01553 0.01320 0.06942 0.00006 MINI INTERN> 4.50184 17.62186 0.00000 16.21705 3.40011 MINI EXTERN> -96.59830 14.32291 0.00000 0.00000 0.00000 MINI CONSTR> 33.51899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10988 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -7.02151 0.00598 0.23276 0.00016 MINI INTERN> 4.46644 17.63747 0.00000 16.21346 3.39916 MINI EXTERN> -96.58865 14.30662 0.00000 0.00000 0.00000 MINI CONSTR> 33.54398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -7.03662 0.01511 0.07335 0.00007 MINI INTERN> 4.50190 17.60530 0.00000 16.19543 3.39751 MINI EXTERN> -96.62811 14.32431 0.00000 0.00000 0.00000 MINI CONSTR> 33.56704 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10986 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -7.04127 0.00465 0.24855 0.00017 MINI INTERN> 4.46819 17.62215 0.00000 16.19283 3.39622 MINI EXTERN> -96.61577 14.30442 0.00000 0.00000 0.00000 MINI CONSTR> 33.59069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -7.05077 0.00950 0.28115 0.00018 MINI INTERN> 4.46381 17.61405 0.00000 16.18105 3.39608 MINI EXTERN> -96.63451 14.31341 0.00000 0.00000 0.00000 MINI CONSTR> 33.61534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10986 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -7.06701 0.01625 0.08353 0.00008 MINI INTERN> 4.50280 17.58089 0.00000 16.16368 3.39366 MINI EXTERN> -96.67146 14.32644 0.00000 0.00000 0.00000 MINI CONSTR> 33.63697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -7.07592 0.00890 0.06571 0.00008 MINI INTERN> 4.49667 17.57759 0.00000 16.15576 3.39266 MINI EXTERN> -96.68008 14.32465 0.00000 0.00000 0.00000 MINI CONSTR> 33.65682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10986 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -7.08595 0.01003 0.06828 0.00008 MINI INTERN> 4.49769 17.56918 0.00000 16.14506 3.39133 MINI EXTERN> -96.69455 14.32529 0.00000 0.00000 0.00000 MINI CONSTR> 33.68005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -7.09547 0.00952 0.07046 0.00009 MINI INTERN> 4.49751 17.56160 0.00000 16.13493 3.39016 MINI EXTERN> -96.70818 14.32635 0.00000 0.00000 0.00000 MINI CONSTR> 33.70217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10985 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -7.10520 0.00972 0.11588 0.00009 MINI INTERN> 4.50679 17.54813 0.00000 16.12206 3.38867 MINI EXTERN> -96.72820 14.33060 0.00000 0.00000 0.00000 MINI CONSTR> 33.72675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -7.11482 0.00962 0.08420 0.00009 MINI INTERN> 4.49821 17.54541 0.00000 16.11385 3.38772 MINI EXTERN> -96.73653 14.32890 0.00000 0.00000 0.00000 MINI CONSTR> 33.74763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10985 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -7.12406 0.00924 0.09801 0.00010 MINI INTERN> 4.50237 17.53597 0.00000 16.10315 3.38628 MINI EXTERN> -96.75136 14.32974 0.00000 0.00000 0.00000 MINI CONSTR> 33.76979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -7.13311 0.00905 0.10691 0.00010 MINI INTERN> 4.50148 17.52866 0.00000 16.09308 3.38528 MINI EXTERN> -96.76490 14.33187 0.00000 0.00000 0.00000 MINI CONSTR> 33.79143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10985 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -7.14106 0.00796 0.14912 0.00010 MINI INTERN> 4.51040 17.51724 0.00000 16.08199 3.38382 MINI EXTERN> -96.78154 14.33433 0.00000 0.00000 0.00000 MINI CONSTR> 33.81269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -7.15095 0.00989 0.10772 0.00011 MINI INTERN> 4.49838 17.51589 0.00000 16.07414 3.38306 MINI EXTERN> -96.78867 14.33288 0.00000 0.00000 0.00000 MINI CONSTR> 33.83338 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10985 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -7.15814 0.00718 0.15970 0.00011 MINI INTERN> 4.50663 17.50468 0.00000 16.06322 3.38193 MINI EXTERN> -96.80580 14.33752 0.00000 0.00000 0.00000 MINI CONSTR> 33.85368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -7.16630 0.00817 0.18195 0.00011 MINI INTERN> 4.51455 17.49502 0.00000 16.05302 3.38007 MINI EXTERN> -96.81909 14.33552 0.00000 0.00000 0.00000 MINI CONSTR> 33.87460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10984 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -7.17479 0.00849 0.16839 0.00012 MINI INTERN> 4.50938 17.48986 0.00000 16.04418 3.37956 MINI EXTERN> -96.83075 14.33907 0.00000 0.00000 0.00000 MINI CONSTR> 33.89391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -7.18294 0.00815 0.20373 0.00012 MINI INTERN> 4.51633 17.48059 0.00000 16.03371 3.37761 MINI EXTERN> -96.84356 14.33642 0.00000 0.00000 0.00000 MINI CONSTR> 33.91595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10983 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -7.19126 0.00832 0.18474 0.00013 MINI INTERN> 4.51372 17.47474 0.00000 16.02502 3.37689 MINI EXTERN> -96.85509 14.33900 0.00000 0.00000 0.00000 MINI CONSTR> 33.93444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -7.19957 0.00830 0.20024 0.00013 MINI INTERN> 4.50087 17.47310 0.00000 16.01656 3.37668 MINI EXTERN> -96.86408 14.34206 0.00000 0.00000 0.00000 MINI CONSTR> 33.95524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10983 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -7.21020 0.01064 0.06255 0.00006 MINI INTERN> 4.48326 17.47783 0.00000 16.01243 3.37519 MINI EXTERN> -96.86069 14.32931 0.00000 0.00000 0.00000 MINI CONSTR> 33.97247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -7.21491 0.00471 0.20953 0.00014 MINI INTERN> 4.51670 17.45370 0.00000 15.99701 3.37348 MINI EXTERN> -96.89091 14.34166 0.00000 0.00000 0.00000 MINI CONSTR> 33.99346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10983 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -7.22245 0.00754 0.23584 0.00015 MINI INTERN> 4.50007 17.45397 0.00000 15.98919 3.37362 MINI EXTERN> -96.89846 14.34556 0.00000 0.00000 0.00000 MINI CONSTR> 34.01359 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -7.23053 0.00809 0.22558 0.00015 MINI INTERN> 4.51803 17.43944 0.00000 15.97799 3.37136 MINI EXTERN> -96.91539 14.34497 0.00000 0.00000 0.00000 MINI CONSTR> 34.03306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10983 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -7.23818 0.00765 0.24491 0.00016 MINI INTERN> 4.50825 17.43646 0.00000 15.96920 3.37109 MINI EXTERN> -96.92539 14.34883 0.00000 0.00000 0.00000 MINI CONSTR> 34.05338 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -7.25105 0.01287 0.07479 0.00007 MINI INTERN> 4.47838 17.44714 0.00000 15.96666 3.36961 MINI EXTERN> -96.91537 14.33090 0.00000 0.00000 0.00000 MINI CONSTR> 34.07162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10981 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -7.25820 0.00715 0.05907 0.00007 MINI INTERN> 4.48108 17.43936 0.00000 15.95796 3.36868 MINI EXTERN> -96.92739 14.33356 0.00000 0.00000 0.00000 MINI CONSTR> 34.08854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -7.26619 0.00799 0.06138 0.00007 MINI INTERN> 4.48016 17.43339 0.00000 15.94891 3.36753 MINI EXTERN> -96.93788 14.33359 0.00000 0.00000 0.00000 MINI CONSTR> 34.10811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10980 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -7.27394 0.00775 0.06167 0.00008 MINI INTERN> 4.47919 17.42735 0.00000 15.93998 3.36651 MINI EXTERN> -96.94854 14.33447 0.00000 0.00000 0.00000 MINI CONSTR> 34.12711 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -7.28181 0.00787 0.10406 0.00008 MINI INTERN> 4.47307 17.42471 0.00000 15.93140 3.36531 MINI EXTERN> -96.95586 14.33137 0.00000 0.00000 0.00000 MINI CONSTR> 34.14819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10979 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -7.28878 0.00697 0.05953 0.00008 MINI INTERN> 4.47879 17.41504 0.00000 15.92262 3.36447 MINI EXTERN> -96.96945 14.33622 0.00000 0.00000 0.00000 MINI CONSTR> 34.16354 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -7.29627 0.00748 0.12195 0.00008 MINI INTERN> 4.46889 17.41446 0.00000 15.91447 3.36345 MINI EXTERN> -96.97514 14.33274 0.00000 0.00000 0.00000 MINI CONSTR> 34.18487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10979 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -7.30391 0.00764 0.09090 0.00009 MINI INTERN> 4.47475 17.40523 0.00000 15.90532 3.36215 MINI EXTERN> -96.98759 14.33417 0.00000 0.00000 0.00000 MINI CONSTR> 34.20207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -7.31032 0.00641 0.13172 0.00009 MINI INTERN> 4.46731 17.40366 0.00000 15.89791 3.36137 MINI EXTERN> -96.99377 14.33285 0.00000 0.00000 0.00000 MINI CONSTR> 34.22035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10979 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -7.31855 0.00823 0.08606 0.00009 MINI INTERN> 4.47475 17.39277 0.00000 15.88789 3.36010 MINI EXTERN> -97.00842 14.33612 0.00000 0.00000 0.00000 MINI CONSTR> 34.23824 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -7.32465 0.00610 0.13992 0.00010 MINI INTERN> 4.46704 17.39191 0.00000 15.88069 3.35922 MINI EXTERN> -97.01360 14.33348 0.00000 0.00000 0.00000 MINI CONSTR> 34.25662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10979 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -7.33219 0.00754 0.14793 0.00010 MINI INTERN> 4.46478 17.38600 0.00000 15.87135 3.35846 MINI EXTERN> -97.02503 14.33626 0.00000 0.00000 0.00000 MINI CONSTR> 34.27600 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -7.33869 0.00650 0.16845 0.00011 MINI INTERN> 4.46892 17.37951 0.00000 15.86293 3.35683 MINI EXTERN> -97.03389 14.33322 0.00000 0.00000 0.00000 MINI CONSTR> 34.29378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10978 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -7.34553 0.00684 0.15511 0.00011 MINI INTERN> 4.46380 17.37551 0.00000 15.85530 3.35637 MINI EXTERN> -97.04259 14.33594 0.00000 0.00000 0.00000 MINI CONSTR> 34.31014 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -7.35224 0.00671 0.18589 0.00011 MINI INTERN> 4.46883 17.36807 0.00000 15.84591 3.35476 MINI EXTERN> -97.05328 14.33410 0.00000 0.00000 0.00000 MINI CONSTR> 34.32937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10978 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -7.35899 0.00675 0.16892 0.00012 MINI INTERN> 4.46434 17.36407 0.00000 15.83852 3.35419 MINI EXTERN> -97.06142 14.33607 0.00000 0.00000 0.00000 MINI CONSTR> 34.34524 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 -7.35899 0.00675 0.16892 0.00014 STPD INTERN> 4.46434 17.36407 0.00000 15.83852 3.35419 STPD EXTERN> -97.06142 14.33607 0.00000 0.00000 0.00000 STPD CONSTR> 34.34524 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 10978 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10978 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 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 -7.35899 0.00675 0.16892 0.00000 MINI INTERN> 4.46434 17.36407 0.00000 15.83852 3.35419 MINI EXTERN> -97.06142 14.33607 0.00000 0.00000 0.00000 MINI CONSTR> 34.34524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -8.03343 0.67444 0.11869 0.06627 MINI INTERN> 4.47861 16.35916 0.00000 14.44299 3.22962 MINI EXTERN> -99.14250 14.69230 0.00000 0.00000 0.00000 MINI CONSTR> 37.90639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -8.04730 0.01387 0.09568 0.00693 MINI INTERN> 4.40672 16.36375 0.00000 14.40400 3.19892 MINI EXTERN> -99.03344 14.67484 0.00000 0.00000 0.00000 MINI CONSTR> 37.93791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -8.07100 0.02370 0.14466 0.02037 MINI INTERN> 4.35270 16.25215 0.00000 14.35495 3.22732 MINI EXTERN> -98.74757 14.61050 0.00000 0.00000 0.00000 MINI CONSTR> 37.87895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -8.10666 0.03566 0.14266 0.01913 MINI INTERN> 4.38378 16.25256 0.00000 14.29755 3.18684 MINI EXTERN> -98.47295 14.49531 0.00000 0.00000 0.00000 MINI CONSTR> 37.75025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -8.14082 0.03416 0.14402 0.02524 MINI INTERN> 4.39907 16.36166 0.00000 14.25038 3.19805 MINI EXTERN> -98.56340 14.58903 0.00000 0.00000 0.00000 MINI CONSTR> 37.62440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -8.16490 0.02408 0.11585 0.02126 MINI INTERN> 4.46035 16.34267 0.00000 14.19992 3.20615 MINI EXTERN> -98.49906 14.59013 0.00000 0.00000 0.00000 MINI CONSTR> 37.53495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -8.17890 0.01400 0.07323 0.01115 MINI INTERN> 4.43029 16.27038 0.00000 14.15869 3.21814 MINI EXTERN> -98.39823 14.65609 0.00000 0.00000 0.00000 MINI CONSTR> 37.48574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -8.18802 0.00912 0.07637 0.00976 MINI INTERN> 4.40691 16.29877 0.00000 14.15993 3.22898 MINI EXTERN> -98.42835 14.68123 0.00000 0.00000 0.00000 MINI CONSTR> 37.46451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -8.19621 0.00819 0.07160 0.00974 MINI INTERN> 4.42073 16.27129 0.00000 14.14985 3.21750 MINI EXTERN> -98.38003 14.66751 0.00000 0.00000 0.00000 MINI CONSTR> 37.45692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -8.20208 0.00587 0.05882 0.00681 MINI INTERN> 4.40726 16.26672 0.00000 14.15846 3.21588 MINI EXTERN> -98.43572 14.72874 0.00000 0.00000 0.00000 MINI CONSTR> 37.45658 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -8.20752 0.00544 0.05530 0.00742 MINI INTERN> 4.42309 16.26116 0.00000 14.16907 3.22067 MINI EXTERN> -98.47472 14.74083 0.00000 0.00000 0.00000 MINI CONSTR> 37.45237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -8.21152 0.00400 0.04500 0.00651 MINI INTERN> 4.43283 16.26702 0.00000 14.17087 3.23295 MINI EXTERN> -98.45346 14.70022 0.00000 0.00000 0.00000 MINI CONSTR> 37.43804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -8.21443 0.00291 0.04057 0.00525 MINI INTERN> 4.42564 16.27187 0.00000 14.15930 3.22771 MINI EXTERN> -98.40655 14.69204 0.00000 0.00000 0.00000 MINI CONSTR> 37.41555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -8.21638 0.00195 0.02668 0.00322 MINI INTERN> 4.42904 16.27655 0.00000 14.16750 3.22375 MINI EXTERN> -98.34739 14.64137 0.00000 0.00000 0.00000 MINI CONSTR> 37.39279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -8.21770 0.00132 0.02917 0.00411 MINI INTERN> 4.42039 16.29195 0.00000 14.17650 3.23184 MINI EXTERN> -98.33713 14.62641 0.00000 0.00000 0.00000 MINI CONSTR> 37.37234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -8.21901 0.00132 0.02765 0.00295 MINI INTERN> 4.42524 16.29373 0.00000 14.19160 3.22539 MINI EXTERN> -98.31870 14.61474 0.00000 0.00000 0.00000 MINI CONSTR> 37.34899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -8.21993 0.00092 0.01941 0.00260 MINI INTERN> 4.43106 16.29594 0.00000 14.19511 3.22637 MINI EXTERN> -98.30763 14.60803 0.00000 0.00000 0.00000 MINI CONSTR> 37.33119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -8.22065 0.00072 0.02071 0.00321 MINI INTERN> 4.42819 16.30797 0.00000 14.20255 3.22629 MINI EXTERN> -98.29779 14.59618 0.00000 0.00000 0.00000 MINI CONSTR> 37.31596 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -8.22129 0.00064 0.01819 0.00242 MINI INTERN> 4.42817 16.31947 0.00000 14.22511 3.22416 MINI EXTERN> -98.30017 14.57756 0.00000 0.00000 0.00000 MINI CONSTR> 37.30440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -8.22193 0.00063 0.01938 0.00274 MINI INTERN> 4.42510 16.31887 0.00000 14.23670 3.22976 MINI EXTERN> -98.30017 14.57104 0.00000 0.00000 0.00000 MINI CONSTR> 37.29677 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 -8.22193 0.00063 0.01938 0.02000 CONJ INTERN> 4.42510 16.31887 0.00000 14.23670 3.22976 CONJ EXTERN> -98.30017 14.57104 0.00000 0.00000 0.00000 CONJ CONSTR> 37.29677 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "9600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.20307 ( PROT LYS 1 HT2 ) 0.20307 ( PROT LYS 1 N ) 0.25384 ( PROT LYS 1 HT3 ) 0.20307 ( PROT LYS 1 CA ) 0.25384 ( PROT LYS 1 CB ) 0.20307 ( PROT LYS 1 CG ) 0.20307 ( PROT LYS 1 CD ) 0.20307 ( PROT LYS 1 CE ) 0.20307 ( PROT LYS 1 NZ ) 0.20307 ( PROT LYS 1 HZ1 ) 0.20307 ( PROT LYS 1 HZ2 ) 0.20307 ( PROT LYS 1 HZ3 ) 0.20307 ( PROT LYS 1 C ) 0.25384 ( PROT LYS 1 O ) 0.25384 ( PROT MET 2 N ) 0.25384 ( PROT MET 2 H ) 0.20307 ( PROT MET 2 CA ) 0.25384 ( PROT MET 2 CB ) 0.20307 ( PROT MET 2 CG ) 0.20307 ( PROT MET 2 SD ) 0.20307 ( PROT MET 2 CE ) 0.20307 ( PROT MET 2 C ) 0.25384 ( PROT MET 2 O ) 0.25384 ( PROT LYS 3 N ) 0.25384 ( PROT LYS 3 H ) 0.20307 ( PROT LYS 3 CA ) 0.25384 ( PROT LYS 3 CB ) 0.20307 ( PROT LYS 3 CG ) 0.20307 ( PROT LYS 3 CD ) 0.20307 ( PROT LYS 3 CE ) 0.20307 ( PROT LYS 3 NZ ) 0.20307 ( PROT LYS 3 HZ1 ) 0.20307 ( PROT LYS 3 HZ2 ) 0.20307 ( PROT LYS 3 HZ3 ) 0.20307 ( PROT LYS 3 C ) 0.25384 ( PROT LYS 3 O ) 0.25384 ( PROT ALA 4 N ) 0.25384 ( PROT ALA 4 H ) 0.20307 ( PROT ALA 4 CA ) 0.25384 ( PROT ALA 4 CB ) 0.20307 ( PROT ALA 4 C ) 0.25384 ( PROT ALA 4 O ) 0.25384 ( PROT VAL 5 N ) 0.25384 ( PROT VAL 5 H ) 0.20307 ( PROT VAL 5 CA ) 0.25384 ( PROT VAL 5 CB ) 0.20307 ( PROT VAL 5 CG1 ) 0.20307 ( PROT VAL 5 CG2 ) 0.20307 ( PROT VAL 5 C ) 0.25384 ( PROT VAL 5 O ) 0.25384 ( PROT MET 6 N ) 0.25384 ( PROT MET 6 H ) 0.20307 ( PROT MET 6 CA ) 0.25384 ( PROT MET 6 CB ) 0.20307 ( PROT MET 6 CG ) 0.20307 ( PROT MET 6 SD ) 0.20307 ( PROT MET 6 CE ) 0.20307 ( PROT MET 6 C ) 0.25384 ( PROT MET 6 O ) 0.25384 ( PROT ILE 7 N ) 0.25384 ( PROT ILE 7 H ) 0.20307 ( PROT ILE 7 CA ) 0.25384 ( PROT ILE 7 CB ) 0.20307 ( PROT ILE 7 CG2 ) 0.20307 ( PROT ILE 7 CG1 ) 0.20307 ( PROT ILE 7 CD ) 0.20307 ( PROT ILE 7 C ) 0.25384 ( PROT ILE 7 O ) 0.25384 ( PROT GLY 8 N ) 0.25384 ( PROT GLY 8 H ) 0.20307 ( PROT GLY 8 CA ) 0.25384 ( PROT GLY 8 C ) 0.25384 ( PROT GLY 8 O ) 0.25384 ( PROT ALA 9 N ) 0.25384 ( PROT ALA 9 H ) 0.20307 ( PROT ALA 9 CA ) 0.25384 ( PROT ALA 9 CB ) 0.20307 ( PROT ALA 9 C ) 0.25384 ( PROT ALA 9 O ) 0.25384 ( PROT CYS 10 N ) 0.25384 ( PROT CYS 10 H ) 0.20307 ( PROT CYS 10 CA ) 0.25384 ( PROT CYS 10 CB ) 0.20307 ( PROT CYS 10 SG ) 0.20307 ( PROT CYS 10 C ) 0.25384 ( PROT CYS 10 O ) 0.25384 ( PROT PHE 11 N ) 0.25384 ( PROT PHE 11 H ) 0.20307 ( PROT PHE 11 CA ) 0.25384 ( PROT PHE 11 CB ) 0.20307 ( PROT PHE 11 CG ) 0.20307 ( PROT PHE 11 CD1 ) 0.20307 ( PROT PHE 11 CD2 ) 0.20307 ( PROT PHE 11 CE1 ) 0.20307 ( PROT PHE 11 CE2 ) 0.20307 ( PROT PHE 11 CZ ) 0.20307 ( PROT PHE 11 C ) 0.25384 ( PROT PHE 11 O ) 0.25384 ( PROT LEU 12 N ) 0.25384 ( PROT LEU 12 H ) 0.20307 ( PROT LEU 12 CA ) 0.25384 ( PROT LEU 12 CB ) 0.20307 ( PROT LEU 12 CG ) 0.20307 ( PROT LEU 12 CD1 ) 0.20307 ( PROT LEU 12 CD2 ) 0.20307 ( PROT LEU 12 C ) 0.25384 ( PROT LEU 12 O ) 0.25384 ( PROT ILE 13 N ) 0.25384 ( PROT ILE 13 H ) 0.20307 ( PROT ILE 13 CA ) 0.25384 ( PROT ILE 13 CB ) 0.20307 ( PROT ILE 13 CG2 ) 0.20307 ( PROT ILE 13 CG1 ) 0.20307 ( PROT ILE 13 CD ) 0.20307 ( PROT ILE 13 C ) 0.25384 ( PROT ILE 13 O ) 0.25384 ( PROT ASH 14 N ) 0.25384 ( PROT ASH 14 H ) 0.20307 ( PROT ASH 14 CA ) 0.25384 ( PROT ASH 14 CB ) 0.20307 ( PROT ASH 14 CG ) 0.20307 ( PROT ASH 14 OD1 ) 0.20307 ( PROT ASH 14 OD2 ) 0.20307 ( PROT ASH 14 HD2 ) 0.20307 ( PROT ASH 14 C ) 0.25384 ( PROT ASH 14 O ) 0.25384 ( PROT PHE 15 N ) 0.25384 ( PROT PHE 15 H ) 0.20307 ( PROT PHE 15 CA ) 0.25384 ( PROT PHE 15 CB ) 0.20307 ( PROT PHE 15 CG ) 0.20307 ( PROT PHE 15 CD1 ) 0.20307 ( PROT PHE 15 CD2 ) 0.20307 ( PROT PHE 15 CE1 ) 0.20307 ( PROT PHE 15 CE2 ) 0.20307 ( PROT PHE 15 CZ ) 0.20307 ( PROT PHE 15 C ) 0.25384 ( PROT PHE 15 O ) 0.25384 ( PROT MET 16 N ) 0.25384 ( PROT MET 16 H ) 0.20307 ( PROT MET 16 CA ) 0.25384 ( PROT MET 16 CB ) 0.20307 ( PROT MET 16 CG ) 0.20307 ( PROT MET 16 SD ) 0.20307 ( PROT MET 16 CE ) 0.20307 ( PROT MET 16 C ) 0.25384 ( PROT MET 16 O ) 0.25384 ( PROT PHE 17 N ) 0.25384 ( PROT PHE 17 H ) 0.20307 ( PROT PHE 17 CA ) 0.25384 ( PROT PHE 17 CB ) 0.20307 ( PROT PHE 17 CG ) 0.20307 ( PROT PHE 17 CD1 ) 0.20307 ( PROT PHE 17 CD2 ) 0.20307 ( PROT PHE 17 CE1 ) 0.20307 ( PROT PHE 17 CE2 ) 0.20307 ( PROT PHE 17 CZ ) 0.20307 ( PROT PHE 17 C ) 0.25384 ( PROT PHE 17 O ) 0.25384 ( PROT PHE 18 N ) 0.25384 ( PROT PHE 18 H ) 0.20307 ( PROT PHE 18 CA ) 0.25384 ( PROT PHE 18 CB ) 0.20307 ( PROT PHE 18 CG ) 0.20307 ( PROT PHE 18 CD1 ) 0.20307 ( PROT PHE 18 CD2 ) 0.20307 ( PROT PHE 18 CE1 ) 0.20307 ( PROT PHE 18 CE2 ) 0.20307 ( PROT PHE 18 CZ ) 0.20307 ( PROT PHE 18 C ) 0.25384 ( PROT PHE 18 O ) 0.25384 ( PROT GLU 19 N ) 0.25384 ( PROT GLU 19 H ) 0.20307 ( PROT GLU 19 CA ) 0.25384 ( PROT GLU 19 CB ) 0.20307 ( PROT GLU 19 CG ) 0.20307 ( PROT GLU 19 CD ) 0.20307 ( PROT GLU 19 OE1 ) 0.20307 ( PROT GLU 19 OE2 ) 0.20307 ( PROT GLU 19 C ) 0.25384 ( PROT GLU 19 OT1 ) 0.20307 ( PROT GLU 19 OT2 ) 0.20307 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40244 5.28790 -8.68956 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00211 0.00452 -0.00365 ROTATION MATRIX 1.000000 0.000040 0.000328 -0.000040 1.000000 0.000277 -0.000328 -0.000277 1.000000 AXIS OF ROTATION IS 0.642690 -0.760606 0.091806 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 110.8720 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.778369 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.7784" Parameter: A <- "0.7784" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.72035 5.25462 -8.79386 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.00551 0.00980 -0.00051 ROTATION MATRIX 0.999866 0.014664 0.007210 -0.014559 0.999790 -0.014448 -0.007420 0.014341 0.999870 AXIS OF ROTATION IS -0.661019 -0.335920 0.670978 ANGLE IS 1.25 CENTER OF ROTATION 9.423566 5.074476 -9.176423 SHIFT IS 0.000009 TOTAL SQUARE DIFF IS 6.5183 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.585722 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.7784" RDCMND substituted energy or value "?RMS" to " 0.5857" Parameter: A <- "0.7784 0.5857" 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 0.7784 0.5857 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 " 37.30" Parameter: H <- "37.30" 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 -45.51870 37.29677 0.30563 ENER INTERN> 4.42510 16.31887 0.00000 14.23670 3.22976 ENER EXTERN> -98.30017 14.57104 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 " -45.52" Parameter: B <- "-45.52" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 14.57" Parameter: C <- "14.57" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -98.30" Parameter: C <- " -83.73" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -83.73" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.43" Parameter: D <- "4.43" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 16.32" Parameter: D <- " 20.75" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 14.24" Parameter: D <- " 34.99" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.23" Parameter: D <- " 38.22" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 38.22" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 9600 ENER= -45.52 GRMS= 0.31 ELEC= 14.57 VDW= -98.30 RDTITL> *EXTERNAL= -83.73 INTERNAL= 38.22 USER= 0.00 HARM= 37.30 RDTITL> *BOND= 4.43 ANGL= 16.32 DIHE= 14.24 IMPR= 3.23 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= -45.52 GRMS= 0.31 ELEC= 14.57 VDW= -98.30 RDTITL> *EXTERNAL= -83.73 INTERNAL= 38.22 USER= 0.00 HARM= 37.30 RDTITL> *BOND= 4.43 ANGL= 16.32 DIHE= 14.24 IMPR= 3.23 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= -45.52 GRMS= 0.31 ELEC= 14.57 VDW= -98.30 RDTITL> *EXTERNAL= -83.73 INTERNAL= 38.22 USER= 0.00 HARM= 37.30 RDTITL> *BOND= 4.43 ANGL= 16.32 DIHE= 14.24 IMPR= 3.23 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 9600 0.7784 0.5857 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 10978 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10943 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 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 -20.89511 -24.62360 0.11173 0.02000 MINI INTERN> 4.42510 16.31887 0.00000 14.23670 3.22976 MINI EXTERN> -98.30017 14.57104 0.00000 0.00000 0.00000 MINI CONSTR> 24.62360 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -20.98721 0.09211 1.32808 0.00150 MINI INTERN> 4.80745 16.93755 0.00000 14.54970 3.21588 MINI EXTERN> -101.89516 15.78365 0.00000 0.00000 0.00000 MINI CONSTR> 25.61372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10938 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -21.19550 0.20828 0.77411 0.00065 MINI INTERN> 4.78760 16.49806 0.00000 14.43840 3.24839 MINI EXTERN> -101.31072 15.53296 0.00000 0.00000 0.00000 MINI CONSTR> 25.60981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -21.29303 0.09753 0.45450 0.00028 MINI INTERN> 4.60647 16.48802 0.00000 14.39913 3.24352 MINI EXTERN> -100.96111 15.30747 0.00000 0.00000 0.00000 MINI CONSTR> 25.62347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10937 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -21.33046 0.03743 0.09903 0.00012 MINI INTERN> 4.59159 16.40654 0.00000 14.37114 3.24733 MINI EXTERN> -100.84603 15.26384 0.00000 0.00000 0.00000 MINI CONSTR> 25.63514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -21.35019 0.01973 0.09607 0.00013 MINI INTERN> 4.56993 16.37103 0.00000 14.34290 3.24831 MINI EXTERN> -100.72556 15.19010 0.00000 0.00000 0.00000 MINI CONSTR> 25.65309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10937 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -21.36631 0.01613 0.13877 0.00013 MINI INTERN> 4.56641 16.33315 0.00000 14.31816 3.24756 MINI EXTERN> -100.64384 15.13889 0.00000 0.00000 0.00000 MINI CONSTR> 25.67335 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -21.37962 0.01331 0.17588 0.00013 MINI INTERN> 4.56927 16.29918 0.00000 14.29828 3.24624 MINI EXTERN> -100.59424 15.10841 0.00000 0.00000 0.00000 MINI CONSTR> 25.69323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10936 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -21.39107 0.01145 0.21085 0.00014 MINI INTERN> 4.59252 16.26261 0.00000 14.28096 3.24239 MINI EXTERN> -100.56350 15.08149 0.00000 0.00000 0.00000 MINI CONSTR> 25.71247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -21.40259 0.01152 0.21539 0.00014 MINI INTERN> 4.59207 16.24048 0.00000 14.26598 3.24143 MINI EXTERN> -100.54349 15.06889 0.00000 0.00000 0.00000 MINI CONSTR> 25.73205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10932 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -21.41373 0.01114 0.22210 0.00015 MINI INTERN> 4.60168 16.22150 0.00000 14.25183 3.23914 MINI EXTERN> -100.53043 15.05065 0.00000 0.00000 0.00000 MINI CONSTR> 25.75190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -21.42454 0.01081 0.21606 0.00016 MINI INTERN> 4.59727 16.20795 0.00000 14.23945 3.23858 MINI EXTERN> -100.52386 15.04438 0.00000 0.00000 0.00000 MINI CONSTR> 25.77170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10932 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -21.43862 0.01408 0.07068 0.00007 MINI INTERN> 4.49977 16.26777 0.00000 14.23515 3.24615 MINI EXTERN> -100.50141 15.02354 0.00000 0.00000 0.00000 MINI CONSTR> 25.79041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -21.44414 0.00552 0.25159 0.00017 MINI INTERN> 4.60252 16.18079 0.00000 14.21596 3.23663 MINI EXTERN> -100.52465 15.03211 0.00000 0.00000 0.00000 MINI CONSTR> 25.81249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10932 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -21.45251 0.00838 0.29456 0.00017 MINI INTERN> 4.59168 16.18607 0.00000 14.20795 3.23574 MINI EXTERN> -100.52157 15.01539 0.00000 0.00000 0.00000 MINI CONSTR> 25.83222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -21.46888 0.01636 0.08052 0.00007 MINI INTERN> 4.48204 16.24652 0.00000 14.20656 3.24409 MINI EXTERN> -100.50481 15.00553 0.00000 0.00000 0.00000 MINI CONSTR> 25.85119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10932 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -21.47785 0.00898 0.06849 0.00008 MINI INTERN> 4.49119 16.23048 0.00000 14.19778 3.24226 MINI EXTERN> -100.51334 15.00434 0.00000 0.00000 0.00000 MINI CONSTR> 25.86943 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -21.48725 0.00939 0.06931 0.00008 MINI INTERN> 4.48881 16.22311 0.00000 14.18960 3.24132 MINI EXTERN> -100.52089 15.00156 0.00000 0.00000 0.00000 MINI CONSTR> 25.88924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10930 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -21.49679 0.00955 0.06660 0.00008 MINI INTERN> 4.49019 16.21352 0.00000 14.18112 3.24011 MINI EXTERN> -100.53129 15.00005 0.00000 0.00000 0.00000 MINI CONSTR> 25.90952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -21.50641 0.00962 0.07018 0.00009 MINI INTERN> 4.48497 16.20841 0.00000 14.17325 3.23945 MINI EXTERN> -100.54131 14.99840 0.00000 0.00000 0.00000 MINI CONSTR> 25.93042 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10931 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -21.51592 0.00951 0.11661 0.00009 MINI INTERN> 4.45752 16.21967 0.00000 14.16694 3.24052 MINI EXTERN> -100.54659 14.99283 0.00000 0.00000 0.00000 MINI CONSTR> 25.95318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -21.52513 0.00921 0.09348 0.00009 MINI INTERN> 4.46913 16.20320 0.00000 14.15854 3.23869 MINI EXTERN> -100.56270 14.99564 0.00000 0.00000 0.00000 MINI CONSTR> 25.97237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10929 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -21.53369 0.00856 0.10651 0.00010 MINI INTERN> 4.46366 16.19961 0.00000 14.15208 3.23799 MINI EXTERN> -100.57277 14.99370 0.00000 0.00000 0.00000 MINI CONSTR> 25.99204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -21.54245 0.00876 0.10971 0.00010 MINI INTERN> 4.46533 16.19182 0.00000 14.14496 3.23673 MINI EXTERN> -100.58588 14.99277 0.00000 0.00000 0.00000 MINI CONSTR> 26.01182 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10929 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -21.55002 0.00757 0.15033 0.00010 MINI INTERN> 4.44960 16.19518 0.00000 14.13971 3.23701 MINI EXTERN> -100.59364 14.99072 0.00000 0.00000 0.00000 MINI CONSTR> 26.03140 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -21.55871 0.00869 0.16125 0.00011 MINI INTERN> 4.45291 16.18788 0.00000 14.13235 3.23564 MINI EXTERN> -100.60859 14.98932 0.00000 0.00000 0.00000 MINI CONSTR> 26.05177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10928 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -21.56665 0.00794 0.17115 0.00011 MINI INTERN> 4.44472 16.18514 0.00000 14.12659 3.23541 MINI EXTERN> -100.61949 14.99003 0.00000 0.00000 0.00000 MINI CONSTR> 26.07096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -21.57486 0.00821 0.18232 0.00012 MINI INTERN> 4.44652 16.17863 0.00000 14.11988 3.23414 MINI EXTERN> -100.63344 14.98868 0.00000 0.00000 0.00000 MINI CONSTR> 26.09072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10928 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -21.58291 0.00805 0.17225 0.00012 MINI INTERN> 4.44836 16.16996 0.00000 14.11344 3.23328 MINI EXTERN> -100.64816 14.99157 0.00000 0.00000 0.00000 MINI CONSTR> 26.10864 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -21.59092 0.00801 0.18922 0.00012 MINI INTERN> 4.45534 16.16173 0.00000 14.10629 3.23161 MINI EXTERN> -100.66432 14.99005 0.00000 0.00000 0.00000 MINI CONSTR> 26.12838 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10928 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -21.59896 0.00804 0.18377 0.00013 MINI INTERN> 4.44802 16.15787 0.00000 14.10037 3.23163 MINI EXTERN> -100.67763 14.99371 0.00000 0.00000 0.00000 MINI CONSTR> 26.14706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -21.60902 0.01006 0.06123 0.00006 MINI INTERN> 4.50084 16.11961 0.00000 14.08810 3.22737 MINI EXTERN> -100.71481 15.00615 0.00000 0.00000 0.00000 MINI CONSTR> 26.16373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10928 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -21.61337 0.00435 0.20487 0.00014 MINI INTERN> 4.44689 16.14739 0.00000 14.08897 3.22977 MINI EXTERN> -100.70266 14.99308 0.00000 0.00000 0.00000 MINI CONSTR> 26.18319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -21.62078 0.00742 0.22461 0.00014 MINI INTERN> 4.46133 16.13599 0.00000 14.08152 3.22753 MINI EXTERN> -100.72098 14.99173 0.00000 0.00000 0.00000 MINI CONSTR> 26.20210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10927 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -21.62779 0.00701 0.23700 0.00015 MINI INTERN> 4.44695 16.13609 0.00000 14.07618 3.22851 MINI EXTERN> -100.73332 14.99735 0.00000 0.00000 0.00000 MINI CONSTR> 26.22046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -21.63976 0.01197 0.06892 0.00006 MINI INTERN> 4.50300 16.09753 0.00000 14.06272 3.22419 MINI EXTERN> -100.77567 15.01102 0.00000 0.00000 0.00000 MINI CONSTR> 26.23745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10926 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -21.64206 0.00230 0.23565 0.00016 MINI INTERN> 4.44636 16.12620 0.00000 14.06545 3.22644 MINI EXTERN> -100.75711 14.99527 0.00000 0.00000 0.00000 MINI CONSTR> 26.25534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -21.65457 0.01251 0.08187 0.00007 MINI INTERN> 4.50625 16.08570 0.00000 14.04990 3.22259 MINI EXTERN> -100.80740 15.01454 0.00000 0.00000 0.00000 MINI CONSTR> 26.27386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10925 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -21.66106 0.00649 0.05728 0.00007 MINI INTERN> 4.49540 16.08781 0.00000 14.04634 3.22246 MINI EXTERN> -100.81392 15.01201 0.00000 0.00000 0.00000 MINI CONSTR> 26.28884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -21.66834 0.00728 0.06117 0.00007 MINI INTERN> 4.49717 16.08201 0.00000 14.03997 3.22167 MINI EXTERN> -100.82980 15.01384 0.00000 0.00000 0.00000 MINI CONSTR> 26.30679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10924 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -21.67550 0.00717 0.10357 0.00008 MINI INTERN> 4.50986 16.07014 0.00000 14.03151 3.22041 MINI EXTERN> -100.85303 15.01938 0.00000 0.00000 0.00000 MINI CONSTR> 26.32622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -21.68275 0.00724 0.07189 0.00008 MINI INTERN> 4.50090 16.07042 0.00000 14.02735 3.21999 MINI EXTERN> -100.86105 15.01694 0.00000 0.00000 0.00000 MINI CONSTR> 26.34271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10922 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -21.68978 0.00703 0.08416 0.00008 MINI INTERN> 4.50192 16.06492 0.00000 14.02091 3.21939 MINI EXTERN> -100.87736 15.01978 0.00000 0.00000 0.00000 MINI CONSTR> 26.36067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -21.69627 0.00650 0.09799 0.00009 MINI INTERN> 4.50626 16.05865 0.00000 14.01455 3.21851 MINI EXTERN> -100.89366 15.02187 0.00000 0.00000 0.00000 MINI CONSTR> 26.37754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10922 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -21.70222 0.00595 0.13106 0.00009 MINI INTERN> 4.51422 16.05071 0.00000 14.00769 3.21753 MINI EXTERN> -100.91193 15.02519 0.00000 0.00000 0.00000 MINI CONSTR> 26.39438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -21.70929 0.00707 0.12947 0.00009 MINI INTERN> 4.51174 16.04687 0.00000 14.00194 3.21703 MINI EXTERN> -100.92566 15.02673 0.00000 0.00000 0.00000 MINI CONSTR> 26.41206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10922 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -21.71623 0.00694 0.10860 0.00010 MINI INTERN> 4.50831 16.04470 0.00000 13.99718 3.21624 MINI EXTERN> -100.93583 15.02490 0.00000 0.00000 0.00000 MINI CONSTR> 26.42828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -21.72160 0.00538 0.14185 0.00010 MINI INTERN> 4.51472 16.03789 0.00000 13.99060 3.21556 MINI EXTERN> -100.95354 15.02905 0.00000 0.00000 0.00000 MINI CONSTR> 26.44412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10922 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -21.72838 0.00678 0.15524 0.00010 MINI INTERN> 4.51557 16.03235 0.00000 13.98414 3.21494 MINI EXTERN> -100.96964 15.03185 0.00000 0.00000 0.00000 MINI CONSTR> 26.46240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -21.73428 0.00590 0.17507 0.00011 MINI INTERN> 4.52218 16.02577 0.00000 13.97805 3.21360 MINI EXTERN> -100.98457 15.03166 0.00000 0.00000 0.00000 MINI CONSTR> 26.47903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10921 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -21.74041 0.00613 0.16074 0.00011 MINI INTERN> 4.51793 16.02386 0.00000 13.97321 3.21344 MINI EXTERN> -100.99600 15.03346 0.00000 0.00000 0.00000 MINI CONSTR> 26.49370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -21.74690 0.00649 0.16997 0.00011 MINI INTERN> 4.51532 16.02023 0.00000 13.96738 3.21310 MINI EXTERN> -101.01003 15.03597 0.00000 0.00000 0.00000 MINI CONSTR> 26.51114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10921 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -21.75513 0.00823 0.05535 0.00005 MINI INTERN> 4.48263 16.03215 0.00000 13.96794 3.21307 MINI EXTERN> -100.99974 15.02315 0.00000 0.00000 0.00000 MINI CONSTR> 26.52568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -21.75834 0.00321 0.18125 0.00012 MINI INTERN> 4.52161 16.01030 0.00000 13.95630 3.21124 MINI EXTERN> -101.03689 15.03722 0.00000 0.00000 0.00000 MINI CONSTR> 26.54189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10921 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -21.76713 0.00879 0.05792 0.00005 MINI INTERN> 4.48159 16.02469 0.00000 13.95744 3.21172 MINI EXTERN> -101.02416 15.02461 0.00000 0.00000 0.00000 MINI CONSTR> 26.55698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -21.76952 0.00239 0.19882 0.00013 MINI INTERN> 4.51615 16.00494 0.00000 13.94585 3.21078 MINI EXTERN> -101.06179 15.04189 0.00000 0.00000 0.00000 MINI CONSTR> 26.57266 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10921 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -21.77875 0.00923 0.06448 0.00006 MINI INTERN> 4.47921 16.01808 0.00000 13.94731 3.21048 MINI EXTERN> -101.04731 15.02584 0.00000 0.00000 0.00000 MINI CONSTR> 26.58765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -21.78043 0.00168 0.20875 0.00014 MINI INTERN> 4.52571 15.99380 0.00000 13.93468 3.20864 MINI EXTERN> -101.08883 15.04293 0.00000 0.00000 0.00000 MINI CONSTR> 26.60263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10921 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -21.79032 0.00989 0.07220 0.00006 MINI INTERN> 4.47738 16.01129 0.00000 13.93706 3.20915 MINI EXTERN> -101.07061 15.02692 0.00000 0.00000 0.00000 MINI CONSTR> 26.61849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -21.79543 0.00511 0.04990 0.00006 MINI INTERN> 4.48364 16.00468 0.00000 13.93144 3.20847 MINI EXTERN> -101.08568 15.03068 0.00000 0.00000 0.00000 MINI CONSTR> 26.63134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10921 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -21.80137 0.00593 0.05298 0.00007 MINI INTERN> 4.48231 16.00142 0.00000 13.92622 3.20777 MINI EXTERN> -101.09725 15.03093 0.00000 0.00000 0.00000 MINI CONSTR> 26.64723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -21.80701 0.00565 0.09315 0.00007 MINI INTERN> 4.47274 16.00231 0.00000 13.92215 3.20731 MINI EXTERN> -101.10372 15.02826 0.00000 0.00000 0.00000 MINI CONSTR> 26.66394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10920 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -21.81274 0.00572 0.06316 0.00007 MINI INTERN> 4.47967 15.99517 0.00000 13.91607 3.20644 MINI EXTERN> -101.11969 15.03161 0.00000 0.00000 0.00000 MINI CONSTR> 26.67801 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -21.81827 0.00553 0.07507 0.00007 MINI INTERN> 4.47599 15.99305 0.00000 13.91116 3.20603 MINI EXTERN> -101.13028 15.03242 0.00000 0.00000 0.00000 MINI CONSTR> 26.69336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10919 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -21.82297 0.00470 0.11152 0.00008 MINI INTERN> 4.47026 15.99286 0.00000 13.90746 3.20532 MINI EXTERN> -101.13625 15.02944 0.00000 0.00000 0.00000 MINI CONSTR> 26.70795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -21.82891 0.00594 0.07224 0.00008 MINI INTERN> 4.47640 15.98569 0.00000 13.90106 3.20474 MINI EXTERN> -101.15344 15.03456 0.00000 0.00000 0.00000 MINI CONSTR> 26.72208 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10918 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -21.83338 0.00447 0.11859 0.00008 MINI INTERN> 4.46843 15.98663 0.00000 13.89766 3.20415 MINI EXTERN> -101.15810 15.03113 0.00000 0.00000 0.00000 MINI CONSTR> 26.73672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -21.83897 0.00559 0.11983 0.00009 MINI INTERN> 4.46972 15.98234 0.00000 13.89217 3.20331 MINI EXTERN> -101.17047 15.03189 0.00000 0.00000 0.00000 MINI CONSTR> 26.75206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10918 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -21.84460 0.00563 0.09846 0.00009 MINI INTERN> 4.47146 15.97742 0.00000 13.88647 3.20292 MINI EXTERN> -101.18483 15.03577 0.00000 0.00000 0.00000 MINI CONSTR> 26.76619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -21.84864 0.00404 0.13087 0.00009 MINI INTERN> 4.46611 15.97726 0.00000 13.88298 3.20239 MINI EXTERN> -101.19065 15.03385 0.00000 0.00000 0.00000 MINI CONSTR> 26.77941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10918 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -21.85348 0.00484 0.14551 0.00010 MINI INTERN> 4.47216 15.97155 0.00000 13.87765 3.20106 MINI EXTERN> -101.20273 15.03322 0.00000 0.00000 0.00000 MINI CONSTR> 26.79360 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -21.85843 0.00495 0.14120 0.00010 MINI INTERN> 4.46468 15.97114 0.00000 13.87331 3.20130 MINI EXTERN> -101.21207 15.03601 0.00000 0.00000 0.00000 MINI CONSTR> 26.80720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10918 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -21.86459 0.00616 0.04777 0.00004 MINI INTERN> 4.48720 15.95636 0.00000 13.86498 3.20007 MINI EXTERN> -101.23791 15.04528 0.00000 0.00000 0.00000 MINI CONSTR> 26.81942 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -21.86744 0.00285 0.15723 0.00011 MINI INTERN> 4.46208 15.96623 0.00000 13.86452 3.20014 MINI EXTERN> -101.23062 15.03654 0.00000 0.00000 0.00000 MINI CONSTR> 26.83366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10918 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -21.87414 0.00670 0.05072 0.00005 MINI INTERN> 4.48789 15.94950 0.00000 13.85533 3.19888 MINI EXTERN> -101.25963 15.04772 0.00000 0.00000 0.00000 MINI CONSTR> 26.84618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -21.87628 0.00214 0.17264 0.00011 MINI INTERN> 4.46793 15.95808 0.00000 13.85531 3.19810 MINI EXTERN> -101.25063 15.03538 0.00000 0.00000 0.00000 MINI CONSTR> 26.85956 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10918 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -21.88036 0.00408 0.19565 0.00012 MINI INTERN> 4.46166 15.95694 0.00000 13.85016 3.19892 MINI EXTERN> -101.26341 15.04246 0.00000 0.00000 0.00000 MINI CONSTR> 26.87291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -21.88792 0.00756 0.05456 0.00005 MINI INTERN> 4.48878 15.93964 0.00000 13.84128 3.19711 MINI EXTERN> -101.29080 15.05099 0.00000 0.00000 0.00000 MINI CONSTR> 26.88509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10918 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -21.89213 0.00421 0.04533 0.00005 MINI INTERN> 4.48598 15.93818 0.00000 13.83766 3.19657 MINI EXTERN> -101.29763 15.05038 0.00000 0.00000 0.00000 MINI CONSTR> 26.89673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -21.89675 0.00463 0.04664 0.00005 MINI INTERN> 4.48627 15.93481 0.00000 13.83284 3.19601 MINI EXTERN> -101.30836 15.05177 0.00000 0.00000 0.00000 MINI CONSTR> 26.90992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10918 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -21.90128 0.00453 0.04686 0.00006 MINI INTERN> 4.48658 15.93159 0.00000 13.82820 3.19537 MINI EXTERN> -101.31842 15.05259 0.00000 0.00000 0.00000 MINI CONSTR> 26.92282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -21.90593 0.00465 0.07639 0.00006 MINI INTERN> 4.49274 15.92524 0.00000 13.82186 3.19471 MINI EXTERN> -101.33442 15.05676 0.00000 0.00000 0.00000 MINI CONSTR> 26.93720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10917 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -21.90996 0.00403 0.04556 0.00006 MINI INTERN> 4.48598 15.92591 0.00000 13.81939 3.19423 MINI EXTERN> -101.33720 15.05411 0.00000 0.00000 0.00000 MINI CONSTR> 26.94763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -21.91436 0.00440 0.09055 0.00006 MINI INTERN> 4.49612 15.91785 0.00000 13.81246 3.19337 MINI EXTERN> -101.35530 15.05905 0.00000 0.00000 0.00000 MINI CONSTR> 26.96210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10917 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -21.91881 0.00446 0.06658 0.00007 MINI INTERN> 4.48942 15.91789 0.00000 13.80911 3.19313 MINI EXTERN> -101.36088 15.05865 0.00000 0.00000 0.00000 MINI CONSTR> 26.97386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -21.92288 0.00407 0.07780 0.00007 MINI INTERN> 4.49269 15.91346 0.00000 13.80415 3.19246 MINI EXTERN> -101.37235 15.06057 0.00000 0.00000 0.00000 MINI CONSTR> 26.98614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -21.92664 0.00376 0.10350 0.00007 MINI INTERN> 4.49840 15.90808 0.00000 13.79887 3.19167 MINI EXTERN> -101.38504 15.06294 0.00000 0.00000 0.00000 MINI CONSTR> 26.99843 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -21.93093 0.00429 0.10792 0.00007 MINI INTERN> 4.49486 15.90652 0.00000 13.79450 3.19148 MINI EXTERN> -101.39408 15.06464 0.00000 0.00000 0.00000 MINI CONSTR> 27.01116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -21.93486 0.00392 0.11626 0.00008 MINI INTERN> 4.50059 15.90130 0.00000 13.78961 3.19041 MINI EXTERN> -101.40510 15.06513 0.00000 0.00000 0.00000 MINI CONSTR> 27.02321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -21.93880 0.00394 0.12405 0.00008 MINI INTERN> 4.49844 15.89918 0.00000 13.78511 3.19028 MINI EXTERN> -101.41491 15.06780 0.00000 0.00000 0.00000 MINI CONSTR> 27.03531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -21.94277 0.00397 0.11697 0.00008 MINI INTERN> 4.50068 15.89564 0.00000 13.78104 3.18934 MINI EXTERN> -101.42317 15.06718 0.00000 0.00000 0.00000 MINI CONSTR> 27.04651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -21.94646 0.00369 0.14302 0.00008 MINI INTERN> 4.49732 15.89408 0.00000 13.77639 3.18940 MINI EXTERN> -101.43330 15.07047 0.00000 0.00000 0.00000 MINI CONSTR> 27.05919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -21.95032 0.00386 0.13047 0.00009 MINI INTERN> 4.49842 15.89094 0.00000 13.77245 3.18872 MINI EXTERN> -101.44148 15.07089 0.00000 0.00000 0.00000 MINI CONSTR> 27.06974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -21.95540 0.00508 0.04307 0.00004 MINI INTERN> 4.47994 15.89719 0.00000 13.77219 3.18815 MINI EXTERN> -101.43497 15.06183 0.00000 0.00000 0.00000 MINI CONSTR> 27.08028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -21.95777 0.00236 0.13816 0.00009 MINI INTERN> 4.50211 15.88392 0.00000 13.76357 3.18745 MINI EXTERN> -101.46071 15.07332 0.00000 0.00000 0.00000 MINI CONSTR> 27.09257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -21.96326 0.00549 0.04441 0.00004 MINI INTERN> 4.47915 15.89203 0.00000 13.76371 3.18706 MINI EXTERN> -101.45228 15.06338 0.00000 0.00000 0.00000 MINI CONSTR> 27.10371 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -21.96520 0.00194 0.14805 0.00010 MINI INTERN> 4.50608 15.87696 0.00000 13.75481 3.18596 MINI EXTERN> -101.47915 15.07453 0.00000 0.00000 0.00000 MINI CONSTR> 27.11561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -21.96886 0.00365 0.16531 0.00011 MINI INTERN> 4.49670 15.87825 0.00000 13.75117 3.18634 MINI EXTERN> -101.48559 15.07656 0.00000 0.00000 0.00000 MINI CONSTR> 27.12772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -21.97480 0.00595 0.04903 0.00005 MINI INTERN> 4.47783 15.88454 0.00000 13.75114 3.18539 MINI EXTERN> -101.47753 15.06535 0.00000 0.00000 0.00000 MINI CONSTR> 27.13847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -21.97595 0.00115 0.16823 0.00011 MINI INTERN> 4.50290 15.87021 0.00000 13.74214 3.18498 MINI EXTERN> -101.50551 15.07957 0.00000 0.00000 0.00000 MINI CONSTR> 27.14974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10915 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -21.98210 0.00615 0.05868 0.00005 MINI INTERN> 4.47530 15.88056 0.00000 13.74326 3.18442 MINI EXTERN> -101.49284 15.06637 0.00000 0.00000 0.00000 MINI CONSTR> 27.16083 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 -21.98210 0.00615 0.05868 0.00006 STPD INTERN> 4.47530 15.88056 0.00000 13.74326 3.18442 STPD EXTERN> -101.49284 15.06637 0.00000 0.00000 0.00000 STPD CONSTR> 27.16083 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 10915 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10915 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 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 -21.98210 0.00615 0.05868 0.00000 MINI INTERN> 4.47530 15.88056 0.00000 13.74326 3.18442 MINI EXTERN> -101.49284 15.06637 0.00000 0.00000 0.00000 MINI CONSTR> 27.16083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -22.35482 0.37272 0.05452 0.01666 MINI INTERN> 4.50483 15.42956 0.00000 12.97216 3.09574 MINI EXTERN> -103.16613 15.29334 0.00000 0.00000 0.00000 MINI CONSTR> 29.51567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -22.36439 0.00957 0.12212 0.00932 MINI INTERN> 4.45396 15.42512 0.00000 12.95402 3.05244 MINI EXTERN> -103.09234 15.32655 0.00000 0.00000 0.00000 MINI CONSTR> 29.51585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -22.39895 0.03456 0.16100 0.03906 MINI INTERN> 4.40126 15.33434 0.00000 12.90586 3.07484 MINI EXTERN> -102.92671 15.34597 0.00000 0.00000 0.00000 MINI CONSTR> 29.46549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -22.44341 0.04446 0.14216 0.02734 MINI INTERN> 4.45383 15.45142 0.00000 12.83052 3.05756 MINI EXTERN> -102.83150 15.19831 0.00000 0.00000 0.00000 MINI CONSTR> 29.39645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -22.46345 0.02004 0.09878 0.01334 MINI INTERN> 4.45803 15.49316 0.00000 12.77235 3.04031 MINI EXTERN> -102.81775 15.22298 0.00000 0.00000 0.00000 MINI CONSTR> 29.36748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -22.47326 0.00981 0.07354 0.00965 MINI INTERN> 4.49658 15.45857 0.00000 12.74712 3.06297 MINI EXTERN> -102.78109 15.18859 0.00000 0.00000 0.00000 MINI CONSTR> 29.35399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -22.48124 0.00798 0.06706 0.00860 MINI INTERN> 4.47478 15.42508 0.00000 12.72902 3.05650 MINI EXTERN> -102.73004 15.21439 0.00000 0.00000 0.00000 MINI CONSTR> 29.34902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -22.48993 0.00870 0.07828 0.01208 MINI INTERN> 4.44907 15.39838 0.00000 12.71089 3.05256 MINI EXTERN> -102.72392 15.27072 0.00000 0.00000 0.00000 MINI CONSTR> 29.35236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -22.49760 0.00767 0.06298 0.01203 MINI INTERN> 4.48384 15.39726 0.00000 12.68755 3.04578 MINI EXTERN> -102.69328 15.21988 0.00000 0.00000 0.00000 MINI CONSTR> 29.36137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -22.50297 0.00536 0.04692 0.00644 MINI INTERN> 4.46647 15.43368 0.00000 12.68302 3.05027 MINI EXTERN> -102.71643 15.21187 0.00000 0.00000 0.00000 MINI CONSTR> 29.36816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -22.50622 0.00325 0.04611 0.00546 MINI INTERN> 4.46699 15.42346 0.00000 12.69030 3.05304 MINI EXTERN> -102.72032 15.21183 0.00000 0.00000 0.00000 MINI CONSTR> 29.36848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -22.50905 0.00284 0.03946 0.00525 MINI INTERN> 4.47902 15.42456 0.00000 12.69336 3.06559 MINI EXTERN> -102.72489 15.19049 0.00000 0.00000 0.00000 MINI CONSTR> 29.36281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -22.51125 0.00220 0.03191 0.00422 MINI INTERN> 4.47821 15.42953 0.00000 12.69159 3.07052 MINI EXTERN> -102.73775 15.20330 0.00000 0.00000 0.00000 MINI CONSTR> 29.35334 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -22.51284 0.00159 0.03209 0.00408 MINI INTERN> 4.47562 15.43093 0.00000 12.70793 3.06517 MINI EXTERN> -102.73139 15.19749 0.00000 0.00000 0.00000 MINI CONSTR> 29.34142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -22.51431 0.00147 0.02667 0.00416 MINI INTERN> 4.47070 15.44109 0.00000 12.72164 3.07101 MINI EXTERN> -102.73254 15.18821 0.00000 0.00000 0.00000 MINI CONSTR> 29.32558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -22.51567 0.00136 0.03170 0.00383 MINI INTERN> 4.47656 15.44955 0.00000 12.73226 3.07034 MINI EXTERN> -102.70561 15.15463 0.00000 0.00000 0.00000 MINI CONSTR> 29.30660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -22.51689 0.00122 0.02366 0.00382 MINI INTERN> 4.47645 15.44667 0.00000 12.74218 3.06961 MINI EXTERN> -102.68916 15.14963 0.00000 0.00000 0.00000 MINI CONSTR> 29.28774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -22.51776 0.00086 0.02200 0.00378 MINI INTERN> 4.47286 15.44539 0.00000 12.76301 3.06860 MINI EXTERN> -102.67626 15.13486 0.00000 0.00000 0.00000 MINI CONSTR> 29.27378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -22.51851 0.00075 0.02148 0.00303 MINI INTERN> 4.47623 15.45726 0.00000 12.78365 3.06903 MINI EXTERN> -102.70879 15.14181 0.00000 0.00000 0.00000 MINI CONSTR> 29.26231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -22.51913 0.00062 0.01868 0.00274 MINI INTERN> 4.47200 15.45777 0.00000 12.78864 3.06909 MINI EXTERN> -102.71315 15.15376 0.00000 0.00000 0.00000 MINI CONSTR> 29.25275 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 -22.51913 0.00062 0.01868 0.02000 CONJ INTERN> 4.47200 15.45777 0.00000 12.78864 3.06909 CONJ EXTERN> -102.71315 15.15376 0.00000 0.00000 0.00000 CONJ CONSTR> 29.25275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "10200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.13199 ( PROT LYS 1 HT2 ) 0.13199 ( PROT LYS 1 N ) 0.16499 ( PROT LYS 1 HT3 ) 0.13199 ( PROT LYS 1 CA ) 0.16499 ( PROT LYS 1 CB ) 0.13199 ( PROT LYS 1 CG ) 0.13199 ( PROT LYS 1 CD ) 0.13199 ( PROT LYS 1 CE ) 0.13199 ( PROT LYS 1 NZ ) 0.13199 ( PROT LYS 1 HZ1 ) 0.13199 ( PROT LYS 1 HZ2 ) 0.13199 ( PROT LYS 1 HZ3 ) 0.13199 ( PROT LYS 1 C ) 0.16499 ( PROT LYS 1 O ) 0.16499 ( PROT MET 2 N ) 0.16499 ( PROT MET 2 H ) 0.13199 ( PROT MET 2 CA ) 0.16499 ( PROT MET 2 CB ) 0.13199 ( PROT MET 2 CG ) 0.13199 ( PROT MET 2 SD ) 0.13199 ( PROT MET 2 CE ) 0.13199 ( PROT MET 2 C ) 0.16499 ( PROT MET 2 O ) 0.16499 ( PROT LYS 3 N ) 0.16499 ( PROT LYS 3 H ) 0.13199 ( PROT LYS 3 CA ) 0.16499 ( PROT LYS 3 CB ) 0.13199 ( PROT LYS 3 CG ) 0.13199 ( PROT LYS 3 CD ) 0.13199 ( PROT LYS 3 CE ) 0.13199 ( PROT LYS 3 NZ ) 0.13199 ( PROT LYS 3 HZ1 ) 0.13199 ( PROT LYS 3 HZ2 ) 0.13199 ( PROT LYS 3 HZ3 ) 0.13199 ( PROT LYS 3 C ) 0.16499 ( PROT LYS 3 O ) 0.16499 ( PROT ALA 4 N ) 0.16499 ( PROT ALA 4 H ) 0.13199 ( PROT ALA 4 CA ) 0.16499 ( PROT ALA 4 CB ) 0.13199 ( PROT ALA 4 C ) 0.16499 ( PROT ALA 4 O ) 0.16499 ( PROT VAL 5 N ) 0.16499 ( PROT VAL 5 H ) 0.13199 ( PROT VAL 5 CA ) 0.16499 ( PROT VAL 5 CB ) 0.13199 ( PROT VAL 5 CG1 ) 0.13199 ( PROT VAL 5 CG2 ) 0.13199 ( PROT VAL 5 C ) 0.16499 ( PROT VAL 5 O ) 0.16499 ( PROT MET 6 N ) 0.16499 ( PROT MET 6 H ) 0.13199 ( PROT MET 6 CA ) 0.16499 ( PROT MET 6 CB ) 0.13199 ( PROT MET 6 CG ) 0.13199 ( PROT MET 6 SD ) 0.13199 ( PROT MET 6 CE ) 0.13199 ( PROT MET 6 C ) 0.16499 ( PROT MET 6 O ) 0.16499 ( PROT ILE 7 N ) 0.16499 ( PROT ILE 7 H ) 0.13199 ( PROT ILE 7 CA ) 0.16499 ( PROT ILE 7 CB ) 0.13199 ( PROT ILE 7 CG2 ) 0.13199 ( PROT ILE 7 CG1 ) 0.13199 ( PROT ILE 7 CD ) 0.13199 ( PROT ILE 7 C ) 0.16499 ( PROT ILE 7 O ) 0.16499 ( PROT GLY 8 N ) 0.16499 ( PROT GLY 8 H ) 0.13199 ( PROT GLY 8 CA ) 0.16499 ( PROT GLY 8 C ) 0.16499 ( PROT GLY 8 O ) 0.16499 ( PROT ALA 9 N ) 0.16499 ( PROT ALA 9 H ) 0.13199 ( PROT ALA 9 CA ) 0.16499 ( PROT ALA 9 CB ) 0.13199 ( PROT ALA 9 C ) 0.16499 ( PROT ALA 9 O ) 0.16499 ( PROT CYS 10 N ) 0.16499 ( PROT CYS 10 H ) 0.13199 ( PROT CYS 10 CA ) 0.16499 ( PROT CYS 10 CB ) 0.13199 ( PROT CYS 10 SG ) 0.13199 ( PROT CYS 10 C ) 0.16499 ( PROT CYS 10 O ) 0.16499 ( PROT PHE 11 N ) 0.16499 ( PROT PHE 11 H ) 0.13199 ( PROT PHE 11 CA ) 0.16499 ( PROT PHE 11 CB ) 0.13199 ( PROT PHE 11 CG ) 0.13199 ( PROT PHE 11 CD1 ) 0.13199 ( PROT PHE 11 CD2 ) 0.13199 ( PROT PHE 11 CE1 ) 0.13199 ( PROT PHE 11 CE2 ) 0.13199 ( PROT PHE 11 CZ ) 0.13199 ( PROT PHE 11 C ) 0.16499 ( PROT PHE 11 O ) 0.16499 ( PROT LEU 12 N ) 0.16499 ( PROT LEU 12 H ) 0.13199 ( PROT LEU 12 CA ) 0.16499 ( PROT LEU 12 CB ) 0.13199 ( PROT LEU 12 CG ) 0.13199 ( PROT LEU 12 CD1 ) 0.13199 ( PROT LEU 12 CD2 ) 0.13199 ( PROT LEU 12 C ) 0.16499 ( PROT LEU 12 O ) 0.16499 ( PROT ILE 13 N ) 0.16499 ( PROT ILE 13 H ) 0.13199 ( PROT ILE 13 CA ) 0.16499 ( PROT ILE 13 CB ) 0.13199 ( PROT ILE 13 CG2 ) 0.13199 ( PROT ILE 13 CG1 ) 0.13199 ( PROT ILE 13 CD ) 0.13199 ( PROT ILE 13 C ) 0.16499 ( PROT ILE 13 O ) 0.16499 ( PROT ASH 14 N ) 0.16499 ( PROT ASH 14 H ) 0.13199 ( PROT ASH 14 CA ) 0.16499 ( PROT ASH 14 CB ) 0.13199 ( PROT ASH 14 CG ) 0.13199 ( PROT ASH 14 OD1 ) 0.13199 ( PROT ASH 14 OD2 ) 0.13199 ( PROT ASH 14 HD2 ) 0.13199 ( PROT ASH 14 C ) 0.16499 ( PROT ASH 14 O ) 0.16499 ( PROT PHE 15 N ) 0.16499 ( PROT PHE 15 H ) 0.13199 ( PROT PHE 15 CA ) 0.16499 ( PROT PHE 15 CB ) 0.13199 ( PROT PHE 15 CG ) 0.13199 ( PROT PHE 15 CD1 ) 0.13199 ( PROT PHE 15 CD2 ) 0.13199 ( PROT PHE 15 CE1 ) 0.13199 ( PROT PHE 15 CE2 ) 0.13199 ( PROT PHE 15 CZ ) 0.13199 ( PROT PHE 15 C ) 0.16499 ( PROT PHE 15 O ) 0.16499 ( PROT MET 16 N ) 0.16499 ( PROT MET 16 H ) 0.13199 ( PROT MET 16 CA ) 0.16499 ( PROT MET 16 CB ) 0.13199 ( PROT MET 16 CG ) 0.13199 ( PROT MET 16 SD ) 0.13199 ( PROT MET 16 CE ) 0.13199 ( PROT MET 16 C ) 0.16499 ( PROT MET 16 O ) 0.16499 ( PROT PHE 17 N ) 0.16499 ( PROT PHE 17 H ) 0.13199 ( PROT PHE 17 CA ) 0.16499 ( PROT PHE 17 CB ) 0.13199 ( PROT PHE 17 CG ) 0.13199 ( PROT PHE 17 CD1 ) 0.13199 ( PROT PHE 17 CD2 ) 0.13199 ( PROT PHE 17 CE1 ) 0.13199 ( PROT PHE 17 CE2 ) 0.13199 ( PROT PHE 17 CZ ) 0.13199 ( PROT PHE 17 C ) 0.16499 ( PROT PHE 17 O ) 0.16499 ( PROT PHE 18 N ) 0.16499 ( PROT PHE 18 H ) 0.13199 ( PROT PHE 18 CA ) 0.16499 ( PROT PHE 18 CB ) 0.13199 ( PROT PHE 18 CG ) 0.13199 ( PROT PHE 18 CD1 ) 0.13199 ( PROT PHE 18 CD2 ) 0.13199 ( PROT PHE 18 CE1 ) 0.13199 ( PROT PHE 18 CE2 ) 0.13199 ( PROT PHE 18 CZ ) 0.13199 ( PROT PHE 18 C ) 0.16499 ( PROT PHE 18 O ) 0.16499 ( PROT GLU 19 N ) 0.16499 ( PROT GLU 19 H ) 0.13199 ( PROT GLU 19 CA ) 0.16499 ( PROT GLU 19 CB ) 0.13199 ( PROT GLU 19 CG ) 0.13199 ( PROT GLU 19 CD ) 0.13199 ( PROT GLU 19 OE1 ) 0.13199 ( PROT GLU 19 OE2 ) 0.13199 ( PROT GLU 19 C ) 0.16499 ( PROT GLU 19 OT1 ) 0.13199 ( PROT GLU 19 OT2 ) 0.13199 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40161 5.28715 -8.68931 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00294 0.00526 -0.00390 ROTATION MATRIX 1.000000 -0.000312 0.000240 0.000312 1.000000 0.000698 -0.000241 -0.000698 1.000000 AXIS OF ROTATION IS 0.870831 -0.300012 -0.389418 ANGLE IS 0.05 TOTAL SQUARE DIFF IS 134.0304 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.855808 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.8558" Parameter: A <- "0.8558" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.72827 5.26424 -8.79820 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.01343 0.00018 0.00383 ROTATION MATRIX 0.999927 0.011540 0.003657 -0.011494 0.999859 -0.012243 -0.003798 0.012201 0.999918 AXIS OF ROTATION IS -0.710493 -0.216685 0.669513 ANGLE IS 0.99 TOTAL SQUARE DIFF IS 8.0627 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.651422 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.8558" RDCMND substituted energy or value "?RMS" to " 0.6514" Parameter: A <- "0.8558 0.6514" 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 0.8558 0.6514 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 " 29.25" Parameter: H <- "29.25" 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 -51.77188 29.25275 0.21790 ENER INTERN> 4.47200 15.45777 0.00000 12.78864 3.06909 ENER EXTERN> -102.71315 15.15376 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 " -51.77" Parameter: B <- "-51.77" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 15.15" Parameter: C <- "15.15" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -102.71" Parameter: C <- " -87.56" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -87.56" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.47" Parameter: D <- "4.47" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 15.46" Parameter: D <- " 19.93" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 12.79" Parameter: D <- " 32.72" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.07" Parameter: D <- " 35.79" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 35.79" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 10200 ENER= -51.77 GRMS= 0.22 ELEC= 15.15 VDW= -102.71 RDTITL> *EXTERNAL= -87.56 INTERNAL= 35.79 USER= 0.00 HARM= 29.25 RDTITL> *BOND= 4.47 ANGL= 15.46 DIHE= 12.79 IMPR= 3.07 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 10915 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10878 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 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 -32.56898 -19.20290 0.07956 0.02000 MINI INTERN> 4.47200 15.45777 0.00000 12.78864 3.06909 MINI EXTERN> -102.71315 15.15376 0.00000 0.00000 0.00000 MINI CONSTR> 19.20290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -32.34448 -0.22451 1.86005 0.00150 MINI INTERN> 5.27829 15.87907 0.00000 13.02254 3.06854 MINI EXTERN> -105.68322 16.18031 0.00000 0.00000 0.00000 MINI CONSTR> 19.90999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10866 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -32.76474 0.42027 0.66733 0.00065 MINI INTERN> 4.72831 15.72681 0.00000 12.92630 3.07785 MINI EXTERN> -105.11075 15.98191 0.00000 0.00000 0.00000 MINI CONSTR> 19.90483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -32.82687 0.06213 0.32932 0.00028 MINI INTERN> 4.67130 15.63545 0.00000 12.90171 3.08080 MINI EXTERN> -104.87383 15.84796 0.00000 0.00000 0.00000 MINI CONSTR> 19.90973 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10866 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -32.85387 0.02699 0.13451 0.00012 MINI INTERN> 4.63305 15.59373 0.00000 12.87124 3.08566 MINI EXTERN> -104.72564 15.77307 0.00000 0.00000 0.00000 MINI CONSTR> 19.91503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -32.86437 0.01050 0.15725 0.00013 MINI INTERN> 4.60898 15.56894 0.00000 12.85045 3.08851 MINI EXTERN> -104.61797 15.71416 0.00000 0.00000 0.00000 MINI CONSTR> 19.92256 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10865 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -32.87238 0.00801 0.19341 0.00013 MINI INTERN> 4.60648 15.53795 0.00000 12.83454 3.08623 MINI EXTERN> -104.54529 15.67702 0.00000 0.00000 0.00000 MINI CONSTR> 19.93069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -32.87931 0.00692 0.21699 0.00013 MINI INTERN> 4.58280 15.53176 0.00000 12.82000 3.09078 MINI EXTERN> -104.48914 15.64509 0.00000 0.00000 0.00000 MINI CONSTR> 19.93940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10865 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -32.88971 0.01041 0.05621 0.00006 MINI INTERN> 4.58539 15.50612 0.00000 12.80821 3.08768 MINI EXTERN> -104.45124 15.62635 0.00000 0.00000 0.00000 MINI CONSTR> 19.94778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -32.89196 0.00225 0.23501 0.00014 MINI INTERN> 4.57487 15.50203 0.00000 12.79667 3.08664 MINI EXTERN> -104.41668 15.60629 0.00000 0.00000 0.00000 MINI CONSTR> 19.95821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10864 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -32.90251 0.01054 0.06507 0.00006 MINI INTERN> 4.57622 15.47771 0.00000 12.78651 3.08652 MINI EXTERN> -104.39179 15.59455 0.00000 0.00000 0.00000 MINI CONSTR> 19.96778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -32.90799 0.00549 0.05091 0.00006 MINI INTERN> 4.56981 15.47123 0.00000 12.77845 3.08635 MINI EXTERN> -104.37516 15.58431 0.00000 0.00000 0.00000 MINI CONSTR> 19.97701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10864 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -32.91365 0.00566 0.05314 0.00007 MINI INTERN> 4.56702 15.46133 0.00000 12.77009 3.08559 MINI EXTERN> -104.36126 15.57611 0.00000 0.00000 0.00000 MINI CONSTR> 19.98745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -32.91920 0.00555 0.08744 0.00007 MINI INTERN> 4.56959 15.44651 0.00000 12.76144 3.08409 MINI EXTERN> -104.35035 15.57038 0.00000 0.00000 0.00000 MINI CONSTR> 19.99915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10863 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -32.92483 0.00563 0.06280 0.00007 MINI INTERN> 4.56399 15.44291 0.00000 12.75477 3.08389 MINI EXTERN> -104.34521 15.56521 0.00000 0.00000 0.00000 MINI CONSTR> 20.00960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -32.93006 0.00523 0.07488 0.00007 MINI INTERN> 4.56413 15.43407 0.00000 12.74783 3.08271 MINI EXTERN> -104.34169 15.56212 0.00000 0.00000 0.00000 MINI CONSTR> 20.02077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10863 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -32.93541 0.00535 0.07400 0.00008 MINI INTERN> 4.56294 15.42743 0.00000 12.74149 3.08200 MINI EXTERN> -104.34098 15.55962 0.00000 0.00000 0.00000 MINI CONSTR> 20.03207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -32.93988 0.00447 0.11150 0.00008 MINI INTERN> 4.56580 15.41776 0.00000 12.73518 3.08059 MINI EXTERN> -104.34181 15.55924 0.00000 0.00000 0.00000 MINI CONSTR> 20.04335 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -32.94455 0.00467 0.12477 0.00008 MINI INTERN> 4.56824 15.40984 0.00000 12.72985 3.07988 MINI EXTERN> -104.34439 15.55778 0.00000 0.00000 0.00000 MINI CONSTR> 20.05426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -32.94911 0.00457 0.12675 0.00009 MINI INTERN> 4.56702 15.40475 0.00000 12.72466 3.07916 MINI EXTERN> -104.34779 15.55834 0.00000 0.00000 0.00000 MINI CONSTR> 20.06474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -32.95369 0.00458 0.13358 0.00009 MINI INTERN> 4.56666 15.40094 0.00000 12.71941 3.07794 MINI EXTERN> -104.35238 15.55817 0.00000 0.00000 0.00000 MINI CONSTR> 20.07555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -32.95831 0.00461 0.13079 0.00009 MINI INTERN> 4.56386 15.39752 0.00000 12.71503 3.07807 MINI EXTERN> -104.35776 15.55904 0.00000 0.00000 0.00000 MINI CONSTR> 20.08593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -32.96259 0.00428 0.14403 0.00010 MINI INTERN> 4.56566 15.39541 0.00000 12.71038 3.07646 MINI EXTERN> -104.36393 15.55705 0.00000 0.00000 0.00000 MINI CONSTR> 20.09638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -32.96688 0.00430 0.14190 0.00010 MINI INTERN> 4.56464 15.39144 0.00000 12.70597 3.07588 MINI EXTERN> -104.36998 15.55861 0.00000 0.00000 0.00000 MINI CONSTR> 20.10655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -32.97259 0.00571 0.04487 0.00004 MINI INTERN> 4.54844 15.40274 0.00000 12.70312 3.07751 MINI EXTERN> -104.37764 15.55734 0.00000 0.00000 0.00000 MINI CONSTR> 20.11590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -32.97493 0.00234 0.16358 0.00011 MINI INTERN> 4.56758 15.38181 0.00000 12.69764 3.07462 MINI EXTERN> -104.38390 15.56008 0.00000 0.00000 0.00000 MINI CONSTR> 20.12724 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -32.97860 0.00367 0.18512 0.00011 MINI INTERN> 4.55469 15.38656 0.00000 12.69379 3.07593 MINI EXTERN> -104.39185 15.56484 0.00000 0.00000 0.00000 MINI CONSTR> 20.13745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -32.98284 0.00424 0.17561 0.00012 MINI INTERN> 4.55909 15.37942 0.00000 12.68956 3.07456 MINI EXTERN> -104.39891 15.56584 0.00000 0.00000 0.00000 MINI CONSTR> 20.14759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -32.98960 0.00676 0.05410 0.00005 MINI INTERN> 4.54688 15.39123 0.00000 12.68708 3.07538 MINI EXTERN> -104.40929 15.56176 0.00000 0.00000 0.00000 MINI CONSTR> 20.15737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -32.99337 0.00377 0.04480 0.00005 MINI INTERN> 4.54784 15.38688 0.00000 12.68355 3.07479 MINI EXTERN> -104.41652 15.56364 0.00000 0.00000 0.00000 MINI CONSTR> 20.16645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -32.99731 0.00395 0.04582 0.00005 MINI INTERN> 4.54782 15.38419 0.00000 12.67992 3.07429 MINI EXTERN> -104.42483 15.56500 0.00000 0.00000 0.00000 MINI CONSTR> 20.17629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -33.00128 0.00397 0.04615 0.00006 MINI INTERN> 4.54819 15.38126 0.00000 12.67627 3.07374 MINI EXTERN> -104.43334 15.56636 0.00000 0.00000 0.00000 MINI CONSTR> 20.18624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10860 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -33.00543 0.00414 0.07356 0.00006 MINI INTERN> 4.54520 15.38164 0.00000 12.67242 3.07369 MINI EXTERN> -104.44375 15.56781 0.00000 0.00000 0.00000 MINI CONSTR> 20.19756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -33.00929 0.00386 0.06273 0.00006 MINI INTERN> 4.54752 15.37724 0.00000 12.66893 3.07286 MINI EXTERN> -104.45185 15.56905 0.00000 0.00000 0.00000 MINI CONSTR> 20.20696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10858 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -33.01309 0.00380 0.06687 0.00006 MINI INTERN> 4.54640 15.37538 0.00000 12.66545 3.07262 MINI EXTERN> -104.46078 15.57104 0.00000 0.00000 0.00000 MINI CONSTR> 20.21681 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -33.01691 0.00382 0.07058 0.00006 MINI INTERN> 4.54783 15.37230 0.00000 12.66194 3.07193 MINI EXTERN> -104.46976 15.57214 0.00000 0.00000 0.00000 MINI CONSTR> 20.22672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10858 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -33.02029 0.00338 0.09601 0.00007 MINI INTERN> 4.54504 15.37241 0.00000 12.65864 3.07204 MINI EXTERN> -104.47927 15.57425 0.00000 0.00000 0.00000 MINI CONSTR> 20.23661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -33.02387 0.00358 0.10546 0.00007 MINI INTERN> 4.54885 15.36837 0.00000 12.65521 3.07100 MINI EXTERN> -104.48814 15.57456 0.00000 0.00000 0.00000 MINI CONSTR> 20.24628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10858 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -33.02743 0.00356 0.10534 0.00007 MINI INTERN> 4.54727 15.36717 0.00000 12.65200 3.07090 MINI EXTERN> -104.49716 15.57668 0.00000 0.00000 0.00000 MINI CONSTR> 20.25572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -33.03104 0.00361 0.11699 0.00007 MINI INTERN> 4.54453 15.36590 0.00000 12.64852 3.07096 MINI EXTERN> -104.50645 15.57975 0.00000 0.00000 0.00000 MINI CONSTR> 20.26576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10857 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -33.03461 0.00357 0.10994 0.00008 MINI INTERN> 4.54887 15.36175 0.00000 12.64536 3.06983 MINI EXTERN> -104.51491 15.57971 0.00000 0.00000 0.00000 MINI CONSTR> 20.27479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -33.03795 0.00334 0.12374 0.00008 MINI INTERN> 4.54453 15.36077 0.00000 12.64203 3.07020 MINI EXTERN> -104.52353 15.58381 0.00000 0.00000 0.00000 MINI CONSTR> 20.28425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10856 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -33.04145 0.00350 0.11837 0.00008 MINI INTERN> 4.54553 15.35884 0.00000 12.63894 3.06968 MINI EXTERN> -104.53263 15.58472 0.00000 0.00000 0.00000 MINI CONSTR> 20.29346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -33.04484 0.00339 0.12244 0.00009 MINI INTERN> 4.55068 15.35452 0.00000 12.63572 3.06844 MINI EXTERN> -104.54140 15.58448 0.00000 0.00000 0.00000 MINI CONSTR> 20.30271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10856 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -33.04823 0.00339 0.12184 0.00009 MINI INTERN> 4.54663 15.35449 0.00000 12.63263 3.06880 MINI EXTERN> -104.55046 15.58770 0.00000 0.00000 0.00000 MINI CONSTR> 20.31197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -33.05274 0.00451 0.04154 0.00004 MINI INTERN> 4.55115 15.34522 0.00000 12.62897 3.06730 MINI EXTERN> -104.55603 15.59021 0.00000 0.00000 0.00000 MINI CONSTR> 20.32044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10856 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -33.05456 0.00182 0.13860 0.00010 MINI INTERN> 4.54652 15.35103 0.00000 12.62644 3.06818 MINI EXTERN> -104.56821 15.59120 0.00000 0.00000 0.00000 MINI CONSTR> 20.33028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -33.05737 0.00281 0.16914 0.00010 MINI INTERN> 4.55659 15.34327 0.00000 12.62300 3.06609 MINI EXTERN> -104.57599 15.59021 0.00000 0.00000 0.00000 MINI CONSTR> 20.33947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10856 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -33.06278 0.00542 0.04716 0.00004 MINI INTERN> 4.55183 15.33853 0.00000 12.61953 3.06606 MINI EXTERN> -104.58211 15.59545 0.00000 0.00000 0.00000 MINI CONSTR> 20.34793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -33.06395 0.00117 0.15255 0.00011 MINI INTERN> 4.54742 15.34528 0.00000 12.61736 3.06709 MINI EXTERN> -104.59432 15.59603 0.00000 0.00000 0.00000 MINI CONSTR> 20.35718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10856 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -33.06939 0.00544 0.05430 0.00005 MINI INTERN> 4.55205 15.33413 0.00000 12.61320 3.06529 MINI EXTERN> -104.59961 15.59920 0.00000 0.00000 0.00000 MINI CONSTR> 20.36635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -33.07229 0.00290 0.03998 0.00005 MINI INTERN> 4.55184 15.33335 0.00000 12.61074 3.06502 MINI EXTERN> -104.60740 15.60017 0.00000 0.00000 0.00000 MINI CONSTR> 20.37399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10856 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -33.07544 0.00315 0.04152 0.00005 MINI INTERN> 4.55192 15.33130 0.00000 12.60773 3.06465 MINI EXTERN> -104.61578 15.60196 0.00000 0.00000 0.00000 MINI CONSTR> 20.38278 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -33.07862 0.00318 0.03938 0.00005 MINI INTERN> 4.55167 15.32968 0.00000 12.60475 3.06435 MINI EXTERN> -104.62441 15.60370 0.00000 0.00000 0.00000 MINI CONSTR> 20.39163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10856 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -33.08187 0.00325 0.07156 0.00005 MINI INTERN> 4.55385 15.32526 0.00000 12.60102 3.06356 MINI EXTERN> -104.63334 15.60597 0.00000 0.00000 0.00000 MINI CONSTR> 20.40181 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -33.08514 0.00327 0.05333 0.00006 MINI INTERN> 4.55185 15.32512 0.00000 12.59829 3.06358 MINI EXTERN> -104.64212 15.60780 0.00000 0.00000 0.00000 MINI CONSTR> 20.41034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10856 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -33.08806 0.00292 0.06435 0.00006 MINI INTERN> 4.55224 15.32278 0.00000 12.59528 3.06317 MINI EXTERN> -104.65019 15.60969 0.00000 0.00000 0.00000 MINI CONSTR> 20.41898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -33.09075 0.00269 0.08351 0.00006 MINI INTERN> 4.55456 15.31928 0.00000 12.59222 3.06242 MINI EXTERN> -104.65786 15.61113 0.00000 0.00000 0.00000 MINI CONSTR> 20.42749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10855 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -33.09421 0.00346 0.05593 0.00006 MINI INTERN> 4.55240 15.31936 0.00000 12.58948 3.06248 MINI EXTERN> -104.66700 15.61288 0.00000 0.00000 0.00000 MINI CONSTR> 20.43620 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -33.09676 0.00255 0.08914 0.00006 MINI INTERN> 4.55451 15.31549 0.00000 12.58624 3.06178 MINI EXTERN> -104.67463 15.61488 0.00000 0.00000 0.00000 MINI CONSTR> 20.44497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10855 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -33.09974 0.00298 0.10289 0.00007 MINI INTERN> 4.55759 15.31255 0.00000 12.58311 3.06094 MINI EXTERN> -104.68359 15.61554 0.00000 0.00000 0.00000 MINI CONSTR> 20.45412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -33.10245 0.00271 0.10683 0.00007 MINI INTERN> 4.55744 15.31057 0.00000 12.58025 3.06062 MINI EXTERN> -104.69120 15.61757 0.00000 0.00000 0.00000 MINI CONSTR> 20.46231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10855 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -33.10529 0.00284 0.10202 0.00007 MINI INTERN> 4.55391 15.31054 0.00000 12.57760 3.06092 MINI EXTERN> -104.69897 15.62045 0.00000 0.00000 0.00000 MINI CONSTR> 20.47027 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -33.10798 0.00269 0.11202 0.00007 MINI INTERN> 4.55866 15.30734 0.00000 12.57486 3.05982 MINI EXTERN> -104.70710 15.61999 0.00000 0.00000 0.00000 MINI CONSTR> 20.47845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10855 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -33.11074 0.00276 0.10806 0.00008 MINI INTERN> 4.55796 15.30550 0.00000 12.57205 3.05958 MINI EXTERN> -104.71451 15.62221 0.00000 0.00000 0.00000 MINI CONSTR> 20.48647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -33.11344 0.00270 0.11109 0.00008 MINI INTERN> 4.55411 15.30543 0.00000 12.56928 3.05993 MINI EXTERN> -104.72232 15.62550 0.00000 0.00000 0.00000 MINI CONSTR> 20.49463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10855 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -33.11702 0.00358 0.03623 0.00003 MINI INTERN> 4.55277 15.30739 0.00000 12.56743 3.05987 MINI EXTERN> -104.73138 15.62500 0.00000 0.00000 0.00000 MINI CONSTR> 20.50189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -33.11844 0.00142 0.13028 0.00009 MINI INTERN> 4.55368 15.30242 0.00000 12.56381 3.05943 MINI EXTERN> -104.73759 15.62921 0.00000 0.00000 0.00000 MINI CONSTR> 20.51060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10855 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -33.12081 0.00238 0.14522 0.00009 MINI INTERN> 4.56154 15.29801 0.00000 12.56115 3.05782 MINI EXTERN> -104.74536 15.62756 0.00000 0.00000 0.00000 MINI CONSTR> 20.51846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -33.12357 0.00276 0.13449 0.00009 MINI INTERN> 4.55940 15.29612 0.00000 12.55824 3.05778 MINI EXTERN> -104.75227 15.63073 0.00000 0.00000 0.00000 MINI CONSTR> 20.52643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10855 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -33.12788 0.00431 0.04338 0.00004 MINI INTERN> 4.55279 15.30132 0.00000 12.55644 3.05862 MINI EXTERN> -104.76285 15.63149 0.00000 0.00000 0.00000 MINI CONSTR> 20.53431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -33.13031 0.00243 0.03509 0.00004 MINI INTERN> 4.55362 15.29898 0.00000 12.55391 3.05817 MINI EXTERN> -104.76932 15.63295 0.00000 0.00000 0.00000 MINI CONSTR> 20.54138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10854 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -33.13287 0.00256 0.03624 0.00004 MINI INTERN> 4.55367 15.29752 0.00000 12.55129 3.05786 MINI EXTERN> -104.77679 15.63448 0.00000 0.00000 0.00000 MINI CONSTR> 20.54909 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -33.13537 0.00250 0.03719 0.00004 MINI INTERN> 4.55367 15.29609 0.00000 12.54871 3.05757 MINI EXTERN> -104.78411 15.63603 0.00000 0.00000 0.00000 MINI CONSTR> 20.55667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -33.13789 0.00252 0.03720 0.00005 MINI INTERN> 4.55352 15.29464 0.00000 12.54608 3.05730 MINI EXTERN> -104.79144 15.63769 0.00000 0.00000 0.00000 MINI CONSTR> 20.56431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -33.14052 0.00262 0.06206 0.00005 MINI INTERN> 4.55376 15.29396 0.00000 12.54327 3.05700 MINI EXTERN> -104.80044 15.63889 0.00000 0.00000 0.00000 MINI CONSTR> 20.57305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -33.14304 0.00252 0.05180 0.00005 MINI INTERN> 4.55291 15.29236 0.00000 12.54067 3.05682 MINI EXTERN> -104.80717 15.64101 0.00000 0.00000 0.00000 MINI CONSTR> 20.58036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -33.14543 0.00239 0.05630 0.00005 MINI INTERN> 4.55332 15.29099 0.00000 12.53814 3.05648 MINI EXTERN> -104.81449 15.64229 0.00000 0.00000 0.00000 MINI CONSTR> 20.58784 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -33.14797 0.00254 0.05541 0.00005 MINI INTERN> 4.55447 15.28883 0.00000 12.53545 3.05596 MINI EXTERN> -104.82179 15.64354 0.00000 0.00000 0.00000 MINI CONSTR> 20.59558 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -33.15012 0.00215 0.07750 0.00005 MINI INTERN> 4.55298 15.28897 0.00000 12.53299 3.05601 MINI EXTERN> -104.82958 15.64533 0.00000 0.00000 0.00000 MINI CONSTR> 20.60318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -33.15276 0.00264 0.06263 0.00006 MINI INTERN> 4.55518 15.28570 0.00000 12.53028 3.05526 MINI EXTERN> -104.83618 15.64641 0.00000 0.00000 0.00000 MINI CONSTR> 20.61060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -33.15473 0.00197 0.08438 0.00006 MINI INTERN> 4.55520 15.28522 0.00000 12.52794 3.05507 MINI EXTERN> -104.84348 15.64758 0.00000 0.00000 0.00000 MINI CONSTR> 20.61774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -33.15694 0.00221 0.09487 0.00006 MINI INTERN> 4.55240 15.28534 0.00000 12.52543 3.05531 MINI EXTERN> -104.85080 15.65017 0.00000 0.00000 0.00000 MINI CONSTR> 20.62521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -33.15925 0.00231 0.09103 0.00006 MINI INTERN> 4.55570 15.28236 0.00000 12.52297 3.05444 MINI EXTERN> -104.85730 15.65042 0.00000 0.00000 0.00000 MINI CONSTR> 20.63216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -33.16145 0.00220 0.09943 0.00007 MINI INTERN> 4.55184 15.28236 0.00000 12.52042 3.05482 MINI EXTERN> -104.86402 15.65371 0.00000 0.00000 0.00000 MINI CONSTR> 20.63941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -33.16375 0.00230 0.09412 0.00007 MINI INTERN> 4.55317 15.28090 0.00000 12.51803 3.05434 MINI EXTERN> -104.87110 15.65439 0.00000 0.00000 0.00000 MINI CONSTR> 20.64650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -33.16665 0.00290 0.03313 0.00003 MINI INTERN> 4.55590 15.27501 0.00000 12.51519 3.05330 MINI EXTERN> -104.87537 15.65625 0.00000 0.00000 0.00000 MINI CONSTR> 20.65308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -33.16800 0.00136 0.10780 0.00007 MINI INTERN> 4.55265 15.27866 0.00000 12.51312 3.05392 MINI EXTERN> -104.88471 15.65762 0.00000 0.00000 0.00000 MINI CONSTR> 20.66074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -33.17110 0.00309 0.03443 0.00003 MINI INTERN> 4.55613 15.27204 0.00000 12.51026 3.05269 MINI EXTERN> -104.88863 15.65924 0.00000 0.00000 0.00000 MINI CONSTR> 20.66717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -33.17226 0.00117 0.11166 0.00008 MINI INTERN> 4.55568 15.27510 0.00000 12.50831 3.05289 MINI EXTERN> -104.89810 15.65924 0.00000 0.00000 0.00000 MINI CONSTR> 20.67463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -33.17559 0.00333 0.03686 0.00003 MINI INTERN> 4.55668 15.26885 0.00000 12.50522 3.05201 MINI EXTERN> -104.90208 15.66222 0.00000 0.00000 0.00000 MINI CONSTR> 20.68151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -33.17625 0.00066 0.13356 0.00008 MINI INTERN> 4.55172 15.27363 0.00000 12.50337 3.05304 MINI EXTERN> -104.91087 15.66429 0.00000 0.00000 0.00000 MINI CONSTR> 20.68858 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -33.17988 0.00364 0.03923 0.00004 MINI INTERN> 4.55701 15.26589 0.00000 12.50036 3.05139 MINI EXTERN> -104.91498 15.66515 0.00000 0.00000 0.00000 MINI CONSTR> 20.69531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -33.18186 0.00198 0.03218 0.00004 MINI INTERN> 4.55641 15.26532 0.00000 12.49827 3.05126 MINI EXTERN> -104.92107 15.66645 0.00000 0.00000 0.00000 MINI CONSTR> 20.70150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10852 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -33.18394 0.00208 0.03332 0.00004 MINI INTERN> 4.55661 15.26383 0.00000 12.49589 3.05094 MINI EXTERN> -104.92732 15.66789 0.00000 0.00000 0.00000 MINI CONSTR> 20.70823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -33.18599 0.00205 0.03392 0.00004 MINI INTERN> 4.55689 15.26235 0.00000 12.49355 3.05062 MINI EXTERN> -104.93350 15.66925 0.00000 0.00000 0.00000 MINI CONSTR> 20.71487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10852 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -33.18810 0.00211 0.03212 0.00004 MINI INTERN> 4.55710 15.26104 0.00000 12.49117 3.05031 MINI EXTERN> -104.93996 15.67057 0.00000 0.00000 0.00000 MINI CONSTR> 20.72167 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -33.19026 0.00216 0.05907 0.00004 MINI INTERN> 4.55787 15.25816 0.00000 12.48819 3.04982 MINI EXTERN> -104.94656 15.67274 0.00000 0.00000 0.00000 MINI CONSTR> 20.72953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10852 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -33.19245 0.00219 0.04347 0.00005 MINI INTERN> 4.55831 15.25731 0.00000 12.48599 3.04950 MINI EXTERN> -104.95316 15.67352 0.00000 0.00000 0.00000 MINI CONSTR> 20.73609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -33.19439 0.00195 0.05309 0.00005 MINI INTERN> 4.55887 15.25545 0.00000 12.48357 3.04912 MINI EXTERN> -104.95915 15.67498 0.00000 0.00000 0.00000 MINI CONSTR> 20.74276 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10852 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -33.19618 0.00179 0.06860 0.00005 MINI INTERN> 4.55857 15.25374 0.00000 12.48113 3.04888 MINI EXTERN> -104.96482 15.67699 0.00000 0.00000 0.00000 MINI CONSTR> 20.74933 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 -33.19618 0.00179 0.06860 0.00006 STPD INTERN> 4.55857 15.25374 0.00000 12.48113 3.04888 STPD EXTERN> -104.96482 15.67699 0.00000 0.00000 0.00000 STPD CONSTR> 20.74933 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 10852 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10852 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 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 -33.19618 0.00179 0.06860 0.00000 MINI INTERN> 4.55857 15.25374 0.00000 12.48113 3.04888 MINI EXTERN> -104.96482 15.67699 0.00000 0.00000 0.00000 MINI CONSTR> 20.74933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -33.42554 0.22936 0.03689 0.00824 MINI INTERN> 4.60543 14.99668 0.00000 11.98172 2.99259 MINI EXTERN> -106.31535 16.01280 0.00000 0.00000 0.00000 MINI CONSTR> 22.30059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -33.43316 0.00762 0.11592 0.00993 MINI INTERN> 4.58216 14.95615 0.00000 11.96520 2.96486 MINI EXTERN> -106.28714 16.07543 0.00000 0.00000 0.00000 MINI CONSTR> 22.31017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -33.46026 0.02709 0.14690 0.03769 MINI INTERN> 4.53043 14.89924 0.00000 11.92776 2.96698 MINI EXTERN> -106.26332 16.15414 0.00000 0.00000 0.00000 MINI CONSTR> 22.32452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -33.49215 0.03190 0.11127 0.02095 MINI INTERN> 4.55977 14.96479 0.00000 11.86502 2.96784 MINI EXTERN> -106.19523 16.00666 0.00000 0.00000 0.00000 MINI CONSTR> 22.33901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -33.50446 0.01231 0.07816 0.01148 MINI INTERN> 4.56672 14.98842 0.00000 11.82338 2.95944 MINI EXTERN> -106.16517 15.98054 0.00000 0.00000 0.00000 MINI CONSTR> 22.34221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -33.51134 0.00688 0.06593 0.00943 MINI INTERN> 4.59902 14.98825 0.00000 11.81014 2.97080 MINI EXTERN> -106.14553 15.92465 0.00000 0.00000 0.00000 MINI CONSTR> 22.34133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -33.51798 0.00664 0.06140 0.00893 MINI INTERN> 4.58744 14.94284 0.00000 11.78643 2.96548 MINI EXTERN> -106.05870 15.91752 0.00000 0.00000 0.00000 MINI CONSTR> 22.34100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -33.52584 0.00786 0.06921 0.01332 MINI INTERN> 4.55344 14.91085 0.00000 11.76112 2.95109 MINI EXTERN> -105.99140 15.94446 0.00000 0.00000 0.00000 MINI CONSTR> 22.34459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -33.53167 0.00583 0.05741 0.01041 MINI INTERN> 4.58394 14.92277 0.00000 11.74487 2.95460 MINI EXTERN> -105.97463 15.88589 0.00000 0.00000 0.00000 MINI CONSTR> 22.35088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -33.53693 0.00525 0.05110 0.00727 MINI INTERN> 4.57021 14.94916 0.00000 11.72967 2.95541 MINI EXTERN> -105.96342 15.86320 0.00000 0.00000 0.00000 MINI CONSTR> 22.35884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -33.54099 0.00406 0.05229 0.00888 MINI INTERN> 4.57026 14.92363 0.00000 11.72958 2.95672 MINI EXTERN> -105.98114 15.89314 0.00000 0.00000 0.00000 MINI CONSTR> 22.36683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -33.54463 0.00364 0.04075 0.00700 MINI INTERN> 4.57690 14.91959 0.00000 11.72021 2.97104 MINI EXTERN> -106.01090 15.90463 0.00000 0.00000 0.00000 MINI CONSTR> 22.37390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -33.54728 0.00265 0.03761 0.00557 MINI INTERN> 4.57753 14.91877 0.00000 11.72395 2.98194 MINI EXTERN> -106.04104 15.91428 0.00000 0.00000 0.00000 MINI CONSTR> 22.37729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -33.54964 0.00236 0.03450 0.00601 MINI INTERN> 4.58218 14.92233 0.00000 11.74321 2.97155 MINI EXTERN> -106.07524 15.92861 0.00000 0.00000 0.00000 MINI CONSTR> 22.37772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -33.55188 0.00224 0.03940 0.00681 MINI INTERN> 4.57458 14.93759 0.00000 11.76053 2.97754 MINI EXTERN> -106.09687 15.92097 0.00000 0.00000 0.00000 MINI CONSTR> 22.37378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -33.55438 0.00250 0.03842 0.00603 MINI INTERN> 4.57789 14.95848 0.00000 11.77822 2.97754 MINI EXTERN> -106.07298 15.86141 0.00000 0.00000 0.00000 MINI CONSTR> 22.36506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -33.55616 0.00178 0.02704 0.00534 MINI INTERN> 4.57931 14.95450 0.00000 11.78391 2.97465 MINI EXTERN> -106.06692 15.86309 0.00000 0.00000 0.00000 MINI CONSTR> 22.35530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -33.55747 0.00131 0.02609 0.00474 MINI INTERN> 4.57680 14.95194 0.00000 11.79952 2.97443 MINI EXTERN> -106.04135 15.83580 0.00000 0.00000 0.00000 MINI CONSTR> 22.34538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -33.55864 0.00117 0.02662 0.00407 MINI INTERN> 4.57738 14.95455 0.00000 11.81456 2.97647 MINI EXTERN> -106.06155 15.84485 0.00000 0.00000 0.00000 MINI CONSTR> 22.33510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -33.55951 0.00087 0.02267 0.00389 MINI INTERN> 4.57589 14.94288 0.00000 11.81513 2.97209 MINI EXTERN> -106.05008 15.85803 0.00000 0.00000 0.00000 MINI CONSTR> 22.32655 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 -33.55951 0.00087 0.02267 0.02000 CONJ INTERN> 4.57589 14.94288 0.00000 11.81513 2.97209 CONJ EXTERN> -106.05008 15.85803 0.00000 0.00000 0.00000 CONJ CONSTR> 22.32655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "10800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.85797E-01 ( PROT LYS 1 HT2 ) 0.85797E-01 ( PROT LYS 1 N ) 0.10725 ( PROT LYS 1 HT3 ) 0.85797E-01 ( PROT LYS 1 CA ) 0.10725 ( PROT LYS 1 CB ) 0.85797E-01 ( PROT LYS 1 CG ) 0.85797E-01 ( PROT LYS 1 CD ) 0.85797E-01 ( PROT LYS 1 CE ) 0.85797E-01 ( PROT LYS 1 NZ ) 0.85797E-01 ( PROT LYS 1 HZ1 ) 0.85797E-01 ( PROT LYS 1 HZ2 ) 0.85797E-01 ( PROT LYS 1 HZ3 ) 0.85797E-01 ( PROT LYS 1 C ) 0.10725 ( PROT LYS 1 O ) 0.10725 ( PROT MET 2 N ) 0.10725 ( PROT MET 2 H ) 0.85797E-01 ( PROT MET 2 CA ) 0.10725 ( PROT MET 2 CB ) 0.85797E-01 ( PROT MET 2 CG ) 0.85797E-01 ( PROT MET 2 SD ) 0.85797E-01 ( PROT MET 2 CE ) 0.85797E-01 ( PROT MET 2 C ) 0.10725 ( PROT MET 2 O ) 0.10725 ( PROT LYS 3 N ) 0.10725 ( PROT LYS 3 H ) 0.85797E-01 ( PROT LYS 3 CA ) 0.10725 ( PROT LYS 3 CB ) 0.85797E-01 ( PROT LYS 3 CG ) 0.85797E-01 ( PROT LYS 3 CD ) 0.85797E-01 ( PROT LYS 3 CE ) 0.85797E-01 ( PROT LYS 3 NZ ) 0.85797E-01 ( PROT LYS 3 HZ1 ) 0.85797E-01 ( PROT LYS 3 HZ2 ) 0.85797E-01 ( PROT LYS 3 HZ3 ) 0.85797E-01 ( PROT LYS 3 C ) 0.10725 ( PROT LYS 3 O ) 0.10725 ( PROT ALA 4 N ) 0.10725 ( PROT ALA 4 H ) 0.85797E-01 ( PROT ALA 4 CA ) 0.10725 ( PROT ALA 4 CB ) 0.85797E-01 ( PROT ALA 4 C ) 0.10725 ( PROT ALA 4 O ) 0.10725 ( PROT VAL 5 N ) 0.10725 ( PROT VAL 5 H ) 0.85797E-01 ( PROT VAL 5 CA ) 0.10725 ( PROT VAL 5 CB ) 0.85797E-01 ( PROT VAL 5 CG1 ) 0.85797E-01 ( PROT VAL 5 CG2 ) 0.85797E-01 ( PROT VAL 5 C ) 0.10725 ( PROT VAL 5 O ) 0.10725 ( PROT MET 6 N ) 0.10725 ( PROT MET 6 H ) 0.85797E-01 ( PROT MET 6 CA ) 0.10725 ( PROT MET 6 CB ) 0.85797E-01 ( PROT MET 6 CG ) 0.85797E-01 ( PROT MET 6 SD ) 0.85797E-01 ( PROT MET 6 CE ) 0.85797E-01 ( PROT MET 6 C ) 0.10725 ( PROT MET 6 O ) 0.10725 ( PROT ILE 7 N ) 0.10725 ( PROT ILE 7 H ) 0.85797E-01 ( PROT ILE 7 CA ) 0.10725 ( PROT ILE 7 CB ) 0.85797E-01 ( PROT ILE 7 CG2 ) 0.85797E-01 ( PROT ILE 7 CG1 ) 0.85797E-01 ( PROT ILE 7 CD ) 0.85797E-01 ( PROT ILE 7 C ) 0.10725 ( PROT ILE 7 O ) 0.10725 ( PROT GLY 8 N ) 0.10725 ( PROT GLY 8 H ) 0.85797E-01 ( PROT GLY 8 CA ) 0.10725 ( PROT GLY 8 C ) 0.10725 ( PROT GLY 8 O ) 0.10725 ( PROT ALA 9 N ) 0.10725 ( PROT ALA 9 H ) 0.85797E-01 ( PROT ALA 9 CA ) 0.10725 ( PROT ALA 9 CB ) 0.85797E-01 ( PROT ALA 9 C ) 0.10725 ( PROT ALA 9 O ) 0.10725 ( PROT CYS 10 N ) 0.10725 ( PROT CYS 10 H ) 0.85797E-01 ( PROT CYS 10 CA ) 0.10725 ( PROT CYS 10 CB ) 0.85797E-01 ( PROT CYS 10 SG ) 0.85797E-01 ( PROT CYS 10 C ) 0.10725 ( PROT CYS 10 O ) 0.10725 ( PROT PHE 11 N ) 0.10725 ( PROT PHE 11 H ) 0.85797E-01 ( PROT PHE 11 CA ) 0.10725 ( PROT PHE 11 CB ) 0.85797E-01 ( PROT PHE 11 CG ) 0.85797E-01 ( PROT PHE 11 CD1 ) 0.85797E-01 ( PROT PHE 11 CD2 ) 0.85797E-01 ( PROT PHE 11 CE1 ) 0.85797E-01 ( PROT PHE 11 CE2 ) 0.85797E-01 ( PROT PHE 11 CZ ) 0.85797E-01 ( PROT PHE 11 C ) 0.10725 ( PROT PHE 11 O ) 0.10725 ( PROT LEU 12 N ) 0.10725 ( PROT LEU 12 H ) 0.85797E-01 ( PROT LEU 12 CA ) 0.10725 ( PROT LEU 12 CB ) 0.85797E-01 ( PROT LEU 12 CG ) 0.85797E-01 ( PROT LEU 12 CD1 ) 0.85797E-01 ( PROT LEU 12 CD2 ) 0.85797E-01 ( PROT LEU 12 C ) 0.10725 ( PROT LEU 12 O ) 0.10725 ( PROT ILE 13 N ) 0.10725 ( PROT ILE 13 H ) 0.85797E-01 ( PROT ILE 13 CA ) 0.10725 ( PROT ILE 13 CB ) 0.85797E-01 ( PROT ILE 13 CG2 ) 0.85797E-01 ( PROT ILE 13 CG1 ) 0.85797E-01 ( PROT ILE 13 CD ) 0.85797E-01 ( PROT ILE 13 C ) 0.10725 ( PROT ILE 13 O ) 0.10725 ( PROT ASH 14 N ) 0.10725 ( PROT ASH 14 H ) 0.85797E-01 ( PROT ASH 14 CA ) 0.10725 ( PROT ASH 14 CB ) 0.85797E-01 ( PROT ASH 14 CG ) 0.85797E-01 ( PROT ASH 14 OD1 ) 0.85797E-01 ( PROT ASH 14 OD2 ) 0.85797E-01 ( PROT ASH 14 HD2 ) 0.85797E-01 ( PROT ASH 14 C ) 0.10725 ( PROT ASH 14 O ) 0.10725 ( PROT PHE 15 N ) 0.10725 ( PROT PHE 15 H ) 0.85797E-01 ( PROT PHE 15 CA ) 0.10725 ( PROT PHE 15 CB ) 0.85797E-01 ( PROT PHE 15 CG ) 0.85797E-01 ( PROT PHE 15 CD1 ) 0.85797E-01 ( PROT PHE 15 CD2 ) 0.85797E-01 ( PROT PHE 15 CE1 ) 0.85797E-01 ( PROT PHE 15 CE2 ) 0.85797E-01 ( PROT PHE 15 CZ ) 0.85797E-01 ( PROT PHE 15 C ) 0.10725 ( PROT PHE 15 O ) 0.10725 ( PROT MET 16 N ) 0.10725 ( PROT MET 16 H ) 0.85797E-01 ( PROT MET 16 CA ) 0.10725 ( PROT MET 16 CB ) 0.85797E-01 ( PROT MET 16 CG ) 0.85797E-01 ( PROT MET 16 SD ) 0.85797E-01 ( PROT MET 16 CE ) 0.85797E-01 ( PROT MET 16 C ) 0.10725 ( PROT MET 16 O ) 0.10725 ( PROT PHE 17 N ) 0.10725 ( PROT PHE 17 H ) 0.85797E-01 ( PROT PHE 17 CA ) 0.10725 ( PROT PHE 17 CB ) 0.85797E-01 ( PROT PHE 17 CG ) 0.85797E-01 ( PROT PHE 17 CD1 ) 0.85797E-01 ( PROT PHE 17 CD2 ) 0.85797E-01 ( PROT PHE 17 CE1 ) 0.85797E-01 ( PROT PHE 17 CE2 ) 0.85797E-01 ( PROT PHE 17 CZ ) 0.85797E-01 ( PROT PHE 17 C ) 0.10725 ( PROT PHE 17 O ) 0.10725 ( PROT PHE 18 N ) 0.10725 ( PROT PHE 18 H ) 0.85797E-01 ( PROT PHE 18 CA ) 0.10725 ( PROT PHE 18 CB ) 0.85797E-01 ( PROT PHE 18 CG ) 0.85797E-01 ( PROT PHE 18 CD1 ) 0.85797E-01 ( PROT PHE 18 CD2 ) 0.85797E-01 ( PROT PHE 18 CE1 ) 0.85797E-01 ( PROT PHE 18 CE2 ) 0.85797E-01 ( PROT PHE 18 CZ ) 0.85797E-01 ( PROT PHE 18 C ) 0.10725 ( PROT PHE 18 O ) 0.10725 ( PROT GLU 19 N ) 0.10725 ( PROT GLU 19 H ) 0.85797E-01 ( PROT GLU 19 CA ) 0.10725 ( PROT GLU 19 CB ) 0.85797E-01 ( PROT GLU 19 CG ) 0.85797E-01 ( PROT GLU 19 CD ) 0.85797E-01 ( PROT GLU 19 OE1 ) 0.85797E-01 ( PROT GLU 19 OE2 ) 0.85797E-01 ( PROT GLU 19 C ) 0.10725 ( PROT GLU 19 OT1 ) 0.85797E-01 ( PROT GLU 19 OT2 ) 0.85797E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.40042 5.28615 -8.68876 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00412 0.00627 -0.00446 ROTATION MATRIX 1.000000 -0.000589 0.000355 0.000588 0.999999 0.001118 -0.000355 -0.001118 0.999999 AXIS OF ROTATION IS 0.851955 -0.270562 -0.448296 ANGLE IS 0.08 TOTAL SQUARE DIFF IS 157.6561 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.928175 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.9282" Parameter: A <- "0.9282" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.73562 5.27561 -8.80313 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.02078 -0.01119 0.00876 ROTATION MATRIX 0.999968 0.007918 -0.000644 -0.007924 0.999925 -0.009326 0.000570 0.009331 0.999956 AXIS OF ROTATION IS -0.761337 0.049567 0.646458 ANGLE IS 0.70 TOTAL SQUARE DIFF IS 9.5301 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.708226 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.9282" RDCMND substituted energy or value "?RMS" to " 0.7082" Parameter: A <- "0.9282 0.7082" 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 0.9282 0.7082 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 " 22.33" Parameter: H <- "22.33" 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 -55.88606 22.32655 0.15431 ENER INTERN> 4.57589 14.94288 0.00000 11.81513 2.97209 ENER EXTERN> -106.05008 15.85803 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 " -55.89" Parameter: B <- "-55.89" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 15.86" Parameter: C <- "15.86" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -106.05" Parameter: C <- " -90.19" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -90.19" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.58" Parameter: D <- "4.58" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.94" Parameter: D <- " 19.52" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.82" Parameter: D <- " 31.34" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.97" Parameter: D <- " 34.31" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 34.31" 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= -55.89 GRMS= 0.15 ELEC= 15.86 VDW= -106.05 RDTITL> *EXTERNAL= -90.19 INTERNAL= 34.31 USER= 0.00 HARM= 22.33 RDTITL> *BOND= 4.58 ANGL= 14.94 DIHE= 11.82 IMPR= 2.97 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 "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= -55.89 GRMS= 0.15 ELEC= 15.86 VDW= -106.05 RDTITL> *EXTERNAL= -90.19 INTERNAL= 34.31 USER= 0.00 HARM= 22.33 RDTITL> *BOND= 4.58 ANGL= 14.94 DIHE= 11.82 IMPR= 2.97 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= -55.89 GRMS= 0.15 ELEC= 15.86 VDW= -106.05 RDTITL> *EXTERNAL= -90.19 INTERNAL= 34.31 USER= 0.00 HARM= 22.33 RDTITL> *BOND= 4.58 ANGL= 14.94 DIHE= 11.82 IMPR= 2.97 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 10800 0.9282 0.7082 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 10852 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10833 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 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 -41.27618 -14.60988 0.05860 0.02000 MINI INTERN> 4.57589 14.94288 0.00000 11.81513 2.97209 MINI EXTERN> -106.05008 15.85803 0.00000 0.00000 0.00000 MINI CONSTR> 14.60988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -35.83219 -5.44399 7.75016 0.00360 MINI INTERN> 10.22208 15.58470 0.00000 11.97967 2.98263 MINI EXTERN> -108.83379 17.14763 0.00000 0.00000 0.00000 MINI CONSTR> 15.08488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -41.31308 5.48088 0.99358 0.00065 MINI INTERN> 4.99741 15.23857 0.00000 11.93736 2.96859 MINI EXTERN> -108.25498 16.71702 0.00000 0.00000 0.00000 MINI CONSTR> 15.08294 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -41.41824 0.10516 0.42958 0.00028 MINI INTERN> 4.74790 15.23984 0.00000 11.89783 2.98646 MINI EXTERN> -107.87609 16.50357 0.00000 0.00000 0.00000 MINI CONSTR> 15.08226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -41.44833 0.03009 0.14781 0.00012 MINI INTERN> 4.75180 15.12914 0.00000 11.87524 2.98379 MINI EXTERN> -107.72790 16.45618 0.00000 0.00000 0.00000 MINI CONSTR> 15.08341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -41.45473 0.00641 0.22525 0.00013 MINI INTERN> 4.73318 15.09822 0.00000 11.85854 2.98629 MINI EXTERN> -107.61632 16.39971 0.00000 0.00000 0.00000 MINI CONSTR> 15.08566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -41.46017 0.00543 0.22778 0.00013 MINI INTERN> 4.71794 15.08256 0.00000 11.84736 2.98752 MINI EXTERN> -107.54853 16.36502 0.00000 0.00000 0.00000 MINI CONSTR> 15.08797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -41.46884 0.00867 0.07944 0.00006 MINI INTERN> 4.69490 15.07297 0.00000 11.83690 2.98850 MINI EXTERN> -107.48720 16.33424 0.00000 0.00000 0.00000 MINI CONSTR> 15.09084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -41.47288 0.00404 0.06223 0.00006 MINI INTERN> 4.68854 15.05632 0.00000 11.82832 2.98855 MINI EXTERN> -107.44267 16.31427 0.00000 0.00000 0.00000 MINI CONSTR> 15.09380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -41.47591 0.00303 0.10721 0.00006 MINI INTERN> 4.68138 15.04336 0.00000 11.81998 2.98853 MINI EXTERN> -107.40255 16.29612 0.00000 0.00000 0.00000 MINI CONSTR> 15.09727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -41.47909 0.00317 0.11307 0.00006 MINI INTERN> 4.67607 15.03158 0.00000 11.81259 2.98833 MINI EXTERN> -107.37051 16.28194 0.00000 0.00000 0.00000 MINI CONSTR> 15.10091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -41.48190 0.00281 0.12392 0.00006 MINI INTERN> 4.67161 15.02159 0.00000 11.80592 2.98801 MINI EXTERN> -107.34423 16.27048 0.00000 0.00000 0.00000 MINI CONSTR> 15.10472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -41.48451 0.00261 0.11689 0.00007 MINI INTERN> 4.66834 15.01380 0.00000 11.80066 2.98768 MINI EXTERN> -107.32559 16.26247 0.00000 0.00000 0.00000 MINI CONSTR> 15.10814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -41.48725 0.00274 0.11984 0.00007 MINI INTERN> 4.66495 15.00583 0.00000 11.79489 2.98724 MINI EXTERN> -107.30699 16.25450 0.00000 0.00000 0.00000 MINI CONSTR> 15.11233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -41.49076 0.00351 0.03744 0.00003 MINI INTERN> 4.66357 14.99786 0.00000 11.79015 2.98692 MINI EXTERN> -107.29417 16.24872 0.00000 0.00000 0.00000 MINI CONSTR> 15.11618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -41.49189 0.00113 0.13093 0.00007 MINI INTERN> 4.66015 14.99351 0.00000 11.78545 2.98630 MINI EXTERN> -107.28155 16.24386 0.00000 0.00000 0.00000 MINI CONSTR> 15.12039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -41.49426 0.00238 0.13603 0.00008 MINI INTERN> 4.65813 14.98795 0.00000 11.78093 2.98577 MINI EXTERN> -107.27164 16.23976 0.00000 0.00000 0.00000 MINI CONSTR> 15.12483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -41.49806 0.00380 0.04090 0.00003 MINI INTERN> 4.65802 14.98081 0.00000 11.77689 2.98538 MINI EXTERN> -107.26504 16.23666 0.00000 0.00000 0.00000 MINI CONSTR> 15.12921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -41.50007 0.00201 0.03373 0.00003 MINI INTERN> 4.65661 14.97711 0.00000 11.77363 2.98492 MINI EXTERN> -107.25991 16.23460 0.00000 0.00000 0.00000 MINI CONSTR> 15.13297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -41.50234 0.00228 0.03321 0.00004 MINI INTERN> 4.65547 14.97287 0.00000 11.77001 2.98439 MINI EXTERN> -107.25528 16.23273 0.00000 0.00000 0.00000 MINI CONSTR> 15.13747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -41.50464 0.00229 0.03320 0.00004 MINI INTERN> 4.65453 14.96886 0.00000 11.76650 2.98386 MINI EXTERN> -107.25185 16.23134 0.00000 0.00000 0.00000 MINI CONSTR> 15.14212 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -41.50698 0.00234 0.06053 0.00004 MINI INTERN> 4.65471 14.96401 0.00000 11.76278 2.98329 MINI EXTERN> -107.24964 16.23043 0.00000 0.00000 0.00000 MINI CONSTR> 15.14745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -41.50909 0.00211 0.04243 0.00004 MINI INTERN> 4.65355 14.96142 0.00000 11.76001 2.98282 MINI EXTERN> -107.24839 16.22989 0.00000 0.00000 0.00000 MINI CONSTR> 15.15161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -41.51126 0.00217 0.04156 0.00004 MINI INTERN> 4.65303 14.95832 0.00000 11.75706 2.98232 MINI EXTERN> -107.24795 16.22967 0.00000 0.00000 0.00000 MINI CONSTR> 15.15629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -41.51344 0.00218 0.04297 0.00004 MINI INTERN> 4.65269 14.95528 0.00000 11.75417 2.98182 MINI EXTERN> -107.24825 16.22973 0.00000 0.00000 0.00000 MINI CONSTR> 15.16112 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -41.51557 0.00212 0.04920 0.00004 MINI INTERN> 4.65263 14.95228 0.00000 11.75140 2.98134 MINI EXTERN> -107.24925 16.23005 0.00000 0.00000 0.00000 MINI CONSTR> 15.16598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -41.51721 0.00165 0.08018 0.00005 MINI INTERN> 4.65364 14.94901 0.00000 11.74898 2.98094 MINI EXTERN> -107.25093 16.23066 0.00000 0.00000 0.00000 MINI CONSTR> 15.17049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -41.51925 0.00204 0.08201 0.00005 MINI INTERN> 4.65360 14.94644 0.00000 11.74649 2.98050 MINI EXTERN> -107.25285 16.23134 0.00000 0.00000 0.00000 MINI CONSTR> 15.17523 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -41.52127 0.00202 0.08651 0.00005 MINI INTERN> 4.65375 14.94383 0.00000 11.74404 2.98006 MINI EXTERN> -107.25528 16.23224 0.00000 0.00000 0.00000 MINI CONSTR> 15.18007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -41.52319 0.00192 0.09465 0.00005 MINI INTERN> 4.65413 14.94123 0.00000 11.74170 2.97965 MINI EXTERN> -107.25808 16.23330 0.00000 0.00000 0.00000 MINI CONSTR> 15.18489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -41.52502 0.00183 0.09095 0.00005 MINI INTERN> 4.65399 14.93952 0.00000 11.73967 2.97930 MINI EXTERN> -107.26062 16.23404 0.00000 0.00000 0.00000 MINI CONSTR> 15.18908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -41.52690 0.00188 0.09581 0.00006 MINI INTERN> 4.65431 14.93722 0.00000 11.73750 2.97892 MINI EXTERN> -107.26387 16.23523 0.00000 0.00000 0.00000 MINI CONSTR> 15.19378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -41.52884 0.00194 0.09925 0.00006 MINI INTERN> 4.65462 14.93490 0.00000 11.73534 2.97853 MINI EXTERN> -107.26746 16.23661 0.00000 0.00000 0.00000 MINI CONSTR> 15.19861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -41.53081 0.00197 0.10058 0.00006 MINI INTERN> 4.65483 14.93271 0.00000 11.73321 2.97815 MINI EXTERN> -107.27129 16.23808 0.00000 0.00000 0.00000 MINI CONSTR> 15.20349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10823 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -41.53337 0.00256 0.03163 0.00003 MINI INTERN> 4.65036 14.93605 0.00000 11.73084 2.97777 MINI EXTERN> -107.27326 16.23704 0.00000 0.00000 0.00000 MINI CONSTR> 15.20783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -41.53428 0.00092 0.10988 0.00006 MINI INTERN> 4.65567 14.92877 0.00000 11.72938 2.97750 MINI EXTERN> -107.27886 16.24078 0.00000 0.00000 0.00000 MINI CONSTR> 15.21248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10822 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -41.53614 0.00185 0.11239 0.00007 MINI INTERN> 4.65594 14.92681 0.00000 11.72743 2.97715 MINI EXTERN> -107.28310 16.24241 0.00000 0.00000 0.00000 MINI CONSTR> 15.21723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -41.53801 0.00187 0.11584 0.00007 MINI INTERN> 4.65614 14.92489 0.00000 11.72546 2.97679 MINI EXTERN> -107.28761 16.24421 0.00000 0.00000 0.00000 MINI CONSTR> 15.22211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10822 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -41.53984 0.00183 0.12108 0.00007 MINI INTERN> 4.65625 14.92316 0.00000 11.72351 2.97642 MINI EXTERN> -107.29229 16.24607 0.00000 0.00000 0.00000 MINI CONSTR> 15.22704 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -41.54284 0.00300 0.03810 0.00003 MINI INTERN> 4.65075 14.92906 0.00000 11.72074 2.97615 MINI EXTERN> -107.29436 16.24310 0.00000 0.00000 0.00000 MINI CONSTR> 15.23172 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10822 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -41.54443 0.00158 0.02944 0.00003 MINI INTERN> 4.65118 14.92725 0.00000 11.71926 2.97588 MINI EXTERN> -107.29840 16.24477 0.00000 0.00000 0.00000 MINI CONSTR> 15.23564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -41.54629 0.00186 0.02915 0.00003 MINI INTERN> 4.65140 14.92583 0.00000 11.71736 2.97558 MINI EXTERN> -107.30311 16.24623 0.00000 0.00000 0.00000 MINI CONSTR> 15.24043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10822 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -41.54819 0.00190 0.02911 0.00003 MINI INTERN> 4.65164 14.92439 0.00000 11.71542 2.97529 MINI EXTERN> -107.30803 16.24774 0.00000 0.00000 0.00000 MINI CONSTR> 15.24535 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -41.55010 0.00191 0.02951 0.00004 MINI INTERN> 4.65191 14.92298 0.00000 11.71349 2.97499 MINI EXTERN> -107.31306 16.24926 0.00000 0.00000 0.00000 MINI CONSTR> 15.25032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -41.55199 0.00190 0.05500 0.00004 MINI INTERN> 4.65294 14.92134 0.00000 11.71127 2.97477 MINI EXTERN> -107.31832 16.25018 0.00000 0.00000 0.00000 MINI CONSTR> 15.25582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -41.55379 0.00180 0.03703 0.00004 MINI INTERN> 4.65284 14.92002 0.00000 11.70970 2.97446 MINI EXTERN> -107.32315 16.25216 0.00000 0.00000 0.00000 MINI CONSTR> 15.26017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -41.55543 0.00163 0.02935 0.00004 MINI INTERN> 4.65266 14.91915 0.00000 11.70813 2.97418 MINI EXTERN> -107.32770 16.25379 0.00000 0.00000 0.00000 MINI CONSTR> 15.26437 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -41.55716 0.00173 0.06629 0.00004 MINI INTERN> 4.65495 14.91628 0.00000 11.70604 2.97402 MINI EXTERN> -107.33324 16.25493 0.00000 0.00000 0.00000 MINI CONSTR> 15.26987 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -41.55910 0.00193 0.03861 0.00004 MINI INTERN> 4.65397 14.91588 0.00000 11.70442 2.97366 MINI EXTERN> -107.33828 16.25692 0.00000 0.00000 0.00000 MINI CONSTR> 15.27432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -41.56091 0.00182 0.04645 0.00004 MINI INTERN> 4.65484 14.91408 0.00000 11.70257 2.97341 MINI EXTERN> -107.34374 16.25855 0.00000 0.00000 0.00000 MINI CONSTR> 15.27938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -41.56230 0.00139 0.07198 0.00005 MINI INTERN> 4.65667 14.91167 0.00000 11.70094 2.97325 MINI EXTERN> -107.34860 16.25985 0.00000 0.00000 0.00000 MINI CONSTR> 15.28392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -41.56408 0.00177 0.07453 0.00005 MINI INTERN> 4.65738 14.91003 0.00000 11.69918 2.97299 MINI EXTERN> -107.35406 16.26156 0.00000 0.00000 0.00000 MINI CONSTR> 15.28884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10820 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -41.56581 0.00174 0.07991 0.00005 MINI INTERN> 4.65824 14.90834 0.00000 11.69742 2.97274 MINI EXTERN> -107.35957 16.26322 0.00000 0.00000 0.00000 MINI CONSTR> 15.29380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -41.56744 0.00163 0.08794 0.00005 MINI INTERN> 4.65919 14.90666 0.00000 11.69571 2.97251 MINI EXTERN> -107.36493 16.26481 0.00000 0.00000 0.00000 MINI CONSTR> 15.29862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10820 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -41.56901 0.00157 0.08328 0.00005 MINI INTERN> 4.65899 14.90608 0.00000 11.69419 2.97228 MINI EXTERN> -107.36951 16.26624 0.00000 0.00000 0.00000 MINI CONSTR> 15.30274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -41.57068 0.00167 0.08737 0.00006 MINI INTERN> 4.65966 14.90464 0.00000 11.69249 2.97204 MINI EXTERN> -107.37492 16.26785 0.00000 0.00000 0.00000 MINI CONSTR> 15.30755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10820 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -41.57239 0.00171 0.09020 0.00006 MINI INTERN> 4.66028 14.90326 0.00000 11.69076 2.97181 MINI EXTERN> -107.38045 16.26951 0.00000 0.00000 0.00000 MINI CONSTR> 15.31244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -41.57411 0.00173 0.09070 0.00006 MINI INTERN> 4.66068 14.90207 0.00000 11.68904 2.97158 MINI EXTERN> -107.38596 16.27119 0.00000 0.00000 0.00000 MINI CONSTR> 15.31730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10820 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -41.57632 0.00220 0.02922 0.00003 MINI INTERN> 4.65376 14.90769 0.00000 11.68705 2.97108 MINI EXTERN> -107.39058 16.27317 0.00000 0.00000 0.00000 MINI CONSTR> 15.32152 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -41.57704 0.00072 0.10022 0.00006 MINI INTERN> 4.66188 14.89960 0.00000 11.68596 2.97117 MINI EXTERN> -107.39584 16.27416 0.00000 0.00000 0.00000 MINI CONSTR> 15.32602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10820 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -41.57865 0.00161 0.10351 0.00007 MINI INTERN> 4.66255 14.89825 0.00000 11.68430 2.97097 MINI EXTERN> -107.40130 16.27581 0.00000 0.00000 0.00000 MINI CONSTR> 15.33077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -41.58024 0.00159 0.10836 0.00007 MINI INTERN> 4.66336 14.89678 0.00000 11.68263 2.97077 MINI EXTERN> -107.40684 16.27749 0.00000 0.00000 0.00000 MINI CONSTR> 15.33556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10820 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -41.58284 0.00259 0.03415 0.00003 MINI INTERN> 4.65391 14.90461 0.00000 11.68035 2.97012 MINI EXTERN> -107.41162 16.27969 0.00000 0.00000 0.00000 MINI CONSTR> 15.34010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -41.58420 0.00136 0.02647 0.00003 MINI INTERN> 4.65513 14.90275 0.00000 11.67909 2.96999 MINI EXTERN> -107.41600 16.28096 0.00000 0.00000 0.00000 MINI CONSTR> 15.34388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10820 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -41.58580 0.00160 0.02620 0.00003 MINI INTERN> 4.65538 14.90179 0.00000 11.67745 2.96977 MINI EXTERN> -107.42126 16.28258 0.00000 0.00000 0.00000 MINI CONSTR> 15.34848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -41.58743 0.00163 0.02618 0.00003 MINI INTERN> 4.65558 14.90087 0.00000 11.67578 2.96954 MINI EXTERN> -107.42665 16.28425 0.00000 0.00000 0.00000 MINI CONSTR> 15.35320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -41.58906 0.00163 0.02669 0.00003 MINI INTERN> 4.65565 14.90008 0.00000 11.67409 2.96931 MINI EXTERN> -107.43205 16.28593 0.00000 0.00000 0.00000 MINI CONSTR> 15.35792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -41.59061 0.00155 0.05330 0.00004 MINI INTERN> 4.65329 14.90189 0.00000 11.67207 2.96890 MINI EXTERN> -107.43764 16.28786 0.00000 0.00000 0.00000 MINI CONSTR> 15.36303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -41.59216 0.00155 0.03344 0.00004 MINI INTERN> 4.65515 14.89925 0.00000 11.67078 2.96881 MINI EXTERN> -107.44246 16.28923 0.00000 0.00000 0.00000 MINI CONSTR> 15.36709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -41.59373 0.00157 0.03367 0.00004 MINI INTERN> 4.65533 14.89837 0.00000 11.66914 2.96859 MINI EXTERN> -107.44775 16.29088 0.00000 0.00000 0.00000 MINI CONSTR> 15.37171 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -41.59530 0.00157 0.03629 0.00004 MINI INTERN> 4.65529 14.89773 0.00000 11.66747 2.96835 MINI EXTERN> -107.45308 16.29256 0.00000 0.00000 0.00000 MINI CONSTR> 15.37638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -41.59657 0.00127 0.06455 0.00004 MINI INTERN> 4.65330 14.89929 0.00000 11.66566 2.96799 MINI EXTERN> -107.45803 16.29425 0.00000 0.00000 0.00000 MINI CONSTR> 15.38095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -41.59805 0.00148 0.06475 0.00004 MINI INTERN> 4.65352 14.89841 0.00000 11.66411 2.96778 MINI EXTERN> -107.46307 16.29583 0.00000 0.00000 0.00000 MINI CONSTR> 15.38536 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -41.59955 0.00150 0.06657 0.00004 MINI INTERN> 4.65368 14.89759 0.00000 11.66250 2.96757 MINI EXTERN> -107.46824 16.29745 0.00000 0.00000 0.00000 MINI CONSTR> 15.38990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10821 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -41.60104 0.00148 0.07063 0.00005 MINI INTERN> 4.65373 14.89690 0.00000 11.66086 2.96734 MINI EXTERN> -107.47346 16.29910 0.00000 0.00000 0.00000 MINI CONSTR> 15.39450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -41.60244 0.00140 0.07776 0.00005 MINI INTERN> 4.65360 14.89643 0.00000 11.65923 2.96710 MINI EXTERN> -107.47856 16.30073 0.00000 0.00000 0.00000 MINI CONSTR> 15.39902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10820 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -41.60378 0.00134 0.07445 0.00005 MINI INTERN> 4.65399 14.89545 0.00000 11.65789 2.96694 MINI EXTERN> -107.48307 16.30213 0.00000 0.00000 0.00000 MINI CONSTR> 15.40290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -41.60517 0.00140 0.07830 0.00005 MINI INTERN> 4.65407 14.89476 0.00000 11.65632 2.96673 MINI EXTERN> -107.48806 16.30371 0.00000 0.00000 0.00000 MINI CONSTR> 15.40730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -41.60661 0.00143 0.08107 0.00005 MINI INTERN> 4.65428 14.89390 0.00000 11.65474 2.96652 MINI EXTERN> -107.49316 16.30533 0.00000 0.00000 0.00000 MINI CONSTR> 15.41178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -41.60806 0.00145 0.08201 0.00005 MINI INTERN> 4.65460 14.89292 0.00000 11.65318 2.96633 MINI EXTERN> -107.49829 16.30695 0.00000 0.00000 0.00000 MINI CONSTR> 15.41625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -41.60993 0.00187 0.02621 0.00002 MINI INTERN> 4.65999 14.88674 0.00000 11.65229 2.96647 MINI EXTERN> -107.50393 16.30832 0.00000 0.00000 0.00000 MINI CONSTR> 15.42018 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -41.61057 0.00064 0.09021 0.00006 MINI INTERN> 4.65465 14.89180 0.00000 11.65030 2.96593 MINI EXTERN> -107.50749 16.30989 0.00000 0.00000 0.00000 MINI CONSTR> 15.42435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -41.61194 0.00137 0.09288 0.00006 MINI INTERN> 4.65491 14.89093 0.00000 11.64877 2.96574 MINI EXTERN> -107.51246 16.31148 0.00000 0.00000 0.00000 MINI CONSTR> 15.42870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -41.61330 0.00136 0.09670 0.00006 MINI INTERN> 4.65515 14.89007 0.00000 11.64721 2.96554 MINI EXTERN> -107.51750 16.31310 0.00000 0.00000 0.00000 MINI CONSTR> 15.43312 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -41.61551 0.00221 0.02881 0.00003 MINI INTERN> 4.66106 14.88332 0.00000 11.64628 2.96568 MINI EXTERN> -107.52381 16.31458 0.00000 0.00000 0.00000 MINI CONSTR> 15.43739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -41.61668 0.00117 0.02420 0.00003 MINI INTERN> 4.66067 14.88313 0.00000 11.64498 2.96549 MINI EXTERN> -107.52779 16.31589 0.00000 0.00000 0.00000 MINI CONSTR> 15.44097 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -41.61802 0.00134 0.02391 0.00003 MINI INTERN> 4.66082 14.88239 0.00000 11.64351 2.96529 MINI EXTERN> -107.53258 16.31741 0.00000 0.00000 0.00000 MINI CONSTR> 15.44514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -41.61939 0.00137 0.02386 0.00003 MINI INTERN> 4.66103 14.88159 0.00000 11.64201 2.96509 MINI EXTERN> -107.53749 16.31897 0.00000 0.00000 0.00000 MINI CONSTR> 15.44942 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -41.62076 0.00137 0.02427 0.00003 MINI INTERN> 4.66131 14.88073 0.00000 11.64050 2.96490 MINI EXTERN> -107.54245 16.32053 0.00000 0.00000 0.00000 MINI CONSTR> 15.45372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -41.62208 0.00132 0.04779 0.00003 MINI INTERN> 4.66341 14.87840 0.00000 11.63899 2.96476 MINI EXTERN> -107.54822 16.32218 0.00000 0.00000 0.00000 MINI CONSTR> 15.45840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -41.62339 0.00131 0.03033 0.00003 MINI INTERN> 4.66234 14.87867 0.00000 11.63760 2.96454 MINI EXTERN> -107.55220 16.32357 0.00000 0.00000 0.00000 MINI CONSTR> 15.46210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -41.62472 0.00133 0.03011 0.00004 MINI INTERN> 4.66251 14.87791 0.00000 11.63612 2.96434 MINI EXTERN> -107.55701 16.32510 0.00000 0.00000 0.00000 MINI CONSTR> 15.46631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -41.62606 0.00134 0.03157 0.00004 MINI INTERN> 4.66283 14.87704 0.00000 11.63461 2.96415 MINI EXTERN> -107.56194 16.32665 0.00000 0.00000 0.00000 MINI CONSTR> 15.47060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -41.62736 0.00130 0.03707 0.00004 MINI INTERN> 4.66342 14.87597 0.00000 11.63314 2.96396 MINI EXTERN> -107.56688 16.32818 0.00000 0.00000 0.00000 MINI CONSTR> 15.47485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -41.62836 0.00100 0.05918 0.00004 MINI INTERN> 4.66502 14.87426 0.00000 11.63187 2.96383 MINI EXTERN> -107.57157 16.32953 0.00000 0.00000 0.00000 MINI CONSTR> 15.47871 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -41.62962 0.00126 0.06083 0.00004 MINI INTERN> 4.66532 14.87345 0.00000 11.63041 2.96364 MINI EXTERN> -107.57627 16.33101 0.00000 0.00000 0.00000 MINI CONSTR> 15.48282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -41.63087 0.00125 0.06457 0.00004 MINI INTERN> 4.66576 14.87254 0.00000 11.62894 2.96345 MINI EXTERN> -107.58104 16.33250 0.00000 0.00000 0.00000 MINI CONSTR> 15.48698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -41.63205 0.00118 0.07107 0.00004 MINI INTERN> 4.66638 14.87153 0.00000 11.62751 2.96328 MINI EXTERN> -107.58576 16.33396 0.00000 0.00000 0.00000 MINI CONSTR> 15.49106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -41.63317 0.00113 0.06799 0.00005 MINI INTERN> 4.66633 14.87102 0.00000 11.62627 2.96311 MINI EXTERN> -107.58971 16.33525 0.00000 0.00000 0.00000 MINI CONSTR> 15.49457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -41.63435 0.00118 0.07162 0.00005 MINI INTERN> 4.66676 14.87016 0.00000 11.62486 2.96293 MINI EXTERN> -107.59426 16.33667 0.00000 0.00000 0.00000 MINI CONSTR> 15.49854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -41.63556 0.00121 0.07432 0.00005 MINI INTERN> 4.66714 14.86931 0.00000 11.62341 2.96274 MINI EXTERN> -107.59888 16.33812 0.00000 0.00000 0.00000 MINI CONSTR> 15.50260 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 -41.63556 0.00121 0.07432 0.00006 STPD INTERN> 4.66714 14.86931 0.00000 11.62341 2.96274 STPD EXTERN> -107.59888 16.33812 0.00000 0.00000 0.00000 STPD CONSTR> 15.50260 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 10819 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10819 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 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 -41.63556 0.00121 0.07432 0.00000 MINI INTERN> 4.66714 14.86931 0.00000 11.62341 2.96274 MINI EXTERN> -107.59888 16.33812 0.00000 0.00000 0.00000 MINI CONSTR> 15.50260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -41.78808 0.15252 0.02626 0.00314 MINI INTERN> 4.72215 14.72603 0.00000 11.29446 2.92218 MINI EXTERN> -108.68301 16.70750 0.00000 0.00000 0.00000 MINI CONSTR> 16.52261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -41.79403 0.00595 0.09117 0.01240 MINI INTERN> 4.71878 14.65399 0.00000 11.28453 2.90370 MINI EXTERN> -108.67420 16.78036 0.00000 0.00000 0.00000 MINI CONSTR> 16.53880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -41.81349 0.01946 0.13474 0.03272 MINI INTERN> 4.67660 14.63681 0.00000 11.25553 2.90166 MINI EXTERN> -108.76026 16.89377 0.00000 0.00000 0.00000 MINI CONSTR> 16.58239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -41.83522 0.02173 0.08313 0.03068 MINI INTERN> 4.67868 14.67850 0.00000 11.22218 2.90744 MINI EXTERN> -108.70215 16.75223 0.00000 0.00000 0.00000 MINI CONSTR> 16.62791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -41.84543 0.01020 0.06825 0.01389 MINI INTERN> 4.69215 14.68824 0.00000 11.18793 2.90766 MINI EXTERN> -108.68149 16.71597 0.00000 0.00000 0.00000 MINI CONSTR> 16.64411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -41.85247 0.00704 0.06009 0.01189 MINI INTERN> 4.73168 14.70246 0.00000 11.18576 2.91237 MINI EXTERN> -108.63649 16.60180 0.00000 0.00000 0.00000 MINI CONSTR> 16.64996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -41.85941 0.00694 0.05907 0.01183 MINI INTERN> 4.71796 14.65550 0.00000 11.15534 2.90766 MINI EXTERN> -108.49409 16.54493 0.00000 0.00000 0.00000 MINI CONSTR> 16.65329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -41.86631 0.00690 0.05218 0.01269 MINI INTERN> 4.68166 14.65155 0.00000 11.13749 2.89080 MINI EXTERN> -108.46034 16.57460 0.00000 0.00000 0.00000 MINI CONSTR> 16.65794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -41.87079 0.00448 0.05353 0.00850 MINI INTERN> 4.69628 14.65388 0.00000 11.13759 2.90261 MINI EXTERN> -108.42380 16.49943 0.00000 0.00000 0.00000 MINI CONSTR> 16.66323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -41.87514 0.00435 0.05052 0.00922 MINI INTERN> 4.68146 14.66249 0.00000 11.10660 2.89535 MINI EXTERN> -108.40402 16.51182 0.00000 0.00000 0.00000 MINI CONSTR> 16.67116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -41.88007 0.00493 0.05589 0.01403 MINI INTERN> 4.69053 14.64004 0.00000 11.09765 2.88878 MINI EXTERN> -108.44308 16.56091 0.00000 0.00000 0.00000 MINI CONSTR> 16.68510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -41.88439 0.00432 0.04698 0.00907 MINI INTERN> 4.70662 14.62927 0.00000 11.07014 2.90879 MINI EXTERN> -108.45677 16.55761 0.00000 0.00000 0.00000 MINI CONSTR> 16.69995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -41.88797 0.00357 0.04285 0.00882 MINI INTERN> 4.69447 14.63573 0.00000 11.08745 2.92356 MINI EXTERN> -108.50826 16.56491 0.00000 0.00000 0.00000 MINI CONSTR> 16.71416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -41.89092 0.00296 0.03726 0.00648 MINI INTERN> 4.69557 14.64311 0.00000 11.09654 2.90773 MINI EXTERN> -108.55615 16.59637 0.00000 0.00000 0.00000 MINI CONSTR> 16.72591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -41.89361 0.00269 0.03780 0.00906 MINI INTERN> 4.70494 14.65865 0.00000 11.10958 2.91322 MINI EXTERN> -108.56978 16.55559 0.00000 0.00000 0.00000 MINI CONSTR> 16.73419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -41.89578 0.00217 0.03551 0.00562 MINI INTERN> 4.70027 14.68019 0.00000 11.12645 2.91665 MINI EXTERN> -108.57076 16.51317 0.00000 0.00000 0.00000 MINI CONSTR> 16.73825 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -41.89762 0.00184 0.02985 0.00436 MINI INTERN> 4.69422 14.66511 0.00000 11.12624 2.91393 MINI EXTERN> -108.55493 16.51941 0.00000 0.00000 0.00000 MINI CONSTR> 16.73839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -41.89905 0.00143 0.02806 0.00515 MINI INTERN> 4.70081 14.66129 0.00000 11.13414 2.91521 MINI EXTERN> -108.53620 16.49023 0.00000 0.00000 0.00000 MINI CONSTR> 16.73548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -41.90054 0.00149 0.02429 0.00449 MINI INTERN> 4.70243 14.65836 0.00000 11.14825 2.91062 MINI EXTERN> -108.56799 16.51790 0.00000 0.00000 0.00000 MINI CONSTR> 16.72990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -41.90178 0.00124 0.02579 0.00491 MINI INTERN> 4.69703 14.65188 0.00000 11.15213 2.90758 MINI EXTERN> -108.54411 16.51029 0.00000 0.00000 0.00000 MINI CONSTR> 16.72341 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 -41.90178 0.00124 0.02579 0.02000 CONJ INTERN> 4.69703 14.65188 0.00000 11.15213 2.90758 CONJ EXTERN> -108.54411 16.51029 0.00000 0.00000 0.00000 CONJ CONSTR> 16.72341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "11400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.55768E-01 ( PROT LYS 1 HT2 ) 0.55768E-01 ( PROT LYS 1 N ) 0.69710E-01 ( PROT LYS 1 HT3 ) 0.55768E-01 ( PROT LYS 1 CA ) 0.69710E-01 ( PROT LYS 1 CB ) 0.55768E-01 ( PROT LYS 1 CG ) 0.55768E-01 ( PROT LYS 1 CD ) 0.55768E-01 ( PROT LYS 1 CE ) 0.55768E-01 ( PROT LYS 1 NZ ) 0.55768E-01 ( PROT LYS 1 HZ1 ) 0.55768E-01 ( PROT LYS 1 HZ2 ) 0.55768E-01 ( PROT LYS 1 HZ3 ) 0.55768E-01 ( PROT LYS 1 C ) 0.69710E-01 ( PROT LYS 1 O ) 0.69710E-01 ( PROT MET 2 N ) 0.69710E-01 ( PROT MET 2 H ) 0.55768E-01 ( PROT MET 2 CA ) 0.69710E-01 ( PROT MET 2 CB ) 0.55768E-01 ( PROT MET 2 CG ) 0.55768E-01 ( PROT MET 2 SD ) 0.55768E-01 ( PROT MET 2 CE ) 0.55768E-01 ( PROT MET 2 C ) 0.69710E-01 ( PROT MET 2 O ) 0.69710E-01 ( PROT LYS 3 N ) 0.69710E-01 ( PROT LYS 3 H ) 0.55768E-01 ( PROT LYS 3 CA ) 0.69710E-01 ( PROT LYS 3 CB ) 0.55768E-01 ( PROT LYS 3 CG ) 0.55768E-01 ( PROT LYS 3 CD ) 0.55768E-01 ( PROT LYS 3 CE ) 0.55768E-01 ( PROT LYS 3 NZ ) 0.55768E-01 ( PROT LYS 3 HZ1 ) 0.55768E-01 ( PROT LYS 3 HZ2 ) 0.55768E-01 ( PROT LYS 3 HZ3 ) 0.55768E-01 ( PROT LYS 3 C ) 0.69710E-01 ( PROT LYS 3 O ) 0.69710E-01 ( PROT ALA 4 N ) 0.69710E-01 ( PROT ALA 4 H ) 0.55768E-01 ( PROT ALA 4 CA ) 0.69710E-01 ( PROT ALA 4 CB ) 0.55768E-01 ( PROT ALA 4 C ) 0.69710E-01 ( PROT ALA 4 O ) 0.69710E-01 ( PROT VAL 5 N ) 0.69710E-01 ( PROT VAL 5 H ) 0.55768E-01 ( PROT VAL 5 CA ) 0.69710E-01 ( PROT VAL 5 CB ) 0.55768E-01 ( PROT VAL 5 CG1 ) 0.55768E-01 ( PROT VAL 5 CG2 ) 0.55768E-01 ( PROT VAL 5 C ) 0.69710E-01 ( PROT VAL 5 O ) 0.69710E-01 ( PROT MET 6 N ) 0.69710E-01 ( PROT MET 6 H ) 0.55768E-01 ( PROT MET 6 CA ) 0.69710E-01 ( PROT MET 6 CB ) 0.55768E-01 ( PROT MET 6 CG ) 0.55768E-01 ( PROT MET 6 SD ) 0.55768E-01 ( PROT MET 6 CE ) 0.55768E-01 ( PROT MET 6 C ) 0.69710E-01 ( PROT MET 6 O ) 0.69710E-01 ( PROT ILE 7 N ) 0.69710E-01 ( PROT ILE 7 H ) 0.55768E-01 ( PROT ILE 7 CA ) 0.69710E-01 ( PROT ILE 7 CB ) 0.55768E-01 ( PROT ILE 7 CG2 ) 0.55768E-01 ( PROT ILE 7 CG1 ) 0.55768E-01 ( PROT ILE 7 CD ) 0.55768E-01 ( PROT ILE 7 C ) 0.69710E-01 ( PROT ILE 7 O ) 0.69710E-01 ( PROT GLY 8 N ) 0.69710E-01 ( PROT GLY 8 H ) 0.55768E-01 ( PROT GLY 8 CA ) 0.69710E-01 ( PROT GLY 8 C ) 0.69710E-01 ( PROT GLY 8 O ) 0.69710E-01 ( PROT ALA 9 N ) 0.69710E-01 ( PROT ALA 9 H ) 0.55768E-01 ( PROT ALA 9 CA ) 0.69710E-01 ( PROT ALA 9 CB ) 0.55768E-01 ( PROT ALA 9 C ) 0.69710E-01 ( PROT ALA 9 O ) 0.69710E-01 ( PROT CYS 10 N ) 0.69710E-01 ( PROT CYS 10 H ) 0.55768E-01 ( PROT CYS 10 CA ) 0.69710E-01 ( PROT CYS 10 CB ) 0.55768E-01 ( PROT CYS 10 SG ) 0.55768E-01 ( PROT CYS 10 C ) 0.69710E-01 ( PROT CYS 10 O ) 0.69710E-01 ( PROT PHE 11 N ) 0.69710E-01 ( PROT PHE 11 H ) 0.55768E-01 ( PROT PHE 11 CA ) 0.69710E-01 ( PROT PHE 11 CB ) 0.55768E-01 ( PROT PHE 11 CG ) 0.55768E-01 ( PROT PHE 11 CD1 ) 0.55768E-01 ( PROT PHE 11 CD2 ) 0.55768E-01 ( PROT PHE 11 CE1 ) 0.55768E-01 ( PROT PHE 11 CE2 ) 0.55768E-01 ( PROT PHE 11 CZ ) 0.55768E-01 ( PROT PHE 11 C ) 0.69710E-01 ( PROT PHE 11 O ) 0.69710E-01 ( PROT LEU 12 N ) 0.69710E-01 ( PROT LEU 12 H ) 0.55768E-01 ( PROT LEU 12 CA ) 0.69710E-01 ( PROT LEU 12 CB ) 0.55768E-01 ( PROT LEU 12 CG ) 0.55768E-01 ( PROT LEU 12 CD1 ) 0.55768E-01 ( PROT LEU 12 CD2 ) 0.55768E-01 ( PROT LEU 12 C ) 0.69710E-01 ( PROT LEU 12 O ) 0.69710E-01 ( PROT ILE 13 N ) 0.69710E-01 ( PROT ILE 13 H ) 0.55768E-01 ( PROT ILE 13 CA ) 0.69710E-01 ( PROT ILE 13 CB ) 0.55768E-01 ( PROT ILE 13 CG2 ) 0.55768E-01 ( PROT ILE 13 CG1 ) 0.55768E-01 ( PROT ILE 13 CD ) 0.55768E-01 ( PROT ILE 13 C ) 0.69710E-01 ( PROT ILE 13 O ) 0.69710E-01 ( PROT ASH 14 N ) 0.69710E-01 ( PROT ASH 14 H ) 0.55768E-01 ( PROT ASH 14 CA ) 0.69710E-01 ( PROT ASH 14 CB ) 0.55768E-01 ( PROT ASH 14 CG ) 0.55768E-01 ( PROT ASH 14 OD1 ) 0.55768E-01 ( PROT ASH 14 OD2 ) 0.55768E-01 ( PROT ASH 14 HD2 ) 0.55768E-01 ( PROT ASH 14 C ) 0.69710E-01 ( PROT ASH 14 O ) 0.69710E-01 ( PROT PHE 15 N ) 0.69710E-01 ( PROT PHE 15 H ) 0.55768E-01 ( PROT PHE 15 CA ) 0.69710E-01 ( PROT PHE 15 CB ) 0.55768E-01 ( PROT PHE 15 CG ) 0.55768E-01 ( PROT PHE 15 CD1 ) 0.55768E-01 ( PROT PHE 15 CD2 ) 0.55768E-01 ( PROT PHE 15 CE1 ) 0.55768E-01 ( PROT PHE 15 CE2 ) 0.55768E-01 ( PROT PHE 15 CZ ) 0.55768E-01 ( PROT PHE 15 C ) 0.69710E-01 ( PROT PHE 15 O ) 0.69710E-01 ( PROT MET 16 N ) 0.69710E-01 ( PROT MET 16 H ) 0.55768E-01 ( PROT MET 16 CA ) 0.69710E-01 ( PROT MET 16 CB ) 0.55768E-01 ( PROT MET 16 CG ) 0.55768E-01 ( PROT MET 16 SD ) 0.55768E-01 ( PROT MET 16 CE ) 0.55768E-01 ( PROT MET 16 C ) 0.69710E-01 ( PROT MET 16 O ) 0.69710E-01 ( PROT PHE 17 N ) 0.69710E-01 ( PROT PHE 17 H ) 0.55768E-01 ( PROT PHE 17 CA ) 0.69710E-01 ( PROT PHE 17 CB ) 0.55768E-01 ( PROT PHE 17 CG ) 0.55768E-01 ( PROT PHE 17 CD1 ) 0.55768E-01 ( PROT PHE 17 CD2 ) 0.55768E-01 ( PROT PHE 17 CE1 ) 0.55768E-01 ( PROT PHE 17 CE2 ) 0.55768E-01 ( PROT PHE 17 CZ ) 0.55768E-01 ( PROT PHE 17 C ) 0.69710E-01 ( PROT PHE 17 O ) 0.69710E-01 ( PROT PHE 18 N ) 0.69710E-01 ( PROT PHE 18 H ) 0.55768E-01 ( PROT PHE 18 CA ) 0.69710E-01 ( PROT PHE 18 CB ) 0.55768E-01 ( PROT PHE 18 CG ) 0.55768E-01 ( PROT PHE 18 CD1 ) 0.55768E-01 ( PROT PHE 18 CD2 ) 0.55768E-01 ( PROT PHE 18 CE1 ) 0.55768E-01 ( PROT PHE 18 CE2 ) 0.55768E-01 ( PROT PHE 18 CZ ) 0.55768E-01 ( PROT PHE 18 C ) 0.69710E-01 ( PROT PHE 18 O ) 0.69710E-01 ( PROT GLU 19 N ) 0.69710E-01 ( PROT GLU 19 H ) 0.55768E-01 ( PROT GLU 19 CA ) 0.69710E-01 ( PROT GLU 19 CB ) 0.55768E-01 ( PROT GLU 19 CG ) 0.55768E-01 ( PROT GLU 19 CD ) 0.55768E-01 ( PROT GLU 19 OE1 ) 0.55768E-01 ( PROT GLU 19 OE2 ) 0.55768E-01 ( PROT GLU 19 C ) 0.69710E-01 ( PROT GLU 19 OT1 ) 0.55768E-01 ( PROT GLU 19 OT2 ) 0.55768E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.39831 5.28422 -8.68766 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00623 0.00820 -0.00556 ROTATION MATRIX 0.999999 -0.000873 0.000859 0.000872 0.999998 0.001623 -0.000861 -0.001622 0.999998 AXIS OF ROTATION IS 0.798041 -0.423081 -0.429107 ANGLE IS 0.12 TOTAL SQUARE DIFF IS 182.0147 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 0.997304 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.9973" Parameter: A <- "0.9973" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.74165 5.28793 -8.80743 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.02681 -0.02351 0.01306 ROTATION MATRIX 0.999976 0.004263 -0.005409 -0.004295 0.999973 -0.005996 0.005383 0.006019 0.999967 AXIS OF ROTATION IS -0.657368 0.590466 0.468207 ANGLE IS 0.52 TOTAL SQUARE DIFF IS 10.8982 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.757357 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.9973" RDCMND substituted energy or value "?RMS" to " 0.7574" Parameter: A <- "0.9973 0.7574" 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 0.9973 0.7574 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 " 16.72" Parameter: H <- "16.72" 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 -58.62520 16.72341 0.10908 ENER INTERN> 4.69703 14.65188 0.00000 11.15213 2.90758 ENER EXTERN> -108.54411 16.51029 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 " -58.63" Parameter: B <- "-58.63" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 16.51" Parameter: C <- "16.51" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -108.54" Parameter: C <- " -92.03" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -92.03" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.70" Parameter: D <- "4.70" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.65" Parameter: D <- " 19.35" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.15" Parameter: D <- " 30.50" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.91" Parameter: D <- " 33.41" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 33.41" 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= -58.63 GRMS= 0.11 ELEC= 16.51 VDW= -108.54 RDTITL> *EXTERNAL= -92.03 INTERNAL= 33.41 USER= 0.00 HARM= 16.72 RDTITL> *BOND= 4.70 ANGL= 14.65 DIHE= 11.15 IMPR= 2.91 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: 6/ 4/14 16:26:43 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 183 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 10819 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10788 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 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 -47.69148 -10.93372 0.04530 0.02000 MINI INTERN> 4.69703 14.65188 0.00000 11.15213 2.90758 MINI EXTERN> -108.54411 16.51029 0.00000 0.00000 0.00000 MINI CONSTR> 10.93372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -43.57528 -4.11620 6.82141 0.00360 MINI INTERN> 8.99833 15.57194 0.00000 11.22430 2.97935 MINI EXTERN> -110.79780 17.21953 0.00000 0.00000 0.00000 MINI CONSTR> 11.22906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -47.74676 4.17148 0.19374 0.00065 MINI INTERN> 4.96604 15.09758 0.00000 11.22451 2.94515 MINI EXTERN> -110.38068 17.17307 0.00000 0.00000 0.00000 MINI CONSTR> 11.22757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -47.75886 0.01209 0.50401 0.00028 MINI INTERN> 4.82599 14.97383 0.00000 11.20177 2.92984 MINI EXTERN> -109.94693 17.03070 0.00000 0.00000 0.00000 MINI CONSTR> 11.22594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -47.78873 0.02987 0.18193 0.00012 MINI INTERN> 4.87547 14.87142 0.00000 11.17997 2.93329 MINI EXTERN> -109.85174 16.97670 0.00000 0.00000 0.00000 MINI CONSTR> 11.22615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -47.79745 0.00873 0.04836 0.00005 MINI INTERN> 4.82679 14.86110 0.00000 11.17626 2.92900 MINI EXTERN> -109.76457 16.94725 0.00000 0.00000 0.00000 MINI CONSTR> 11.22672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -47.79894 0.00148 0.19577 0.00013 MINI INTERN> 4.85520 14.80696 0.00000 11.16143 2.92878 MINI EXTERN> -109.69057 16.91146 0.00000 0.00000 0.00000 MINI CONSTR> 11.22781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -47.80586 0.00693 0.07439 0.00006 MINI INTERN> 4.78839 14.82001 0.00000 11.16154 2.92550 MINI EXTERN> -109.62773 16.89726 0.00000 0.00000 0.00000 MINI CONSTR> 11.22916 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -47.80893 0.00306 0.05438 0.00006 MINI INTERN> 4.78568 14.80040 0.00000 11.15453 2.92461 MINI EXTERN> -109.58649 16.88172 0.00000 0.00000 0.00000 MINI CONSTR> 11.23063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -47.81091 0.00198 0.08708 0.00006 MINI INTERN> 4.77119 14.79210 0.00000 11.14991 2.92342 MINI EXTERN> -109.55091 16.87106 0.00000 0.00000 0.00000 MINI CONSTR> 11.23231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -47.81305 0.00215 0.09904 0.00006 MINI INTERN> 4.76044 14.78304 0.00000 11.14474 2.92253 MINI EXTERN> -109.51946 16.86131 0.00000 0.00000 0.00000 MINI CONSTR> 11.23434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -47.81492 0.00186 0.09539 0.00006 MINI INTERN> 4.75914 14.77207 0.00000 11.14016 2.92168 MINI EXTERN> -109.49891 16.85479 0.00000 0.00000 0.00000 MINI CONSTR> 11.23616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -47.81752 0.00260 0.02837 0.00003 MINI INTERN> 4.78235 14.74601 0.00000 11.13216 2.92164 MINI EXTERN> -109.48365 16.84579 0.00000 0.00000 0.00000 MINI CONSTR> 11.23818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -47.81828 0.00076 0.10274 0.00007 MINI INTERN> 4.74999 14.75800 0.00000 11.13225 2.92009 MINI EXTERN> -109.46421 16.84517 0.00000 0.00000 0.00000 MINI CONSTR> 11.24043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10780 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -47.81984 0.00157 0.10800 0.00007 MINI INTERN> 4.74487 14.75331 0.00000 11.12883 2.91930 MINI EXTERN> -109.45079 16.84183 0.00000 0.00000 0.00000 MINI CONSTR> 11.24280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -47.82241 0.00256 0.03541 0.00003 MINI INTERN> 4.78081 14.72199 0.00000 11.12038 2.91955 MINI EXTERN> -109.44519 16.83496 0.00000 0.00000 0.00000 MINI CONSTR> 11.24509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10780 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -47.82370 0.00129 0.02476 0.00003 MINI INTERN> 4.77301 14.72222 0.00000 11.11866 2.91900 MINI EXTERN> -109.43767 16.83401 0.00000 0.00000 0.00000 MINI CONSTR> 11.24706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -47.82520 0.00150 0.02498 0.00003 MINI INTERN> 4.77229 14.71692 0.00000 11.11563 2.91836 MINI EXTERN> -109.43063 16.83263 0.00000 0.00000 0.00000 MINI CONSTR> 11.24961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10780 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -47.82660 0.00140 0.04801 0.00003 MINI INTERN> 4.78342 14.70380 0.00000 11.11125 2.91770 MINI EXTERN> -109.42589 16.83070 0.00000 0.00000 0.00000 MINI CONSTR> 11.25241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -47.82799 0.00139 0.03159 0.00004 MINI INTERN> 4.77492 14.70568 0.00000 11.10993 2.91721 MINI EXTERN> -109.42147 16.83101 0.00000 0.00000 0.00000 MINI CONSTR> 11.25473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -47.82927 0.00128 0.03962 0.00004 MINI INTERN> 4.77812 14.69974 0.00000 11.10725 2.91660 MINI EXTERN> -109.41869 16.83040 0.00000 0.00000 0.00000 MINI CONSTR> 11.25729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -47.83034 0.00107 0.05594 0.00004 MINI INTERN> 4.78358 14.69289 0.00000 11.10440 2.91642 MINI EXTERN> -109.41726 16.82993 0.00000 0.00000 0.00000 MINI CONSTR> 11.25971 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -47.83162 0.00129 0.05678 0.00004 MINI INTERN> 4.78399 14.68943 0.00000 11.10247 2.91566 MINI EXTERN> -109.41570 16.83022 0.00000 0.00000 0.00000 MINI CONSTR> 11.26232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -47.83272 0.00110 0.06737 0.00004 MINI INTERN> 4.78246 14.68770 0.00000 11.10052 2.91570 MINI EXTERN> -109.41499 16.83105 0.00000 0.00000 0.00000 MINI CONSTR> 11.26484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -47.83387 0.00115 0.06136 0.00004 MINI INTERN> 4.78404 14.68478 0.00000 11.09879 2.91524 MINI EXTERN> -109.41471 16.83086 0.00000 0.00000 0.00000 MINI CONSTR> 11.26714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -47.83507 0.00120 0.06850 0.00004 MINI INTERN> 4.78587 14.68071 0.00000 11.09675 2.91481 MINI EXTERN> -109.41502 16.83190 0.00000 0.00000 0.00000 MINI CONSTR> 11.26992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -47.83619 0.00112 0.06775 0.00005 MINI INTERN> 4.78531 14.67955 0.00000 11.09549 2.91418 MINI EXTERN> -109.41528 16.83225 0.00000 0.00000 0.00000 MINI CONSTR> 11.27231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -47.83729 0.00109 0.07046 0.00005 MINI INTERN> 4.78108 14.68056 0.00000 11.09417 2.91441 MINI EXTERN> -109.41601 16.83370 0.00000 0.00000 0.00000 MINI CONSTR> 11.27480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -47.83869 0.00140 0.02256 0.00002 MINI INTERN> 4.76130 14.69329 0.00000 11.09563 2.91343 MINI EXTERN> -109.41519 16.83590 0.00000 0.00000 0.00000 MINI CONSTR> 11.27696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -47.83933 0.00065 0.07544 0.00005 MINI INTERN> 4.78612 14.67453 0.00000 11.09083 2.91389 MINI EXTERN> -109.41866 16.83431 0.00000 0.00000 0.00000 MINI CONSTR> 11.27964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10780 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -47.84098 0.00165 0.02239 0.00002 MINI INTERN> 4.76112 14.69047 0.00000 11.09282 2.91278 MINI EXTERN> -109.41824 16.83788 0.00000 0.00000 0.00000 MINI CONSTR> 11.28221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -47.84153 0.00055 0.08101 0.00006 MINI INTERN> 4.78848 14.66978 0.00000 11.08789 2.91313 MINI EXTERN> -109.42224 16.83651 0.00000 0.00000 0.00000 MINI CONSTR> 11.28493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10780 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -47.84262 0.00109 0.08545 0.00006 MINI INTERN> 4.78790 14.66851 0.00000 11.08655 2.91293 MINI EXTERN> -109.42435 16.83822 0.00000 0.00000 0.00000 MINI CONSTR> 11.28764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -47.84432 0.00171 0.02788 0.00002 MINI INTERN> 4.75762 14.68951 0.00000 11.08934 2.91187 MINI EXTERN> -109.42416 16.84138 0.00000 0.00000 0.00000 MINI CONSTR> 11.29011 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -47.84460 0.00028 0.08952 0.00006 MINI INTERN> 4.78989 14.66527 0.00000 11.08394 2.91251 MINI EXTERN> -109.42868 16.83990 0.00000 0.00000 0.00000 MINI CONSTR> 11.29258 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -47.84646 0.00185 0.03011 0.00003 MINI INTERN> 4.75684 14.68819 0.00000 11.08707 2.91133 MINI EXTERN> -109.42891 16.84373 0.00000 0.00000 0.00000 MINI CONSTR> 11.29529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -47.84739 0.00093 0.02131 0.00003 MINI INTERN> 4.76211 14.68335 0.00000 11.08546 2.91113 MINI EXTERN> -109.43144 16.84455 0.00000 0.00000 0.00000 MINI CONSTR> 11.29745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -47.84845 0.00106 0.02317 0.00003 MINI INTERN> 4.76081 14.68349 0.00000 11.08450 2.91083 MINI EXTERN> -109.43405 16.84588 0.00000 0.00000 0.00000 MINI CONSTR> 11.30008 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -47.84948 0.00103 0.03959 0.00003 MINI INTERN> 4.75409 14.68790 0.00000 11.08417 2.91050 MINI EXTERN> -109.43660 16.84756 0.00000 0.00000 0.00000 MINI CONSTR> 11.30289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -47.85054 0.00105 0.02700 0.00003 MINI INTERN> 4.75902 14.68337 0.00000 11.08250 2.91039 MINI EXTERN> -109.43960 16.84849 0.00000 0.00000 0.00000 MINI CONSTR> 11.30529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -47.85156 0.00102 0.03252 0.00003 MINI INTERN> 4.75844 14.68327 0.00000 11.08157 2.91003 MINI EXTERN> -109.44250 16.84969 0.00000 0.00000 0.00000 MINI CONSTR> 11.30794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -47.85241 0.00085 0.04771 0.00003 MINI INTERN> 4.75260 14.68715 0.00000 11.08134 2.90975 MINI EXTERN> -109.44503 16.85138 0.00000 0.00000 0.00000 MINI CONSTR> 11.31041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -47.85350 0.00110 0.03132 0.00003 MINI INTERN> 4.75829 14.68200 0.00000 11.07953 2.90975 MINI EXTERN> -109.44831 16.85237 0.00000 0.00000 0.00000 MINI CONSTR> 11.31285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -47.85432 0.00082 0.05086 0.00004 MINI INTERN> 4.75231 14.68623 0.00000 11.07943 2.90932 MINI EXTERN> -109.45096 16.85398 0.00000 0.00000 0.00000 MINI CONSTR> 11.31538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -47.85536 0.00104 0.05121 0.00004 MINI INTERN> 4.75241 14.68576 0.00000 11.07834 2.90921 MINI EXTERN> -109.45424 16.85509 0.00000 0.00000 0.00000 MINI CONSTR> 11.31806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -47.85644 0.00108 0.04017 0.00004 MINI INTERN> 4.75608 14.68217 0.00000 11.07681 2.90918 MINI EXTERN> -109.45762 16.85638 0.00000 0.00000 0.00000 MINI CONSTR> 11.32057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -47.85718 0.00074 0.05651 0.00004 MINI INTERN> 4.75191 14.68503 0.00000 11.07656 2.90881 MINI EXTERN> -109.46035 16.85794 0.00000 0.00000 0.00000 MINI CONSTR> 11.32291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -47.85807 0.00089 0.06375 0.00004 MINI INTERN> 4.75586 14.68198 0.00000 11.07537 2.90828 MINI EXTERN> -109.46356 16.85861 0.00000 0.00000 0.00000 MINI CONSTR> 11.32540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -47.85900 0.00093 0.05925 0.00004 MINI INTERN> 4.75241 14.68383 0.00000 11.07481 2.90823 MINI EXTERN> -109.46657 16.86052 0.00000 0.00000 0.00000 MINI CONSTR> 11.32778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -47.85994 0.00094 0.06183 0.00004 MINI INTERN> 4.75207 14.68377 0.00000 11.07390 2.90810 MINI EXTERN> -109.46991 16.86178 0.00000 0.00000 0.00000 MINI CONSTR> 11.33035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -47.86090 0.00096 0.06321 0.00005 MINI INTERN> 4.75187 14.68356 0.00000 11.07293 2.90801 MINI EXTERN> -109.47329 16.86307 0.00000 0.00000 0.00000 MINI CONSTR> 11.33295 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -47.86213 0.00123 0.02098 0.00002 MINI INTERN> 4.76922 14.66905 0.00000 11.06979 2.90790 MINI EXTERN> -109.47716 16.86382 0.00000 0.00000 0.00000 MINI CONSTR> 11.33525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -47.86259 0.00046 0.07136 0.00005 MINI INTERN> 4.75093 14.68358 0.00000 11.07134 2.90763 MINI EXTERN> -109.47966 16.86581 0.00000 0.00000 0.00000 MINI CONSTR> 11.33778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -47.86346 0.00087 0.07897 0.00005 MINI INTERN> 4.75541 14.68044 0.00000 11.07004 2.90739 MINI EXTERN> -109.48341 16.86634 0.00000 0.00000 0.00000 MINI CONSTR> 11.34033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -47.86485 0.00139 0.02419 0.00002 MINI INTERN> 4.77110 14.66637 0.00000 11.06691 2.90736 MINI EXTERN> -109.48704 16.86784 0.00000 0.00000 0.00000 MINI CONSTR> 11.34261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -47.86511 0.00026 0.08137 0.00006 MINI INTERN> 4.75375 14.68095 0.00000 11.06871 2.90685 MINI EXTERN> -109.48956 16.86922 0.00000 0.00000 0.00000 MINI CONSTR> 11.34497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -47.86655 0.00144 0.02855 0.00002 MINI INTERN> 4.77280 14.66441 0.00000 11.06503 2.90704 MINI EXTERN> -109.49346 16.87031 0.00000 0.00000 0.00000 MINI CONSTR> 11.34732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -47.86732 0.00076 0.02036 0.00002 MINI INTERN> 4.76953 14.66671 0.00000 11.06471 2.90699 MINI EXTERN> -109.49601 16.87146 0.00000 0.00000 0.00000 MINI CONSTR> 11.34929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -47.86821 0.00089 0.03264 0.00003 MINI INTERN> 4.77399 14.66286 0.00000 11.06323 2.90679 MINI EXTERN> -109.49976 16.87277 0.00000 0.00000 0.00000 MINI CONSTR> 11.35192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -47.86897 0.00077 0.02028 0.00003 MINI INTERN> 4.76971 14.66596 0.00000 11.06309 2.90671 MINI EXTERN> -109.50227 16.87397 0.00000 0.00000 0.00000 MINI CONSTR> 11.35386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -47.86981 0.00084 0.03840 0.00003 MINI INTERN> 4.77492 14.66146 0.00000 11.06142 2.90665 MINI EXTERN> -109.50603 16.87529 0.00000 0.00000 0.00000 MINI CONSTR> 11.35648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -47.87067 0.00086 0.02855 0.00003 MINI INTERN> 4.77287 14.66297 0.00000 11.06105 2.90635 MINI EXTERN> -109.50901 16.87641 0.00000 0.00000 0.00000 MINI CONSTR> 11.35868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -47.87146 0.00078 0.03352 0.00003 MINI INTERN> 4.77432 14.66157 0.00000 11.06003 2.90629 MINI EXTERN> -109.51220 16.87758 0.00000 0.00000 0.00000 MINI CONSTR> 11.36096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -47.87218 0.00073 0.04449 0.00003 MINI INTERN> 4.77617 14.65970 0.00000 11.05885 2.90637 MINI EXTERN> -109.51541 16.87890 0.00000 0.00000 0.00000 MINI CONSTR> 11.36324 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -47.87306 0.00088 0.03403 0.00003 MINI INTERN> 4.77448 14.66095 0.00000 11.05848 2.90599 MINI EXTERN> -109.51844 16.88003 0.00000 0.00000 0.00000 MINI CONSTR> 11.36546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -47.87373 0.00067 0.04726 0.00003 MINI INTERN> 4.77766 14.65826 0.00000 11.05722 2.90603 MINI EXTERN> -109.52161 16.88105 0.00000 0.00000 0.00000 MINI CONSTR> 11.36767 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -47.87448 0.00076 0.05522 0.00003 MINI INTERN> 4.77607 14.65886 0.00000 11.05641 2.90617 MINI EXTERN> -109.52484 16.88282 0.00000 0.00000 0.00000 MINI CONSTR> 11.37001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -47.87527 0.00079 0.05002 0.00004 MINI INTERN> 4.77830 14.65718 0.00000 11.05555 2.90587 MINI EXTERN> -109.52785 16.88354 0.00000 0.00000 0.00000 MINI CONSTR> 11.37213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -47.87608 0.00082 0.05712 0.00004 MINI INTERN> 4.77780 14.65706 0.00000 11.05465 2.90585 MINI EXTERN> -109.53139 16.88530 0.00000 0.00000 0.00000 MINI CONSTR> 11.37465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -47.87685 0.00077 0.05576 0.00004 MINI INTERN> 4.77917 14.65609 0.00000 11.05398 2.90537 MINI EXTERN> -109.53433 16.88608 0.00000 0.00000 0.00000 MINI CONSTR> 11.37679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -47.87761 0.00075 0.05809 0.00004 MINI INTERN> 4.77681 14.65731 0.00000 11.05327 2.90566 MINI EXTERN> -109.53751 16.88784 0.00000 0.00000 0.00000 MINI CONSTR> 11.37901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -47.87836 0.00076 0.05608 0.00004 MINI INTERN> 4.77966 14.65510 0.00000 11.05227 2.90540 MINI EXTERN> -109.54058 16.88861 0.00000 0.00000 0.00000 MINI CONSTR> 11.38118 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -47.87939 0.00103 0.01888 0.00002 MINI INTERN> 4.76950 14.66275 0.00000 11.05319 2.90476 MINI EXTERN> -109.54337 16.89045 0.00000 0.00000 0.00000 MINI CONSTR> 11.38332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -47.87984 0.00044 0.06355 0.00004 MINI INTERN> 4.78102 14.65354 0.00000 11.05053 2.90518 MINI EXTERN> -109.54697 16.89115 0.00000 0.00000 0.00000 MINI CONSTR> 11.38571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -47.88100 0.00117 0.01921 0.00002 MINI INTERN> 4.76981 14.66204 0.00000 11.05160 2.90448 MINI EXTERN> -109.54998 16.89306 0.00000 0.00000 0.00000 MINI CONSTR> 11.38799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -47.88135 0.00035 0.06980 0.00005 MINI INTERN> 4.78046 14.65332 0.00000 11.04899 2.90497 MINI EXTERN> -109.55351 16.89406 0.00000 0.00000 0.00000 MINI CONSTR> 11.39035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -47.88253 0.00117 0.02276 0.00002 MINI INTERN> 4.76923 14.66208 0.00000 11.05021 2.90418 MINI EXTERN> -109.55635 16.89562 0.00000 0.00000 0.00000 MINI CONSTR> 11.39250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -47.88277 0.00025 0.07279 0.00005 MINI INTERN> 4.78264 14.65128 0.00000 11.04734 2.90456 MINI EXTERN> -109.55953 16.89626 0.00000 0.00000 0.00000 MINI CONSTR> 11.39467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -47.88408 0.00130 0.02319 0.00002 MINI INTERN> 4.76965 14.66131 0.00000 11.04864 2.90393 MINI EXTERN> -109.56283 16.89816 0.00000 0.00000 0.00000 MINI CONSTR> 11.39705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -47.88475 0.00067 0.01868 0.00002 MINI INTERN> 4.77100 14.65996 0.00000 11.04780 2.90381 MINI EXTERN> -109.56552 16.89922 0.00000 0.00000 0.00000 MINI CONSTR> 11.39897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -47.88551 0.00076 0.03007 0.00002 MINI INTERN> 4.76882 14.66162 0.00000 11.04736 2.90364 MINI EXTERN> -109.56901 16.90065 0.00000 0.00000 0.00000 MINI CONSTR> 11.40141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -47.88618 0.00067 0.01835 0.00002 MINI INTERN> 4.77153 14.65912 0.00000 11.04634 2.90356 MINI EXTERN> -109.57154 16.90159 0.00000 0.00000 0.00000 MINI CONSTR> 11.40321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -47.88691 0.00074 0.03536 0.00003 MINI INTERN> 4.76879 14.66132 0.00000 11.04603 2.90330 MINI EXTERN> -109.57505 16.90301 0.00000 0.00000 0.00000 MINI CONSTR> 11.40569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -47.88764 0.00073 0.02715 0.00003 MINI INTERN> 4.76998 14.65998 0.00000 11.04509 2.90332 MINI EXTERN> -109.57794 16.90422 0.00000 0.00000 0.00000 MINI CONSTR> 11.40770 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -47.88832 0.00067 0.03070 0.00003 MINI INTERN> 4.76948 14.66023 0.00000 11.04453 2.90313 MINI EXTERN> -109.58088 16.90541 0.00000 0.00000 0.00000 MINI CONSTR> 11.40979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -47.88901 0.00070 0.03170 0.00003 MINI INTERN> 4.76982 14.65981 0.00000 11.04385 2.90291 MINI EXTERN> -109.58383 16.90654 0.00000 0.00000 0.00000 MINI CONSTR> 11.41189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -47.88963 0.00062 0.04240 0.00003 MINI INTERN> 4.76810 14.66102 0.00000 11.04340 2.90283 MINI EXTERN> -109.58685 16.90787 0.00000 0.00000 0.00000 MINI CONSTR> 11.41400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -47.89031 0.00068 0.04744 0.00003 MINI INTERN> 4.76965 14.65981 0.00000 11.04263 2.90248 MINI EXTERN> -109.58984 16.90881 0.00000 0.00000 0.00000 MINI CONSTR> 11.41615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -47.89096 0.00065 0.04829 0.00003 MINI INTERN> 4.76846 14.66051 0.00000 11.04212 2.90238 MINI EXTERN> -109.59270 16.91011 0.00000 0.00000 0.00000 MINI CONSTR> 11.41817 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -47.89161 0.00066 0.05092 0.00003 MINI INTERN> 4.76751 14.66092 0.00000 11.04145 2.90245 MINI EXTERN> -109.59569 16.91150 0.00000 0.00000 0.00000 MINI CONSTR> 11.42024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -47.89228 0.00067 0.04865 0.00003 MINI INTERN> 4.76893 14.65976 0.00000 11.04076 2.90210 MINI EXTERN> -109.59840 16.91237 0.00000 0.00000 0.00000 MINI CONSTR> 11.42220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -47.89292 0.00064 0.05410 0.00004 MINI INTERN> 4.76834 14.65969 0.00000 11.03988 2.90242 MINI EXTERN> -109.60143 16.91389 0.00000 0.00000 0.00000 MINI CONSTR> 11.42428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -47.89359 0.00067 0.05106 0.00004 MINI INTERN> 4.76788 14.66003 0.00000 11.03945 2.90205 MINI EXTERN> -109.60420 16.91492 0.00000 0.00000 0.00000 MINI CONSTR> 11.42628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -47.89443 0.00085 0.01773 0.00002 MINI INTERN> 4.77517 14.65370 0.00000 11.03763 2.90215 MINI EXTERN> -109.60682 16.91559 0.00000 0.00000 0.00000 MINI CONSTR> 11.42815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -47.89483 0.00039 0.05849 0.00004 MINI INTERN> 4.76739 14.66002 0.00000 11.03818 2.90187 MINI EXTERN> -109.60990 16.91731 0.00000 0.00000 0.00000 MINI CONSTR> 11.43031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -47.89573 0.00091 0.01860 0.00002 MINI INTERN> 4.77576 14.65284 0.00000 11.03622 2.90194 MINI EXTERN> -109.61247 16.91782 0.00000 0.00000 0.00000 MINI CONSTR> 11.43215 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -47.89607 0.00033 0.06097 0.00004 MINI INTERN> 4.76800 14.65945 0.00000 11.03705 2.90126 MINI EXTERN> -109.61536 16.91927 0.00000 0.00000 0.00000 MINI CONSTR> 11.43426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -47.89666 0.00060 0.07114 0.00004 MINI INTERN> 4.76820 14.65869 0.00000 11.03592 2.90180 MINI EXTERN> -109.61851 16.92085 0.00000 0.00000 0.00000 MINI CONSTR> 11.43638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -47.89732 0.00066 0.06676 0.00005 MINI INTERN> 4.76707 14.65982 0.00000 11.03579 2.90113 MINI EXTERN> -109.62125 16.92171 0.00000 0.00000 0.00000 MINI CONSTR> 11.43840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -47.89839 0.00107 0.02070 0.00002 MINI INTERN> 4.77688 14.65115 0.00000 11.03337 2.90147 MINI EXTERN> -109.62411 16.92242 0.00000 0.00000 0.00000 MINI CONSTR> 11.44043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -47.89899 0.00059 0.01688 0.00002 MINI INTERN> 4.77601 14.65170 0.00000 11.03293 2.90134 MINI EXTERN> -109.62666 16.92346 0.00000 0.00000 0.00000 MINI CONSTR> 11.44223 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 -47.89899 0.00059 0.01688 0.00002 STPD INTERN> 4.77601 14.65170 0.00000 11.03293 2.90134 STPD EXTERN> -109.62666 16.92346 0.00000 0.00000 0.00000 STPD CONSTR> 11.44223 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 10778 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 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 -47.89899 0.00059 0.01688 0.00000 MINI INTERN> 4.77601 14.65170 0.00000 11.03293 2.90134 MINI EXTERN> -109.62666 16.92346 0.00000 0.00000 0.00000 MINI CONSTR> 11.44223 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -48.00240 0.10341 0.02140 0.00378 MINI INTERN> 4.83838 14.57834 0.00000 10.83229 2.86791 MINI EXTERN> -110.50149 17.27937 0.00000 0.00000 0.00000 MINI CONSTR> 12.10279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -48.00544 0.00304 0.07193 0.00761 MINI INTERN> 4.82538 14.53162 0.00000 10.82896 2.85706 MINI EXTERN> -110.48101 17.31868 0.00000 0.00000 0.00000 MINI CONSTR> 12.11387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -48.01776 0.01232 0.11631 0.02486 MINI INTERN> 4.78178 14.51030 0.00000 10.81225 2.85819 MINI EXTERN> -110.54713 17.41301 0.00000 0.00000 0.00000 MINI CONSTR> 12.15384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -48.03511 0.01735 0.07852 0.03327 MINI INTERN> 4.80919 14.52903 0.00000 10.78573 2.85774 MINI EXTERN> -110.54747 17.32245 0.00000 0.00000 0.00000 MINI CONSTR> 12.20822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -48.04466 0.00955 0.07804 0.01717 MINI INTERN> 4.81419 14.54938 0.00000 10.76205 2.86333 MINI EXTERN> -110.53970 17.27179 0.00000 0.00000 0.00000 MINI CONSTR> 12.23428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -48.05320 0.00854 0.07074 0.01499 MINI INTERN> 4.85140 14.57644 0.00000 10.77707 2.86860 MINI EXTERN> -110.52245 17.14322 0.00000 0.00000 0.00000 MINI CONSTR> 12.25252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -48.06131 0.00810 0.05893 0.01561 MINI INTERN> 4.83867 14.53945 0.00000 10.75951 2.86366 MINI EXTERN> -110.40597 17.07711 0.00000 0.00000 0.00000 MINI CONSTR> 12.26627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -48.06829 0.00698 0.05747 0.01493 MINI INTERN> 4.80763 14.51171 0.00000 10.75569 2.85166 MINI EXTERN> -110.33662 17.06460 0.00000 0.00000 0.00000 MINI CONSTR> 12.27704 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -48.07250 0.00422 0.04920 0.00859 MINI INTERN> 4.82013 14.49997 0.00000 10.75942 2.85496 MINI EXTERN> -110.32144 17.03038 0.00000 0.00000 0.00000 MINI CONSTR> 12.28407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -48.07616 0.00365 0.03909 0.00739 MINI INTERN> 4.80724 14.50742 0.00000 10.73480 2.85672 MINI EXTERN> -110.29585 17.02221 0.00000 0.00000 0.00000 MINI CONSTR> 12.29131 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -48.08006 0.00390 0.05450 0.01005 MINI INTERN> 4.81670 14.49813 0.00000 10.73079 2.84860 MINI EXTERN> -110.30661 17.03013 0.00000 0.00000 0.00000 MINI CONSTR> 12.30220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -48.08416 0.00410 0.05144 0.01053 MINI INTERN> 4.81226 14.49555 0.00000 10.70236 2.85755 MINI EXTERN> -110.33359 17.06533 0.00000 0.00000 0.00000 MINI CONSTR> 12.31638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -48.08810 0.00394 0.04610 0.01116 MINI INTERN> 4.81078 14.48398 0.00000 10.70513 2.87618 MINI EXTERN> -110.36065 17.06358 0.00000 0.00000 0.00000 MINI CONSTR> 12.33291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -48.09194 0.00384 0.04025 0.00977 MINI INTERN> 4.81844 14.50792 0.00000 10.70636 2.86401 MINI EXTERN> -110.42250 17.08272 0.00000 0.00000 0.00000 MINI CONSTR> 12.35111 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -48.09466 0.00272 0.04263 0.00723 MINI INTERN> 4.81453 14.52848 0.00000 10.71652 2.87316 MINI EXTERN> -110.47647 17.08433 0.00000 0.00000 0.00000 MINI CONSTR> 12.36479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -48.09685 0.00219 0.03067 0.00717 MINI INTERN> 4.82384 14.55585 0.00000 10.72781 2.87090 MINI EXTERN> -110.48049 17.02985 0.00000 0.00000 0.00000 MINI CONSTR> 12.37539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -48.09847 0.00161 0.02710 0.00519 MINI INTERN> 4.81986 14.54790 0.00000 10.72586 2.86738 MINI EXTERN> -110.46815 17.02665 0.00000 0.00000 0.00000 MINI CONSTR> 12.38204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -48.09962 0.00116 0.02277 0.00357 MINI INTERN> 4.82166 14.53519 0.00000 10.72868 2.87192 MINI EXTERN> -110.45853 17.01595 0.00000 0.00000 0.00000 MINI CONSTR> 12.38549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -48.10062 0.00100 0.02561 0.00513 MINI INTERN> 4.82548 14.54280 0.00000 10.73397 2.87013 MINI EXTERN> -110.48500 17.02508 0.00000 0.00000 0.00000 MINI CONSTR> 12.38694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -48.10173 0.00111 0.02413 0.00462 MINI INTERN> 4.81494 14.53521 0.00000 10.73853 2.86474 MINI EXTERN> -110.47299 17.03079 0.00000 0.00000 0.00000 MINI CONSTR> 12.38705 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 -48.10173 0.00111 0.02413 0.02000 CONJ INTERN> 4.81494 14.53521 0.00000 10.73853 2.86474 CONJ EXTERN> -110.47299 17.03079 0.00000 0.00000 0.00000 CONJ CONSTR> 12.38705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "12000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.36249E-01 ( PROT LYS 1 HT2 ) 0.36249E-01 ( PROT LYS 1 N ) 0.45311E-01 ( PROT LYS 1 HT3 ) 0.36249E-01 ( PROT LYS 1 CA ) 0.45311E-01 ( PROT LYS 1 CB ) 0.36249E-01 ( PROT LYS 1 CG ) 0.36249E-01 ( PROT LYS 1 CD ) 0.36249E-01 ( PROT LYS 1 CE ) 0.36249E-01 ( PROT LYS 1 NZ ) 0.36249E-01 ( PROT LYS 1 HZ1 ) 0.36249E-01 ( PROT LYS 1 HZ2 ) 0.36249E-01 ( PROT LYS 1 HZ3 ) 0.36249E-01 ( PROT LYS 1 C ) 0.45311E-01 ( PROT LYS 1 O ) 0.45311E-01 ( PROT MET 2 N ) 0.45311E-01 ( PROT MET 2 H ) 0.36249E-01 ( PROT MET 2 CA ) 0.45311E-01 ( PROT MET 2 CB ) 0.36249E-01 ( PROT MET 2 CG ) 0.36249E-01 ( PROT MET 2 SD ) 0.36249E-01 ( PROT MET 2 CE ) 0.36249E-01 ( PROT MET 2 C ) 0.45311E-01 ( PROT MET 2 O ) 0.45311E-01 ( PROT LYS 3 N ) 0.45311E-01 ( PROT LYS 3 H ) 0.36249E-01 ( PROT LYS 3 CA ) 0.45311E-01 ( PROT LYS 3 CB ) 0.36249E-01 ( PROT LYS 3 CG ) 0.36249E-01 ( PROT LYS 3 CD ) 0.36249E-01 ( PROT LYS 3 CE ) 0.36249E-01 ( PROT LYS 3 NZ ) 0.36249E-01 ( PROT LYS 3 HZ1 ) 0.36249E-01 ( PROT LYS 3 HZ2 ) 0.36249E-01 ( PROT LYS 3 HZ3 ) 0.36249E-01 ( PROT LYS 3 C ) 0.45311E-01 ( PROT LYS 3 O ) 0.45311E-01 ( PROT ALA 4 N ) 0.45311E-01 ( PROT ALA 4 H ) 0.36249E-01 ( PROT ALA 4 CA ) 0.45311E-01 ( PROT ALA 4 CB ) 0.36249E-01 ( PROT ALA 4 C ) 0.45311E-01 ( PROT ALA 4 O ) 0.45311E-01 ( PROT VAL 5 N ) 0.45311E-01 ( PROT VAL 5 H ) 0.36249E-01 ( PROT VAL 5 CA ) 0.45311E-01 ( PROT VAL 5 CB ) 0.36249E-01 ( PROT VAL 5 CG1 ) 0.36249E-01 ( PROT VAL 5 CG2 ) 0.36249E-01 ( PROT VAL 5 C ) 0.45311E-01 ( PROT VAL 5 O ) 0.45311E-01 ( PROT MET 6 N ) 0.45311E-01 ( PROT MET 6 H ) 0.36249E-01 ( PROT MET 6 CA ) 0.45311E-01 ( PROT MET 6 CB ) 0.36249E-01 ( PROT MET 6 CG ) 0.36249E-01 ( PROT MET 6 SD ) 0.36249E-01 ( PROT MET 6 CE ) 0.36249E-01 ( PROT MET 6 C ) 0.45311E-01 ( PROT MET 6 O ) 0.45311E-01 ( PROT ILE 7 N ) 0.45311E-01 ( PROT ILE 7 H ) 0.36249E-01 ( PROT ILE 7 CA ) 0.45311E-01 ( PROT ILE 7 CB ) 0.36249E-01 ( PROT ILE 7 CG2 ) 0.36249E-01 ( PROT ILE 7 CG1 ) 0.36249E-01 ( PROT ILE 7 CD ) 0.36249E-01 ( PROT ILE 7 C ) 0.45311E-01 ( PROT ILE 7 O ) 0.45311E-01 ( PROT GLY 8 N ) 0.45311E-01 ( PROT GLY 8 H ) 0.36249E-01 ( PROT GLY 8 CA ) 0.45311E-01 ( PROT GLY 8 C ) 0.45311E-01 ( PROT GLY 8 O ) 0.45311E-01 ( PROT ALA 9 N ) 0.45311E-01 ( PROT ALA 9 H ) 0.36249E-01 ( PROT ALA 9 CA ) 0.45311E-01 ( PROT ALA 9 CB ) 0.36249E-01 ( PROT ALA 9 C ) 0.45311E-01 ( PROT ALA 9 O ) 0.45311E-01 ( PROT CYS 10 N ) 0.45311E-01 ( PROT CYS 10 H ) 0.36249E-01 ( PROT CYS 10 CA ) 0.45311E-01 ( PROT CYS 10 CB ) 0.36249E-01 ( PROT CYS 10 SG ) 0.36249E-01 ( PROT CYS 10 C ) 0.45311E-01 ( PROT CYS 10 O ) 0.45311E-01 ( PROT PHE 11 N ) 0.45311E-01 ( PROT PHE 11 H ) 0.36249E-01 ( PROT PHE 11 CA ) 0.45311E-01 ( PROT PHE 11 CB ) 0.36249E-01 ( PROT PHE 11 CG ) 0.36249E-01 ( PROT PHE 11 CD1 ) 0.36249E-01 ( PROT PHE 11 CD2 ) 0.36249E-01 ( PROT PHE 11 CE1 ) 0.36249E-01 ( PROT PHE 11 CE2 ) 0.36249E-01 ( PROT PHE 11 CZ ) 0.36249E-01 ( PROT PHE 11 C ) 0.45311E-01 ( PROT PHE 11 O ) 0.45311E-01 ( PROT LEU 12 N ) 0.45311E-01 ( PROT LEU 12 H ) 0.36249E-01 ( PROT LEU 12 CA ) 0.45311E-01 ( PROT LEU 12 CB ) 0.36249E-01 ( PROT LEU 12 CG ) 0.36249E-01 ( PROT LEU 12 CD1 ) 0.36249E-01 ( PROT LEU 12 CD2 ) 0.36249E-01 ( PROT LEU 12 C ) 0.45311E-01 ( PROT LEU 12 O ) 0.45311E-01 ( PROT ILE 13 N ) 0.45311E-01 ( PROT ILE 13 H ) 0.36249E-01 ( PROT ILE 13 CA ) 0.45311E-01 ( PROT ILE 13 CB ) 0.36249E-01 ( PROT ILE 13 CG2 ) 0.36249E-01 ( PROT ILE 13 CG1 ) 0.36249E-01 ( PROT ILE 13 CD ) 0.36249E-01 ( PROT ILE 13 C ) 0.45311E-01 ( PROT ILE 13 O ) 0.45311E-01 ( PROT ASH 14 N ) 0.45311E-01 ( PROT ASH 14 H ) 0.36249E-01 ( PROT ASH 14 CA ) 0.45311E-01 ( PROT ASH 14 CB ) 0.36249E-01 ( PROT ASH 14 CG ) 0.36249E-01 ( PROT ASH 14 OD1 ) 0.36249E-01 ( PROT ASH 14 OD2 ) 0.36249E-01 ( PROT ASH 14 HD2 ) 0.36249E-01 ( PROT ASH 14 C ) 0.45311E-01 ( PROT ASH 14 O ) 0.45311E-01 ( PROT PHE 15 N ) 0.45311E-01 ( PROT PHE 15 H ) 0.36249E-01 ( PROT PHE 15 CA ) 0.45311E-01 ( PROT PHE 15 CB ) 0.36249E-01 ( PROT PHE 15 CG ) 0.36249E-01 ( PROT PHE 15 CD1 ) 0.36249E-01 ( PROT PHE 15 CD2 ) 0.36249E-01 ( PROT PHE 15 CE1 ) 0.36249E-01 ( PROT PHE 15 CE2 ) 0.36249E-01 ( PROT PHE 15 CZ ) 0.36249E-01 ( PROT PHE 15 C ) 0.45311E-01 ( PROT PHE 15 O ) 0.45311E-01 ( PROT MET 16 N ) 0.45311E-01 ( PROT MET 16 H ) 0.36249E-01 ( PROT MET 16 CA ) 0.45311E-01 ( PROT MET 16 CB ) 0.36249E-01 ( PROT MET 16 CG ) 0.36249E-01 ( PROT MET 16 SD ) 0.36249E-01 ( PROT MET 16 CE ) 0.36249E-01 ( PROT MET 16 C ) 0.45311E-01 ( PROT MET 16 O ) 0.45311E-01 ( PROT PHE 17 N ) 0.45311E-01 ( PROT PHE 17 H ) 0.36249E-01 ( PROT PHE 17 CA ) 0.45311E-01 ( PROT PHE 17 CB ) 0.36249E-01 ( PROT PHE 17 CG ) 0.36249E-01 ( PROT PHE 17 CD1 ) 0.36249E-01 ( PROT PHE 17 CD2 ) 0.36249E-01 ( PROT PHE 17 CE1 ) 0.36249E-01 ( PROT PHE 17 CE2 ) 0.36249E-01 ( PROT PHE 17 CZ ) 0.36249E-01 ( PROT PHE 17 C ) 0.45311E-01 ( PROT PHE 17 O ) 0.45311E-01 ( PROT PHE 18 N ) 0.45311E-01 ( PROT PHE 18 H ) 0.36249E-01 ( PROT PHE 18 CA ) 0.45311E-01 ( PROT PHE 18 CB ) 0.36249E-01 ( PROT PHE 18 CG ) 0.36249E-01 ( PROT PHE 18 CD1 ) 0.36249E-01 ( PROT PHE 18 CD2 ) 0.36249E-01 ( PROT PHE 18 CE1 ) 0.36249E-01 ( PROT PHE 18 CE2 ) 0.36249E-01 ( PROT PHE 18 CZ ) 0.36249E-01 ( PROT PHE 18 C ) 0.45311E-01 ( PROT PHE 18 O ) 0.45311E-01 ( PROT GLU 19 N ) 0.45311E-01 ( PROT GLU 19 H ) 0.36249E-01 ( PROT GLU 19 CA ) 0.45311E-01 ( PROT GLU 19 CB ) 0.36249E-01 ( PROT GLU 19 CG ) 0.36249E-01 ( PROT GLU 19 CD ) 0.36249E-01 ( PROT GLU 19 OE1 ) 0.36249E-01 ( PROT GLU 19 OE2 ) 0.36249E-01 ( PROT GLU 19 C ) 0.45311E-01 ( PROT GLU 19 OT1 ) 0.36249E-01 ( PROT GLU 19 OT2 ) 0.36249E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.39516 5.28029 -8.68558 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.00938 0.01212 -0.00763 ROTATION MATRIX 0.999997 -0.000718 0.002232 0.000714 0.999998 0.001718 -0.002234 -0.001716 0.999996 AXIS OF ROTATION IS 0.590793 -0.768280 -0.246391 ANGLE IS 0.17 TOTAL SQUARE DIFF IS 207.8297 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 1.065683 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.0657" Parameter: A <- "1.0657" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.74622 5.30030 -8.81114 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.03137 -0.03588 0.01677 ROTATION MATRIX 0.999946 0.000824 -0.010339 -0.000851 0.999996 -0.002526 0.010337 0.002534 0.999943 AXIS OF ROTATION IS -0.236975 0.968343 0.078451 ANGLE IS 0.61 TOTAL SQUARE DIFF IS 12.1928 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.801080 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.0657" RDCMND substituted energy or value "?RMS" to " 0.8011" Parameter: A <- "1.0657 0.8011" 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 1.0657 0.8011 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 " 12.39" Parameter: H <- "12.39" 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 -60.48878 12.38705 0.07647 ENER INTERN> 4.81494 14.53521 0.00000 10.73853 2.86474 ENER EXTERN> -110.47299 17.03079 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 " -60.49" Parameter: B <- "-60.49" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 17.03" Parameter: C <- "17.03" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -110.47" Parameter: C <- " -93.44" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -93.44" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.81" Parameter: D <- "4.81" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.54" Parameter: D <- " 19.35" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.74" Parameter: D <- " 30.09" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.86" Parameter: D <- " 32.95" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 32.95" 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= -60.49 GRMS= 0.08 ELEC= 17.03 VDW= -110.47 RDTITL> *EXTERNAL= -93.44 INTERNAL= 32.95 USER= 0.00 HARM= 12.39 RDTITL> *BOND= 4.81 ANGL= 14.54 DIHE= 10.74 IMPR= 2.86 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= -60.49 GRMS= 0.08 ELEC= 17.03 VDW= -110.47 RDTITL> *EXTERNAL= -93.44 INTERNAL= 32.95 USER= 0.00 HARM= 12.39 RDTITL> *BOND= 4.81 ANGL= 14.54 DIHE= 10.74 IMPR= 2.86 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= -60.49 GRMS= 0.08 ELEC= 17.03 VDW= -110.47 RDTITL> *EXTERNAL= -93.44 INTERNAL= 32.95 USER= 0.00 HARM= 12.39 RDTITL> *BOND= 4.81 ANGL= 14.54 DIHE= 10.74 IMPR= 2.86 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 12000 1.0657 0.8011 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "12000" and "12000". IF test evaluated as false. Skipping command CHARMM> CHARMM> ! now do a minimization without any constraint CHARMM> cons harm clear CHARMM> ! check that constraint==0 CHARMM> scalar cons show ( PROT LYS 1 HT1 ) 0.0000 ( PROT LYS 1 HT2 ) 0.0000 ( PROT LYS 1 N ) 0.0000 ( PROT LYS 1 HT3 ) 0.0000 ( PROT LYS 1 CA ) 0.0000 ( PROT LYS 1 CB ) 0.0000 ( PROT LYS 1 CG ) 0.0000 ( PROT LYS 1 CD ) 0.0000 ( PROT LYS 1 CE ) 0.0000 ( PROT LYS 1 NZ ) 0.0000 ( PROT LYS 1 HZ1 ) 0.0000 ( PROT LYS 1 HZ2 ) 0.0000 ( PROT LYS 1 HZ3 ) 0.0000 ( PROT LYS 1 C ) 0.0000 ( PROT LYS 1 O ) 0.0000 ( PROT MET 2 N ) 0.0000 ( PROT MET 2 H ) 0.0000 ( PROT MET 2 CA ) 0.0000 ( PROT MET 2 CB ) 0.0000 ( PROT MET 2 CG ) 0.0000 ( PROT MET 2 SD ) 0.0000 ( PROT MET 2 CE ) 0.0000 ( PROT MET 2 C ) 0.0000 ( PROT MET 2 O ) 0.0000 ( PROT LYS 3 N ) 0.0000 ( PROT LYS 3 H ) 0.0000 ( PROT LYS 3 CA ) 0.0000 ( PROT LYS 3 CB ) 0.0000 ( PROT LYS 3 CG ) 0.0000 ( PROT LYS 3 CD ) 0.0000 ( PROT LYS 3 CE ) 0.0000 ( PROT LYS 3 NZ ) 0.0000 ( PROT LYS 3 HZ1 ) 0.0000 ( PROT LYS 3 HZ2 ) 0.0000 ( PROT LYS 3 HZ3 ) 0.0000 ( PROT LYS 3 C ) 0.0000 ( PROT LYS 3 O ) 0.0000 ( PROT ALA 4 N ) 0.0000 ( PROT ALA 4 H ) 0.0000 ( PROT ALA 4 CA ) 0.0000 ( PROT ALA 4 CB ) 0.0000 ( PROT ALA 4 C ) 0.0000 ( PROT ALA 4 O ) 0.0000 ( PROT VAL 5 N ) 0.0000 ( PROT VAL 5 H ) 0.0000 ( PROT VAL 5 CA ) 0.0000 ( PROT VAL 5 CB ) 0.0000 ( PROT VAL 5 CG1 ) 0.0000 ( PROT VAL 5 CG2 ) 0.0000 ( PROT VAL 5 C ) 0.0000 ( PROT VAL 5 O ) 0.0000 ( PROT MET 6 N ) 0.0000 ( PROT MET 6 H ) 0.0000 ( PROT MET 6 CA ) 0.0000 ( PROT MET 6 CB ) 0.0000 ( PROT MET 6 CG ) 0.0000 ( PROT MET 6 SD ) 0.0000 ( PROT MET 6 CE ) 0.0000 ( PROT MET 6 C ) 0.0000 ( PROT MET 6 O ) 0.0000 ( PROT ILE 7 N ) 0.0000 ( PROT ILE 7 H ) 0.0000 ( PROT ILE 7 CA ) 0.0000 ( PROT ILE 7 CB ) 0.0000 ( PROT ILE 7 CG2 ) 0.0000 ( PROT ILE 7 CG1 ) 0.0000 ( PROT ILE 7 CD ) 0.0000 ( PROT ILE 7 C ) 0.0000 ( PROT ILE 7 O ) 0.0000 ( PROT GLY 8 N ) 0.0000 ( PROT GLY 8 H ) 0.0000 ( PROT GLY 8 CA ) 0.0000 ( PROT GLY 8 C ) 0.0000 ( PROT GLY 8 O ) 0.0000 ( PROT ALA 9 N ) 0.0000 ( PROT ALA 9 H ) 0.0000 ( PROT ALA 9 CA ) 0.0000 ( PROT ALA 9 CB ) 0.0000 ( PROT ALA 9 C ) 0.0000 ( PROT ALA 9 O ) 0.0000 ( PROT CYS 10 N ) 0.0000 ( PROT CYS 10 H ) 0.0000 ( PROT CYS 10 CA ) 0.0000 ( PROT CYS 10 CB ) 0.0000 ( PROT CYS 10 SG ) 0.0000 ( PROT CYS 10 C ) 0.0000 ( PROT CYS 10 O ) 0.0000 ( PROT PHE 11 N ) 0.0000 ( PROT PHE 11 H ) 0.0000 ( PROT PHE 11 CA ) 0.0000 ( PROT PHE 11 CB ) 0.0000 ( PROT PHE 11 CG ) 0.0000 ( PROT PHE 11 CD1 ) 0.0000 ( PROT PHE 11 CD2 ) 0.0000 ( PROT PHE 11 CE1 ) 0.0000 ( PROT PHE 11 CE2 ) 0.0000 ( PROT PHE 11 CZ ) 0.0000 ( PROT PHE 11 C ) 0.0000 ( PROT PHE 11 O ) 0.0000 ( PROT LEU 12 N ) 0.0000 ( PROT LEU 12 H ) 0.0000 ( PROT LEU 12 CA ) 0.0000 ( PROT LEU 12 CB ) 0.0000 ( PROT LEU 12 CG ) 0.0000 ( PROT LEU 12 CD1 ) 0.0000 ( PROT LEU 12 CD2 ) 0.0000 ( PROT LEU 12 C ) 0.0000 ( PROT LEU 12 O ) 0.0000 ( PROT ILE 13 N ) 0.0000 ( PROT ILE 13 H ) 0.0000 ( PROT ILE 13 CA ) 0.0000 ( PROT ILE 13 CB ) 0.0000 ( PROT ILE 13 CG2 ) 0.0000 ( PROT ILE 13 CG1 ) 0.0000 ( PROT ILE 13 CD ) 0.0000 ( PROT ILE 13 C ) 0.0000 ( PROT ILE 13 O ) 0.0000 ( PROT ASH 14 N ) 0.0000 ( PROT ASH 14 H ) 0.0000 ( PROT ASH 14 CA ) 0.0000 ( PROT ASH 14 CB ) 0.0000 ( PROT ASH 14 CG ) 0.0000 ( PROT ASH 14 OD1 ) 0.0000 ( PROT ASH 14 OD2 ) 0.0000 ( PROT ASH 14 HD2 ) 0.0000 ( PROT ASH 14 C ) 0.0000 ( PROT ASH 14 O ) 0.0000 ( PROT PHE 15 N ) 0.0000 ( PROT PHE 15 H ) 0.0000 ( PROT PHE 15 CA ) 0.0000 ( PROT PHE 15 CB ) 0.0000 ( PROT PHE 15 CG ) 0.0000 ( PROT PHE 15 CD1 ) 0.0000 ( PROT PHE 15 CD2 ) 0.0000 ( PROT PHE 15 CE1 ) 0.0000 ( PROT PHE 15 CE2 ) 0.0000 ( PROT PHE 15 CZ ) 0.0000 ( PROT PHE 15 C ) 0.0000 ( PROT PHE 15 O ) 0.0000 ( PROT MET 16 N ) 0.0000 ( PROT MET 16 H ) 0.0000 ( PROT MET 16 CA ) 0.0000 ( PROT MET 16 CB ) 0.0000 ( PROT MET 16 CG ) 0.0000 ( PROT MET 16 SD ) 0.0000 ( PROT MET 16 CE ) 0.0000 ( PROT MET 16 C ) 0.0000 ( PROT MET 16 O ) 0.0000 ( PROT PHE 17 N ) 0.0000 ( PROT PHE 17 H ) 0.0000 ( PROT PHE 17 CA ) 0.0000 ( PROT PHE 17 CB ) 0.0000 ( PROT PHE 17 CG ) 0.0000 ( PROT PHE 17 CD1 ) 0.0000 ( PROT PHE 17 CD2 ) 0.0000 ( PROT PHE 17 CE1 ) 0.0000 ( PROT PHE 17 CE2 ) 0.0000 ( PROT PHE 17 CZ ) 0.0000 ( PROT PHE 17 C ) 0.0000 ( PROT PHE 17 O ) 0.0000 ( PROT PHE 18 N ) 0.0000 ( PROT PHE 18 H ) 0.0000 ( PROT PHE 18 CA ) 0.0000 ( PROT PHE 18 CB ) 0.0000 ( PROT PHE 18 CG ) 0.0000 ( PROT PHE 18 CD1 ) 0.0000 ( PROT PHE 18 CD2 ) 0.0000 ( PROT PHE 18 CE1 ) 0.0000 ( PROT PHE 18 CE2 ) 0.0000 ( PROT PHE 18 CZ ) 0.0000 ( PROT PHE 18 C ) 0.0000 ( PROT PHE 18 O ) 0.0000 ( PROT GLU 19 N ) 0.0000 ( PROT GLU 19 H ) 0.0000 ( PROT GLU 19 CA ) 0.0000 ( PROT GLU 19 CB ) 0.0000 ( PROT GLU 19 CG ) 0.0000 ( PROT GLU 19 CD ) 0.0000 ( PROT GLU 19 OE1 ) 0.0000 ( PROT GLU 19 OE2 ) 0.0000 ( PROT GLU 19 C ) 0.0000 ( PROT GLU 19 OT1 ) 0.0000 ( PROT GLU 19 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 10778 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10748 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 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 -60.48878 12.38705 0.07647 0.00000 MINI INTERN> 4.81494 14.53521 0.00000 10.73853 2.86474 MINI EXTERN> -110.47299 17.03079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -62.76850 2.27972 0.19100 0.04224 MINI INTERN> 5.15624 14.39463 0.00000 10.92337 2.73644 MINI EXTERN> -114.34246 18.36327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10601 ATOM PAIRS WERE FOUND FOR ATOM LIST 315 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -62.76850 2.27972 0.19100 0.00000 MINI INTERN> 5.15624 14.39463 0.00000 10.92337 2.73644 MINI EXTERN> -114.34246 18.36327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -63.35205 0.58356 0.10048 0.02894 MINI INTERN> 5.12999 14.45488 0.00000 10.66431 2.78204 MINI EXTERN> -113.89082 17.50754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10633 ATOM PAIRS WERE FOUND FOR ATOM LIST 314 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -63.35205 0.58356 0.10048 0.00000 MINI INTERN> 5.12999 14.45488 0.00000 10.66431 2.78204 MINI EXTERN> -113.89082 17.50754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -63.61043 0.25837 0.11252 0.02006 MINI INTERN> 5.25389 14.39654 0.00000 10.90486 2.78569 MINI EXTERN> -114.89996 17.94855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10585 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -63.61043 0.25837 0.11252 0.00000 MINI INTERN> 5.25389 14.39654 0.00000 10.90486 2.78569 MINI EXTERN> -114.89996 17.94855 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -63.76236 0.15193 0.08032 0.01146 MINI INTERN> 5.20744 14.41490 0.00000 10.75740 2.80778 MINI EXTERN> -114.58941 17.63953 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10607 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -63.76236 0.15193 0.08032 0.00000 MINI INTERN> 5.20744 14.41490 0.00000 10.75740 2.80778 MINI EXTERN> -114.58941 17.63953 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -63.85745 0.09509 0.06004 0.01134 MINI INTERN> 5.30120 14.38651 0.00000 10.95331 2.81029 MINI EXTERN> -115.21703 17.90828 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10585 ATOM PAIRS WERE FOUND FOR ATOM LIST 314 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -63.85745 0.09509 0.06004 0.00000 MINI INTERN> 5.30120 14.38651 0.00000 10.95331 2.81029 MINI EXTERN> -115.21703 17.90828 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -63.91934 0.06189 0.05953 0.00615 MINI INTERN> 5.26427 14.41203 0.00000 10.84787 2.82350 MINI EXTERN> -114.99518 17.72818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10602 ATOM PAIRS WERE FOUND FOR ATOM LIST 315 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -63.91934 0.06189 0.05953 0.00000 MINI INTERN> 5.26427 14.41203 0.00000 10.84787 2.82350 MINI EXTERN> -114.99518 17.72818 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -63.96053 0.04119 0.03996 0.00818 MINI INTERN> 5.32034 14.39291 0.00000 11.00004 2.82361 MINI EXTERN> -115.37534 17.87790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10590 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -63.96053 0.04119 0.03996 0.00000 MINI INTERN> 5.32034 14.39291 0.00000 11.00004 2.82361 MINI EXTERN> -115.37534 17.87790 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -63.98854 0.02801 0.03892 0.00418 MINI INTERN> 5.29773 14.41047 0.00000 10.92217 2.83315 MINI EXTERN> -115.22764 17.77560 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10600 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -63.98854 0.02801 0.03892 0.00000 MINI INTERN> 5.29773 14.41047 0.00000 10.92217 2.83315 MINI EXTERN> -115.22764 17.77560 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -64.00803 0.01950 0.02851 0.00577 MINI INTERN> 5.33339 14.39739 0.00000 11.03376 2.83225 MINI EXTERN> -115.47049 17.86567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10591 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -64.00803 0.01950 0.02851 0.00000 MINI INTERN> 5.33339 14.39739 0.00000 11.03376 2.83225 MINI EXTERN> -115.47049 17.86567 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -64.02189 0.01386 0.03133 0.00320 MINI INTERN> 5.31849 14.41027 0.00000 10.97672 2.83859 MINI EXTERN> -115.36968 17.80371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10596 ATOM PAIRS WERE FOUND FOR ATOM LIST 315 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -64.02189 0.01386 0.03133 0.00000 MINI INTERN> 5.31849 14.41027 0.00000 10.97672 2.83859 MINI EXTERN> -115.36968 17.80371 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -64.03193 0.01004 0.02104 0.00424 MINI INTERN> 5.34319 14.39945 0.00000 11.05836 2.83694 MINI EXTERN> -115.53171 17.86184 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10592 ATOM PAIRS WERE FOUND FOR ATOM LIST 315 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -64.03193 0.01004 0.02104 0.00000 MINI INTERN> 5.34319 14.39945 0.00000 11.05836 2.83694 MINI EXTERN> -115.53171 17.86184 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -64.03938 0.00744 0.02102 0.00242 MINI INTERN> 5.33198 14.41058 0.00000 11.01632 2.84062 MINI EXTERN> -115.46005 17.82116 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10595 ATOM PAIRS WERE FOUND FOR ATOM LIST 314 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -64.03938 0.00744 0.02102 0.00000 MINI INTERN> 5.33198 14.41058 0.00000 11.01632 2.84062 MINI EXTERN> -115.46005 17.82116 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -64.04506 0.00568 0.01661 0.00337 MINI INTERN> 5.34881 14.40256 0.00000 11.07665 2.83890 MINI EXTERN> -115.57328 17.86129 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10591 ATOM PAIRS WERE FOUND FOR ATOM LIST 314 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -64.04506 0.00568 0.01661 0.00000 MINI INTERN> 5.34881 14.40256 0.00000 11.07665 2.83890 MINI EXTERN> -115.57328 17.86129 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -64.04952 0.00446 0.01499 0.00198 MINI INTERN> 5.34019 14.41225 0.00000 11.04449 2.84085 MINI EXTERN> -115.51856 17.83126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10593 ATOM PAIRS WERE FOUND FOR ATOM LIST 314 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -64.04952 0.00446 0.01499 0.00000 MINI INTERN> 5.34019 14.41225 0.00000 11.04449 2.84085 MINI EXTERN> -115.51856 17.83126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -64.05311 0.00359 0.01378 0.00285 MINI INTERN> 5.35277 14.40578 0.00000 11.08975 2.83911 MINI EXTERN> -115.60211 17.86158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10591 ATOM PAIRS WERE FOUND FOR ATOM LIST 314 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -64.05311 0.00359 0.01378 0.00000 MINI INTERN> 5.35277 14.40578 0.00000 11.08975 2.83911 MINI EXTERN> -115.60211 17.86158 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -64.05603 0.00292 0.01176 0.00164 MINI INTERN> 5.34531 14.41518 0.00000 11.06380 2.84010 MINI EXTERN> -115.55855 17.83814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10595 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -64.05603 0.00292 0.01176 0.00000 MINI INTERN> 5.34531 14.41518 0.00000 11.06380 2.84010 MINI EXTERN> -115.55855 17.83814 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -64.05842 0.00238 0.01141 0.00229 MINI INTERN> 5.35532 14.40978 0.00000 11.09780 2.83842 MINI EXTERN> -115.62229 17.86256 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10592 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -64.05842 0.00238 0.01141 0.00000 MINI INTERN> 5.35532 14.40978 0.00000 11.09780 2.83842 MINI EXTERN> -115.62229 17.86256 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -64.06039 0.00197 0.00980 0.00138 MINI INTERN> 5.34929 14.41762 0.00000 11.07717 2.83895 MINI EXTERN> -115.58749 17.84406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10597 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -64.06039 0.00197 0.00980 0.00000 MINI INTERN> 5.34929 14.41762 0.00000 11.07717 2.83895 MINI EXTERN> -115.58749 17.84406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -64.06203 0.00165 0.00979 0.00192 MINI INTERN> 5.35719 14.41312 0.00000 11.10350 2.83741 MINI EXTERN> -115.63746 17.86421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10595 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -64.06203 0.00165 0.00979 0.00000 MINI INTERN> 5.35719 14.41312 0.00000 11.10350 2.83741 MINI EXTERN> -115.63746 17.86421 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -64.06344 0.00141 0.01458 0.00124 MINI INTERN> 5.35249 14.41941 0.00000 11.08695 2.83789 MINI EXTERN> -115.60941 17.84922 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 -64.06344 0.00141 0.01458 0.02000 CONJ INTERN> 5.35249 14.41941 0.00000 11.08695 2.83789 CONJ EXTERN> -115.60941 17.84922 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 10595 atom pairs and 768 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10597 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 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 -64.06344 0.00141 0.01458 0.00000 MINI INTERN> 5.35249 14.41941 0.00000 11.08695 2.83789 MINI EXTERN> -115.60941 17.84922 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -64.06464 0.00120 0.00740 0.00162 MINI INTERN> 5.35877 14.41610 0.00000 11.10782 2.83604 MINI EXTERN> -115.64872 17.86535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10595 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -64.06464 0.00120 0.00740 0.00000 MINI INTERN> 5.35877 14.41610 0.00000 11.10782 2.83604 MINI EXTERN> -115.64872 17.86535 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -64.06566 0.00102 0.00920 0.00099 MINI INTERN> 5.35399 14.42224 0.00000 11.09420 2.83641 MINI EXTERN> -115.62534 17.85284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10597 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -64.06566 0.00102 0.00920 0.00000 MINI INTERN> 5.35399 14.42224 0.00000 11.09420 2.83641 MINI EXTERN> -115.62534 17.85284 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -64.06653 0.00087 0.00632 0.00145 MINI INTERN> 5.35963 14.41904 0.00000 11.11092 2.83479 MINI EXTERN> -115.65720 17.86629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10596 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -64.06653 0.00087 0.00632 0.00000 MINI INTERN> 5.35963 14.41904 0.00000 11.11092 2.83479 MINI EXTERN> -115.65720 17.86629 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -64.06728 0.00075 0.00766 0.00088 MINI INTERN> 5.35560 14.42434 0.00000 11.09985 2.83503 MINI EXTERN> -115.63747 17.85537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10597 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -64.06728 0.00075 0.00766 0.00000 MINI INTERN> 5.35560 14.42434 0.00000 11.09985 2.83503 MINI EXTERN> -115.63747 17.85537 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -64.06794 0.00065 0.00536 0.00125 MINI INTERN> 5.36027 14.42177 0.00000 11.11330 2.83356 MINI EXTERN> -115.66366 17.86682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10596 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -64.06794 0.00065 0.00536 0.00000 MINI INTERN> 5.36027 14.42177 0.00000 11.11330 2.83356 MINI EXTERN> -115.66366 17.86682 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -64.06849 0.00056 0.00555 0.00072 MINI INTERN> 5.35698 14.42635 0.00000 11.10418 2.83372 MINI EXTERN> -115.64729 17.85755 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10595 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -64.06849 0.00056 0.00555 0.00000 MINI INTERN> 5.35698 14.42635 0.00000 11.10418 2.83372 MINI EXTERN> -115.64729 17.85755 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -64.06897 0.00047 0.00461 0.00105 MINI INTERN> 5.36080 14.42417 0.00000 11.11485 2.83248 MINI EXTERN> -115.66880 17.86754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10597 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -64.06897 0.00047 0.00461 0.00000 MINI INTERN> 5.36080 14.42417 0.00000 11.11485 2.83248 MINI EXTERN> -115.66880 17.86754 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -64.06937 0.00040 0.00462 0.00061 MINI INTERN> 5.35804 14.42811 0.00000 11.10746 2.83261 MINI EXTERN> -115.65516 17.85957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10597 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -64.06937 0.00040 0.00462 0.00000 MINI INTERN> 5.35804 14.42811 0.00000 11.10746 2.83261 MINI EXTERN> -115.65516 17.85957 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -64.06971 0.00035 0.00395 0.00090 MINI INTERN> 5.36128 14.42618 0.00000 11.11593 2.83155 MINI EXTERN> -115.67292 17.86826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10598 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -64.06971 0.00035 0.00395 0.00000 MINI INTERN> 5.36128 14.42618 0.00000 11.11593 2.83155 MINI EXTERN> -115.67292 17.86826 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -64.07001 0.00030 0.00535 0.00057 MINI INTERN> 5.35883 14.42954 0.00000 11.11021 2.83164 MINI EXTERN> -115.66154 17.86131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10598 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -64.07001 0.00030 0.00535 0.00000 MINI INTERN> 5.35883 14.42954 0.00000 11.11021 2.83164 MINI EXTERN> -115.66154 17.86131 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -64.07027 0.00026 0.00335 0.00080 MINI INTERN> 5.36166 14.42769 0.00000 11.11695 2.83071 MINI EXTERN> -115.67624 17.86896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 312 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -64.07027 0.00026 0.00335 0.00000 MINI INTERN> 5.36166 14.42769 0.00000 11.11695 2.83071 MINI EXTERN> -115.67624 17.86896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -64.07052 0.00025 0.01379 0.00055 MINI INTERN> 5.35995 14.42926 0.00000 11.11363 2.83088 MINI EXTERN> -115.66720 17.86297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -64.07052 0.00025 0.01379 0.00000 MINI INTERN> 5.35995 14.42926 0.00000 11.11363 2.83088 MINI EXTERN> -115.66720 17.86297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -64.07072 0.00021 0.00253 0.00053 MINI INTERN> 5.36221 14.42874 0.00000 11.11887 2.83002 MINI EXTERN> -115.67924 17.86867 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 312 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -64.07072 0.00021 0.00253 0.00000 MINI INTERN> 5.36221 14.42874 0.00000 11.11887 2.83002 MINI EXTERN> -115.67924 17.86867 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -64.07089 0.00017 0.00837 0.00068 MINI INTERN> 5.36044 14.43008 0.00000 11.11633 2.83014 MINI EXTERN> -115.67180 17.86392 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -64.07089 0.00017 0.00837 0.00000 MINI INTERN> 5.36044 14.43008 0.00000 11.11633 2.83014 MINI EXTERN> -115.67180 17.86392 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -64.07104 0.00014 0.00203 0.00044 MINI INTERN> 5.36235 14.42958 0.00000 11.12065 2.82930 MINI EXTERN> -115.68231 17.86940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 312 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -64.07104 0.00014 0.00203 0.00000 MINI INTERN> 5.36235 14.42958 0.00000 11.12065 2.82930 MINI EXTERN> -115.68231 17.86940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -64.07115 0.00011 0.00376 0.00047 MINI INTERN> 5.36128 14.43015 0.00000 11.11859 2.82941 MINI EXTERN> -115.67634 17.86576 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 313 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -64.07115 0.00011 0.00376 0.00000 MINI INTERN> 5.36128 14.43015 0.00000 11.11859 2.82941 MINI EXTERN> -115.67634 17.86576 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -64.07125 0.00010 0.00169 0.00040 MINI INTERN> 5.36252 14.43002 0.00000 11.12227 2.82873 MINI EXTERN> -115.68495 17.87016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 312 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -64.07125 0.00010 0.00169 0.00000 MINI INTERN> 5.36252 14.43002 0.00000 11.12227 2.82873 MINI EXTERN> -115.68495 17.87016 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -64.07134 0.00009 0.00395 0.00047 MINI INTERN> 5.36153 14.43054 0.00000 11.12081 2.82894 MINI EXTERN> -115.67961 17.86646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 312 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -64.07134 0.00009 0.00395 0.00000 MINI INTERN> 5.36153 14.43054 0.00000 11.12081 2.82894 MINI EXTERN> -115.67961 17.86646 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -64.07142 0.00008 0.00180 0.00042 MINI INTERN> 5.36265 14.43050 0.00000 11.12388 2.82821 MINI EXTERN> -115.68710 17.87043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16654 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10599 ATOM PAIRS WERE FOUND FOR ATOM LIST 312 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -64.07142 0.00008 0.00180 0.00000 MINI INTERN> 5.36265 14.43050 0.00000 11.12388 2.82821 MINI EXTERN> -115.68710 17.87043 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -64.07150 0.00008 0.00305 0.00040 MINI INTERN> 5.36149 14.43122 0.00000 11.12252 2.82830 MINI EXTERN> -115.68220 17.86717 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 -64.07150 0.00008 0.00305 0.02000 CONJ INTERN> 5.36149 14.43122 0.00000 11.12252 2.82830 CONJ EXTERN> -115.68220 17.86717 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> 183 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.37442 5.25655 -8.67290 CENTER OF REFERENCE COORDINATE SET 9.40455 5.29242 -8.69322 NET TRANSLATION OF ROTATED ATOMS 0.03013 0.03586 -0.02032 ROTATION MATRIX 0.999951 -0.000904 0.009893 0.000860 0.999990 0.004480 -0.009897 -0.004471 0.999941 AXIS OF ROTATION IS 0.410779 -0.908132 -0.080974 ANGLE IS 0.62 TOTAL SQUARE DIFF IS 433.8866 DENOMINATOR IS 183.0000 THUS RMS DIFF IS 1.539794 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.5398" Parameter: A <- "1.5398" CHARMM> set a @a ?RMS Parameter: A -> "1.5398" RDCMND substituted energy or value "?RMS" to " 1.5398" Parameter: A <- "1.5398 1.5398" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 183 CENTER OF ATOMS BEFORE TRANSLATION 9.74862 5.32315 -8.84249 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.03377 -0.05873 0.04812 ROTATION MATRIX 0.999930 0.005413 -0.010546 -0.005480 0.999965 -0.006310 0.010512 0.006368 0.999924 AXIS OF ROTATION IS -0.471549 0.783244 0.405180 ANGLE IS 0.77 TOTAL SQUARE DIFF IS 21.0210 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 1.051840 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.5398 1.5398" RDCMND substituted energy or value "?RMS" to " 1.0518" Parameter: A <- "1.5398 1.5398 1.0518" 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 1.5398 1.5398 1.0518 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" $$$$$$ New timer profile $$$$$ List time 0.00 Other: 0.00 Electrostatic & VDW 13.57 Other: 0.00 Nonbond force 13.61 Other: 0.04 Bond energy 0.13 Other: 0.00 Angle energy 0.94 Other: 0.00 Dihedral energy 0.56 Other: 0.00 Restraints energy 0.01 Other: 0.00 INTRNL energy 1.71 Other: 0.06 Energy time 15.43 Other: 0.11 Total time 16.78 Other: 1.35 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47522 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL 2 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 28758 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 16.78 SECONDS CPU TIME: 0.00 SECONDS