1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 33b1 August 15, 2006 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.6.32-573.7.1.el6.x86_64(x86_64)@kont Created on 2/15/16 at 20:37: 3 by user: annesc Maximum number of ATOMS: 360720, and RESidues: 120240 Current HEAP size: 10240000, and STACK size: 10000000 RDTITL> * GENERATE PSF AND CHARMM COORDINATE SET FOR RDTITL> * HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * CHARMM> CHARMM> set name "helix_allh" Parameter: NAME <- ""helix_allh"" CHARMM> set output mini_@name ! this is the output : replace by any other complexe name ! Parameter: NAME -> ""helix_allh"" Parameter: OUTPUT <- "MINI_"helix_allh"" CHARMM> CHARMM> CHARMM> ! Read in Topology and Parameter files CHARMM> !_____________________________________ CHARMM> CHARMM> open unit 1 card read name "../lib/toph19_eef1.1.inp" VOPEN> Attempting to open::../lib/toph19_eef1.1.inp:: OPNLGU> Unit 1 opened for READONLY access to ../lib/toph19_eef1.1.inp CHARMM> read RTF card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 TITLE> * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL TITLE> * THIS DIFFERS FROM TOPH19_EEF1.INP IN: TITLE> * SCALED DOWN PARTIAL CHARGE DISTRIBUTIONS OF PSEUDO-IONIC AND TITLE> * POLAR SIDECHAINS, CTER, NTER TITLE> * INCLUDES (DE-)PROTONATED IONIC SIDECHAINS, PSEUDO-IONIC HIS AND AIB TITLE> * IN TYR CZ IS NOW TYPE CR TITLE> * THIS IS WORK IN PROGRESS. NO EXTENSIVE TESTS HAVE BEEN MADE. TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 card read name "../lib/param19_eef1.1.inp" VOPEN> Attempting to open::../lib/param19_eef1.1.inp:: OPNLGU> Unit 1 opened for READONLY access to ../lib/param19_eef1.1.inp CHARMM> read PARA card unit 1 PARAMETER FILE BEING READ FROM UNIT 1 TITLE> * - PARAMETER FILE PARAM19 * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 TITLE> * PARRDR> NOTE: atom type "CR " is removed from previous group PARRDR> NOTE: atom type "OC " is removed from previous group PARRDR> NOTE: atom type "OT " is removed from previous group PARRDR> NOTE: atom type "OH2 " is removed from previous group PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> CHARMM> CHARMM> ! Read in structure and psf file of the Bovine alpha lactalbumine 1f6r CHARMM> !_____________________________________________________________________ CHARMM> CHARMM> open read unit 9 card name ../lib/@name.psf Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../lib/helix_allh.psf:: OPNLGU> Unit 9 opened for READONLY access to ../lib/helix_allh.psf CHARMM> read psf card unit 9 MAINIO> Protein structure file being read from unit 9. TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 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 = 17 Number of atoms = 164 Number of groups = 62 Number of bonds = 165 Number of angles = 238 Number of dihedrals = 88 Number of impropers = 79 Number of cross-terms = 0 Number of HB acceptors = 27 Number of HB donors = 28 Number of NB exclusions = 6 Total charge = 0.00000 CHARMM> close unit 9 VCLOSE: Closing unit 9 with status "KEEP" CHARMM> CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 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 409 exclusions and 291 interactions(1-4) found 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9408 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 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 9408 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9408 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 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 3486.26699 0.00000 494.43868 ENER INTERN> 165.46712 98.15010 0.00000 1.53675 4.10922 ENER EXTERN> 3283.76459 -66.76079 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> 164 atoms have been selected out of 164 CHARMM> define water sele ( segid solv) end SELRPN> 0 atoms have been selected out of 164 CHARMM> define nonh sele ( .not. hydrogen ) end SELRPN> 136 atoms have been selected out of 164 CHARMM> define trace sele ( type ca ) end SELRPN> 17 atoms have been selected out of 164 CHARMM> define back sele ( type n .or. type ca .or. type c ) end SELRPN> 51 atoms have been selected out of 164 CHARMM> define main sele ( type n .or. type ca .or. type c .or. type o) end SELRPN> 67 atoms have been selected out of 164 CHARMM> define side sele ( (.not. main) ) end SELRPN> 97 atoms have been selected out of 164 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: 164 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 164 atoms are restrained. CHARMM> CHARMM> ! { very tight on backbone of pcna } CHARMM> SCALar CONSTraint SET 250. SELEct ( prot .AND. main ) END SELRPN> 67 atoms have been selected out of 164 CHARMM> CHARMM> ! { quite tight on sidechains of pcna } CHARMM> SCALar CONSTraint SET 200. SELEct ( prot .AND. side ) END SELRPN> 97 atoms have been selected out of 164 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 ASP 1 HT1 ) 200.00 ( PROT ASP 1 HT2 ) 200.00 ( PROT ASP 1 N ) 250.00 ( PROT ASP 1 HT3 ) 200.00 ( PROT ASP 1 CA ) 250.00 ( PROT ASP 1 CB ) 200.00 ( PROT ASP 1 CG ) 200.00 ( PROT ASP 1 OD1 ) 200.00 ( PROT ASP 1 OD2 ) 200.00 ( PROT ASP 1 C ) 250.00 ( PROT ASP 1 O ) 250.00 ( PROT TYR 2 N ) 250.00 ( PROT TYR 2 H ) 200.00 ( PROT TYR 2 CA ) 250.00 ( PROT TYR 2 CB ) 200.00 ( PROT TYR 2 CG ) 200.00 ( PROT TYR 2 CD1 ) 200.00 ( PROT TYR 2 CE1 ) 200.00 ( PROT TYR 2 CD2 ) 200.00 ( PROT TYR 2 CE2 ) 200.00 ( PROT TYR 2 CZ ) 200.00 ( PROT TYR 2 OH ) 200.00 ( PROT TYR 2 HH ) 200.00 ( PROT TYR 2 C ) 250.00 ( PROT TYR 2 O ) 250.00 ( PROT ALA 3 N ) 250.00 ( PROT ALA 3 H ) 200.00 ( PROT ALA 3 CA ) 250.00 ( PROT ALA 3 CB ) 200.00 ( PROT ALA 3 C ) 250.00 ( PROT ALA 3 O ) 250.00 ( PROT PHE 4 N ) 250.00 ( PROT PHE 4 H ) 200.00 ( PROT PHE 4 CA ) 250.00 ( PROT PHE 4 CB ) 200.00 ( PROT PHE 4 CG ) 200.00 ( PROT PHE 4 CD1 ) 200.00 ( PROT PHE 4 CD2 ) 200.00 ( PROT PHE 4 CE1 ) 200.00 ( PROT PHE 4 CE2 ) 200.00 ( PROT PHE 4 CZ ) 200.00 ( PROT PHE 4 C ) 250.00 ( PROT PHE 4 O ) 250.00 ( PROT ILE 5 N ) 250.00 ( PROT ILE 5 H ) 200.00 ( PROT ILE 5 CA ) 250.00 ( PROT ILE 5 CB ) 200.00 ( PROT ILE 5 CG2 ) 200.00 ( PROT ILE 5 CG1 ) 200.00 ( PROT ILE 5 CD ) 200.00 ( PROT ILE 5 C ) 250.00 ( PROT ILE 5 O ) 250.00 ( PROT ALA 6 N ) 250.00 ( PROT ALA 6 H ) 200.00 ( PROT ALA 6 CA ) 250.00 ( PROT ALA 6 CB ) 200.00 ( PROT ALA 6 C ) 250.00 ( PROT ALA 6 O ) 250.00 ( PROT SER 7 N ) 250.00 ( PROT SER 7 H ) 200.00 ( PROT SER 7 CA ) 250.00 ( PROT SER 7 CB ) 200.00 ( PROT SER 7 OG ) 200.00 ( PROT SER 7 HG ) 200.00 ( PROT SER 7 C ) 250.00 ( PROT SER 7 O ) 250.00 ( PROT LEU 8 N ) 250.00 ( PROT LEU 8 H ) 200.00 ( PROT LEU 8 CA ) 250.00 ( PROT LEU 8 CB ) 200.00 ( PROT LEU 8 CG ) 200.00 ( PROT LEU 8 CD1 ) 200.00 ( PROT LEU 8 CD2 ) 200.00 ( PROT LEU 8 C ) 250.00 ( PROT LEU 8 O ) 250.00 ( PROT VAL 9 N ) 250.00 ( PROT VAL 9 H ) 200.00 ( PROT VAL 9 CA ) 250.00 ( PROT VAL 9 CB ) 200.00 ( PROT VAL 9 CG1 ) 200.00 ( PROT VAL 9 CG2 ) 200.00 ( PROT VAL 9 C ) 250.00 ( PROT VAL 9 O ) 250.00 ( PROT VAL 10 N ) 250.00 ( PROT VAL 10 H ) 200.00 ( PROT VAL 10 CA ) 250.00 ( PROT VAL 10 CB ) 200.00 ( PROT VAL 10 CG1 ) 200.00 ( PROT VAL 10 CG2 ) 200.00 ( PROT VAL 10 C ) 250.00 ( PROT VAL 10 O ) 250.00 ( PROT ILE 11 N ) 250.00 ( PROT ILE 11 H ) 200.00 ( PROT ILE 11 CA ) 250.00 ( PROT ILE 11 CB ) 200.00 ( PROT ILE 11 CG2 ) 200.00 ( PROT ILE 11 CG1 ) 200.00 ( PROT ILE 11 CD ) 200.00 ( PROT ILE 11 C ) 250.00 ( PROT ILE 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 ASP 13 N ) 250.00 ( PROT ASP 13 H ) 200.00 ( PROT ASP 13 CA ) 250.00 ( PROT ASP 13 CB ) 200.00 ( PROT ASP 13 CG ) 200.00 ( PROT ASP 13 OD1 ) 200.00 ( PROT ASP 13 OD2 ) 200.00 ( PROT ASP 13 C ) 250.00 ( PROT ASP 13 O ) 250.00 ( PROT ASP 14 N ) 250.00 ( PROT ASP 14 H ) 200.00 ( PROT ASP 14 CA ) 250.00 ( PROT ASP 14 CB ) 200.00 ( PROT ASP 14 CG ) 200.00 ( PROT ASP 14 OD1 ) 200.00 ( PROT ASP 14 OD2 ) 200.00 ( PROT ASP 14 C ) 250.00 ( PROT ASP 14 O ) 250.00 ( PROT VAL 15 N ) 250.00 ( PROT VAL 15 H ) 200.00 ( PROT VAL 15 CA ) 250.00 ( PROT VAL 15 CB ) 200.00 ( PROT VAL 15 CG1 ) 200.00 ( PROT VAL 15 CG2 ) 200.00 ( PROT VAL 15 C ) 250.00 ( PROT VAL 15 O ) 250.00 ( PROT ASN 16 N ) 250.00 ( PROT ASN 16 H ) 200.00 ( PROT ASN 16 CA ) 250.00 ( PROT ASN 16 CB ) 200.00 ( PROT ASN 16 CG ) 200.00 ( PROT ASN 16 OD1 ) 200.00 ( PROT ASN 16 ND2 ) 200.00 ( PROT ASN 16 HD21 ) 200.00 ( PROT ASN 16 HD22 ) 200.00 ( PROT ASN 16 C ) 250.00 ( PROT ASN 16 O ) 250.00 ( PROT ARG 17 N ) 250.00 ( PROT ARG 17 H ) 200.00 ( PROT ARG 17 CA ) 250.00 ( PROT ARG 17 CB ) 200.00 ( PROT ARG 17 CG ) 200.00 ( PROT ARG 17 CD ) 200.00 ( PROT ARG 17 NE ) 200.00 ( PROT ARG 17 HE ) 200.00 ( PROT ARG 17 CZ ) 200.00 ( PROT ARG 17 NH1 ) 200.00 ( PROT ARG 17 HH11 ) 200.00 ( PROT ARG 17 HH12 ) 200.00 ( PROT ARG 17 NH2 ) 200.00 ( PROT ARG 17 HH21 ) 200.00 ( PROT ARG 17 HH22 ) 200.00 ( PROT ARG 17 C ) 250.00 ( PROT ARG 17 OT1 ) 200.00 ( PROT ARG 17 OT2 ) 200.00 CHARMM> CHARMM> !stop ! OK CHARMM> CHARMM> !do @2 steps of steepest descent with constraints CHARMM> label mini CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 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 9408 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9408 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 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 3486.26699 0.00000 494.43868 0.02000 MINI INTERN> 165.46712 98.15010 0.00000 1.53675 4.10922 MINI EXTERN> 3283.76459 -66.76079 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 863.97855 2622.28844 54.30933 0.02074 MINI INTERN> 271.84479 42.85817 0.00000 2.70965 8.23898 MINI EXTERN> 233.79861 -6.10292 0.00000 0.00000 0.00000 MINI CONSTR> 310.63127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9384 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 672.23290 191.74565 4.92082 0.00373 MINI INTERN> 47.09568 46.97507 0.00000 2.60763 8.26962 MINI EXTERN> 304.84517 -16.96701 0.00000 0.00000 0.00000 MINI CONSTR> 279.40673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 671.92252 0.31038 4.53326 0.00161 MINI INTERN> 30.57517 50.40563 0.00000 2.53583 8.52445 MINI EXTERN> 314.04647 -18.78833 0.00000 0.00000 0.00000 MINI CONSTR> 284.62330 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9386 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 670.60437 1.31815 0.65400 0.00029 MINI INTERN> 37.00242 48.44281 0.00000 2.57576 8.35738 MINI EXTERN> 308.55232 -18.19752 0.00000 0.00000 0.00000 MINI CONSTR> 283.87119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 670.57607 0.02830 0.21875 0.00013 MINI INTERN> 37.30663 48.10573 0.00000 2.59051 8.31666 MINI EXTERN> 309.82492 -18.23283 0.00000 0.00000 0.00000 MINI CONSTR> 282.66445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9386 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 670.57281 0.00326 0.06256 0.00005 MINI INTERN> 37.16636 48.20881 0.00000 2.58533 8.32883 MINI EXTERN> 309.49982 -18.23433 0.00000 0.00000 0.00000 MINI CONSTR> 283.01798 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 670.57277 0.00004 0.05774 0.00002 MINI INTERN> 37.22647 48.16353 0.00000 2.58757 8.32331 MINI EXTERN> 309.62757 -18.23290 0.00000 0.00000 0.00000 MINI CONSTR> 282.87722 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> 38 670.57252 0.00025 0.00403 0.00001 STPD INTERN> 37.19703 48.18622 0.00000 2.58644 8.32623 STPD EXTERN> 309.56045 -18.23355 0.00000 0.00000 0.00000 STPD CONSTR> 282.94970 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 9386 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9386 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 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> 0 670.57252 0.00025 0.00403 0.00000 MINI INTERN> 37.19703 48.18622 0.00000 2.58644 8.32623 MINI EXTERN> 309.56045 -18.23355 0.00000 0.00000 0.00000 MINI CONSTR> 282.94970 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> 1 670.57252 0.00000 0.00017 0.02000 CONJ INTERN> 37.19888 48.18487 0.00000 2.58650 8.32601 CONJ EXTERN> 309.56472 -18.23346 0.00000 0.00000 0.00000 CONJ CONSTR> 282.94499 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 ASP 1 HT1 ) 130.00 ( PROT ASP 1 HT2 ) 130.00 ( PROT ASP 1 N ) 162.50 ( PROT ASP 1 HT3 ) 130.00 ( PROT ASP 1 CA ) 162.50 ( PROT ASP 1 CB ) 130.00 ( PROT ASP 1 CG ) 130.00 ( PROT ASP 1 OD1 ) 130.00 ( PROT ASP 1 OD2 ) 130.00 ( PROT ASP 1 C ) 162.50 ( PROT ASP 1 O ) 162.50 ( PROT TYR 2 N ) 162.50 ( PROT TYR 2 H ) 130.00 ( PROT TYR 2 CA ) 162.50 ( PROT TYR 2 CB ) 130.00 ( PROT TYR 2 CG ) 130.00 ( PROT TYR 2 CD1 ) 130.00 ( PROT TYR 2 CE1 ) 130.00 ( PROT TYR 2 CD2 ) 130.00 ( PROT TYR 2 CE2 ) 130.00 ( PROT TYR 2 CZ ) 130.00 ( PROT TYR 2 OH ) 130.00 ( PROT TYR 2 HH ) 130.00 ( PROT TYR 2 C ) 162.50 ( PROT TYR 2 O ) 162.50 ( PROT ALA 3 N ) 162.50 ( PROT ALA 3 H ) 130.00 ( PROT ALA 3 CA ) 162.50 ( PROT ALA 3 CB ) 130.00 ( PROT ALA 3 C ) 162.50 ( PROT ALA 3 O ) 162.50 ( PROT PHE 4 N ) 162.50 ( PROT PHE 4 H ) 130.00 ( PROT PHE 4 CA ) 162.50 ( PROT PHE 4 CB ) 130.00 ( PROT PHE 4 CG ) 130.00 ( PROT PHE 4 CD1 ) 130.00 ( PROT PHE 4 CD2 ) 130.00 ( PROT PHE 4 CE1 ) 130.00 ( PROT PHE 4 CE2 ) 130.00 ( PROT PHE 4 CZ ) 130.00 ( PROT PHE 4 C ) 162.50 ( PROT PHE 4 O ) 162.50 ( PROT ILE 5 N ) 162.50 ( PROT ILE 5 H ) 130.00 ( PROT ILE 5 CA ) 162.50 ( PROT ILE 5 CB ) 130.00 ( PROT ILE 5 CG2 ) 130.00 ( PROT ILE 5 CG1 ) 130.00 ( PROT ILE 5 CD ) 130.00 ( PROT ILE 5 C ) 162.50 ( PROT ILE 5 O ) 162.50 ( PROT ALA 6 N ) 162.50 ( PROT ALA 6 H ) 130.00 ( PROT ALA 6 CA ) 162.50 ( PROT ALA 6 CB ) 130.00 ( PROT ALA 6 C ) 162.50 ( PROT ALA 6 O ) 162.50 ( PROT SER 7 N ) 162.50 ( PROT SER 7 H ) 130.00 ( PROT SER 7 CA ) 162.50 ( PROT SER 7 CB ) 130.00 ( PROT SER 7 OG ) 130.00 ( PROT SER 7 HG ) 130.00 ( PROT SER 7 C ) 162.50 ( PROT SER 7 O ) 162.50 ( PROT LEU 8 N ) 162.50 ( PROT LEU 8 H ) 130.00 ( PROT LEU 8 CA ) 162.50 ( PROT LEU 8 CB ) 130.00 ( PROT LEU 8 CG ) 130.00 ( PROT LEU 8 CD1 ) 130.00 ( PROT LEU 8 CD2 ) 130.00 ( PROT LEU 8 C ) 162.50 ( PROT LEU 8 O ) 162.50 ( PROT VAL 9 N ) 162.50 ( PROT VAL 9 H ) 130.00 ( PROT VAL 9 CA ) 162.50 ( PROT VAL 9 CB ) 130.00 ( PROT VAL 9 CG1 ) 130.00 ( PROT VAL 9 CG2 ) 130.00 ( PROT VAL 9 C ) 162.50 ( PROT VAL 9 O ) 162.50 ( PROT VAL 10 N ) 162.50 ( PROT VAL 10 H ) 130.00 ( PROT VAL 10 CA ) 162.50 ( PROT VAL 10 CB ) 130.00 ( PROT VAL 10 CG1 ) 130.00 ( PROT VAL 10 CG2 ) 130.00 ( PROT VAL 10 C ) 162.50 ( PROT VAL 10 O ) 162.50 ( PROT ILE 11 N ) 162.50 ( PROT ILE 11 H ) 130.00 ( PROT ILE 11 CA ) 162.50 ( PROT ILE 11 CB ) 130.00 ( PROT ILE 11 CG2 ) 130.00 ( PROT ILE 11 CG1 ) 130.00 ( PROT ILE 11 CD ) 130.00 ( PROT ILE 11 C ) 162.50 ( PROT ILE 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 ASP 13 N ) 162.50 ( PROT ASP 13 H ) 130.00 ( PROT ASP 13 CA ) 162.50 ( PROT ASP 13 CB ) 130.00 ( PROT ASP 13 CG ) 130.00 ( PROT ASP 13 OD1 ) 130.00 ( PROT ASP 13 OD2 ) 130.00 ( PROT ASP 13 C ) 162.50 ( PROT ASP 13 O ) 162.50 ( PROT ASP 14 N ) 162.50 ( PROT ASP 14 H ) 130.00 ( PROT ASP 14 CA ) 162.50 ( PROT ASP 14 CB ) 130.00 ( PROT ASP 14 CG ) 130.00 ( PROT ASP 14 OD1 ) 130.00 ( PROT ASP 14 OD2 ) 130.00 ( PROT ASP 14 C ) 162.50 ( PROT ASP 14 O ) 162.50 ( PROT VAL 15 N ) 162.50 ( PROT VAL 15 H ) 130.00 ( PROT VAL 15 CA ) 162.50 ( PROT VAL 15 CB ) 130.00 ( PROT VAL 15 CG1 ) 130.00 ( PROT VAL 15 CG2 ) 130.00 ( PROT VAL 15 C ) 162.50 ( PROT VAL 15 O ) 162.50 ( PROT ASN 16 N ) 162.50 ( PROT ASN 16 H ) 130.00 ( PROT ASN 16 CA ) 162.50 ( PROT ASN 16 CB ) 130.00 ( PROT ASN 16 CG ) 130.00 ( PROT ASN 16 OD1 ) 130.00 ( PROT ASN 16 ND2 ) 130.00 ( PROT ASN 16 HD21 ) 130.00 ( PROT ASN 16 HD22 ) 130.00 ( PROT ASN 16 C ) 162.50 ( PROT ASN 16 O ) 162.50 ( PROT ARG 17 N ) 162.50 ( PROT ARG 17 H ) 130.00 ( PROT ARG 17 CA ) 162.50 ( PROT ARG 17 CB ) 130.00 ( PROT ARG 17 CG ) 130.00 ( PROT ARG 17 CD ) 130.00 ( PROT ARG 17 NE ) 130.00 ( PROT ARG 17 HE ) 130.00 ( PROT ARG 17 CZ ) 130.00 ( PROT ARG 17 NH1 ) 130.00 ( PROT ARG 17 HH11 ) 130.00 ( PROT ARG 17 HH12 ) 130.00 ( PROT ARG 17 NH2 ) 130.00 ( PROT ARG 17 HH21 ) 130.00 ( PROT ARG 17 HH22 ) 130.00 ( PROT ARG 17 C ) 162.50 ( PROT ARG 17 OT1 ) 130.00 ( PROT ARG 17 OT2 ) 130.00 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96519 3.71262 -6.80350 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS -0.00137 -0.00129 0.00150 ROTATION MATRIX 1.000000 -0.000022 -0.000054 0.000022 1.000000 0.000083 0.000054 -0.000083 1.000000 AXIS OF ROTATION IS 0.819755 0.531658 -0.212937 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 1.2235 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.086373 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.0864" Parameter: A <- "0.0864" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.76534 3.78285 -6.96679 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS 0.00684 0.00886 -0.01045 ROTATION MATRIX 0.999948 0.007233 0.007249 -0.007175 0.999942 -0.008081 -0.007307 0.008028 0.999941 AXIS OF ROTATION IS -0.618227 -0.558604 0.552953 ANGLE IS 0.75 TOTAL SQUARE DIFF IS 0.0260 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.039134 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.0864" RDCMND substituted energy or value "?RMS" to " 0.0391" Parameter: A <- "0.0864 0.0391" 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 0.0864 0.0391 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 " 282.94" Parameter: H <- "282.94" 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> 0 387.62753 282.94499 23.18213 ENER INTERN> 37.19888 48.18487 0.00000 2.58650 8.32601 ENER EXTERN> 309.56472 -18.23346 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 " 387.63" Parameter: B <- "387.63" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -18.23" Parameter: C <- "-18.23" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 309.56" Parameter: C <- " 291.33" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 291.33" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 37.20" Parameter: D <- "37.20" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 48.18" Parameter: D <- " 85.38" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 2.59" Parameter: D <- " 87.97" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.33" Parameter: D <- " 96.30" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 96.30" 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= 387.63 GRMS= 23.18 ELEC= -18.23 VDW= 309.56 RDTITL> *EXTERNAL= 291.33 INTERNAL= 96.30 USER= 0.00 HARM= 282.94 RDTITL> *BOND= 37.20 ANGL= 48.18 DIHE= 2.59 IMPR= 8.33 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9386 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9386 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 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> 0 631.83508 -244.20755 11.52770 0.02000 MINI INTERN> 37.19888 48.18487 0.00000 2.58650 8.32601 MINI EXTERN> 309.56472 -18.23346 0.00000 0.00000 0.00000 MINI CONSTR> 244.20755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 584.54345 47.29163 18.36950 0.00864 MINI INTERN> 82.32589 42.40744 0.00000 3.33561 7.70574 MINI EXTERN> 224.14274 -14.02674 0.00000 0.00000 0.00000 MINI CONSTR> 238.65278 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9377 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 558.68666 25.85679 1.51408 0.00156 MINI INTERN> 34.67462 50.00626 0.00000 3.21112 8.27357 MINI EXTERN> 241.57318 -17.49187 0.00000 0.00000 0.00000 MINI CONSTR> 238.43977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 558.17756 0.50910 1.13507 0.00067 MINI INTERN> 33.82370 51.01152 0.00000 3.18861 8.39645 MINI EXTERN> 237.43936 -17.38776 0.00000 0.00000 0.00000 MINI CONSTR> 241.70568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9377 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 558.03864 0.13892 0.07242 0.00012 MINI INTERN> 33.90262 50.52797 0.00000 3.19704 8.30586 MINI EXTERN> 239.20523 -17.47198 0.00000 0.00000 0.00000 MINI CONSTR> 240.37190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 558.03747 0.00117 0.08309 0.00005 MINI INTERN> 33.88447 50.44386 0.00000 3.19646 8.29352 MINI EXTERN> 239.60027 -17.49579 0.00000 0.00000 0.00000 MINI CONSTR> 240.11468 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> 28 558.03676 0.00071 0.00954 0.00002 STPD INTERN> 33.87361 50.49245 0.00000 3.19726 8.29988 STPD EXTERN> 239.35479 -17.48042 0.00000 0.00000 0.00000 STPD CONSTR> 240.29918 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 9377 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9377 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 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> 0 558.03676 0.00071 0.00954 0.00000 MINI INTERN> 33.87361 50.49245 0.00000 3.19726 8.29988 MINI EXTERN> 239.35479 -17.48042 0.00000 0.00000 0.00000 MINI CONSTR> 240.29918 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> 1 558.03675 0.00001 0.00378 0.02000 CONJ INTERN> 33.87734 50.48758 0.00000 3.19685 8.29903 CONJ EXTERN> 239.37876 -17.48226 0.00000 0.00000 0.00000 CONJ CONSTR> 240.27945 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 ASP 1 HT1 ) 84.500 ( PROT ASP 1 HT2 ) 84.500 ( PROT ASP 1 N ) 105.63 ( PROT ASP 1 HT3 ) 84.500 ( PROT ASP 1 CA ) 105.63 ( PROT ASP 1 CB ) 84.500 ( PROT ASP 1 CG ) 84.500 ( PROT ASP 1 OD1 ) 84.500 ( PROT ASP 1 OD2 ) 84.500 ( PROT ASP 1 C ) 105.63 ( PROT ASP 1 O ) 105.63 ( PROT TYR 2 N ) 105.63 ( PROT TYR 2 H ) 84.500 ( PROT TYR 2 CA ) 105.63 ( PROT TYR 2 CB ) 84.500 ( PROT TYR 2 CG ) 84.500 ( PROT TYR 2 CD1 ) 84.500 ( PROT TYR 2 CE1 ) 84.500 ( PROT TYR 2 CD2 ) 84.500 ( PROT TYR 2 CE2 ) 84.500 ( PROT TYR 2 CZ ) 84.500 ( PROT TYR 2 OH ) 84.500 ( PROT TYR 2 HH ) 84.500 ( PROT TYR 2 C ) 105.63 ( PROT TYR 2 O ) 105.63 ( PROT ALA 3 N ) 105.63 ( PROT ALA 3 H ) 84.500 ( PROT ALA 3 CA ) 105.63 ( PROT ALA 3 CB ) 84.500 ( PROT ALA 3 C ) 105.63 ( PROT ALA 3 O ) 105.63 ( PROT PHE 4 N ) 105.63 ( PROT PHE 4 H ) 84.500 ( PROT PHE 4 CA ) 105.63 ( PROT PHE 4 CB ) 84.500 ( PROT PHE 4 CG ) 84.500 ( PROT PHE 4 CD1 ) 84.500 ( PROT PHE 4 CD2 ) 84.500 ( PROT PHE 4 CE1 ) 84.500 ( PROT PHE 4 CE2 ) 84.500 ( PROT PHE 4 CZ ) 84.500 ( PROT PHE 4 C ) 105.63 ( PROT PHE 4 O ) 105.63 ( PROT ILE 5 N ) 105.63 ( PROT ILE 5 H ) 84.500 ( PROT ILE 5 CA ) 105.63 ( PROT ILE 5 CB ) 84.500 ( PROT ILE 5 CG2 ) 84.500 ( PROT ILE 5 CG1 ) 84.500 ( PROT ILE 5 CD ) 84.500 ( PROT ILE 5 C ) 105.63 ( PROT ILE 5 O ) 105.63 ( PROT ALA 6 N ) 105.63 ( PROT ALA 6 H ) 84.500 ( PROT ALA 6 CA ) 105.63 ( PROT ALA 6 CB ) 84.500 ( PROT ALA 6 C ) 105.63 ( PROT ALA 6 O ) 105.63 ( PROT SER 7 N ) 105.63 ( PROT SER 7 H ) 84.500 ( PROT SER 7 CA ) 105.63 ( PROT SER 7 CB ) 84.500 ( PROT SER 7 OG ) 84.500 ( PROT SER 7 HG ) 84.500 ( PROT SER 7 C ) 105.63 ( PROT SER 7 O ) 105.63 ( PROT LEU 8 N ) 105.63 ( PROT LEU 8 H ) 84.500 ( PROT LEU 8 CA ) 105.63 ( PROT LEU 8 CB ) 84.500 ( PROT LEU 8 CG ) 84.500 ( PROT LEU 8 CD1 ) 84.500 ( PROT LEU 8 CD2 ) 84.500 ( PROT LEU 8 C ) 105.63 ( PROT LEU 8 O ) 105.63 ( PROT VAL 9 N ) 105.63 ( PROT VAL 9 H ) 84.500 ( PROT VAL 9 CA ) 105.63 ( PROT VAL 9 CB ) 84.500 ( PROT VAL 9 CG1 ) 84.500 ( PROT VAL 9 CG2 ) 84.500 ( PROT VAL 9 C ) 105.63 ( PROT VAL 9 O ) 105.63 ( PROT VAL 10 N ) 105.63 ( PROT VAL 10 H ) 84.500 ( PROT VAL 10 CA ) 105.63 ( PROT VAL 10 CB ) 84.500 ( PROT VAL 10 CG1 ) 84.500 ( PROT VAL 10 CG2 ) 84.500 ( PROT VAL 10 C ) 105.63 ( PROT VAL 10 O ) 105.63 ( PROT ILE 11 N ) 105.63 ( PROT ILE 11 H ) 84.500 ( PROT ILE 11 CA ) 105.63 ( PROT ILE 11 CB ) 84.500 ( PROT ILE 11 CG2 ) 84.500 ( PROT ILE 11 CG1 ) 84.500 ( PROT ILE 11 CD ) 84.500 ( PROT ILE 11 C ) 105.63 ( PROT ILE 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 ASP 13 N ) 105.63 ( PROT ASP 13 H ) 84.500 ( PROT ASP 13 CA ) 105.63 ( PROT ASP 13 CB ) 84.500 ( PROT ASP 13 CG ) 84.500 ( PROT ASP 13 OD1 ) 84.500 ( PROT ASP 13 OD2 ) 84.500 ( PROT ASP 13 C ) 105.63 ( PROT ASP 13 O ) 105.63 ( PROT ASP 14 N ) 105.63 ( PROT ASP 14 H ) 84.500 ( PROT ASP 14 CA ) 105.63 ( PROT ASP 14 CB ) 84.500 ( PROT ASP 14 CG ) 84.500 ( PROT ASP 14 OD1 ) 84.500 ( PROT ASP 14 OD2 ) 84.500 ( PROT ASP 14 C ) 105.63 ( PROT ASP 14 O ) 105.63 ( PROT VAL 15 N ) 105.63 ( PROT VAL 15 H ) 84.500 ( PROT VAL 15 CA ) 105.63 ( PROT VAL 15 CB ) 84.500 ( PROT VAL 15 CG1 ) 84.500 ( PROT VAL 15 CG2 ) 84.500 ( PROT VAL 15 C ) 105.63 ( PROT VAL 15 O ) 105.63 ( PROT ASN 16 N ) 105.63 ( PROT ASN 16 H ) 84.500 ( PROT ASN 16 CA ) 105.63 ( PROT ASN 16 CB ) 84.500 ( PROT ASN 16 CG ) 84.500 ( PROT ASN 16 OD1 ) 84.500 ( PROT ASN 16 ND2 ) 84.500 ( PROT ASN 16 HD21 ) 84.500 ( PROT ASN 16 HD22 ) 84.500 ( PROT ASN 16 C ) 105.63 ( PROT ASN 16 O ) 105.63 ( PROT ARG 17 N ) 105.63 ( PROT ARG 17 H ) 84.500 ( PROT ARG 17 CA ) 105.63 ( PROT ARG 17 CB ) 84.500 ( PROT ARG 17 CG ) 84.500 ( PROT ARG 17 CD ) 84.500 ( PROT ARG 17 NE ) 84.500 ( PROT ARG 17 HE ) 84.500 ( PROT ARG 17 CZ ) 84.500 ( PROT ARG 17 NH1 ) 84.500 ( PROT ARG 17 HH11 ) 84.500 ( PROT ARG 17 HH12 ) 84.500 ( PROT ARG 17 NH2 ) 84.500 ( PROT ARG 17 HH21 ) 84.500 ( PROT ARG 17 HH22 ) 84.500 ( PROT ARG 17 C ) 105.63 ( PROT ARG 17 OT1 ) 84.500 ( PROT ARG 17 OT2 ) 84.500 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96515 3.71261 -6.80352 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS -0.00133 -0.00128 0.00151 ROTATION MATRIX 1.000000 -0.000027 -0.000068 0.000027 1.000000 0.000105 0.000068 -0.000105 1.000000 AXIS OF ROTATION IS 0.818536 0.535037 -0.209127 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 1.5960 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.098649 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.0986" Parameter: A <- "0.0986" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.76541 3.78228 -6.96613 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS 0.00677 0.00942 -0.01110 ROTATION MATRIX 0.999921 0.008839 0.008976 -0.008750 0.999912 -0.009953 -0.009064 0.009873 0.999910 AXIS OF ROTATION IS -0.618388 -0.562685 0.548618 ANGLE IS 0.92 TOTAL SQUARE DIFF IS 0.0420 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.049733 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.0986" RDCMND substituted energy or value "?RMS" to " 0.0497" Parameter: A <- "0.0986 0.0497" 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 0.0986 0.0497 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 " 240.28" Parameter: H <- "240.28" 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> 0 317.75730 240.27945 17.23740 ENER INTERN> 33.87734 50.48758 0.00000 3.19685 8.29903 ENER EXTERN> 239.37876 -17.48226 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 " 317.76" Parameter: B <- "317.76" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -17.48" Parameter: C <- "-17.48" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 239.38" Parameter: C <- " 221.90" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 221.90" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 33.88" Parameter: D <- "33.88" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 50.49" Parameter: D <- " 84.37" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 3.20" Parameter: D <- " 87.57" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.30" Parameter: D <- " 95.87" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 95.87" 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= 1200 ENER= 317.76 GRMS= 17.24 ELEC= -17.48 VDW= 239.38 RDTITL> *EXTERNAL= 221.90 INTERNAL= 95.87 USER= 0.00 HARM= 240.28 RDTITL> *BOND= 33.88 ANGL= 50.49 DIHE= 3.20 IMPR= 8.30 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 -> "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= 317.76 GRMS= 17.24 ELEC= -17.48 VDW= 239.38 RDTITL> *EXTERNAL= 221.90 INTERNAL= 95.87 USER= 0.00 HARM= 240.28 RDTITL> *BOND= 33.88 ANGL= 50.49 DIHE= 3.20 IMPR= 8.30 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 -> "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= 317.76 GRMS= 17.24 ELEC= -17.48 VDW= 239.38 RDTITL> *EXTERNAL= 221.90 INTERNAL= 95.87 USER= 0.00 HARM= 240.28 RDTITL> *BOND= 33.88 ANGL= 50.49 DIHE= 3.20 IMPR= 8.30 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 1200 0.0986 0.0497 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "1200" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9377 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9377 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 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> 0 532.60040 -214.84310 8.86085 0.02000 MINI INTERN> 33.87734 50.48758 0.00000 3.19685 8.29903 MINI EXTERN> 239.37876 -17.48226 0.00000 0.00000 0.00000 MINI CONSTR> 214.84310 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 493.85980 38.74060 18.25194 0.00864 MINI INTERN> 81.15299 43.60672 0.00000 4.04669 7.41848 MINI EXTERN> 166.00024 -13.57664 0.00000 0.00000 0.00000 MINI CONSTR> 205.21132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9374 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 465.22834 28.63146 1.60642 0.00156 MINI INTERN> 32.04829 52.97599 0.00000 4.04313 7.99308 MINI EXTERN> 182.99836 -17.56289 0.00000 0.00000 0.00000 MINI CONSTR> 202.73237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 463.78279 1.44555 2.79436 0.00161 MINI INTERN> 33.76874 51.60258 0.00000 4.12137 7.80241 MINI EXTERN> 182.19348 -17.49604 0.00000 0.00000 0.00000 MINI CONSTR> 201.79025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9372 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 462.88757 0.89522 1.04745 0.00070 MINI INTERN> 30.81523 53.31397 0.00000 4.04999 8.01959 MINI EXTERN> 180.82873 -17.82326 0.00000 0.00000 0.00000 MINI CONSTR> 203.68332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 462.74762 0.13995 0.47828 0.00030 MINI INTERN> 30.95555 52.82849 0.00000 4.05739 7.88280 MINI EXTERN> 181.69691 -17.83143 0.00000 0.00000 0.00000 MINI CONSTR> 203.15792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9372 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 462.71792 0.02970 0.13934 0.00013 MINI INTERN> 30.96427 52.80749 0.00000 4.06742 7.91766 MINI EXTERN> 181.32354 -17.80797 0.00000 0.00000 0.00000 MINI CONSTR> 203.44551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 462.71546 0.00246 0.08395 0.00006 MINI INTERN> 30.84963 52.80390 0.00000 4.06546 7.90990 MINI EXTERN> 181.53831 -17.83315 0.00000 0.00000 0.00000 MINI CONSTR> 203.38141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9372 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 462.71467 0.00078 0.04766 0.00002 MINI INTERN> 30.95809 52.77133 0.00000 4.06645 7.90975 MINI EXTERN> 181.37747 -17.81170 0.00000 0.00000 0.00000 MINI CONSTR> 203.44329 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> 41 462.71451 0.00016 0.00960 0.00001 STPD INTERN> 30.88387 52.79343 0.00000 4.06648 7.91091 STPD EXTERN> 181.44864 -17.82267 0.00000 0.00000 0.00000 STPD CONSTR> 203.43385 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 9372 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9372 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 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> 0 462.71451 0.00016 0.00960 0.00000 MINI INTERN> 30.88387 52.79343 0.00000 4.06648 7.91091 MINI EXTERN> 181.44864 -17.82267 0.00000 0.00000 0.00000 MINI CONSTR> 203.43385 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> 1 462.71450 0.00001 0.00674 0.02000 CONJ INTERN> 30.86661 52.79707 0.00000 4.06647 7.91131 CONJ EXTERN> 181.46892 -17.82561 0.00000 0.00000 0.00000 CONJ CONSTR> 203.42974 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 ASP 1 HT1 ) 54.925 ( PROT ASP 1 HT2 ) 54.925 ( PROT ASP 1 N ) 68.656 ( PROT ASP 1 HT3 ) 54.925 ( PROT ASP 1 CA ) 68.656 ( PROT ASP 1 CB ) 54.925 ( PROT ASP 1 CG ) 54.925 ( PROT ASP 1 OD1 ) 54.925 ( PROT ASP 1 OD2 ) 54.925 ( PROT ASP 1 C ) 68.656 ( PROT ASP 1 O ) 68.656 ( PROT TYR 2 N ) 68.656 ( PROT TYR 2 H ) 54.925 ( PROT TYR 2 CA ) 68.656 ( PROT TYR 2 CB ) 54.925 ( PROT TYR 2 CG ) 54.925 ( PROT TYR 2 CD1 ) 54.925 ( PROT TYR 2 CE1 ) 54.925 ( PROT TYR 2 CD2 ) 54.925 ( PROT TYR 2 CE2 ) 54.925 ( PROT TYR 2 CZ ) 54.925 ( PROT TYR 2 OH ) 54.925 ( PROT TYR 2 HH ) 54.925 ( PROT TYR 2 C ) 68.656 ( PROT TYR 2 O ) 68.656 ( PROT ALA 3 N ) 68.656 ( PROT ALA 3 H ) 54.925 ( PROT ALA 3 CA ) 68.656 ( PROT ALA 3 CB ) 54.925 ( PROT ALA 3 C ) 68.656 ( PROT ALA 3 O ) 68.656 ( PROT PHE 4 N ) 68.656 ( PROT PHE 4 H ) 54.925 ( PROT PHE 4 CA ) 68.656 ( PROT PHE 4 CB ) 54.925 ( PROT PHE 4 CG ) 54.925 ( PROT PHE 4 CD1 ) 54.925 ( PROT PHE 4 CD2 ) 54.925 ( PROT PHE 4 CE1 ) 54.925 ( PROT PHE 4 CE2 ) 54.925 ( PROT PHE 4 CZ ) 54.925 ( PROT PHE 4 C ) 68.656 ( PROT PHE 4 O ) 68.656 ( PROT ILE 5 N ) 68.656 ( PROT ILE 5 H ) 54.925 ( PROT ILE 5 CA ) 68.656 ( PROT ILE 5 CB ) 54.925 ( PROT ILE 5 CG2 ) 54.925 ( PROT ILE 5 CG1 ) 54.925 ( PROT ILE 5 CD ) 54.925 ( PROT ILE 5 C ) 68.656 ( PROT ILE 5 O ) 68.656 ( PROT ALA 6 N ) 68.656 ( PROT ALA 6 H ) 54.925 ( PROT ALA 6 CA ) 68.656 ( PROT ALA 6 CB ) 54.925 ( PROT ALA 6 C ) 68.656 ( PROT ALA 6 O ) 68.656 ( PROT SER 7 N ) 68.656 ( PROT SER 7 H ) 54.925 ( PROT SER 7 CA ) 68.656 ( PROT SER 7 CB ) 54.925 ( PROT SER 7 OG ) 54.925 ( PROT SER 7 HG ) 54.925 ( PROT SER 7 C ) 68.656 ( PROT SER 7 O ) 68.656 ( PROT LEU 8 N ) 68.656 ( PROT LEU 8 H ) 54.925 ( PROT LEU 8 CA ) 68.656 ( PROT LEU 8 CB ) 54.925 ( PROT LEU 8 CG ) 54.925 ( PROT LEU 8 CD1 ) 54.925 ( PROT LEU 8 CD2 ) 54.925 ( PROT LEU 8 C ) 68.656 ( PROT LEU 8 O ) 68.656 ( PROT VAL 9 N ) 68.656 ( PROT VAL 9 H ) 54.925 ( PROT VAL 9 CA ) 68.656 ( PROT VAL 9 CB ) 54.925 ( PROT VAL 9 CG1 ) 54.925 ( PROT VAL 9 CG2 ) 54.925 ( PROT VAL 9 C ) 68.656 ( PROT VAL 9 O ) 68.656 ( PROT VAL 10 N ) 68.656 ( PROT VAL 10 H ) 54.925 ( PROT VAL 10 CA ) 68.656 ( PROT VAL 10 CB ) 54.925 ( PROT VAL 10 CG1 ) 54.925 ( PROT VAL 10 CG2 ) 54.925 ( PROT VAL 10 C ) 68.656 ( PROT VAL 10 O ) 68.656 ( PROT ILE 11 N ) 68.656 ( PROT ILE 11 H ) 54.925 ( PROT ILE 11 CA ) 68.656 ( PROT ILE 11 CB ) 54.925 ( PROT ILE 11 CG2 ) 54.925 ( PROT ILE 11 CG1 ) 54.925 ( PROT ILE 11 CD ) 54.925 ( PROT ILE 11 C ) 68.656 ( PROT ILE 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 ASP 13 N ) 68.656 ( PROT ASP 13 H ) 54.925 ( PROT ASP 13 CA ) 68.656 ( PROT ASP 13 CB ) 54.925 ( PROT ASP 13 CG ) 54.925 ( PROT ASP 13 OD1 ) 54.925 ( PROT ASP 13 OD2 ) 54.925 ( PROT ASP 13 C ) 68.656 ( PROT ASP 13 O ) 68.656 ( PROT ASP 14 N ) 68.656 ( PROT ASP 14 H ) 54.925 ( PROT ASP 14 CA ) 68.656 ( PROT ASP 14 CB ) 54.925 ( PROT ASP 14 CG ) 54.925 ( PROT ASP 14 OD1 ) 54.925 ( PROT ASP 14 OD2 ) 54.925 ( PROT ASP 14 C ) 68.656 ( PROT ASP 14 O ) 68.656 ( PROT VAL 15 N ) 68.656 ( PROT VAL 15 H ) 54.925 ( PROT VAL 15 CA ) 68.656 ( PROT VAL 15 CB ) 54.925 ( PROT VAL 15 CG1 ) 54.925 ( PROT VAL 15 CG2 ) 54.925 ( PROT VAL 15 C ) 68.656 ( PROT VAL 15 O ) 68.656 ( PROT ASN 16 N ) 68.656 ( PROT ASN 16 H ) 54.925 ( PROT ASN 16 CA ) 68.656 ( PROT ASN 16 CB ) 54.925 ( PROT ASN 16 CG ) 54.925 ( PROT ASN 16 OD1 ) 54.925 ( PROT ASN 16 ND2 ) 54.925 ( PROT ASN 16 HD21 ) 54.925 ( PROT ASN 16 HD22 ) 54.925 ( PROT ASN 16 C ) 68.656 ( PROT ASN 16 O ) 68.656 ( PROT ARG 17 N ) 68.656 ( PROT ARG 17 H ) 54.925 ( PROT ARG 17 CA ) 68.656 ( PROT ARG 17 CB ) 54.925 ( PROT ARG 17 CG ) 54.925 ( PROT ARG 17 CD ) 54.925 ( PROT ARG 17 NE ) 54.925 ( PROT ARG 17 HE ) 54.925 ( PROT ARG 17 CZ ) 54.925 ( PROT ARG 17 NH1 ) 54.925 ( PROT ARG 17 HH11 ) 54.925 ( PROT ARG 17 HH12 ) 54.925 ( PROT ARG 17 NH2 ) 54.925 ( PROT ARG 17 HH21 ) 54.925 ( PROT ARG 17 HH22 ) 54.925 ( PROT ARG 17 C ) 68.656 ( PROT ARG 17 OT1 ) 54.925 ( PROT ARG 17 OT2 ) 54.925 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96500 3.71253 -6.80344 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS -0.00118 -0.00121 0.00144 ROTATION MATRIX 1.000000 -0.000038 -0.000090 0.000038 1.000000 0.000138 0.000090 -0.000138 1.000000 AXIS OF ROTATION IS 0.816628 0.532342 -0.223006 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 2.0793 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.112600 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1126" Parameter: A <- "0.1126" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.76579 3.78177 -6.96578 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS 0.00638 0.00994 -0.01145 ROTATION MATRIX 0.999887 0.010493 0.010806 -0.010364 0.999875 -0.011931 -0.010930 0.011818 0.999870 AXIS OF ROTATION IS -0.619109 -0.566636 0.543717 ANGLE IS 1.10 CENTER OF ROTATION 7.825592 3.598032 -7.103714 SHIFT IS -0.015808 TOTAL SQUARE DIFF IS 0.0644 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.061558 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1126" RDCMND substituted energy or value "?RMS" to " 0.0616" Parameter: A <- "0.1126 0.0616" 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 0.1126 0.0616 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 " 203.43" Parameter: H <- "203.43" 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> 0 259.28476 203.42974 12.78745 ENER INTERN> 30.86661 52.79707 0.00000 4.06647 7.91131 ENER EXTERN> 181.46892 -17.82561 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 " 259.28" Parameter: B <- "259.28" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -17.83" Parameter: C <- "-17.83" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 181.47" Parameter: C <- " 163.64" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 163.64" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 30.87" Parameter: D <- "30.87" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 52.80" Parameter: D <- " 83.67" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 4.07" Parameter: D <- " 87.74" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.91" Parameter: D <- " 95.65" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 95.65" 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= 1800 ENER= 259.28 GRMS= 12.79 ELEC= -17.83 VDW= 181.47 RDTITL> *EXTERNAL= 163.64 INTERNAL= 95.65 USER= 0.00 HARM= 203.43 RDTITL> *BOND= 30.87 ANGL= 52.80 DIHE= 4.07 IMPR= 7.91 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: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9372 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9372 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 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> 0 445.72149 -186.43672 6.72336 0.02000 MINI INTERN> 30.86661 52.79707 0.00000 4.06647 7.91131 MINI EXTERN> 181.46892 -17.82561 0.00000 0.00000 0.00000 MINI CONSTR> 186.43672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 416.05259 29.66890 17.27719 0.00864 MINI INTERN> 72.12675 44.51379 0.00000 5.07108 6.74783 MINI EXTERN> 127.91819 -15.10958 0.00000 0.00000 0.00000 MINI CONSTR> 174.78453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 389.64343 26.40916 6.61319 0.00373 MINI INTERN> 23.02921 60.26174 0.00000 5.11638 7.97275 MINI EXTERN> 137.21803 -19.82592 0.00000 0.00000 0.00000 MINI CONSTR> 175.87124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 383.56044 6.08299 1.76736 0.00161 MINI INTERN> 27.39214 54.08857 0.00000 5.23406 7.30848 MINI EXTERN> 135.78465 -19.09728 0.00000 0.00000 0.00000 MINI CONSTR> 172.84982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 382.27375 1.28670 0.62905 0.00070 MINI INTERN> 27.65727 53.92257 0.00000 5.24871 7.39801 MINI EXTERN> 133.54528 -19.09618 0.00000 0.00000 0.00000 MINI CONSTR> 173.59808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 381.91685 0.35689 1.13583 0.00072 MINI INTERN> 26.39625 54.19297 0.00000 5.26937 7.43903 MINI EXTERN> 133.95102 -19.32958 0.00000 0.00000 0.00000 MINI CONSTR> 173.99780 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 381.69683 0.22002 0.35426 0.00031 MINI INTERN> 27.58199 53.34172 0.00000 5.25826 7.31010 MINI EXTERN> 133.40072 -19.19086 0.00000 0.00000 0.00000 MINI CONSTR> 173.99489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 381.64572 0.05111 0.13141 0.00013 MINI INTERN> 27.25890 53.41337 0.00000 5.26668 7.33082 MINI EXTERN> 133.40963 -19.23504 0.00000 0.00000 0.00000 MINI CONSTR> 174.20135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 381.63043 0.01528 0.22573 0.00014 MINI INTERN> 27.43444 53.27895 0.00000 5.27090 7.33095 MINI EXTERN> 133.18285 -19.20856 0.00000 0.00000 0.00000 MINI CONSTR> 174.34091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 381.62145 0.00898 0.04855 0.00006 MINI INTERN> 27.22967 53.31093 0.00000 5.26910 7.31954 MINI EXTERN> 133.37419 -19.24271 0.00000 0.00000 0.00000 MINI CONSTR> 174.36073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 381.61969 0.00176 0.10076 0.00006 MINI INTERN> 27.15545 53.31011 0.00000 5.26932 7.31584 MINI EXTERN> 133.42443 -19.25407 0.00000 0.00000 0.00000 MINI CONSTR> 174.39862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 381.61821 0.00148 0.03309 0.00003 MINI INTERN> 27.22205 53.27524 0.00000 5.27163 7.32134 MINI EXTERN> 133.32704 -19.24024 0.00000 0.00000 0.00000 MINI CONSTR> 174.44115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 381.61785 0.00036 0.01166 0.00001 MINI INTERN> 27.21695 53.26491 0.00000 5.27151 7.31903 MINI EXTERN> 133.33449 -19.24045 0.00000 0.00000 0.00000 MINI CONSTR> 174.45142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 381.61774 0.00012 0.00712 0.00001 MINI INTERN> 27.20911 53.26197 0.00000 5.27187 7.31934 MINI EXTERN> 133.33391 -19.24064 0.00000 0.00000 0.00000 MINI CONSTR> 174.46217 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> 65 381.61774 0.00012 0.00712 0.00001 STPD INTERN> 27.20911 53.26197 0.00000 5.27187 7.31934 STPD EXTERN> 133.33391 -19.24064 0.00000 0.00000 0.00000 STPD CONSTR> 174.46217 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 9365 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 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> 0 381.61774 0.00012 0.00712 0.00000 MINI INTERN> 27.20911 53.26197 0.00000 5.27187 7.31934 MINI EXTERN> 133.33391 -19.24064 0.00000 0.00000 0.00000 MINI CONSTR> 174.46217 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> 1 381.61772 0.00001 0.00809 0.02000 CONJ INTERN> 27.21505 53.25921 0.00000 5.27203 7.31974 CONJ EXTERN> 133.32595 -19.23941 0.00000 0.00000 0.00000 CONJ CONSTR> 174.46515 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 ASP 1 HT1 ) 35.701 ( PROT ASP 1 HT2 ) 35.701 ( PROT ASP 1 N ) 44.627 ( PROT ASP 1 HT3 ) 35.701 ( PROT ASP 1 CA ) 44.627 ( PROT ASP 1 CB ) 35.701 ( PROT ASP 1 CG ) 35.701 ( PROT ASP 1 OD1 ) 35.701 ( PROT ASP 1 OD2 ) 35.701 ( PROT ASP 1 C ) 44.627 ( PROT ASP 1 O ) 44.627 ( PROT TYR 2 N ) 44.627 ( PROT TYR 2 H ) 35.701 ( PROT TYR 2 CA ) 44.627 ( PROT TYR 2 CB ) 35.701 ( PROT TYR 2 CG ) 35.701 ( PROT TYR 2 CD1 ) 35.701 ( PROT TYR 2 CE1 ) 35.701 ( PROT TYR 2 CD2 ) 35.701 ( PROT TYR 2 CE2 ) 35.701 ( PROT TYR 2 CZ ) 35.701 ( PROT TYR 2 OH ) 35.701 ( PROT TYR 2 HH ) 35.701 ( PROT TYR 2 C ) 44.627 ( PROT TYR 2 O ) 44.627 ( PROT ALA 3 N ) 44.627 ( PROT ALA 3 H ) 35.701 ( PROT ALA 3 CA ) 44.627 ( PROT ALA 3 CB ) 35.701 ( PROT ALA 3 C ) 44.627 ( PROT ALA 3 O ) 44.627 ( PROT PHE 4 N ) 44.627 ( PROT PHE 4 H ) 35.701 ( PROT PHE 4 CA ) 44.627 ( PROT PHE 4 CB ) 35.701 ( PROT PHE 4 CG ) 35.701 ( PROT PHE 4 CD1 ) 35.701 ( PROT PHE 4 CD2 ) 35.701 ( PROT PHE 4 CE1 ) 35.701 ( PROT PHE 4 CE2 ) 35.701 ( PROT PHE 4 CZ ) 35.701 ( PROT PHE 4 C ) 44.627 ( PROT PHE 4 O ) 44.627 ( PROT ILE 5 N ) 44.627 ( PROT ILE 5 H ) 35.701 ( PROT ILE 5 CA ) 44.627 ( PROT ILE 5 CB ) 35.701 ( PROT ILE 5 CG2 ) 35.701 ( PROT ILE 5 CG1 ) 35.701 ( PROT ILE 5 CD ) 35.701 ( PROT ILE 5 C ) 44.627 ( PROT ILE 5 O ) 44.627 ( PROT ALA 6 N ) 44.627 ( PROT ALA 6 H ) 35.701 ( PROT ALA 6 CA ) 44.627 ( PROT ALA 6 CB ) 35.701 ( PROT ALA 6 C ) 44.627 ( PROT ALA 6 O ) 44.627 ( PROT SER 7 N ) 44.627 ( PROT SER 7 H ) 35.701 ( PROT SER 7 CA ) 44.627 ( PROT SER 7 CB ) 35.701 ( PROT SER 7 OG ) 35.701 ( PROT SER 7 HG ) 35.701 ( PROT SER 7 C ) 44.627 ( PROT SER 7 O ) 44.627 ( PROT LEU 8 N ) 44.627 ( PROT LEU 8 H ) 35.701 ( PROT LEU 8 CA ) 44.627 ( PROT LEU 8 CB ) 35.701 ( PROT LEU 8 CG ) 35.701 ( PROT LEU 8 CD1 ) 35.701 ( PROT LEU 8 CD2 ) 35.701 ( PROT LEU 8 C ) 44.627 ( PROT LEU 8 O ) 44.627 ( PROT VAL 9 N ) 44.627 ( PROT VAL 9 H ) 35.701 ( PROT VAL 9 CA ) 44.627 ( PROT VAL 9 CB ) 35.701 ( PROT VAL 9 CG1 ) 35.701 ( PROT VAL 9 CG2 ) 35.701 ( PROT VAL 9 C ) 44.627 ( PROT VAL 9 O ) 44.627 ( PROT VAL 10 N ) 44.627 ( PROT VAL 10 H ) 35.701 ( PROT VAL 10 CA ) 44.627 ( PROT VAL 10 CB ) 35.701 ( PROT VAL 10 CG1 ) 35.701 ( PROT VAL 10 CG2 ) 35.701 ( PROT VAL 10 C ) 44.627 ( PROT VAL 10 O ) 44.627 ( PROT ILE 11 N ) 44.627 ( PROT ILE 11 H ) 35.701 ( PROT ILE 11 CA ) 44.627 ( PROT ILE 11 CB ) 35.701 ( PROT ILE 11 CG2 ) 35.701 ( PROT ILE 11 CG1 ) 35.701 ( PROT ILE 11 CD ) 35.701 ( PROT ILE 11 C ) 44.627 ( PROT ILE 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 ASP 13 N ) 44.627 ( PROT ASP 13 H ) 35.701 ( PROT ASP 13 CA ) 44.627 ( PROT ASP 13 CB ) 35.701 ( PROT ASP 13 CG ) 35.701 ( PROT ASP 13 OD1 ) 35.701 ( PROT ASP 13 OD2 ) 35.701 ( PROT ASP 13 C ) 44.627 ( PROT ASP 13 O ) 44.627 ( PROT ASP 14 N ) 44.627 ( PROT ASP 14 H ) 35.701 ( PROT ASP 14 CA ) 44.627 ( PROT ASP 14 CB ) 35.701 ( PROT ASP 14 CG ) 35.701 ( PROT ASP 14 OD1 ) 35.701 ( PROT ASP 14 OD2 ) 35.701 ( PROT ASP 14 C ) 44.627 ( PROT ASP 14 O ) 44.627 ( PROT VAL 15 N ) 44.627 ( PROT VAL 15 H ) 35.701 ( PROT VAL 15 CA ) 44.627 ( PROT VAL 15 CB ) 35.701 ( PROT VAL 15 CG1 ) 35.701 ( PROT VAL 15 CG2 ) 35.701 ( PROT VAL 15 C ) 44.627 ( PROT VAL 15 O ) 44.627 ( PROT ASN 16 N ) 44.627 ( PROT ASN 16 H ) 35.701 ( PROT ASN 16 CA ) 44.627 ( PROT ASN 16 CB ) 35.701 ( PROT ASN 16 CG ) 35.701 ( PROT ASN 16 OD1 ) 35.701 ( PROT ASN 16 ND2 ) 35.701 ( PROT ASN 16 HD21 ) 35.701 ( PROT ASN 16 HD22 ) 35.701 ( PROT ASN 16 C ) 44.627 ( PROT ASN 16 O ) 44.627 ( PROT ARG 17 N ) 44.627 ( PROT ARG 17 H ) 35.701 ( PROT ARG 17 CA ) 44.627 ( PROT ARG 17 CB ) 35.701 ( PROT ARG 17 CG ) 35.701 ( PROT ARG 17 CD ) 35.701 ( PROT ARG 17 NE ) 35.701 ( PROT ARG 17 HE ) 35.701 ( PROT ARG 17 CZ ) 35.701 ( PROT ARG 17 NH1 ) 35.701 ( PROT ARG 17 HH11 ) 35.701 ( PROT ARG 17 HH12 ) 35.701 ( PROT ARG 17 NH2 ) 35.701 ( PROT ARG 17 HH21 ) 35.701 ( PROT ARG 17 HH22 ) 35.701 ( PROT ARG 17 C ) 44.627 ( PROT ARG 17 OT1 ) 35.701 ( PROT ARG 17 OT2 ) 35.701 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96470 3.71239 -6.80324 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS -0.00088 -0.00106 0.00124 ROTATION MATRIX 1.000000 -0.000057 -0.000121 0.000057 1.000000 0.000188 0.000121 -0.000188 1.000000 AXIS OF ROTATION IS 0.815617 0.522705 -0.248091 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 2.7503 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.129500 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1295" Parameter: A <- "0.1295" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.76643 3.78118 -6.96577 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS 0.00575 0.01052 -0.01146 ROTATION MATRIX 0.999844 0.012214 0.012763 -0.012035 0.999829 -0.014055 -0.012932 0.013899 0.999820 AXIS OF ROTATION IS -0.620481 -0.570346 0.538247 ANGLE IS 1.29 CENTER OF ROTATION 7.808062 3.608132 -7.115767 SHIFT IS -0.015741 TOTAL SQUARE DIFF IS 0.0936 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.074186 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1295" RDCMND substituted energy or value "?RMS" to " 0.0742" Parameter: A <- "0.1295 0.0742" 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 0.1295 0.0742 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 " 174.47" Parameter: H <- "174.47" 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> 0 207.15258 174.46515 9.53655 ENER INTERN> 27.21505 53.25921 0.00000 5.27203 7.31974 ENER EXTERN> 133.32595 -19.23941 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 " 207.15" Parameter: B <- "207.15" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -19.24" Parameter: C <- "-19.24" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 133.33" Parameter: C <- " 114.09" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 114.09" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 27.22" Parameter: D <- "27.22" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 53.26" Parameter: D <- " 80.48" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 5.27" Parameter: D <- " 85.75" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.32" Parameter: D <- " 93.07" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 93.07" 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= 207.15 GRMS= 9.54 ELEC= -19.24 VDW= 133.33 RDTITL> *EXTERNAL= 114.09 INTERNAL= 93.07 USER= 0.00 HARM= 174.47 RDTITL> *BOND= 27.22 ANGL= 53.26 DIHE= 5.27 IMPR= 7.32 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 207.15 GRMS= 9.54 ELEC= -19.24 VDW= 133.33 RDTITL> *EXTERNAL= 114.09 INTERNAL= 93.07 USER= 0.00 HARM= 174.47 RDTITL> *BOND= 27.22 ANGL= 53.26 DIHE= 5.27 IMPR= 7.32 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 207.15 GRMS= 9.54 ELEC= -19.24 VDW= 133.33 RDTITL> *EXTERNAL= 114.09 INTERNAL= 93.07 USER= 0.00 HARM= 174.47 RDTITL> *BOND= 27.22 ANGL= 53.26 DIHE= 5.27 IMPR= 7.32 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 2400 0.1295 0.0742 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "2400" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9365 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 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> 0 368.95053 -161.79795 5.06896 0.02000 MINI INTERN> 27.21505 53.25921 0.00000 5.27203 7.31974 MINI EXTERN> 133.32595 -19.23941 0.00000 0.00000 0.00000 MINI CONSTR> 161.79795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 345.16222 23.78831 14.44422 0.00864 MINI INTERN> 49.05338 46.28355 0.00000 6.61060 5.96944 MINI EXTERN> 104.05178 -18.69196 0.00000 0.00000 0.00000 MINI CONSTR> 151.88543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9356 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 320.00832 25.15390 3.62218 0.00373 MINI INTERN> 26.18029 54.37360 0.00000 6.75941 7.24608 MINI EXTERN> 91.71953 -20.28915 0.00000 0.00000 0.00000 MINI CONSTR> 154.01857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 315.09159 4.91673 1.37327 0.00161 MINI INTERN> 22.93009 52.78546 0.00000 6.75008 6.93295 MINI EXTERN> 95.01693 -21.18223 0.00000 0.00000 0.00000 MINI CONSTR> 151.85831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9354 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 313.36837 1.72321 2.19692 0.00167 MINI INTERN> 24.25328 51.32720 0.00000 6.78310 6.82337 MINI EXTERN> 93.65504 -21.21056 0.00000 0.00000 0.00000 MINI CONSTR> 151.73693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 312.68946 0.67891 2.83901 0.00173 MINI INTERN> 21.04007 52.59416 0.00000 6.79383 6.87868 MINI EXTERN> 94.94061 -21.70140 0.00000 0.00000 0.00000 MINI CONSTR> 152.14352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9352 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 311.63500 1.05447 0.66353 0.00075 MINI INTERN> 22.94278 51.29782 0.00000 6.85006 6.93586 MINI EXTERN> 92.34676 -21.37091 0.00000 0.00000 0.00000 MINI CONSTR> 152.63264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 311.51114 0.12386 1.03236 0.00078 MINI INTERN> 22.53172 51.37444 0.00000 6.86505 6.95975 MINI EXTERN> 92.35456 -21.47112 0.00000 0.00000 0.00000 MINI CONSTR> 152.89675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9352 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 311.34116 0.16999 0.52526 0.00034 MINI INTERN> 22.48734 51.10852 0.00000 6.85838 6.92539 MINI EXTERN> 92.47536 -21.48133 0.00000 0.00000 0.00000 MINI CONSTR> 152.96749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 311.27874 0.06241 0.12820 0.00014 MINI INTERN> 22.61716 50.98398 0.00000 6.86262 6.92124 MINI EXTERN> 92.26757 -21.47700 0.00000 0.00000 0.00000 MINI CONSTR> 153.10318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9352 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 311.25454 0.02420 0.16140 0.00015 MINI INTERN> 22.68806 50.89096 0.00000 6.86513 6.91875 MINI EXTERN> 92.15695 -21.47609 0.00000 0.00000 0.00000 MINI CONSTR> 153.21077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 311.24614 0.00839 0.22374 0.00016 MINI INTERN> 22.45329 50.97033 0.00000 6.86579 6.92284 MINI EXTERN> 92.26921 -21.51231 0.00000 0.00000 0.00000 MINI CONSTR> 153.27699 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9353 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 311.23696 0.00918 0.04540 0.00007 MINI INTERN> 22.57501 50.87565 0.00000 6.86638 6.91958 MINI EXTERN> 92.18459 -21.49229 0.00000 0.00000 0.00000 MINI CONSTR> 153.30805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 311.23435 0.00261 0.09481 0.00007 MINI INTERN> 22.59912 50.83651 0.00000 6.86711 6.91935 MINI EXTERN> 92.15278 -21.48492 0.00000 0.00000 0.00000 MINI CONSTR> 153.34440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9353 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 311.23245 0.00191 0.02545 0.00003 MINI INTERN> 22.57151 50.84826 0.00000 6.86709 6.91908 MINI EXTERN> 92.15361 -21.49441 0.00000 0.00000 0.00000 MINI CONSTR> 153.36731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 311.23184 0.00061 0.04912 0.00003 MINI INTERN> 22.54182 50.85704 0.00000 6.86701 6.91917 MINI EXTERN> 92.16352 -21.50194 0.00000 0.00000 0.00000 MINI CONSTR> 153.38522 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9353 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 311.23134 0.00049 0.01268 0.00001 MINI INTERN> 22.56094 50.83843 0.00000 6.86726 6.91919 MINI EXTERN> 92.14813 -21.49548 0.00000 0.00000 0.00000 MINI CONSTR> 153.39288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 311.23113 0.00021 0.01495 0.00001 MINI INTERN> 22.55696 50.83605 0.00000 6.86725 6.91918 MINI EXTERN> 92.14655 -21.49643 0.00000 0.00000 0.00000 MINI CONSTR> 153.40156 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> 87 311.23107 0.00006 0.00863 0.00001 STPD INTERN> 22.55810 50.83528 0.00000 6.86725 6.91918 STPD EXTERN> 92.14312 -21.49631 0.00000 0.00000 0.00000 STPD CONSTR> 153.40446 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 9353 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9353 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 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> 0 311.23107 0.00006 0.00863 0.00000 MINI INTERN> 22.55810 50.83528 0.00000 6.86725 6.91918 MINI EXTERN> 92.14312 -21.49631 0.00000 0.00000 0.00000 MINI CONSTR> 153.40446 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> 3 311.23086 0.00022 0.00253 0.02000 CONJ INTERN> 22.55253 50.82707 0.00000 6.86721 6.91933 CONJ EXTERN> 92.13463 -21.49652 0.00000 0.00000 0.00000 CONJ CONSTR> 153.42660 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 ASP 1 HT1 ) 23.206 ( PROT ASP 1 HT2 ) 23.206 ( PROT ASP 1 N ) 29.007 ( PROT ASP 1 HT3 ) 23.206 ( PROT ASP 1 CA ) 29.007 ( PROT ASP 1 CB ) 23.206 ( PROT ASP 1 CG ) 23.206 ( PROT ASP 1 OD1 ) 23.206 ( PROT ASP 1 OD2 ) 23.206 ( PROT ASP 1 C ) 29.007 ( PROT ASP 1 O ) 29.007 ( PROT TYR 2 N ) 29.007 ( PROT TYR 2 H ) 23.206 ( PROT TYR 2 CA ) 29.007 ( PROT TYR 2 CB ) 23.206 ( PROT TYR 2 CG ) 23.206 ( PROT TYR 2 CD1 ) 23.206 ( PROT TYR 2 CE1 ) 23.206 ( PROT TYR 2 CD2 ) 23.206 ( PROT TYR 2 CE2 ) 23.206 ( PROT TYR 2 CZ ) 23.206 ( PROT TYR 2 OH ) 23.206 ( PROT TYR 2 HH ) 23.206 ( PROT TYR 2 C ) 29.007 ( PROT TYR 2 O ) 29.007 ( PROT ALA 3 N ) 29.007 ( PROT ALA 3 H ) 23.206 ( PROT ALA 3 CA ) 29.007 ( PROT ALA 3 CB ) 23.206 ( PROT ALA 3 C ) 29.007 ( PROT ALA 3 O ) 29.007 ( PROT PHE 4 N ) 29.007 ( PROT PHE 4 H ) 23.206 ( PROT PHE 4 CA ) 29.007 ( PROT PHE 4 CB ) 23.206 ( PROT PHE 4 CG ) 23.206 ( PROT PHE 4 CD1 ) 23.206 ( PROT PHE 4 CD2 ) 23.206 ( PROT PHE 4 CE1 ) 23.206 ( PROT PHE 4 CE2 ) 23.206 ( PROT PHE 4 CZ ) 23.206 ( PROT PHE 4 C ) 29.007 ( PROT PHE 4 O ) 29.007 ( PROT ILE 5 N ) 29.007 ( PROT ILE 5 H ) 23.206 ( PROT ILE 5 CA ) 29.007 ( PROT ILE 5 CB ) 23.206 ( PROT ILE 5 CG2 ) 23.206 ( PROT ILE 5 CG1 ) 23.206 ( PROT ILE 5 CD ) 23.206 ( PROT ILE 5 C ) 29.007 ( PROT ILE 5 O ) 29.007 ( PROT ALA 6 N ) 29.007 ( PROT ALA 6 H ) 23.206 ( PROT ALA 6 CA ) 29.007 ( PROT ALA 6 CB ) 23.206 ( PROT ALA 6 C ) 29.007 ( PROT ALA 6 O ) 29.007 ( PROT SER 7 N ) 29.007 ( PROT SER 7 H ) 23.206 ( PROT SER 7 CA ) 29.007 ( PROT SER 7 CB ) 23.206 ( PROT SER 7 OG ) 23.206 ( PROT SER 7 HG ) 23.206 ( PROT SER 7 C ) 29.007 ( PROT SER 7 O ) 29.007 ( PROT LEU 8 N ) 29.007 ( PROT LEU 8 H ) 23.206 ( PROT LEU 8 CA ) 29.007 ( PROT LEU 8 CB ) 23.206 ( PROT LEU 8 CG ) 23.206 ( PROT LEU 8 CD1 ) 23.206 ( PROT LEU 8 CD2 ) 23.206 ( PROT LEU 8 C ) 29.007 ( PROT LEU 8 O ) 29.007 ( PROT VAL 9 N ) 29.007 ( PROT VAL 9 H ) 23.206 ( PROT VAL 9 CA ) 29.007 ( PROT VAL 9 CB ) 23.206 ( PROT VAL 9 CG1 ) 23.206 ( PROT VAL 9 CG2 ) 23.206 ( PROT VAL 9 C ) 29.007 ( PROT VAL 9 O ) 29.007 ( PROT VAL 10 N ) 29.007 ( PROT VAL 10 H ) 23.206 ( PROT VAL 10 CA ) 29.007 ( PROT VAL 10 CB ) 23.206 ( PROT VAL 10 CG1 ) 23.206 ( PROT VAL 10 CG2 ) 23.206 ( PROT VAL 10 C ) 29.007 ( PROT VAL 10 O ) 29.007 ( PROT ILE 11 N ) 29.007 ( PROT ILE 11 H ) 23.206 ( PROT ILE 11 CA ) 29.007 ( PROT ILE 11 CB ) 23.206 ( PROT ILE 11 CG2 ) 23.206 ( PROT ILE 11 CG1 ) 23.206 ( PROT ILE 11 CD ) 23.206 ( PROT ILE 11 C ) 29.007 ( PROT ILE 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 ASP 13 N ) 29.007 ( PROT ASP 13 H ) 23.206 ( PROT ASP 13 CA ) 29.007 ( PROT ASP 13 CB ) 23.206 ( PROT ASP 13 CG ) 23.206 ( PROT ASP 13 OD1 ) 23.206 ( PROT ASP 13 OD2 ) 23.206 ( PROT ASP 13 C ) 29.007 ( PROT ASP 13 O ) 29.007 ( PROT ASP 14 N ) 29.007 ( PROT ASP 14 H ) 23.206 ( PROT ASP 14 CA ) 29.007 ( PROT ASP 14 CB ) 23.206 ( PROT ASP 14 CG ) 23.206 ( PROT ASP 14 OD1 ) 23.206 ( PROT ASP 14 OD2 ) 23.206 ( PROT ASP 14 C ) 29.007 ( PROT ASP 14 O ) 29.007 ( PROT VAL 15 N ) 29.007 ( PROT VAL 15 H ) 23.206 ( PROT VAL 15 CA ) 29.007 ( PROT VAL 15 CB ) 23.206 ( PROT VAL 15 CG1 ) 23.206 ( PROT VAL 15 CG2 ) 23.206 ( PROT VAL 15 C ) 29.007 ( PROT VAL 15 O ) 29.007 ( PROT ASN 16 N ) 29.007 ( PROT ASN 16 H ) 23.206 ( PROT ASN 16 CA ) 29.007 ( PROT ASN 16 CB ) 23.206 ( PROT ASN 16 CG ) 23.206 ( PROT ASN 16 OD1 ) 23.206 ( PROT ASN 16 ND2 ) 23.206 ( PROT ASN 16 HD21 ) 23.206 ( PROT ASN 16 HD22 ) 23.206 ( PROT ASN 16 C ) 29.007 ( PROT ASN 16 O ) 29.007 ( PROT ARG 17 N ) 29.007 ( PROT ARG 17 H ) 23.206 ( PROT ARG 17 CA ) 29.007 ( PROT ARG 17 CB ) 23.206 ( PROT ARG 17 CG ) 23.206 ( PROT ARG 17 CD ) 23.206 ( PROT ARG 17 NE ) 23.206 ( PROT ARG 17 HE ) 23.206 ( PROT ARG 17 CZ ) 23.206 ( PROT ARG 17 NH1 ) 23.206 ( PROT ARG 17 HH11 ) 23.206 ( PROT ARG 17 HH12 ) 23.206 ( PROT ARG 17 NH2 ) 23.206 ( PROT ARG 17 HH21 ) 23.206 ( PROT ARG 17 HH22 ) 23.206 ( PROT ARG 17 C ) 29.007 ( PROT ARG 17 OT1 ) 23.206 ( PROT ARG 17 OT2 ) 23.206 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96423 3.71218 -6.80289 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS -0.00041 -0.00085 0.00089 ROTATION MATRIX 1.000000 -0.000072 -0.000145 0.000072 1.000000 0.000241 0.000145 -0.000241 1.000000 AXIS OF ROTATION IS 0.830490 0.499609 -0.246327 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 3.7343 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.150898 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1509" Parameter: A <- "0.1509" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.76722 3.78062 -6.96601 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS 0.00496 0.01109 -0.01122 ROTATION MATRIX 0.999793 0.013950 0.014811 -0.013708 0.999773 -0.016288 -0.015035 0.016082 0.999758 AXIS OF ROTATION IS -0.622561 -0.574005 0.531918 ANGLE IS 1.49 CENTER OF ROTATION 7.790586 3.618917 -7.127650 SHIFT IS -0.015424 TOTAL SQUARE DIFF IS 0.1301 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.087473 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1509" RDCMND substituted energy or value "?RMS" to " 0.0875" Parameter: A <- "0.1509 0.0875" 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 0.1509 0.0875 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 " 153.43" Parameter: H <- "153.43" 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> 0 157.80425 153.42660 7.19858 ENER INTERN> 22.55253 50.82707 0.00000 6.86721 6.91933 ENER EXTERN> 92.13463 -21.49652 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 " 157.80" Parameter: B <- "157.80" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -21.50" Parameter: C <- "-21.50" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 92.13" Parameter: C <- " 70.63" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 70.63" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 22.55" Parameter: D <- "22.55" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 50.83" Parameter: D <- " 73.38" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 6.87" Parameter: D <- " 80.25" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.92" Parameter: D <- " 87.17" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 87.17" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 3000 ENER= 157.80 GRMS= 7.20 ELEC= -21.50 VDW= 92.13 RDTITL> *EXTERNAL= 70.63 INTERNAL= 87.17 USER= 0.00 HARM= 153.43 RDTITL> *BOND= 22.55 ANGL= 50.83 DIHE= 6.87 IMPR= 6.92 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9353 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9353 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 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> 0 299.33862 -141.53436 3.80822 0.02000 MINI INTERN> 22.55253 50.82707 0.00000 6.86721 6.91933 MINI EXTERN> 92.13463 -21.49652 0.00000 0.00000 0.00000 MINI CONSTR> 141.53436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 285.33182 14.00679 13.69113 0.00864 MINI INTERN> 30.92320 48.79356 0.00000 8.90922 5.78298 MINI EXTERN> 75.77869 -22.33070 0.00000 0.00000 0.00000 MINI CONSTR> 137.47487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9340 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 262.22183 23.11000 4.49295 0.00373 MINI INTERN> 19.31928 50.81370 0.00000 8.81891 7.05506 MINI EXTERN> 60.95444 -22.74841 0.00000 0.00000 0.00000 MINI CONSTR> 138.00884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 256.13482 6.08701 1.51922 0.00161 MINI INTERN> 18.52630 48.66434 0.00000 8.63207 6.97959 MINI EXTERN> 60.03583 -23.37520 0.00000 0.00000 0.00000 MINI CONSTR> 136.67188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 253.37274 2.76209 1.76864 0.00167 MINI INTERN> 18.46820 47.79420 0.00000 8.69586 7.00537 MINI EXTERN> 58.85724 -23.62903 0.00000 0.00000 0.00000 MINI CONSTR> 136.18090 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 252.24497 1.12776 3.16296 0.00173 MINI INTERN> 19.28859 46.96551 0.00000 8.72715 7.07678 MINI EXTERN> 57.56318 -23.46196 0.00000 0.00000 0.00000 MINI CONSTR> 136.08572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 250.67646 1.56852 0.75040 0.00075 MINI INTERN> 17.90020 47.28801 0.00000 8.75813 7.11935 MINI EXTERN> 57.22979 -23.77668 0.00000 0.00000 0.00000 MINI CONSTR> 136.15767 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 250.03705 0.63941 0.58924 0.00078 MINI INTERN> 17.80598 47.05200 0.00000 8.76950 7.12402 MINI EXTERN> 56.94221 -23.84200 0.00000 0.00000 0.00000 MINI CONSTR> 136.18535 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9337 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 249.61820 0.41885 1.14307 0.00080 MINI INTERN> 18.00852 46.83267 0.00000 8.78724 7.14238 MINI EXTERN> 56.48085 -23.92300 0.00000 0.00000 0.00000 MINI CONSTR> 136.28956 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 249.36808 0.25012 1.17755 0.00083 MINI INTERN> 17.55227 46.95221 0.00000 8.79415 7.15676 MINI EXTERN> 56.48964 -23.97427 0.00000 0.00000 0.00000 MINI CONSTR> 136.39732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9337 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 249.08406 0.28402 0.39473 0.00036 MINI INTERN> 17.84111 46.49624 0.00000 8.76410 7.09802 MINI EXTERN> 56.44201 -23.96545 0.00000 0.00000 0.00000 MINI CONSTR> 136.40803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 248.97905 0.10501 0.41467 0.00037 MINI INTERN> 17.85571 46.40703 0.00000 8.75966 7.08828 MINI EXTERN> 56.36971 -23.98173 0.00000 0.00000 0.00000 MINI CONSTR> 136.48040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 248.92062 0.05843 0.59643 0.00039 MINI INTERN> 17.86487 46.38813 0.00000 8.75394 7.08125 MINI EXTERN> 56.31327 -24.02921 0.00000 0.00000 0.00000 MINI CONSTR> 136.54837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 248.85329 0.06733 0.15681 0.00017 MINI INTERN> 17.73907 46.43430 0.00000 8.75885 7.09354 MINI EXTERN> 56.23384 -24.02842 0.00000 0.00000 0.00000 MINI CONSTR> 136.62211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 248.82387 0.02943 0.13202 0.00017 MINI INTERN> 17.73406 46.41107 0.00000 8.75550 7.08946 MINI EXTERN> 56.20233 -24.03835 0.00000 0.00000 0.00000 MINI CONSTR> 136.66979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 248.80424 0.01962 0.26334 0.00018 MINI INTERN> 17.70580 46.41511 0.00000 8.75365 7.08977 MINI EXTERN> 56.15495 -24.04686 0.00000 0.00000 0.00000 MINI CONSTR> 136.73182 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 248.78747 0.01677 0.07631 0.00008 MINI INTERN> 17.76301 46.34798 0.00000 8.74615 7.07615 MINI EXTERN> 56.15774 -24.05382 0.00000 0.00000 0.00000 MINI CONSTR> 136.75027 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 248.77823 0.00925 0.06576 0.00008 MINI INTERN> 17.76235 46.33690 0.00000 8.74298 7.07266 MINI EXTERN> 56.13856 -24.05928 0.00000 0.00000 0.00000 MINI CONSTR> 136.78405 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 248.77296 0.00527 0.13625 0.00008 MINI INTERN> 17.77385 46.31352 0.00000 8.73920 7.06741 MINI EXTERN> 56.12612 -24.05967 0.00000 0.00000 0.00000 MINI CONSTR> 136.81254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 248.76967 0.00329 0.16850 0.00009 MINI INTERN> 17.77425 46.30651 0.00000 8.73668 7.06479 MINI EXTERN> 56.11234 -24.06164 0.00000 0.00000 0.00000 MINI CONSTR> 136.83673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 248.76705 0.00262 0.16394 0.00009 MINI INTERN> 17.76415 46.31189 0.00000 8.73550 7.06445 MINI EXTERN> 56.10029 -24.06515 0.00000 0.00000 0.00000 MINI CONSTR> 136.85592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 248.76322 0.00383 0.06001 0.00004 MINI INTERN> 17.76440 46.32149 0.00000 8.73363 7.06314 MINI EXTERN> 56.08663 -24.07985 0.00000 0.00000 0.00000 MINI CONSTR> 136.87379 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 248.76157 0.00165 0.04584 0.00004 MINI INTERN> 17.76832 46.31483 0.00000 8.73167 7.06079 MINI EXTERN> 56.07898 -24.08153 0.00000 0.00000 0.00000 MINI CONSTR> 136.88851 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 248.76059 0.00099 0.07343 0.00004 MINI INTERN> 17.77267 46.31173 0.00000 8.72985 7.05876 MINI EXTERN> 56.07087 -24.08549 0.00000 0.00000 0.00000 MINI CONSTR> 136.90219 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 248.75959 0.00100 0.07690 0.00004 MINI INTERN> 17.77517 46.30834 0.00000 8.72818 7.05692 MINI EXTERN> 56.06328 -24.08783 0.00000 0.00000 0.00000 MINI CONSTR> 136.91552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 248.75841 0.00118 0.02339 0.00002 MINI INTERN> 17.77128 46.30379 0.00000 8.72700 7.05564 MINI EXTERN> 56.05847 -24.08520 0.00000 0.00000 0.00000 MINI CONSTR> 136.92743 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 248.75778 0.00062 0.01935 0.00002 MINI INTERN> 17.77259 46.30206 0.00000 8.72581 7.05435 MINI EXTERN> 56.05278 -24.08704 0.00000 0.00000 0.00000 MINI CONSTR> 136.93724 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 248.75718 0.00061 0.01796 0.00002 MINI INTERN> 17.77369 46.30003 0.00000 8.72453 7.05295 MINI EXTERN> 56.04673 -24.08861 0.00000 0.00000 0.00000 MINI CONSTR> 136.94786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 248.75667 0.00050 0.03763 0.00002 MINI INTERN> 17.77269 46.29769 0.00000 8.72326 7.05158 MINI EXTERN> 56.04096 -24.08883 0.00000 0.00000 0.00000 MINI CONSTR> 136.95932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 248.75620 0.00048 0.02216 0.00002 MINI INTERN> 17.77484 46.29635 0.00000 8.72220 7.05038 MINI EXTERN> 56.03557 -24.09088 0.00000 0.00000 0.00000 MINI CONSTR> 136.96773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 248.75589 0.00030 0.03962 0.00002 MINI INTERN> 17.77405 46.29474 0.00000 8.72125 7.04934 MINI EXTERN> 56.03109 -24.09102 0.00000 0.00000 0.00000 MINI CONSTR> 136.97646 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 248.75557 0.00032 0.04537 0.00002 MINI INTERN> 17.77410 46.29341 0.00000 8.72027 7.04824 MINI EXTERN> 56.02638 -24.09183 0.00000 0.00000 0.00000 MINI CONSTR> 136.98500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 248.75530 0.00027 0.04362 0.00002 MINI INTERN> 17.77501 46.29224 0.00000 8.71951 7.04736 MINI EXTERN> 56.02233 -24.09269 0.00000 0.00000 0.00000 MINI CONSTR> 136.99154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 248.75492 0.00038 0.01272 0.00001 MINI INTERN> 17.78002 46.29113 0.00000 8.71858 7.04625 MINI EXTERN> 56.01668 -24.09573 0.00000 0.00000 0.00000 MINI CONSTR> 136.99799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 248.75483 0.00009 0.04650 0.00003 MINI INTERN> 17.77580 46.29015 0.00000 8.71800 7.04559 MINI EXTERN> 56.01446 -24.09408 0.00000 0.00000 0.00000 MINI CONSTR> 137.00490 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 248.75446 0.00037 0.01489 0.00001 MINI INTERN> 17.78194 46.28890 0.00000 8.71710 7.04448 MINI EXTERN> 56.00842 -24.09736 0.00000 0.00000 0.00000 MINI CONSTR> 137.01098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 248.75430 0.00017 0.01033 0.00001 MINI INTERN> 17.78147 46.28822 0.00000 8.71659 7.04387 MINI EXTERN> 56.00579 -24.09750 0.00000 0.00000 0.00000 MINI CONSTR> 137.01586 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 248.75411 0.00019 0.02081 0.00001 MINI INTERN> 17.78410 46.28686 0.00000 8.71582 7.04291 MINI EXTERN> 56.00083 -24.09879 0.00000 0.00000 0.00000 MINI CONSTR> 137.02238 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> 189 248.75399 0.00012 0.00949 0.00001 STPD INTERN> 17.78149 46.28681 0.00000 8.71554 7.04258 STPD EXTERN> 56.00004 -24.09814 0.00000 0.00000 0.00000 STPD CONSTR> 137.02567 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 9338 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9338 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 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> 0 248.75399 0.00012 0.00949 0.00000 MINI INTERN> 17.78149 46.28681 0.00000 8.71554 7.04258 MINI EXTERN> 56.00004 -24.09814 0.00000 0.00000 0.00000 MINI CONSTR> 137.02567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 2 248.75234 0.00165 0.00816 0.02000 CONJ INTERN> 17.79137 46.26818 0.00000 8.70385 7.02818 CONJ EXTERN> 55.92418 -24.10567 0.00000 0.00000 0.00000 CONJ CONSTR> 137.14225 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 ASP 1 HT1 ) 15.084 ( PROT ASP 1 HT2 ) 15.084 ( PROT ASP 1 N ) 18.855 ( PROT ASP 1 HT3 ) 15.084 ( PROT ASP 1 CA ) 18.855 ( PROT ASP 1 CB ) 15.084 ( PROT ASP 1 CG ) 15.084 ( PROT ASP 1 OD1 ) 15.084 ( PROT ASP 1 OD2 ) 15.084 ( PROT ASP 1 C ) 18.855 ( PROT ASP 1 O ) 18.855 ( PROT TYR 2 N ) 18.855 ( PROT TYR 2 H ) 15.084 ( PROT TYR 2 CA ) 18.855 ( PROT TYR 2 CB ) 15.084 ( PROT TYR 2 CG ) 15.084 ( PROT TYR 2 CD1 ) 15.084 ( PROT TYR 2 CE1 ) 15.084 ( PROT TYR 2 CD2 ) 15.084 ( PROT TYR 2 CE2 ) 15.084 ( PROT TYR 2 CZ ) 15.084 ( PROT TYR 2 OH ) 15.084 ( PROT TYR 2 HH ) 15.084 ( PROT TYR 2 C ) 18.855 ( PROT TYR 2 O ) 18.855 ( PROT ALA 3 N ) 18.855 ( PROT ALA 3 H ) 15.084 ( PROT ALA 3 CA ) 18.855 ( PROT ALA 3 CB ) 15.084 ( PROT ALA 3 C ) 18.855 ( PROT ALA 3 O ) 18.855 ( PROT PHE 4 N ) 18.855 ( PROT PHE 4 H ) 15.084 ( PROT PHE 4 CA ) 18.855 ( PROT PHE 4 CB ) 15.084 ( PROT PHE 4 CG ) 15.084 ( PROT PHE 4 CD1 ) 15.084 ( PROT PHE 4 CD2 ) 15.084 ( PROT PHE 4 CE1 ) 15.084 ( PROT PHE 4 CE2 ) 15.084 ( PROT PHE 4 CZ ) 15.084 ( PROT PHE 4 C ) 18.855 ( PROT PHE 4 O ) 18.855 ( PROT ILE 5 N ) 18.855 ( PROT ILE 5 H ) 15.084 ( PROT ILE 5 CA ) 18.855 ( PROT ILE 5 CB ) 15.084 ( PROT ILE 5 CG2 ) 15.084 ( PROT ILE 5 CG1 ) 15.084 ( PROT ILE 5 CD ) 15.084 ( PROT ILE 5 C ) 18.855 ( PROT ILE 5 O ) 18.855 ( PROT ALA 6 N ) 18.855 ( PROT ALA 6 H ) 15.084 ( PROT ALA 6 CA ) 18.855 ( PROT ALA 6 CB ) 15.084 ( PROT ALA 6 C ) 18.855 ( PROT ALA 6 O ) 18.855 ( PROT SER 7 N ) 18.855 ( PROT SER 7 H ) 15.084 ( PROT SER 7 CA ) 18.855 ( PROT SER 7 CB ) 15.084 ( PROT SER 7 OG ) 15.084 ( PROT SER 7 HG ) 15.084 ( PROT SER 7 C ) 18.855 ( PROT SER 7 O ) 18.855 ( PROT LEU 8 N ) 18.855 ( PROT LEU 8 H ) 15.084 ( PROT LEU 8 CA ) 18.855 ( PROT LEU 8 CB ) 15.084 ( PROT LEU 8 CG ) 15.084 ( PROT LEU 8 CD1 ) 15.084 ( PROT LEU 8 CD2 ) 15.084 ( PROT LEU 8 C ) 18.855 ( PROT LEU 8 O ) 18.855 ( PROT VAL 9 N ) 18.855 ( PROT VAL 9 H ) 15.084 ( PROT VAL 9 CA ) 18.855 ( PROT VAL 9 CB ) 15.084 ( PROT VAL 9 CG1 ) 15.084 ( PROT VAL 9 CG2 ) 15.084 ( PROT VAL 9 C ) 18.855 ( PROT VAL 9 O ) 18.855 ( PROT VAL 10 N ) 18.855 ( PROT VAL 10 H ) 15.084 ( PROT VAL 10 CA ) 18.855 ( PROT VAL 10 CB ) 15.084 ( PROT VAL 10 CG1 ) 15.084 ( PROT VAL 10 CG2 ) 15.084 ( PROT VAL 10 C ) 18.855 ( PROT VAL 10 O ) 18.855 ( PROT ILE 11 N ) 18.855 ( PROT ILE 11 H ) 15.084 ( PROT ILE 11 CA ) 18.855 ( PROT ILE 11 CB ) 15.084 ( PROT ILE 11 CG2 ) 15.084 ( PROT ILE 11 CG1 ) 15.084 ( PROT ILE 11 CD ) 15.084 ( PROT ILE 11 C ) 18.855 ( PROT ILE 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 ASP 13 N ) 18.855 ( PROT ASP 13 H ) 15.084 ( PROT ASP 13 CA ) 18.855 ( PROT ASP 13 CB ) 15.084 ( PROT ASP 13 CG ) 15.084 ( PROT ASP 13 OD1 ) 15.084 ( PROT ASP 13 OD2 ) 15.084 ( PROT ASP 13 C ) 18.855 ( PROT ASP 13 O ) 18.855 ( PROT ASP 14 N ) 18.855 ( PROT ASP 14 H ) 15.084 ( PROT ASP 14 CA ) 18.855 ( PROT ASP 14 CB ) 15.084 ( PROT ASP 14 CG ) 15.084 ( PROT ASP 14 OD1 ) 15.084 ( PROT ASP 14 OD2 ) 15.084 ( PROT ASP 14 C ) 18.855 ( PROT ASP 14 O ) 18.855 ( PROT VAL 15 N ) 18.855 ( PROT VAL 15 H ) 15.084 ( PROT VAL 15 CA ) 18.855 ( PROT VAL 15 CB ) 15.084 ( PROT VAL 15 CG1 ) 15.084 ( PROT VAL 15 CG2 ) 15.084 ( PROT VAL 15 C ) 18.855 ( PROT VAL 15 O ) 18.855 ( PROT ASN 16 N ) 18.855 ( PROT ASN 16 H ) 15.084 ( PROT ASN 16 CA ) 18.855 ( PROT ASN 16 CB ) 15.084 ( PROT ASN 16 CG ) 15.084 ( PROT ASN 16 OD1 ) 15.084 ( PROT ASN 16 ND2 ) 15.084 ( PROT ASN 16 HD21 ) 15.084 ( PROT ASN 16 HD22 ) 15.084 ( PROT ASN 16 C ) 18.855 ( PROT ASN 16 O ) 18.855 ( PROT ARG 17 N ) 18.855 ( PROT ARG 17 H ) 15.084 ( PROT ARG 17 CA ) 18.855 ( PROT ARG 17 CB ) 15.084 ( PROT ARG 17 CG ) 15.084 ( PROT ARG 17 CD ) 15.084 ( PROT ARG 17 NE ) 15.084 ( PROT ARG 17 HE ) 15.084 ( PROT ARG 17 CZ ) 15.084 ( PROT ARG 17 NH1 ) 15.084 ( PROT ARG 17 HH11 ) 15.084 ( PROT ARG 17 HH12 ) 15.084 ( PROT ARG 17 NH2 ) 15.084 ( PROT ARG 17 HH21 ) 15.084 ( PROT ARG 17 HH22 ) 15.084 ( PROT ARG 17 C ) 18.855 ( PROT ARG 17 OT1 ) 15.084 ( PROT ARG 17 OT2 ) 15.084 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96358 3.71198 -6.80241 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00024 -0.00066 0.00041 ROTATION MATRIX 1.000000 -0.000093 -0.000174 0.000093 1.000000 0.000311 0.000174 -0.000311 1.000000 AXIS OF ROTATION IS 0.844507 0.472894 -0.251354 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 5.1383 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.177005 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1770" Parameter: A <- "0.1770" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.76859 3.78058 -6.96623 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS 0.00359 0.01112 -0.01100 ROTATION MATRIX 0.999741 0.015419 0.016734 -0.015111 0.999717 -0.018367 -0.017012 0.018109 0.999691 AXIS OF ROTATION IS -0.625438 -0.578616 0.523479 ANGLE IS 1.67 CENTER OF ROTATION 7.788964 3.614689 -7.139047 SHIFT IS -0.014441 TOTAL SQUARE DIFF IS 0.1782 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.102387 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1770" RDCMND substituted energy or value "?RMS" to " 0.1024" Parameter: A <- "0.1770 0.1024" 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 0.1770 0.1024 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 " 137.14" Parameter: H <- "137.14" 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> 0 111.61009 137.14225 5.48529 ENER INTERN> 17.79137 46.26818 0.00000 8.70385 7.02818 ENER EXTERN> 55.92418 -24.10567 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 " 111.61" Parameter: B <- "111.61" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -24.11" Parameter: C <- "-24.11" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 55.92" Parameter: C <- " 31.81" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 31.81" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 17.79" Parameter: D <- "17.79" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 46.27" Parameter: D <- " 64.06" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 8.70" Parameter: D <- " 72.76" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.03" Parameter: D <- " 79.79" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 79.79" 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= 3600 ENER= 111.61 GRMS= 5.49 ELEC= -24.11 VDW= 55.92 RDTITL> *EXTERNAL= 31.81 INTERNAL= 79.79 USER= 0.00 HARM= 137.14 RDTITL> *BOND= 17.79 ANGL= 46.27 DIHE= 8.70 IMPR= 7.03 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= 111.61 GRMS= 5.49 ELEC= -24.11 VDW= 55.92 RDTITL> *EXTERNAL= 31.81 INTERNAL= 79.79 USER= 0.00 HARM= 137.14 RDTITL> *BOND= 17.79 ANGL= 46.27 DIHE= 8.70 IMPR= 7.03 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= 111.61 GRMS= 5.49 ELEC= -24.11 VDW= 55.92 RDTITL> *EXTERNAL= 31.81 INTERNAL= 79.79 USER= 0.00 HARM= 137.14 RDTITL> *BOND= 17.79 ANGL= 46.27 DIHE= 8.70 IMPR= 7.03 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 3600 0.1770 0.1024 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "3600" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9338 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9339 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 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> 0 234.94071 -123.33062 2.83110 0.02000 MINI INTERN> 17.79137 46.26818 0.00000 8.70385 7.02818 MINI EXTERN> 55.92418 -24.10567 0.00000 0.00000 0.00000 MINI CONSTR> 123.33062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 215.00623 19.93448 2.39580 0.00360 MINI INTERN> 17.32706 47.47433 0.00000 10.47205 7.52256 MINI EXTERN> 30.32047 -24.12568 0.00000 0.00000 0.00000 MINI CONSTR> 126.01544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9327 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 210.58383 4.42240 5.91314 0.00373 MINI INTERN> 18.18347 43.81239 0.00000 10.82472 7.32079 MINI EXTERN> 31.35004 -24.69402 0.00000 0.00000 0.00000 MINI CONSTR> 123.78645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 206.89227 3.69156 5.95049 0.00387 MINI INTERN> 13.18322 45.22503 0.00000 11.07428 7.22729 MINI EXTERN> 32.78024 -25.46529 0.00000 0.00000 0.00000 MINI CONSTR> 122.86750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 201.40115 5.49112 2.24292 0.00167 MINI INTERN> 16.25755 42.50690 0.00000 10.45681 7.72758 MINI EXTERN> 27.24880 -25.47278 0.00000 0.00000 0.00000 MINI CONSTR> 122.67630 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 199.21669 2.18446 1.70443 0.00173 MINI INTERN> 15.51394 42.21242 0.00000 10.53289 7.74506 MINI EXTERN> 26.64909 -25.61207 0.00000 0.00000 0.00000 MINI CONSTR> 122.17536 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9327 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 198.13688 1.07981 2.62263 0.00180 MINI INTERN> 16.63433 41.63575 0.00000 10.45155 7.83574 MINI EXTERN> 25.36873 -25.68563 0.00000 0.00000 0.00000 MINI CONSTR> 121.89640 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 196.50025 1.63663 0.79423 0.00078 MINI INTERN> 13.52160 42.29424 0.00000 10.72818 7.64538 MINI EXTERN> 26.69709 -25.83787 0.00000 0.00000 0.00000 MINI CONSTR> 121.45164 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9327 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 195.70228 0.79797 0.62162 0.00080 MINI INTERN> 13.65619 42.02850 0.00000 10.70566 7.64901 MINI EXTERN> 26.26861 -25.88411 0.00000 0.00000 0.00000 MINI CONSTR> 121.27841 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 195.03226 0.67003 1.22478 0.00083 MINI INTERN> 12.86798 42.22403 0.00000 10.77899 7.58631 MINI EXTERN> 26.46273 -25.96277 0.00000 0.00000 0.00000 MINI CONSTR> 121.07498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 194.53979 0.49247 1.27110 0.00087 MINI INTERN> 12.78031 42.16053 0.00000 10.77098 7.57265 MINI EXTERN> 26.26125 -26.00087 0.00000 0.00000 0.00000 MINI CONSTR> 120.99495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 194.20607 0.33372 1.47531 0.00090 MINI INTERN> 12.61424 42.18962 0.00000 10.77327 7.55408 MINI EXTERN> 26.15468 -26.03396 0.00000 0.00000 0.00000 MINI CONSTR> 120.95414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 193.94139 0.26468 1.38699 0.00093 MINI INTERN> 12.64450 42.05824 0.00000 10.75586 7.52896 MINI EXTERN> 26.05982 -26.04546 0.00000 0.00000 0.00000 MINI CONSTR> 120.93948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 193.57095 0.37044 0.44685 0.00040 MINI INTERN> 14.06853 41.22486 0.00000 10.58650 7.57271 MINI EXTERN> 25.12836 -26.02733 0.00000 0.00000 0.00000 MINI CONSTR> 121.01733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 193.40568 0.16527 0.35815 0.00042 MINI INTERN> 13.97059 41.21144 0.00000 10.57973 7.54934 MINI EXTERN> 25.09472 -26.04176 0.00000 0.00000 0.00000 MINI CONSTR> 121.04163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 193.27478 0.13091 0.40850 0.00043 MINI INTERN> 14.00736 41.12469 0.00000 10.56074 7.52324 MINI EXTERN> 25.02442 -26.04883 0.00000 0.00000 0.00000 MINI CONSTR> 121.08316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 193.20179 0.07299 0.60133 0.00045 MINI INTERN> 14.18238 40.97983 0.00000 10.53319 7.50063 MINI EXTERN> 24.92387 -26.04838 0.00000 0.00000 0.00000 MINI CONSTR> 121.13028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 193.10013 0.10166 0.18479 0.00019 MINI INTERN> 13.73260 41.24735 0.00000 10.55171 7.50534 MINI EXTERN> 24.94310 -26.07399 0.00000 0.00000 0.00000 MINI CONSTR> 121.19402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 193.04577 0.05436 0.15974 0.00020 MINI INTERN> 13.74836 41.20629 0.00000 10.53765 7.49024 MINI EXTERN> 24.89028 -26.07477 0.00000 0.00000 0.00000 MINI CONSTR> 121.24773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 193.00339 0.04238 0.28649 0.00021 MINI INTERN> 13.66454 41.25153 0.00000 10.52983 7.48391 MINI EXTERN> 24.83891 -26.08180 0.00000 0.00000 0.00000 MINI CONSTR> 121.31647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 192.97201 0.03137 0.32141 0.00022 MINI INTERN> 13.65724 41.24598 0.00000 10.51738 7.47271 MINI EXTERN> 24.79615 -26.08869 0.00000 0.00000 0.00000 MINI CONSTR> 121.37124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 192.94598 0.02603 0.32806 0.00022 MINI INTERN> 13.62033 41.25136 0.00000 10.50930 7.46449 MINI EXTERN> 24.75917 -26.08636 0.00000 0.00000 0.00000 MINI CONSTR> 121.42769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 192.92356 0.02242 0.34448 0.00023 MINI INTERN> 13.64515 41.20729 0.00000 10.49866 7.45126 MINI EXTERN> 24.71954 -26.07966 0.00000 0.00000 0.00000 MINI CONSTR> 121.48133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 192.89694 0.02662 0.09753 0.00010 MINI INTERN> 13.80144 41.06468 0.00000 10.47743 7.42729 MINI EXTERN> 24.67546 -26.06850 0.00000 0.00000 0.00000 MINI CONSTR> 121.51914 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 192.89135 0.00559 0.39585 0.00025 MINI INTERN> 13.63417 41.17634 0.00000 10.47912 7.43262 MINI EXTERN> 24.64700 -26.06466 0.00000 0.00000 0.00000 MINI CONSTR> 121.58676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 192.86575 0.02559 0.11784 0.00011 MINI INTERN> 13.83025 41.01199 0.00000 10.45585 7.40479 MINI EXTERN> 24.59886 -26.06032 0.00000 0.00000 0.00000 MINI CONSTR> 121.62433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 192.85386 0.01190 0.12015 0.00011 MINI INTERN> 13.83165 40.99454 0.00000 10.44722 7.39603 MINI EXTERN> 24.56514 -26.05318 0.00000 0.00000 0.00000 MINI CONSTR> 121.67246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 192.84345 0.01041 0.13085 0.00012 MINI INTERN> 13.84644 40.97227 0.00000 10.43789 7.38638 MINI EXTERN> 24.53126 -26.04940 0.00000 0.00000 0.00000 MINI CONSTR> 121.71861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 192.83297 0.01049 0.12196 0.00012 MINI INTERN> 13.83412 40.96574 0.00000 10.43024 7.37881 MINI EXTERN> 24.49842 -26.04237 0.00000 0.00000 0.00000 MINI CONSTR> 121.76800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 192.82561 0.00735 0.17065 0.00012 MINI INTERN> 13.87240 40.92853 0.00000 10.42007 7.36767 MINI EXTERN> 24.46456 -26.03805 0.00000 0.00000 0.00000 MINI CONSTR> 121.81045 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 192.81901 0.00660 0.22850 0.00013 MINI INTERN> 13.85149 40.92256 0.00000 10.41409 7.36216 MINI EXTERN> 24.43469 -26.02246 0.00000 0.00000 0.00000 MINI CONSTR> 121.85647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 192.81227 0.00674 0.22290 0.00013 MINI INTERN> 13.83590 40.92432 0.00000 10.40893 7.35741 MINI EXTERN> 24.40978 -26.01770 0.00000 0.00000 0.00000 MINI CONSTR> 121.89362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9324 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 192.80501 0.00725 0.19485 0.00014 MINI INTERN> 13.88264 40.88351 0.00000 10.39894 7.34633 MINI EXTERN> 24.37727 -26.01482 0.00000 0.00000 0.00000 MINI CONSTR> 121.93115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 192.79590 0.00912 0.06579 0.00006 MINI INTERN> 13.75082 40.97664 0.00000 10.40149 7.35177 MINI EXTERN> 24.36227 -26.02049 0.00000 0.00000 0.00000 MINI CONSTR> 121.97339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9324 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 192.79061 0.00529 0.05640 0.00006 MINI INTERN> 13.75764 40.96239 0.00000 10.39564 7.34565 MINI EXTERN> 24.33839 -26.01458 0.00000 0.00000 0.00000 MINI CONSTR> 122.00548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 192.78500 0.00561 0.05653 0.00006 MINI INTERN> 13.75427 40.95534 0.00000 10.38990 7.33990 MINI EXTERN> 24.31243 -26.00861 0.00000 0.00000 0.00000 MINI CONSTR> 122.04178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9324 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 192.77977 0.00522 0.05670 0.00007 MINI INTERN> 13.74966 40.94856 0.00000 10.38454 7.33457 MINI EXTERN> 24.28756 -26.00167 0.00000 0.00000 0.00000 MINI CONSTR> 122.07655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 192.77461 0.00516 0.05263 0.00007 MINI INTERN> 13.75248 40.93686 0.00000 10.37870 7.32860 MINI EXTERN> 24.26180 -25.99477 0.00000 0.00000 0.00000 MINI CONSTR> 122.11095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9324 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 192.76974 0.00487 0.09646 0.00007 MINI INTERN> 13.71160 40.95765 0.00000 10.37527 7.32612 MINI EXTERN> 24.23714 -25.98907 0.00000 0.00000 0.00000 MINI CONSTR> 122.15104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 192.76458 0.00516 0.06122 0.00007 MINI INTERN> 13.73696 40.92856 0.00000 10.36827 7.31843 MINI EXTERN> 24.21037 -25.98045 0.00000 0.00000 0.00000 MINI CONSTR> 122.18244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9324 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 192.76025 0.00434 0.08782 0.00008 MINI INTERN> 13.71246 40.93602 0.00000 10.36446 7.31520 MINI EXTERN> 24.18683 -25.97246 0.00000 0.00000 0.00000 MINI CONSTR> 122.21772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 192.75665 0.00360 0.11853 0.00008 MINI INTERN> 13.70320 40.93901 0.00000 10.36021 7.31113 MINI EXTERN> 24.16489 -25.97003 0.00000 0.00000 0.00000 MINI CONSTR> 122.24824 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9324 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 192.75293 0.00371 0.12203 0.00008 MINI INTERN> 13.68547 40.94189 0.00000 10.35681 7.30811 MINI EXTERN> 24.14437 -25.96184 0.00000 0.00000 0.00000 MINI CONSTR> 122.27812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 192.74942 0.00351 0.14143 0.00009 MINI INTERN> 13.68325 40.92907 0.00000 10.35238 7.30371 MINI EXTERN> 24.12178 -25.94865 0.00000 0.00000 0.00000 MINI CONSTR> 122.30788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9324 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 192.74574 0.00368 0.12263 0.00009 MINI INTERN> 13.67761 40.93032 0.00000 10.34857 7.29997 MINI EXTERN> 24.10251 -25.94699 0.00000 0.00000 0.00000 MINI CONSTR> 122.33376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 192.74265 0.00309 0.16097 0.00009 MINI INTERN> 13.66993 40.92138 0.00000 10.34439 7.29602 MINI EXTERN> 24.07864 -25.93303 0.00000 0.00000 0.00000 MINI CONSTR> 122.36532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 192.73938 0.00327 0.14731 0.00010 MINI INTERN> 13.67387 40.91111 0.00000 10.34047 7.29192 MINI EXTERN> 24.06014 -25.92642 0.00000 0.00000 0.00000 MINI CONSTR> 122.38828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 192.73686 0.00252 0.17246 0.00010 MINI INTERN> 13.70205 40.89474 0.00000 10.33465 7.28529 MINI EXTERN> 24.03957 -25.92980 0.00000 0.00000 0.00000 MINI CONSTR> 122.41036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 192.73196 0.00489 0.04699 0.00004 MINI INTERN> 13.75339 40.83759 0.00000 10.32775 7.27688 MINI EXTERN> 24.01645 -25.91101 0.00000 0.00000 0.00000 MINI CONSTR> 122.43091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 192.72934 0.00262 0.04004 0.00004 MINI INTERN> 13.74336 40.83788 0.00000 10.32509 7.27444 MINI EXTERN> 24.00032 -25.90457 0.00000 0.00000 0.00000 MINI CONSTR> 122.45283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 192.72666 0.00268 0.04007 0.00005 MINI INTERN> 13.74207 40.83173 0.00000 10.32164 7.27098 MINI EXTERN> 23.98229 -25.89770 0.00000 0.00000 0.00000 MINI CONSTR> 122.47566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 192.72398 0.00268 0.03749 0.00005 MINI INTERN> 13.73564 40.82877 0.00000 10.31851 7.26797 MINI EXTERN> 23.96444 -25.89035 0.00000 0.00000 0.00000 MINI CONSTR> 122.49899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 192.72137 0.00261 0.06497 0.00005 MINI INTERN> 13.75815 40.80342 0.00000 10.31314 7.26195 MINI EXTERN> 23.94204 -25.88061 0.00000 0.00000 0.00000 MINI CONSTR> 122.52327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 192.71903 0.00234 0.03671 0.00005 MINI INTERN> 13.72969 40.81862 0.00000 10.31216 7.26170 MINI EXTERN> 23.92974 -25.87594 0.00000 0.00000 0.00000 MINI CONSTR> 122.54306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 192.71689 0.00214 0.08021 0.00005 MINI INTERN> 13.75232 40.79134 0.00000 10.30713 7.25602 MINI EXTERN> 23.90850 -25.86410 0.00000 0.00000 0.00000 MINI CONSTR> 122.56568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 192.71478 0.00211 0.07936 0.00006 MINI INTERN> 13.75612 40.78263 0.00000 10.30387 7.25263 MINI EXTERN> 23.89218 -25.85777 0.00000 0.00000 0.00000 MINI CONSTR> 122.58511 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 192.71283 0.00195 0.08909 0.00006 MINI INTERN> 13.75738 40.77899 0.00000 10.30077 7.24946 MINI EXTERN> 23.87631 -25.85446 0.00000 0.00000 0.00000 MINI CONSTR> 122.60438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 192.71093 0.00190 0.08991 0.00006 MINI INTERN> 13.75925 40.77046 0.00000 10.29784 7.24646 MINI EXTERN> 23.86087 -25.84685 0.00000 0.00000 0.00000 MINI CONSTR> 122.62289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 192.70908 0.00185 0.09088 0.00006 MINI INTERN> 13.75806 40.76214 0.00000 10.29517 7.24380 MINI EXTERN> 23.84567 -25.83730 0.00000 0.00000 0.00000 MINI CONSTR> 122.64155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 192.70730 0.00178 0.09771 0.00006 MINI INTERN> 13.74800 40.76838 0.00000 10.29305 7.24190 MINI EXTERN> 23.83210 -25.83582 0.00000 0.00000 0.00000 MINI CONSTR> 122.65969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 192.70549 0.00180 0.08894 0.00007 MINI INTERN> 13.75324 40.75554 0.00000 10.29010 7.23879 MINI EXTERN> 23.81694 -25.82623 0.00000 0.00000 0.00000 MINI CONSTR> 122.67712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 192.70326 0.00223 0.03147 0.00003 MINI INTERN> 13.68973 40.79810 0.00000 10.29176 7.24210 MINI EXTERN> 23.80958 -25.82421 0.00000 0.00000 0.00000 MINI CONSTR> 122.69621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 192.70239 0.00087 0.09884 0.00007 MINI INTERN> 13.75510 40.74146 0.00000 10.28488 7.23343 MINI EXTERN> 23.78854 -25.81216 0.00000 0.00000 0.00000 MINI CONSTR> 122.71114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 192.69994 0.00244 0.03217 0.00003 MINI INTERN> 13.68216 40.79158 0.00000 10.28699 7.23747 MINI EXTERN> 23.78112 -25.81097 0.00000 0.00000 0.00000 MINI CONSTR> 122.73160 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 192.69937 0.00057 0.10562 0.00008 MINI INTERN> 13.75369 40.73000 0.00000 10.27992 7.22838 MINI EXTERN> 23.76062 -25.79828 0.00000 0.00000 0.00000 MINI CONSTR> 122.74505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 192.69678 0.00260 0.03099 0.00003 MINI INTERN> 13.67653 40.78339 0.00000 10.28218 7.23273 MINI EXTERN> 23.75264 -25.79723 0.00000 0.00000 0.00000 MINI CONSTR> 122.76653 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 192.69548 0.00129 0.02694 0.00003 MINI INTERN> 13.67917 40.77646 0.00000 10.27986 7.23031 MINI EXTERN> 23.74040 -25.79143 0.00000 0.00000 0.00000 MINI CONSTR> 122.78070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 192.69421 0.00127 0.04757 0.00004 MINI INTERN> 13.65848 40.78705 0.00000 10.27877 7.22978 MINI EXTERN> 23.72866 -25.78651 0.00000 0.00000 0.00000 MINI CONSTR> 122.79798 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 192.69300 0.00122 0.04112 0.00004 MINI INTERN> 13.66229 40.77761 0.00000 10.27655 7.22740 MINI EXTERN> 23.71669 -25.77897 0.00000 0.00000 0.00000 MINI CONSTR> 122.81144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 192.69197 0.00103 0.05274 0.00004 MINI INTERN> 13.64949 40.78396 0.00000 10.27534 7.22652 MINI EXTERN> 23.70642 -25.77537 0.00000 0.00000 0.00000 MINI CONSTR> 122.82561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 192.69072 0.00125 0.03971 0.00004 MINI INTERN> 13.65872 40.77013 0.00000 10.27271 7.22359 MINI EXTERN> 23.69401 -25.76739 0.00000 0.00000 0.00000 MINI CONSTR> 122.83895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 192.68990 0.00082 0.06250 0.00004 MINI INTERN> 13.64510 40.77523 0.00000 10.27173 7.22298 MINI EXTERN> 23.68470 -25.76208 0.00000 0.00000 0.00000 MINI CONSTR> 122.85224 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 192.68891 0.00099 0.05900 0.00004 MINI INTERN> 13.63797 40.77885 0.00000 10.27033 7.22174 MINI EXTERN> 23.67489 -25.75972 0.00000 0.00000 0.00000 MINI CONSTR> 122.86484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 192.68807 0.00084 0.07760 0.00004 MINI INTERN> 13.63833 40.77065 0.00000 10.26858 7.21987 MINI EXTERN> 23.66258 -25.75011 0.00000 0.00000 0.00000 MINI CONSTR> 122.87816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 192.68720 0.00086 0.07392 0.00005 MINI INTERN> 13.64085 40.76474 0.00000 10.26689 7.21805 MINI EXTERN> 23.65311 -25.74504 0.00000 0.00000 0.00000 MINI CONSTR> 122.88860 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 192.68633 0.00087 0.07069 0.00005 MINI INTERN> 13.63462 40.77032 0.00000 10.26548 7.21680 MINI EXTERN> 23.64447 -25.74544 0.00000 0.00000 0.00000 MINI CONSTR> 122.90009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 192.68519 0.00114 0.02141 0.00002 MINI INTERN> 13.66784 40.73757 0.00000 10.26178 7.21215 MINI EXTERN> 23.63301 -25.73597 0.00000 0.00000 0.00000 MINI CONSTR> 122.90881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 192.68489 0.00030 0.08459 0.00005 MINI INTERN> 13.63708 40.76169 0.00000 10.26204 7.21326 MINI EXTERN> 23.62618 -25.73700 0.00000 0.00000 0.00000 MINI CONSTR> 122.92163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 192.68408 0.00081 0.07542 0.00005 MINI INTERN> 13.61488 40.77168 0.00000 10.26191 7.21372 MINI EXTERN> 23.61867 -25.73059 0.00000 0.00000 0.00000 MINI CONSTR> 122.93382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 192.68284 0.00124 0.02456 0.00002 MINI INTERN> 13.66552 40.72653 0.00000 10.25706 7.20734 MINI EXTERN> 23.60439 -25.72041 0.00000 0.00000 0.00000 MINI CONSTR> 122.94239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 192.68221 0.00062 0.01993 0.00002 MINI INTERN> 13.65985 40.72785 0.00000 10.25614 7.20654 MINI EXTERN> 23.59727 -25.71693 0.00000 0.00000 0.00000 MINI CONSTR> 122.95151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 192.68154 0.00068 0.01919 0.00002 MINI INTERN> 13.65680 40.72615 0.00000 10.25487 7.20531 MINI EXTERN> 23.58881 -25.71215 0.00000 0.00000 0.00000 MINI CONSTR> 122.96175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 192.68090 0.00063 0.03394 0.00003 MINI INTERN> 13.66776 40.71358 0.00000 10.25260 7.20266 MINI EXTERN> 23.57839 -25.70618 0.00000 0.00000 0.00000 MINI CONSTR> 122.97210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 192.68031 0.00060 0.01727 0.00003 MINI INTERN> 13.65160 40.72307 0.00000 10.25248 7.20295 MINI EXTERN> 23.57289 -25.70356 0.00000 0.00000 0.00000 MINI CONSTR> 122.98088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 192.67969 0.00061 0.03835 0.00003 MINI INTERN> 13.66707 40.70680 0.00000 10.24983 7.19978 MINI EXTERN> 23.56141 -25.69689 0.00000 0.00000 0.00000 MINI CONSTR> 122.99170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 192.67910 0.00059 0.03241 0.00003 MINI INTERN> 13.65594 40.71078 0.00000 10.24927 7.19950 MINI EXTERN> 23.55469 -25.69224 0.00000 0.00000 0.00000 MINI CONSTR> 123.00117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 192.67872 0.00039 0.04645 0.00003 MINI INTERN> 13.65726 40.70587 0.00000 10.24807 7.19820 MINI EXTERN> 23.54765 -25.68741 0.00000 0.00000 0.00000 MINI CONSTR> 123.00907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 192.67824 0.00048 0.04523 0.00003 MINI INTERN> 13.66026 40.70081 0.00000 10.24671 7.19670 MINI EXTERN> 23.54036 -25.68359 0.00000 0.00000 0.00000 MINI CONSTR> 123.01698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 192.67779 0.00045 0.04642 0.00003 MINI INTERN> 13.66103 40.69998 0.00000 10.24550 7.19541 MINI EXTERN> 23.53346 -25.68227 0.00000 0.00000 0.00000 MINI CONSTR> 123.02467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 192.67735 0.00044 0.04433 0.00003 MINI INTERN> 13.66134 40.69461 0.00000 10.24441 7.19424 MINI EXTERN> 23.52654 -25.67631 0.00000 0.00000 0.00000 MINI CONSTR> 123.03253 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 192.67679 0.00056 0.01574 0.00001 MINI INTERN> 13.63129 40.71605 0.00000 10.24530 7.19595 MINI EXTERN> 23.52312 -25.67587 0.00000 0.00000 0.00000 MINI CONSTR> 123.04095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 192.67657 0.00023 0.04894 0.00004 MINI INTERN> 13.66264 40.68845 0.00000 10.24219 7.19185 MINI EXTERN> 23.51323 -25.66924 0.00000 0.00000 0.00000 MINI CONSTR> 123.04744 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 192.67595 0.00061 0.01556 0.00002 MINI INTERN> 13.62746 40.71289 0.00000 10.24334 7.19396 MINI EXTERN> 23.50976 -25.66816 0.00000 0.00000 0.00000 MINI CONSTR> 123.05672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 192.67582 0.00013 0.05553 0.00004 MINI INTERN> 13.65984 40.68603 0.00000 10.24021 7.18982 MINI EXTERN> 23.50037 -25.66302 0.00000 0.00000 0.00000 MINI CONSTR> 123.06257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 192.67524 0.00058 0.01986 0.00002 MINI INTERN> 13.62119 40.71265 0.00000 10.24175 7.19243 MINI EXTERN> 23.49803 -25.66178 0.00000 0.00000 0.00000 MINI CONSTR> 123.07098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 192.67492 0.00032 0.01729 0.00002 MINI INTERN> 13.62077 40.71018 0.00000 10.24091 7.19154 MINI EXTERN> 23.49260 -25.65825 0.00000 0.00000 0.00000 MINI CONSTR> 123.07718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 192.67462 0.00031 0.01277 0.00002 MINI INTERN> 13.62442 40.70506 0.00000 10.23983 7.19029 MINI EXTERN> 23.48696 -25.65492 0.00000 0.00000 0.00000 MINI CONSTR> 123.08297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 192.67431 0.00031 0.02542 0.00002 MINI INTERN> 13.61295 40.71155 0.00000 10.23953 7.19024 MINI EXTERN> 23.48147 -25.65229 0.00000 0.00000 0.00000 MINI CONSTR> 123.09085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 192.67402 0.00029 0.02066 0.00002 MINI INTERN> 13.61373 40.70799 0.00000 10.23867 7.18930 MINI EXTERN> 23.47627 -25.64858 0.00000 0.00000 0.00000 MINI CONSTR> 123.09663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 192.67377 0.00024 0.02940 0.00002 MINI INTERN> 13.60973 40.70972 0.00000 10.23805 7.18874 MINI EXTERN> 23.47132 -25.64666 0.00000 0.00000 0.00000 MINI CONSTR> 123.10287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 192.67352 0.00025 0.02958 0.00002 MINI INTERN> 13.60545 40.71034 0.00000 10.23754 7.18828 MINI EXTERN> 23.46669 -25.64352 0.00000 0.00000 0.00000 MINI CONSTR> 123.10873 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> 500 192.67352 0.00025 0.02958 0.00002 STPD INTERN> 13.60545 40.71034 0.00000 10.23754 7.18828 STPD EXTERN> 23.46669 -25.64352 0.00000 0.00000 0.00000 STPD CONSTR> 123.10873 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 9325 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9325 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 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> 0 192.67352 0.00025 0.02958 0.00000 MINI INTERN> 13.60545 40.71034 0.00000 10.23754 7.18828 MINI EXTERN> 23.46669 -25.64352 0.00000 0.00000 0.00000 MINI CONSTR> 123.10873 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> 4 192.66857 0.00495 0.00722 0.02000 CONJ INTERN> 13.56526 40.64646 0.00000 10.21057 7.16302 CONJ EXTERN> 23.26054 -25.52272 0.00000 0.00000 0.00000 CONJ CONSTR> 123.34544 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 ASP 1 HT1 ) 9.8045 ( PROT ASP 1 HT2 ) 9.8045 ( PROT ASP 1 N ) 12.256 ( PROT ASP 1 HT3 ) 9.8045 ( PROT ASP 1 CA ) 12.256 ( PROT ASP 1 CB ) 9.8045 ( PROT ASP 1 CG ) 9.8045 ( PROT ASP 1 OD1 ) 9.8045 ( PROT ASP 1 OD2 ) 9.8045 ( PROT ASP 1 C ) 12.256 ( PROT ASP 1 O ) 12.256 ( PROT TYR 2 N ) 12.256 ( PROT TYR 2 H ) 9.8045 ( PROT TYR 2 CA ) 12.256 ( PROT TYR 2 CB ) 9.8045 ( PROT TYR 2 CG ) 9.8045 ( PROT TYR 2 CD1 ) 9.8045 ( PROT TYR 2 CE1 ) 9.8045 ( PROT TYR 2 CD2 ) 9.8045 ( PROT TYR 2 CE2 ) 9.8045 ( PROT TYR 2 CZ ) 9.8045 ( PROT TYR 2 OH ) 9.8045 ( PROT TYR 2 HH ) 9.8045 ( PROT TYR 2 C ) 12.256 ( PROT TYR 2 O ) 12.256 ( PROT ALA 3 N ) 12.256 ( PROT ALA 3 H ) 9.8045 ( PROT ALA 3 CA ) 12.256 ( PROT ALA 3 CB ) 9.8045 ( PROT ALA 3 C ) 12.256 ( PROT ALA 3 O ) 12.256 ( PROT PHE 4 N ) 12.256 ( PROT PHE 4 H ) 9.8045 ( PROT PHE 4 CA ) 12.256 ( PROT PHE 4 CB ) 9.8045 ( PROT PHE 4 CG ) 9.8045 ( PROT PHE 4 CD1 ) 9.8045 ( PROT PHE 4 CD2 ) 9.8045 ( PROT PHE 4 CE1 ) 9.8045 ( PROT PHE 4 CE2 ) 9.8045 ( PROT PHE 4 CZ ) 9.8045 ( PROT PHE 4 C ) 12.256 ( PROT PHE 4 O ) 12.256 ( PROT ILE 5 N ) 12.256 ( PROT ILE 5 H ) 9.8045 ( PROT ILE 5 CA ) 12.256 ( PROT ILE 5 CB ) 9.8045 ( PROT ILE 5 CG2 ) 9.8045 ( PROT ILE 5 CG1 ) 9.8045 ( PROT ILE 5 CD ) 9.8045 ( PROT ILE 5 C ) 12.256 ( PROT ILE 5 O ) 12.256 ( PROT ALA 6 N ) 12.256 ( PROT ALA 6 H ) 9.8045 ( PROT ALA 6 CA ) 12.256 ( PROT ALA 6 CB ) 9.8045 ( PROT ALA 6 C ) 12.256 ( PROT ALA 6 O ) 12.256 ( PROT SER 7 N ) 12.256 ( PROT SER 7 H ) 9.8045 ( PROT SER 7 CA ) 12.256 ( PROT SER 7 CB ) 9.8045 ( PROT SER 7 OG ) 9.8045 ( PROT SER 7 HG ) 9.8045 ( PROT SER 7 C ) 12.256 ( PROT SER 7 O ) 12.256 ( PROT LEU 8 N ) 12.256 ( PROT LEU 8 H ) 9.8045 ( PROT LEU 8 CA ) 12.256 ( PROT LEU 8 CB ) 9.8045 ( PROT LEU 8 CG ) 9.8045 ( PROT LEU 8 CD1 ) 9.8045 ( PROT LEU 8 CD2 ) 9.8045 ( PROT LEU 8 C ) 12.256 ( PROT LEU 8 O ) 12.256 ( PROT VAL 9 N ) 12.256 ( PROT VAL 9 H ) 9.8045 ( PROT VAL 9 CA ) 12.256 ( PROT VAL 9 CB ) 9.8045 ( PROT VAL 9 CG1 ) 9.8045 ( PROT VAL 9 CG2 ) 9.8045 ( PROT VAL 9 C ) 12.256 ( PROT VAL 9 O ) 12.256 ( PROT VAL 10 N ) 12.256 ( PROT VAL 10 H ) 9.8045 ( PROT VAL 10 CA ) 12.256 ( PROT VAL 10 CB ) 9.8045 ( PROT VAL 10 CG1 ) 9.8045 ( PROT VAL 10 CG2 ) 9.8045 ( PROT VAL 10 C ) 12.256 ( PROT VAL 10 O ) 12.256 ( PROT ILE 11 N ) 12.256 ( PROT ILE 11 H ) 9.8045 ( PROT ILE 11 CA ) 12.256 ( PROT ILE 11 CB ) 9.8045 ( PROT ILE 11 CG2 ) 9.8045 ( PROT ILE 11 CG1 ) 9.8045 ( PROT ILE 11 CD ) 9.8045 ( PROT ILE 11 C ) 12.256 ( PROT ILE 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 ASP 13 N ) 12.256 ( PROT ASP 13 H ) 9.8045 ( PROT ASP 13 CA ) 12.256 ( PROT ASP 13 CB ) 9.8045 ( PROT ASP 13 CG ) 9.8045 ( PROT ASP 13 OD1 ) 9.8045 ( PROT ASP 13 OD2 ) 9.8045 ( PROT ASP 13 C ) 12.256 ( PROT ASP 13 O ) 12.256 ( PROT ASP 14 N ) 12.256 ( PROT ASP 14 H ) 9.8045 ( PROT ASP 14 CA ) 12.256 ( PROT ASP 14 CB ) 9.8045 ( PROT ASP 14 CG ) 9.8045 ( PROT ASP 14 OD1 ) 9.8045 ( PROT ASP 14 OD2 ) 9.8045 ( PROT ASP 14 C ) 12.256 ( PROT ASP 14 O ) 12.256 ( PROT VAL 15 N ) 12.256 ( PROT VAL 15 H ) 9.8045 ( PROT VAL 15 CA ) 12.256 ( PROT VAL 15 CB ) 9.8045 ( PROT VAL 15 CG1 ) 9.8045 ( PROT VAL 15 CG2 ) 9.8045 ( PROT VAL 15 C ) 12.256 ( PROT VAL 15 O ) 12.256 ( PROT ASN 16 N ) 12.256 ( PROT ASN 16 H ) 9.8045 ( PROT ASN 16 CA ) 12.256 ( PROT ASN 16 CB ) 9.8045 ( PROT ASN 16 CG ) 9.8045 ( PROT ASN 16 OD1 ) 9.8045 ( PROT ASN 16 ND2 ) 9.8045 ( PROT ASN 16 HD21 ) 9.8045 ( PROT ASN 16 HD22 ) 9.8045 ( PROT ASN 16 C ) 12.256 ( PROT ASN 16 O ) 12.256 ( PROT ARG 17 N ) 12.256 ( PROT ARG 17 H ) 9.8045 ( PROT ARG 17 CA ) 12.256 ( PROT ARG 17 CB ) 9.8045 ( PROT ARG 17 CG ) 9.8045 ( PROT ARG 17 CD ) 9.8045 ( PROT ARG 17 NE ) 9.8045 ( PROT ARG 17 HE ) 9.8045 ( PROT ARG 17 CZ ) 9.8045 ( PROT ARG 17 NH1 ) 9.8045 ( PROT ARG 17 HH11 ) 9.8045 ( PROT ARG 17 HH12 ) 9.8045 ( PROT ARG 17 NH2 ) 9.8045 ( PROT ARG 17 HH21 ) 9.8045 ( PROT ARG 17 HH22 ) 9.8045 ( PROT ARG 17 C ) 12.256 ( PROT ARG 17 OT1 ) 9.8045 ( PROT ARG 17 OT2 ) 9.8045 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96254 3.71204 -6.80190 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00129 -0.00071 -0.00010 ROTATION MATRIX 1.000000 -0.000134 -0.000221 0.000134 1.000000 0.000414 0.000221 -0.000414 1.000000 AXIS OF ROTATION IS 0.848986 0.451845 -0.273969 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 7.0780 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.207746 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2077" Parameter: A <- "0.2077" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.77240 3.78076 -6.96557 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.00022 0.01095 -0.01166 ROTATION MATRIX 0.999704 0.016152 0.018210 -0.015789 0.999677 -0.019920 -0.018526 0.019626 0.999636 AXIS OF ROTATION IS -0.630530 -0.585733 0.509262 ANGLE IS 1.80 CENTER OF ROTATION 7.812330 3.548253 -7.195540 SHIFT IS -0.012212 TOTAL SQUARE DIFF IS 0.2477 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.120720 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2077" RDCMND substituted energy or value "?RMS" to " 0.1207" Parameter: A <- "0.2077 0.1207" 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 0.2077 0.1207 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 " 123.35" Parameter: H <- "123.35" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 69.32313 123.34544 4.20155 ENER INTERN> 13.56526 40.64646 0.00000 10.21057 7.16302 ENER EXTERN> 23.26054 -25.52272 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 " 69.32" Parameter: B <- "69.32" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -25.52" Parameter: C <- "-25.52" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 23.26" Parameter: C <- " -2.26" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -2.26" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 13.57" Parameter: D <- "13.57" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 40.65" Parameter: D <- " 54.22" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.21" Parameter: D <- " 64.43" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.16" Parameter: D <- " 71.59" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 71.59" 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= 4200 ENER= 69.32 GRMS= 4.20 ELEC= -25.52 VDW= 23.26 RDTITL> *EXTERNAL= -2.26 INTERNAL= 71.59 USER= 0.00 HARM= 123.35 RDTITL> *BOND= 13.57 ANGL= 40.65 DIHE= 10.21 IMPR= 7.16 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9325 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9326 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 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> 0 175.38261 -106.05948 2.07193 0.02000 MINI INTERN> 13.56526 40.64646 0.00000 10.21057 7.16302 MINI EXTERN> 23.26054 -25.52272 0.00000 0.00000 0.00000 MINI CONSTR> 106.05948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 162.25166 13.13095 2.05927 0.00360 MINI INTERN> 13.27166 40.20162 0.00000 11.68560 7.79853 MINI EXTERN> 4.50169 -25.22574 0.00000 0.00000 0.00000 MINI CONSTR> 110.01829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9311 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 159.93441 2.31725 5.45191 0.00373 MINI INTERN> 7.61400 42.61507 0.00000 12.02345 7.74136 MINI EXTERN> 6.36587 -25.92218 0.00000 0.00000 0.00000 MINI CONSTR> 109.49684 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 154.86736 5.06705 1.54188 0.00161 MINI INTERN> 11.88129 37.77395 0.00000 11.88899 7.57511 MINI EXTERN> 2.55602 -25.70112 0.00000 0.00000 0.00000 MINI CONSTR> 108.89313 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9306 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 152.91162 1.95574 2.18022 0.00167 MINI INTERN> 12.99528 36.71671 0.00000 11.87092 7.68858 MINI EXTERN> 0.82713 -25.60730 0.00000 0.00000 0.00000 MINI CONSTR> 108.42031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 151.38228 1.52935 2.52247 0.00173 MINI INTERN> 12.54131 36.85319 0.00000 11.79976 7.79938 MINI EXTERN> 0.16134 -25.80188 0.00000 0.00000 0.00000 MINI CONSTR> 108.02918 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9304 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 150.14423 1.23805 2.82544 0.00180 MINI INTERN> 12.77488 36.26512 0.00000 11.88808 7.73689 MINI EXTERN> -0.50457 -25.62724 0.00000 0.00000 0.00000 MINI CONSTR> 107.61106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 149.21884 0.92539 3.15283 0.00186 MINI INTERN> 12.71380 36.39208 0.00000 11.83977 7.71736 MINI EXTERN> -0.79018 -25.92639 0.00000 0.00000 0.00000 MINI CONSTR> 107.27241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9301 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 147.62374 1.59509 0.84249 0.00080 MINI INTERN> 10.43549 36.98305 0.00000 11.97735 7.63844 MINI EXTERN> -0.44199 -25.94410 0.00000 0.00000 0.00000 MINI CONSTR> 106.97552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 146.88016 0.74359 0.85562 0.00083 MINI INTERN> 10.30622 36.87471 0.00000 11.96877 7.61209 MINI EXTERN> -0.66404 -25.94496 0.00000 0.00000 0.00000 MINI CONSTR> 106.72736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9300 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 146.27593 0.60423 0.94887 0.00087 MINI INTERN> 10.07624 36.86224 0.00000 11.97161 7.57129 MINI EXTERN> -0.75917 -25.96343 0.00000 0.00000 0.00000 MINI CONSTR> 106.51715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 145.82142 0.45451 1.30735 0.00090 MINI INTERN> 9.80446 36.95255 0.00000 11.98127 7.52564 MINI EXTERN> -0.78092 -26.00383 0.00000 0.00000 0.00000 MINI CONSTR> 106.34226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9299 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 145.42944 0.39199 1.51944 0.00093 MINI INTERN> 9.62304 36.93183 0.00000 11.97901 7.49311 MINI EXTERN> -0.84690 -25.96478 0.00000 0.00000 0.00000 MINI CONSTR> 106.21413 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 145.06483 0.36460 1.40590 0.00096 MINI INTERN> 9.56605 36.86442 0.00000 11.96395 7.45262 MINI EXTERN> -0.90727 -25.98965 0.00000 0.00000 0.00000 MINI CONSTR> 106.11471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9298 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 144.58648 0.47836 0.41853 0.00042 MINI INTERN> 10.78492 36.04844 0.00000 11.79838 7.49716 MINI EXTERN> -1.67229 -25.94850 0.00000 0.00000 0.00000 MINI CONSTR> 106.07835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 144.33417 0.25231 0.35065 0.00043 MINI INTERN> 10.69155 36.03728 0.00000 11.78364 7.47189 MINI EXTERN> -1.73221 -25.95071 0.00000 0.00000 0.00000 MINI CONSTR> 106.03273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9298 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 144.10409 0.23008 0.35370 0.00045 MINI INTERN> 10.74572 35.94222 0.00000 11.75331 7.45002 MINI EXTERN> -1.84982 -25.94252 0.00000 0.00000 0.00000 MINI CONSTR> 106.00515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 143.91509 0.18900 0.63378 0.00046 MINI INTERN> 11.07503 35.69127 0.00000 11.69863 7.42742 MINI EXTERN> -2.04979 -25.92265 0.00000 0.00000 0.00000 MINI CONSTR> 105.99518 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9297 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 143.73488 0.18021 0.42302 0.00048 MINI INTERN> 10.82953 35.76156 0.00000 11.69786 7.39807 MINI EXTERN> -2.03055 -25.91694 0.00000 0.00000 0.00000 MINI CONSTR> 105.99536 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 143.62351 0.11137 0.68940 0.00050 MINI INTERN> 11.08074 35.57610 0.00000 11.65584 7.37374 MINI EXTERN> -2.16571 -25.90682 0.00000 0.00000 0.00000 MINI CONSTR> 106.00962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9297 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 143.48255 0.14096 0.24274 0.00022 MINI INTERN> 10.50224 35.89627 0.00000 11.68130 7.36581 MINI EXTERN> -2.07785 -25.91944 0.00000 0.00000 0.00000 MINI CONSTR> 106.03423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 143.42736 0.05520 0.75376 0.00054 MINI INTERN> 11.12474 35.45313 0.00000 11.61283 7.33533 MINI EXTERN> -2.29282 -25.86889 0.00000 0.00000 0.00000 MINI CONSTR> 106.06303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9297 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 143.29473 0.13262 0.24770 0.00023 MINI INTERN> 10.47333 35.84333 0.00000 11.64164 7.33151 MINI EXTERN> -2.19747 -25.90062 0.00000 0.00000 0.00000 MINI CONSTR> 106.10302 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 143.22866 0.06607 0.20101 0.00024 MINI INTERN> 10.49738 35.78848 0.00000 11.62388 7.31471 MINI EXTERN> -2.24787 -25.88451 0.00000 0.00000 0.00000 MINI CONSTR> 106.13660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9297 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 143.16305 0.06561 0.19001 0.00025 MINI INTERN> 10.50095 35.75360 0.00000 11.60537 7.29823 MINI EXTERN> -2.30133 -25.87297 0.00000 0.00000 0.00000 MINI CONSTR> 106.17921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 143.10812 0.05494 0.35073 0.00026 MINI INTERN> 10.36041 35.83090 0.00000 11.59585 7.29000 MINI EXTERN> -2.33474 -25.86799 0.00000 0.00000 0.00000 MINI CONSTR> 106.23369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 143.04899 0.05912 0.21510 0.00027 MINI INTERN> 10.46139 35.72067 0.00000 11.57081 7.26970 MINI EXTERN> -2.40603 -25.84783 0.00000 0.00000 0.00000 MINI CONSTR> 106.28030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 143.01090 0.03809 0.41775 0.00028 MINI INTERN> 10.37110 35.75634 0.00000 11.55891 7.26250 MINI EXTERN> -2.44791 -25.82827 0.00000 0.00000 0.00000 MINI CONSTR> 106.33823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 142.97159 0.03931 0.39824 0.00029 MINI INTERN> 10.35416 35.76032 0.00000 11.54485 7.25016 MINI EXTERN> -2.48979 -25.83315 0.00000 0.00000 0.00000 MINI CONSTR> 106.38505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 142.92664 0.04495 0.14041 0.00012 MINI INTERN> 10.55908 35.54947 0.00000 11.51956 7.22072 MINI EXTERN> -2.55387 -25.78900 0.00000 0.00000 0.00000 MINI CONSTR> 106.42068 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9294 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 142.90657 0.02008 0.42663 0.00031 MINI INTERN> 10.29823 35.74315 0.00000 11.52069 7.23036 MINI EXTERN> -2.57137 -25.79730 0.00000 0.00000 0.00000 MINI CONSTR> 106.48280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 142.86040 0.04617 0.14605 0.00013 MINI INTERN> 10.55889 35.49276 0.00000 11.49078 7.19566 MINI EXTERN> -2.64543 -25.75378 0.00000 0.00000 0.00000 MINI CONSTR> 106.52152 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9294 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 142.83440 0.02600 0.12515 0.00014 MINI INTERN> 10.53724 35.48843 0.00000 11.48018 7.18737 MINI EXTERN> -2.68128 -25.74243 0.00000 0.00000 0.00000 MINI CONSTR> 106.56488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 142.80724 0.02716 0.12198 0.00014 MINI INTERN> 10.52542 35.47079 0.00000 11.46799 7.17748 MINI EXTERN> -2.72270 -25.72490 0.00000 0.00000 0.00000 MINI CONSTR> 106.61316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9294 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 142.78143 0.02581 0.18454 0.00015 MINI INTERN> 10.57827 35.40254 0.00000 11.45140 7.16188 MINI EXTERN> -2.77421 -25.70109 0.00000 0.00000 0.00000 MINI CONSTR> 106.66264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 142.75818 0.02324 0.10952 0.00015 MINI INTERN> 10.50561 35.43977 0.00000 11.44517 7.15918 MINI EXTERN> -2.80315 -25.69390 0.00000 0.00000 0.00000 MINI CONSTR> 106.70551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 142.73417 0.02401 0.21786 0.00016 MINI INTERN> 10.59290 35.34367 0.00000 11.42663 7.14096 MINI EXTERN> -2.86294 -25.66414 0.00000 0.00000 0.00000 MINI CONSTR> 106.75709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 142.71201 0.02216 0.18937 0.00017 MINI INTERN> 10.54623 35.35129 0.00000 11.41798 7.13591 MINI EXTERN> -2.89533 -25.64600 0.00000 0.00000 0.00000 MINI CONSTR> 106.80193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 142.69359 0.01842 0.23745 0.00017 MINI INTERN> 10.58856 35.30155 0.00000 11.40473 7.12398 MINI EXTERN> -2.93892 -25.62944 0.00000 0.00000 0.00000 MINI CONSTR> 106.84314 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 142.67568 0.01791 0.30195 0.00018 MINI INTERN> 10.55549 35.29475 0.00000 11.39658 7.11910 MINI EXTERN> -2.97700 -25.60165 0.00000 0.00000 0.00000 MINI CONSTR> 106.88841 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 142.65671 0.01896 0.26865 0.00019 MINI INTERN> 10.56918 35.26565 0.00000 11.38613 7.11065 MINI EXTERN> -3.01478 -25.58645 0.00000 0.00000 0.00000 MINI CONSTR> 106.92633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 142.63962 0.01710 0.28890 0.00019 MINI INTERN> 10.56834 35.26093 0.00000 11.37611 7.10313 MINI EXTERN> -3.04972 -25.58383 0.00000 0.00000 0.00000 MINI CONSTR> 106.96465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 142.62186 0.01776 0.26592 0.00020 MINI INTERN> 10.58548 35.21840 0.00000 11.36565 7.09493 MINI EXTERN> -3.08890 -25.55703 0.00000 0.00000 0.00000 MINI CONSTR> 107.00333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 142.59964 0.02222 0.09542 0.00009 MINI INTERN> 10.39960 35.34214 0.00000 11.36767 7.10369 MINI EXTERN> -3.10413 -25.55555 0.00000 0.00000 0.00000 MINI CONSTR> 107.04623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 142.59159 0.00805 0.34439 0.00021 MINI INTERN> 10.55482 35.21397 0.00000 11.34904 7.08404 MINI EXTERN> -3.15706 -25.53297 0.00000 0.00000 0.00000 MINI CONSTR> 107.07975 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 142.57614 0.01545 0.33183 0.00022 MINI INTERN> 10.56485 35.16517 0.00000 11.34000 7.07752 MINI EXTERN> -3.19424 -25.49391 0.00000 0.00000 0.00000 MINI CONSTR> 107.11674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 142.55347 0.02267 0.10508 0.00010 MINI INTERN> 10.36107 35.31418 0.00000 11.34400 7.08865 MINI EXTERN> -3.20401 -25.50536 0.00000 0.00000 0.00000 MINI CONSTR> 107.15493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 142.54887 0.00460 0.35010 0.00024 MINI INTERN> 10.56309 35.12988 0.00000 11.32387 7.06658 MINI EXTERN> -3.25978 -25.45886 0.00000 0.00000 0.00000 MINI CONSTR> 107.18408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 142.52615 0.02271 0.12176 0.00010 MINI INTERN> 10.33122 35.29987 0.00000 11.32989 7.08031 MINI EXTERN> -3.26581 -25.47146 0.00000 0.00000 0.00000 MINI CONSTR> 107.22213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 142.51363 0.01252 0.11067 0.00011 MINI INTERN> 10.33363 35.28333 0.00000 11.32246 7.07511 MINI EXTERN> -3.29551 -25.45714 0.00000 0.00000 0.00000 MINI CONSTR> 107.25175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 142.50146 0.01217 0.11781 0.00011 MINI INTERN> 10.31904 35.27546 0.00000 11.31604 7.07145 MINI EXTERN> -3.32421 -25.43909 0.00000 0.00000 0.00000 MINI CONSTR> 107.28278 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 142.49001 0.01144 0.12363 0.00011 MINI INTERN> 10.30441 35.27252 0.00000 11.30989 7.06792 MINI EXTERN> -3.35132 -25.42554 0.00000 0.00000 0.00000 MINI CONSTR> 107.31213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 142.47768 0.01234 0.10611 0.00012 MINI INTERN> 10.31199 35.25018 0.00000 11.30199 7.06227 MINI EXTERN> -3.38241 -25.40843 0.00000 0.00000 0.00000 MINI CONSTR> 107.34210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 142.46719 0.01049 0.14732 0.00012 MINI INTERN> 10.27670 35.25996 0.00000 11.29706 7.06059 MINI EXTERN> -3.40814 -25.39193 0.00000 0.00000 0.00000 MINI CONSTR> 107.37296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9295 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 142.45832 0.00887 0.18697 0.00013 MINI INTERN> 10.26325 35.26400 0.00000 11.29144 7.05734 MINI EXTERN> -3.43221 -25.38456 0.00000 0.00000 0.00000 MINI CONSTR> 107.39907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 142.44921 0.00911 0.19374 0.00013 MINI INTERN> 10.23194 35.27214 0.00000 11.28722 7.05583 MINI EXTERN> -3.45423 -25.36934 0.00000 0.00000 0.00000 MINI CONSTR> 107.42565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9297 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 142.44030 0.00891 0.22215 0.00014 MINI INTERN> 10.22383 35.25867 0.00000 11.28132 7.05226 MINI EXTERN> -3.47996 -25.34846 0.00000 0.00000 0.00000 MINI CONSTR> 107.45263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 142.43146 0.00884 0.19854 0.00014 MINI INTERN> 10.22277 35.25490 0.00000 11.27571 7.04822 MINI EXTERN> -3.50152 -25.34291 0.00000 0.00000 0.00000 MINI CONSTR> 107.47429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 142.42064 0.01082 0.07006 0.00006 MINI INTERN> 10.34289 35.14135 0.00000 11.26297 7.03364 MINI EXTERN> -3.53557 -25.31596 0.00000 0.00000 0.00000 MINI CONSTR> 107.49132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 142.41788 0.00277 0.26296 0.00015 MINI INTERN> 10.25221 35.19623 0.00000 11.26357 7.03822 MINI EXTERN> -3.54778 -25.30149 0.00000 0.00000 0.00000 MINI CONSTR> 107.51692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 142.41116 0.00671 0.27491 0.00016 MINI INTERN> 10.23467 35.19982 0.00000 11.25947 7.03586 MINI EXTERN> -3.56642 -25.29053 0.00000 0.00000 0.00000 MINI CONSTR> 107.53828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 142.39912 0.01204 0.07503 0.00007 MINI INTERN> 10.33713 35.11294 0.00000 11.24779 7.02249 MINI EXTERN> -3.59564 -25.27865 0.00000 0.00000 0.00000 MINI CONSTR> 107.55306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 142.39292 0.00620 0.06192 0.00007 MINI INTERN> 10.32115 35.11763 0.00000 11.24424 7.02033 MINI EXTERN> -3.61116 -25.27041 0.00000 0.00000 0.00000 MINI CONSTR> 107.57113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 142.38665 0.00626 0.06227 0.00007 MINI INTERN> 10.31939 35.10959 0.00000 11.23957 7.01666 MINI EXTERN> -3.62907 -25.25924 0.00000 0.00000 0.00000 MINI CONSTR> 107.58977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 142.38045 0.00621 0.06120 0.00008 MINI INTERN> 10.31379 35.10431 0.00000 11.23511 7.01320 MINI EXTERN> -3.64650 -25.24802 0.00000 0.00000 0.00000 MINI CONSTR> 107.60856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 142.37457 0.00588 0.10588 0.00008 MINI INTERN> 10.34849 35.06861 0.00000 11.22775 7.00576 MINI EXTERN> -3.66936 -25.23409 0.00000 0.00000 0.00000 MINI CONSTR> 107.62742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 142.36884 0.00573 0.09288 0.00008 MINI INTERN> 10.32748 35.07474 0.00000 11.22468 7.00379 MINI EXTERN> -3.68327 -25.22354 0.00000 0.00000 0.00000 MINI CONSTR> 107.64497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 142.36401 0.00483 0.11689 0.00009 MINI INTERN> 10.35119 35.05076 0.00000 11.21879 6.99778 MINI EXTERN> -3.70143 -25.21375 0.00000 0.00000 0.00000 MINI CONSTR> 107.66068 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 142.35804 0.00597 0.08945 0.00009 MINI INTERN> 10.31594 35.06866 0.00000 11.21652 6.99667 MINI EXTERN> -3.71350 -25.20494 0.00000 0.00000 0.00000 MINI CONSTR> 107.67868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 142.35421 0.00383 0.14069 0.00009 MINI INTERN> 10.33164 35.04799 0.00000 11.21155 6.99153 MINI EXTERN> -3.72935 -25.19263 0.00000 0.00000 0.00000 MINI CONSTR> 107.69348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 142.34936 0.00485 0.13063 0.00010 MINI INTERN> 10.35023 35.02996 0.00000 11.20624 6.98582 MINI EXTERN> -3.74517 -25.18548 0.00000 0.00000 0.00000 MINI CONSTR> 107.70777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 142.34527 0.00409 0.17393 0.00010 MINI INTERN> 10.34666 35.03422 0.00000 11.20209 6.98172 MINI EXTERN> -3.75902 -25.18366 0.00000 0.00000 0.00000 MINI CONSTR> 107.72326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 142.34103 0.00424 0.16837 0.00010 MINI INTERN> 10.33263 35.04088 0.00000 11.19942 6.97933 MINI EXTERN> -3.76930 -25.17835 0.00000 0.00000 0.00000 MINI CONSTR> 107.73642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 142.33623 0.00479 0.14423 0.00011 MINI INTERN> 10.35648 35.00990 0.00000 11.19406 6.97313 MINI EXTERN> -3.78536 -25.16234 0.00000 0.00000 0.00000 MINI CONSTR> 107.75036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 142.33149 0.00475 0.15655 0.00011 MINI INTERN> 10.34255 35.01133 0.00000 11.19035 6.96934 MINI EXTERN> -3.79714 -25.15177 0.00000 0.00000 0.00000 MINI CONSTR> 107.76683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 142.32568 0.00581 0.04902 0.00005 MINI INTERN> 10.25563 35.08034 0.00000 11.19228 6.97331 MINI EXTERN> -3.79974 -25.15747 0.00000 0.00000 0.00000 MINI CONSTR> 107.78132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9297 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 142.32415 0.00153 0.19597 0.00012 MINI INTERN> 10.32005 35.01780 0.00000 11.18464 6.96328 MINI EXTERN> -3.81906 -25.13640 0.00000 0.00000 0.00000 MINI CONSTR> 107.79384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 142.31973 0.00443 0.17569 0.00012 MINI INTERN> 10.36302 34.98359 0.00000 11.17807 6.95481 MINI EXTERN> -3.83506 -25.13017 0.00000 0.00000 0.00000 MINI CONSTR> 107.80547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9297 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 142.31309 0.00664 0.05914 0.00005 MINI INTERN> 10.24072 35.07982 0.00000 11.18170 6.96121 MINI EXTERN> -3.83355 -25.13852 0.00000 0.00000 0.00000 MINI CONSTR> 107.82171 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 142.31199 0.00109 0.19328 0.00013 MINI INTERN> 10.35619 34.97962 0.00000 11.17111 6.94649 MINI EXTERN> -3.85689 -25.11588 0.00000 0.00000 0.00000 MINI CONSTR> 107.83135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9298 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 142.30513 0.00686 0.06734 0.00006 MINI INTERN> 10.23281 35.07843 0.00000 11.17490 6.95289 MINI EXTERN> -3.85446 -25.12631 0.00000 0.00000 0.00000 MINI CONSTR> 107.84688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 142.30124 0.00389 0.06152 0.00006 MINI INTERN> 10.23850 35.07211 0.00000 11.17107 6.94793 MINI EXTERN> -3.86506 -25.12153 0.00000 0.00000 0.00000 MINI CONSTR> 107.85822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9298 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 142.29731 0.00393 0.06284 0.00006 MINI INTERN> 10.23455 35.07120 0.00000 11.16777 6.94367 MINI EXTERN> -3.87499 -25.11521 0.00000 0.00000 0.00000 MINI CONSTR> 107.87033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 142.29326 0.00405 0.06848 0.00006 MINI INTERN> 10.23759 35.06774 0.00000 11.16387 6.93847 MINI EXTERN> -3.88574 -25.11103 0.00000 0.00000 0.00000 MINI CONSTR> 107.88235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9298 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 142.28947 0.00379 0.07399 0.00007 MINI INTERN> 10.23789 35.06543 0.00000 11.16042 6.93380 MINI EXTERN> -3.89544 -25.10626 0.00000 0.00000 0.00000 MINI CONSTR> 107.89363 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 142.28596 0.00351 0.10307 0.00007 MINI INTERN> 10.22287 35.07640 0.00000 11.15784 6.93034 MINI EXTERN> -3.90354 -25.10352 0.00000 0.00000 0.00000 MINI CONSTR> 107.90557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9299 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 142.28199 0.00397 0.10020 0.00007 MINI INTERN> 10.21963 35.07614 0.00000 11.15459 6.92577 MINI EXTERN> -3.91285 -25.09831 0.00000 0.00000 0.00000 MINI CONSTR> 107.91702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 142.27789 0.00410 0.09721 0.00007 MINI INTERN> 10.20917 35.08008 0.00000 11.15169 6.92165 MINI EXTERN> -3.92171 -25.09211 0.00000 0.00000 0.00000 MINI CONSTR> 107.92912 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9299 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 142.27306 0.00482 0.06968 0.00008 MINI INTERN> 10.23165 35.05773 0.00000 11.14654 6.91426 MINI EXTERN> -3.93496 -25.08289 0.00000 0.00000 0.00000 MINI CONSTR> 107.94074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 142.26924 0.00382 0.10781 0.00008 MINI INTERN> 10.20337 35.08088 0.00000 11.14442 6.91123 MINI EXTERN> -3.94228 -25.08225 0.00000 0.00000 0.00000 MINI CONSTR> 107.95387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9299 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 142.26437 0.00487 0.09034 0.00008 MINI INTERN> 10.22341 35.05922 0.00000 11.13947 6.90385 MINI EXTERN> -3.95512 -25.07200 0.00000 0.00000 0.00000 MINI CONSTR> 107.96555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 142.26095 0.00343 0.13164 0.00008 MINI INTERN> 10.20970 35.06718 0.00000 11.13690 6.89995 MINI EXTERN> -3.96325 -25.06679 0.00000 0.00000 0.00000 MINI CONSTR> 107.97725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9298 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 142.25648 0.00447 0.12510 0.00009 MINI INTERN> 10.19600 35.07862 0.00000 11.13402 6.89557 MINI EXTERN> -3.97165 -25.06530 0.00000 0.00000 0.00000 MINI CONSTR> 107.98921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 142.25219 0.00429 0.14006 0.00009 MINI INTERN> 10.19736 35.08102 0.00000 11.13009 6.88960 MINI EXTERN> -3.98164 -25.06502 0.00000 0.00000 0.00000 MINI CONSTR> 108.00077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9299 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 142.24775 0.00444 0.14646 0.00009 MINI INTERN> 10.20385 35.06606 0.00000 11.12626 6.88358 MINI EXTERN> -3.99273 -25.05173 0.00000 0.00000 0.00000 MINI CONSTR> 108.01248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 142.24296 0.00479 0.13895 0.00010 MINI INTERN> 10.19103 35.07658 0.00000 11.12324 6.87878 MINI EXTERN> -4.00145 -25.04982 0.00000 0.00000 0.00000 MINI CONSTR> 108.02460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9299 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 142.23848 0.00449 0.15925 0.00010 MINI INTERN> 10.21666 35.06275 0.00000 11.11781 6.87039 MINI EXTERN> -4.01408 -25.05016 0.00000 0.00000 0.00000 MINI CONSTR> 108.03510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 142.23381 0.00467 0.16489 0.00011 MINI INTERN> 10.21647 35.06147 0.00000 11.11413 6.86447 MINI EXTERN> -4.02422 -25.04528 0.00000 0.00000 0.00000 MINI CONSTR> 108.04676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9299 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 142.22744 0.00637 0.05350 0.00005 MINI INTERN> 10.27473 35.00494 0.00000 11.10727 6.85385 MINI EXTERN> -4.04082 -25.02838 0.00000 0.00000 0.00000 MINI CONSTR> 108.05585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 142.22372 0.00372 0.15496 0.00011 MINI INTERN> 10.17543 35.08484 0.00000 11.10911 6.85578 MINI EXTERN> -4.04096 -25.03291 0.00000 0.00000 0.00000 MINI CONSTR> 108.07242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9298 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 142.21789 0.00583 0.17902 0.00012 MINI INTERN> 10.16465 35.09415 0.00000 11.10475 6.84914 MINI EXTERN> -4.05415 -25.02871 0.00000 0.00000 0.00000 MINI CONSTR> 108.08806 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> 500 142.21789 0.00583 0.17902 0.00006 STPD INTERN> 10.16465 35.09415 0.00000 11.10475 6.84914 STPD EXTERN> -4.05415 -25.02871 0.00000 0.00000 0.00000 STPD CONSTR> 108.08806 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 9298 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9298 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 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> 0 142.21722 0.00067 0.08204 0.00000 MINI INTERN> 10.30023 34.98020 0.00000 11.09795 6.83877 MINI EXTERN> -4.06578 -25.01397 0.00000 0.00000 0.00000 MINI CONSTR> 108.07983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 141.98605 0.23117 0.91616 0.05141 MINI INTERN> 9.58167 34.82750 0.00000 10.88062 6.65366 MINI EXTERN> -6.39676 -23.85392 0.00000 0.00000 0.00000 MINI CONSTR> 110.29327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 141.95487 0.03119 0.64008 0.00838 MINI INTERN> 9.67764 34.44149 0.00000 10.85970 6.62081 MINI EXTERN> -6.76507 -23.61411 0.00000 0.00000 0.00000 MINI CONSTR> 110.73442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 141.90795 0.04691 0.76976 0.02001 MINI INTERN> 9.64440 33.71876 0.00000 10.90152 6.59987 MINI EXTERN> -6.74499 -23.32137 0.00000 0.00000 0.00000 MINI CONSTR> 111.10977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 141.87373 0.03423 0.61600 0.01117 MINI INTERN> 9.17277 33.69571 0.00000 10.93136 6.67819 MINI EXTERN> -6.77590 -23.16369 0.00000 0.00000 0.00000 MINI CONSTR> 111.33529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 141.84160 0.03213 0.75854 0.01324 MINI INTERN> 9.31087 33.77366 0.00000 10.85602 6.67607 MINI EXTERN> -7.23602 -22.92657 0.00000 0.00000 0.00000 MINI CONSTR> 111.38758 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 141.80770 0.03390 0.57067 0.01111 MINI INTERN> 9.49514 33.94987 0.00000 10.73644 6.60111 MINI EXTERN> -7.68447 -22.62155 0.00000 0.00000 0.00000 MINI CONSTR> 111.33115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 141.78578 0.02192 0.53163 0.00850 MINI INTERN> 9.22247 34.32567 0.00000 10.66513 6.55509 MINI EXTERN> -7.49787 -22.60298 0.00000 0.00000 0.00000 MINI CONSTR> 111.11827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 141.76512 0.02066 0.57636 0.00843 MINI INTERN> 9.26317 34.41005 0.00000 10.57387 6.55767 MINI EXTERN> -7.09314 -22.67450 0.00000 0.00000 0.00000 MINI CONSTR> 110.72800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 141.74316 0.02196 0.51259 0.00812 MINI INTERN> 9.45120 34.34570 0.00000 10.49480 6.59117 MINI EXTERN> -6.64757 -22.73012 0.00000 0.00000 0.00000 MINI CONSTR> 110.23798 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 141.72214 0.02102 0.50757 0.00910 MINI INTERN> 9.37815 34.56861 0.00000 10.48515 6.60024 MINI EXTERN> -6.28044 -22.81310 0.00000 0.00000 0.00000 MINI CONSTR> 109.78353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 141.70638 0.01575 0.49836 0.00625 MINI INTERN> 9.54712 34.65765 0.00000 10.45812 6.55896 MINI EXTERN> -6.21753 -22.79073 0.00000 0.00000 0.00000 MINI CONSTR> 109.49279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 141.68707 0.01932 0.45044 0.00799 MINI INTERN> 9.71617 34.78548 0.00000 10.38115 6.49826 MINI EXTERN> -6.24736 -22.68514 0.00000 0.00000 0.00000 MINI CONSTR> 109.23850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 141.67362 0.01345 0.43365 0.00583 MINI INTERN> 9.50639 35.05855 0.00000 10.34904 6.48631 MINI EXTERN> -6.18190 -22.69039 0.00000 0.00000 0.00000 MINI CONSTR> 109.14561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 141.66121 0.01240 0.39217 0.00517 MINI INTERN> 9.57193 35.01143 0.00000 10.33712 6.47170 MINI EXTERN> -6.20139 -22.65659 0.00000 0.00000 0.00000 MINI CONSTR> 109.12700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 141.64695 0.01426 0.49990 0.00723 MINI INTERN> 9.77831 34.70700 0.00000 10.34119 6.45045 MINI EXTERN> -6.29147 -22.54941 0.00000 0.00000 0.00000 MINI CONSTR> 109.21088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 141.63085 0.01610 0.39394 0.00665 MINI INTERN> 9.58301 34.67892 0.00000 10.38695 6.45496 MINI EXTERN> -6.36554 -22.50442 0.00000 0.00000 0.00000 MINI CONSTR> 109.39697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 141.61825 0.01260 0.47495 0.00648 MINI INTERN> 9.52506 34.63257 0.00000 10.44385 6.44795 MINI EXTERN> -6.55797 -22.47294 0.00000 0.00000 0.00000 MINI CONSTR> 109.59973 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 141.60283 0.01541 0.40800 0.00677 MINI INTERN> 9.65167 34.39950 0.00000 10.49154 6.41591 MINI EXTERN> -6.79301 -22.43570 0.00000 0.00000 0.00000 MINI CONSTR> 109.87292 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 141.58830 0.01454 0.47525 0.00793 MINI INTERN> 9.54722 34.36092 0.00000 10.52103 6.40675 MINI EXTERN> -6.87509 -22.48180 0.00000 0.00000 0.00000 MINI CONSTR> 110.10927 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 141.57606 0.01224 0.35320 0.00500 MINI INTERN> 9.44692 34.37068 0.00000 10.55620 6.42368 MINI EXTERN> -6.98667 -22.51285 0.00000 0.00000 0.00000 MINI CONSTR> 110.27811 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> 100 141.57606 0.01224 0.35320 0.02000 CONJ INTERN> 9.44692 34.37068 0.00000 10.55620 6.42368 CONJ EXTERN> -6.98667 -22.51285 0.00000 0.00000 0.00000 CONJ CONSTR> 110.27811 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 ASP 1 HT1 ) 6.3729 ( PROT ASP 1 HT2 ) 6.3729 ( PROT ASP 1 N ) 7.9661 ( PROT ASP 1 HT3 ) 6.3729 ( PROT ASP 1 CA ) 7.9661 ( PROT ASP 1 CB ) 6.3729 ( PROT ASP 1 CG ) 6.3729 ( PROT ASP 1 OD1 ) 6.3729 ( PROT ASP 1 OD2 ) 6.3729 ( PROT ASP 1 C ) 7.9661 ( PROT ASP 1 O ) 7.9661 ( PROT TYR 2 N ) 7.9661 ( PROT TYR 2 H ) 6.3729 ( PROT TYR 2 CA ) 7.9661 ( PROT TYR 2 CB ) 6.3729 ( PROT TYR 2 CG ) 6.3729 ( PROT TYR 2 CD1 ) 6.3729 ( PROT TYR 2 CE1 ) 6.3729 ( PROT TYR 2 CD2 ) 6.3729 ( PROT TYR 2 CE2 ) 6.3729 ( PROT TYR 2 CZ ) 6.3729 ( PROT TYR 2 OH ) 6.3729 ( PROT TYR 2 HH ) 6.3729 ( PROT TYR 2 C ) 7.9661 ( PROT TYR 2 O ) 7.9661 ( PROT ALA 3 N ) 7.9661 ( PROT ALA 3 H ) 6.3729 ( PROT ALA 3 CA ) 7.9661 ( PROT ALA 3 CB ) 6.3729 ( PROT ALA 3 C ) 7.9661 ( PROT ALA 3 O ) 7.9661 ( PROT PHE 4 N ) 7.9661 ( PROT PHE 4 H ) 6.3729 ( PROT PHE 4 CA ) 7.9661 ( PROT PHE 4 CB ) 6.3729 ( PROT PHE 4 CG ) 6.3729 ( PROT PHE 4 CD1 ) 6.3729 ( PROT PHE 4 CD2 ) 6.3729 ( PROT PHE 4 CE1 ) 6.3729 ( PROT PHE 4 CE2 ) 6.3729 ( PROT PHE 4 CZ ) 6.3729 ( PROT PHE 4 C ) 7.9661 ( PROT PHE 4 O ) 7.9661 ( PROT ILE 5 N ) 7.9661 ( PROT ILE 5 H ) 6.3729 ( PROT ILE 5 CA ) 7.9661 ( PROT ILE 5 CB ) 6.3729 ( PROT ILE 5 CG2 ) 6.3729 ( PROT ILE 5 CG1 ) 6.3729 ( PROT ILE 5 CD ) 6.3729 ( PROT ILE 5 C ) 7.9661 ( PROT ILE 5 O ) 7.9661 ( PROT ALA 6 N ) 7.9661 ( PROT ALA 6 H ) 6.3729 ( PROT ALA 6 CA ) 7.9661 ( PROT ALA 6 CB ) 6.3729 ( PROT ALA 6 C ) 7.9661 ( PROT ALA 6 O ) 7.9661 ( PROT SER 7 N ) 7.9661 ( PROT SER 7 H ) 6.3729 ( PROT SER 7 CA ) 7.9661 ( PROT SER 7 CB ) 6.3729 ( PROT SER 7 OG ) 6.3729 ( PROT SER 7 HG ) 6.3729 ( PROT SER 7 C ) 7.9661 ( PROT SER 7 O ) 7.9661 ( PROT LEU 8 N ) 7.9661 ( PROT LEU 8 H ) 6.3729 ( PROT LEU 8 CA ) 7.9661 ( PROT LEU 8 CB ) 6.3729 ( PROT LEU 8 CG ) 6.3729 ( PROT LEU 8 CD1 ) 6.3729 ( PROT LEU 8 CD2 ) 6.3729 ( PROT LEU 8 C ) 7.9661 ( PROT LEU 8 O ) 7.9661 ( PROT VAL 9 N ) 7.9661 ( PROT VAL 9 H ) 6.3729 ( PROT VAL 9 CA ) 7.9661 ( PROT VAL 9 CB ) 6.3729 ( PROT VAL 9 CG1 ) 6.3729 ( PROT VAL 9 CG2 ) 6.3729 ( PROT VAL 9 C ) 7.9661 ( PROT VAL 9 O ) 7.9661 ( PROT VAL 10 N ) 7.9661 ( PROT VAL 10 H ) 6.3729 ( PROT VAL 10 CA ) 7.9661 ( PROT VAL 10 CB ) 6.3729 ( PROT VAL 10 CG1 ) 6.3729 ( PROT VAL 10 CG2 ) 6.3729 ( PROT VAL 10 C ) 7.9661 ( PROT VAL 10 O ) 7.9661 ( PROT ILE 11 N ) 7.9661 ( PROT ILE 11 H ) 6.3729 ( PROT ILE 11 CA ) 7.9661 ( PROT ILE 11 CB ) 6.3729 ( PROT ILE 11 CG2 ) 6.3729 ( PROT ILE 11 CG1 ) 6.3729 ( PROT ILE 11 CD ) 6.3729 ( PROT ILE 11 C ) 7.9661 ( PROT ILE 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 ASP 13 N ) 7.9661 ( PROT ASP 13 H ) 6.3729 ( PROT ASP 13 CA ) 7.9661 ( PROT ASP 13 CB ) 6.3729 ( PROT ASP 13 CG ) 6.3729 ( PROT ASP 13 OD1 ) 6.3729 ( PROT ASP 13 OD2 ) 6.3729 ( PROT ASP 13 C ) 7.9661 ( PROT ASP 13 O ) 7.9661 ( PROT ASP 14 N ) 7.9661 ( PROT ASP 14 H ) 6.3729 ( PROT ASP 14 CA ) 7.9661 ( PROT ASP 14 CB ) 6.3729 ( PROT ASP 14 CG ) 6.3729 ( PROT ASP 14 OD1 ) 6.3729 ( PROT ASP 14 OD2 ) 6.3729 ( PROT ASP 14 C ) 7.9661 ( PROT ASP 14 O ) 7.9661 ( PROT VAL 15 N ) 7.9661 ( PROT VAL 15 H ) 6.3729 ( PROT VAL 15 CA ) 7.9661 ( PROT VAL 15 CB ) 6.3729 ( PROT VAL 15 CG1 ) 6.3729 ( PROT VAL 15 CG2 ) 6.3729 ( PROT VAL 15 C ) 7.9661 ( PROT VAL 15 O ) 7.9661 ( PROT ASN 16 N ) 7.9661 ( PROT ASN 16 H ) 6.3729 ( PROT ASN 16 CA ) 7.9661 ( PROT ASN 16 CB ) 6.3729 ( PROT ASN 16 CG ) 6.3729 ( PROT ASN 16 OD1 ) 6.3729 ( PROT ASN 16 ND2 ) 6.3729 ( PROT ASN 16 HD21 ) 6.3729 ( PROT ASN 16 HD22 ) 6.3729 ( PROT ASN 16 C ) 7.9661 ( PROT ASN 16 O ) 7.9661 ( PROT ARG 17 N ) 7.9661 ( PROT ARG 17 H ) 6.3729 ( PROT ARG 17 CA ) 7.9661 ( PROT ARG 17 CB ) 6.3729 ( PROT ARG 17 CG ) 6.3729 ( PROT ARG 17 CD ) 6.3729 ( PROT ARG 17 NE ) 6.3729 ( PROT ARG 17 HE ) 6.3729 ( PROT ARG 17 CZ ) 6.3729 ( PROT ARG 17 NH1 ) 6.3729 ( PROT ARG 17 HH11 ) 6.3729 ( PROT ARG 17 HH12 ) 6.3729 ( PROT ARG 17 NH2 ) 6.3729 ( PROT ARG 17 HH21 ) 6.3729 ( PROT ARG 17 HH22 ) 6.3729 ( PROT ARG 17 C ) 7.9661 ( PROT ARG 17 OT1 ) 6.3729 ( PROT ARG 17 OT2 ) 6.3729 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96196 3.71238 -6.80051 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00186 -0.00106 -0.00149 ROTATION MATRIX 1.000000 -0.000210 -0.000225 0.000210 1.000000 0.000475 0.000225 -0.000475 1.000000 AXIS OF ROTATION IS 0.839006 0.397321 -0.371758 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 9.7196 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.243445 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2434" Parameter: A <- "0.2434" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.77421 3.77797 -6.97137 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.00203 0.01374 -0.00586 ROTATION MATRIX 0.999685 0.016519 0.018903 -0.016119 0.999647 -0.021117 -0.019245 0.020805 0.999598 AXIS OF ROTATION IS -0.640944 -0.583253 0.499005 ANGLE IS 1.87 CENTER OF ROTATION 7.668150 3.638980 -7.279704 SHIFT IS -0.009640 TOTAL SQUARE DIFF IS 0.3343 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.140225 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2434" RDCMND substituted energy or value "?RMS" to " 0.1402" Parameter: A <- "0.2434 0.1402" 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 0.2434 0.1402 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 " 110.28" Parameter: H <- "110.28" 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 31.29795 110.27811 3.18925 ENER INTERN> 9.44692 34.37068 0.00000 10.55620 6.42368 ENER EXTERN> -6.98667 -22.51285 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 " 31.30" Parameter: B <- "31.30" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -22.51" Parameter: C <- "-22.51" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -6.99" Parameter: C <- " -29.50" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -29.50" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 9.45" Parameter: D <- "9.45" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 34.37" Parameter: D <- " 43.82" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.56" Parameter: D <- " 54.38" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.42" Parameter: D <- " 60.80" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 60.80" 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= 31.30 GRMS= 3.19 ELEC= -22.51 VDW= -6.99 RDTITL> *EXTERNAL= -29.50 INTERNAL= 60.80 USER= 0.00 HARM= 110.28 RDTITL> *BOND= 9.45 ANGL= 34.37 DIHE= 10.56 IMPR= 6.42 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= 31.30 GRMS= 3.19 ELEC= -22.51 VDW= -6.99 RDTITL> *EXTERNAL= -29.50 INTERNAL= 60.80 USER= 0.00 HARM= 110.28 RDTITL> *BOND= 9.45 ANGL= 34.37 DIHE= 10.56 IMPR= 6.42 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= 31.30 GRMS= 3.19 ELEC= -22.51 VDW= -6.99 RDTITL> *EXTERNAL= -29.50 INTERNAL= 60.80 USER= 0.00 HARM= 110.28 RDTITL> *BOND= 9.45 ANGL= 34.37 DIHE= 10.56 IMPR= 6.42 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 4800 0.2434 0.1402 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "4800" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9298 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9304 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 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> 0 121.29202 -89.99407 1.51007 0.02000 MINI INTERN> 9.44692 34.37068 0.00000 10.55620 6.42368 MINI EXTERN> -6.98667 -22.51285 0.00000 0.00000 0.00000 MINI CONSTR> 89.99407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 113.86984 7.42218 1.37721 0.00360 MINI INTERN> 9.12392 33.00649 0.00000 11.49754 6.45211 MINI EXTERN> -18.20616 -21.65080 0.00000 0.00000 0.00000 MINI CONSTR> 93.64676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9296 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 110.99990 2.86994 1.78375 0.00156 MINI INTERN> 8.90532 32.61365 0.00000 11.71350 6.37436 MINI EXTERN> -20.93828 -21.43228 0.00000 0.00000 0.00000 MINI CONSTR> 93.76364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 109.93290 1.06700 2.74765 0.00161 MINI INTERN> 9.31198 32.16229 0.00000 11.75219 6.46254 MINI EXTERN> -22.01594 -21.37419 0.00000 0.00000 0.00000 MINI CONSTR> 93.63403 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9293 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 108.34229 1.59062 0.86469 0.00070 MINI INTERN> 8.11777 32.35900 0.00000 11.82330 6.43553 MINI EXTERN> -22.25081 -21.59830 0.00000 0.00000 0.00000 MINI CONSTR> 93.45579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 107.96515 0.37713 3.05441 0.00173 MINI INTERN> 9.13495 31.77964 0.00000 11.83258 6.43513 MINI EXTERN> -23.06102 -21.40470 0.00000 0.00000 0.00000 MINI CONSTR> 93.24857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9291 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 106.36538 1.59977 0.96505 0.00075 MINI INTERN> 7.96059 32.00001 0.00000 11.85845 6.40867 MINI EXTERN> -23.20804 -21.66390 0.00000 0.00000 0.00000 MINI CONSTR> 93.00960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 105.63913 0.72626 0.67174 0.00078 MINI INTERN> 8.04111 31.75807 0.00000 11.85712 6.39806 MINI EXTERN> -23.58931 -21.64269 0.00000 0.00000 0.00000 MINI CONSTR> 92.81677 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9290 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 104.85929 0.77984 1.36387 0.00080 MINI INTERN> 7.81708 31.81879 0.00000 11.86194 6.38013 MINI EXTERN> -23.82380 -21.74713 0.00000 0.00000 0.00000 MINI CONSTR> 92.55228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 104.15002 0.70928 0.86107 0.00083 MINI INTERN> 7.86350 31.57704 0.00000 11.85455 6.36494 MINI EXTERN> -24.13729 -21.71880 0.00000 0.00000 0.00000 MINI CONSTR> 92.34608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9289 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 103.65085 0.49917 1.50175 0.00087 MINI INTERN> 7.74276 31.64468 0.00000 11.84456 6.35344 MINI EXTERN> -24.27669 -21.79852 0.00000 0.00000 0.00000 MINI CONSTR> 92.14062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 103.12700 0.52385 1.63634 0.00090 MINI INTERN> 7.65135 31.62306 0.00000 11.83346 6.34083 MINI EXTERN> -24.43470 -21.83304 0.00000 0.00000 0.00000 MINI CONSTR> 91.94604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9290 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 102.66806 0.45893 1.57420 0.00093 MINI INTERN> 7.65381 31.52187 0.00000 11.82072 6.32716 MINI EXTERN> -24.60078 -21.83867 0.00000 0.00000 0.00000 MINI CONSTR> 91.78395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 102.08616 0.58191 0.48682 0.00040 MINI INTERN> 8.00875 30.99442 0.00000 11.81773 6.29396 MINI EXTERN> -24.94588 -21.69713 0.00000 0.00000 0.00000 MINI CONSTR> 91.61430 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9290 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 101.88656 0.19959 1.72011 0.00100 MINI INTERN> 7.52301 31.48034 0.00000 11.79226 6.30473 MINI EXTERN> -24.81679 -21.88248 0.00000 0.00000 0.00000 MINI CONSTR> 91.48550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 101.54160 0.34496 1.78545 0.00104 MINI INTERN> 7.43476 31.47947 0.00000 11.77785 6.29439 MINI EXTERN> -24.89755 -21.90101 0.00000 0.00000 0.00000 MINI CONSTR> 91.35368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9288 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 101.00065 0.54095 0.59205 0.00045 MINI INTERN> 8.10329 30.69396 0.00000 11.78023 6.24152 MINI EXTERN> -25.32249 -21.69587 0.00000 0.00000 0.00000 MINI CONSTR> 91.20000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 100.74580 0.25485 0.38853 0.00046 MINI INTERN> 7.93210 30.76158 0.00000 11.76813 6.23536 MINI EXTERN> -25.33543 -21.73319 0.00000 0.00000 0.00000 MINI CONSTR> 91.11725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9288 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 100.45803 0.28777 0.75476 0.00048 MINI INTERN> 8.20549 30.50726 0.00000 11.75450 6.20830 MINI EXTERN> -25.52086 -21.68781 0.00000 0.00000 0.00000 MINI CONSTR> 90.99114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 100.21248 0.24555 0.50727 0.00050 MINI INTERN> 8.04561 30.56079 0.00000 11.74077 6.20117 MINI EXTERN> -25.53449 -21.71947 0.00000 0.00000 0.00000 MINI CONSTR> 90.91810 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9288 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 100.03724 0.17525 0.86731 0.00052 MINI INTERN> 8.26133 30.37546 0.00000 11.73058 6.17997 MINI EXTERN> -25.66238 -21.68439 0.00000 0.00000 0.00000 MINI CONSTR> 90.83667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 99.85069 0.18655 0.94109 0.00054 MINI INTERN> 8.30644 30.30370 0.00000 11.71778 6.16587 MINI EXTERN> -25.73270 -21.68021 0.00000 0.00000 0.00000 MINI CONSTR> 90.76980 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 99.68944 0.16125 0.91062 0.00056 MINI INTERN> 8.27988 30.28107 0.00000 11.70730 6.15534 MINI EXTERN> -25.76869 -21.68573 0.00000 0.00000 0.00000 MINI CONSTR> 90.72028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 99.48768 0.20176 0.28478 0.00024 MINI INTERN> 7.78278 30.58306 0.00000 11.69054 6.16452 MINI EXTERN> -25.65016 -21.77824 0.00000 0.00000 0.00000 MINI CONSTR> 90.69519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 99.42097 0.06671 1.00989 0.00060 MINI INTERN> 8.32883 30.18324 0.00000 11.68602 6.13206 MINI EXTERN> -25.86294 -21.68069 0.00000 0.00000 0.00000 MINI CONSTR> 90.63446 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 99.30256 0.11841 1.05952 0.00062 MINI INTERN> 8.35803 30.13450 0.00000 11.67512 6.12083 MINI EXTERN> -25.90795 -21.67753 0.00000 0.00000 0.00000 MINI CONSTR> 90.59955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 99.11473 0.18783 0.36132 0.00027 MINI INTERN> 7.69044 30.56166 0.00000 11.65612 6.13835 MINI EXTERN> -25.72800 -21.80146 0.00000 0.00000 0.00000 MINI CONSTR> 90.59763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 99.02746 0.08727 0.22644 0.00028 MINI INTERN> 7.78429 30.46396 0.00000 11.64867 6.12706 MINI EXTERN> -25.78943 -21.78234 0.00000 0.00000 0.00000 MINI CONSTR> 90.57524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 98.93024 0.09722 0.46438 0.00029 MINI INTERN> 7.62896 30.56241 0.00000 11.63535 6.12338 MINI EXTERN> -25.76269 -21.81673 0.00000 0.00000 0.00000 MINI CONSTR> 90.55956 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 98.84425 0.08599 0.29527 0.00030 MINI INTERN> 7.70831 30.47234 0.00000 11.62728 6.11205 MINI EXTERN> -25.81873 -21.79965 0.00000 0.00000 0.00000 MINI CONSTR> 90.54267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 98.78466 0.05959 0.51358 0.00031 MINI INTERN> 7.60273 30.54420 0.00000 11.61658 6.10942 MINI EXTERN> -25.80081 -21.82431 0.00000 0.00000 0.00000 MINI CONSTR> 90.53686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 98.72099 0.06366 0.56562 0.00032 MINI INTERN> 7.57883 30.54505 0.00000 11.60768 6.10258 MINI EXTERN> -25.81292 -21.83015 0.00000 0.00000 0.00000 MINI CONSTR> 90.52992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 98.66608 0.05491 0.54654 0.00033 MINI INTERN> 7.58723 30.52238 0.00000 11.59962 6.09618 MINI EXTERN> -25.83549 -21.82904 0.00000 0.00000 0.00000 MINI CONSTR> 90.52520 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 98.59507 0.07101 0.16770 0.00014 MINI INTERN> 7.82882 30.30256 0.00000 11.59494 6.07859 MINI EXTERN> -25.94474 -21.77650 0.00000 0.00000 0.00000 MINI CONSTR> 90.51141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 98.57319 0.02189 0.60006 0.00036 MINI INTERN> 7.56593 30.51224 0.00000 11.58395 6.08467 MINI EXTERN> -25.86137 -21.83509 0.00000 0.00000 0.00000 MINI CONSTR> 90.52286 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 98.50427 0.06892 0.17777 0.00015 MINI INTERN> 7.84633 30.25890 0.00000 11.57999 6.06519 MINI EXTERN> -25.98314 -21.77353 0.00000 0.00000 0.00000 MINI CONSTR> 90.51053 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 98.47028 0.03399 0.14120 0.00016 MINI INTERN> 7.81591 30.26924 0.00000 11.57419 6.06113 MINI EXTERN> -25.98434 -21.77934 0.00000 0.00000 0.00000 MINI CONSTR> 90.51349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 98.43457 0.03570 0.13770 0.00017 MINI INTERN> 7.81794 30.25459 0.00000 11.56744 6.05526 MINI EXTERN> -25.99848 -21.77901 0.00000 0.00000 0.00000 MINI CONSTR> 90.51683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 98.40466 0.02991 0.28487 0.00017 MINI INTERN> 7.90503 30.17851 0.00000 11.56056 6.04589 MINI EXTERN> -26.04129 -21.76256 0.00000 0.00000 0.00000 MINI CONSTR> 90.51852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 98.37408 0.03058 0.16838 0.00018 MINI INTERN> 7.84298 30.21237 0.00000 11.55466 6.04337 MINI EXTERN> -26.03111 -21.77424 0.00000 0.00000 0.00000 MINI CONSTR> 90.52605 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 98.35306 0.02103 0.30447 0.00019 MINI INTERN> 7.90739 30.15620 0.00000 11.54871 6.03575 MINI EXTERN> -26.06285 -21.76220 0.00000 0.00000 0.00000 MINI CONSTR> 90.53005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 98.33114 0.02192 0.33651 0.00019 MINI INTERN> 7.91500 30.14246 0.00000 11.54240 6.03076 MINI EXTERN> -26.07542 -21.76117 0.00000 0.00000 0.00000 MINI CONSTR> 90.53711 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 98.31208 0.01906 0.32349 0.00020 MINI INTERN> 7.90739 30.13848 0.00000 11.53810 6.02660 MINI EXTERN> -26.08022 -21.76210 0.00000 0.00000 0.00000 MINI CONSTR> 90.54384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 98.28705 0.02503 0.09810 0.00009 MINI INTERN> 7.77945 30.22183 0.00000 11.53398 6.02716 MINI EXTERN> -26.04545 -21.78595 0.00000 0.00000 0.00000 MINI CONSTR> 90.55604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 98.27936 0.00769 0.35250 0.00021 MINI INTERN> 7.90590 30.12516 0.00000 11.52791 6.01834 MINI EXTERN> -26.09490 -21.76253 0.00000 0.00000 0.00000 MINI CONSTR> 90.55949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 98.25525 0.02411 0.10453 0.00009 MINI INTERN> 7.77291 30.21070 0.00000 11.52487 6.01889 MINI EXTERN> -26.05815 -21.78669 0.00000 0.00000 0.00000 MINI CONSTR> 90.57273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9287 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 98.24332 0.01193 0.08269 0.00010 MINI INTERN> 7.78289 30.19775 0.00000 11.52061 6.01537 MINI EXTERN> -26.06819 -21.78479 0.00000 0.00000 0.00000 MINI CONSTR> 90.57970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 98.23078 0.01255 0.08041 0.00010 MINI INTERN> 7.78228 30.19134 0.00000 11.51636 6.01152 MINI EXTERN> -26.07456 -21.78463 0.00000 0.00000 0.00000 MINI CONSTR> 90.58846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 98.22018 0.01059 0.16509 0.00010 MINI INTERN> 7.76147 30.19897 0.00000 11.51339 6.00770 MINI EXTERN> -26.07232 -21.78778 0.00000 0.00000 0.00000 MINI CONSTR> 90.59875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 98.20948 0.01070 0.09841 0.00011 MINI INTERN> 7.77695 30.18201 0.00000 11.50888 6.00412 MINI EXTERN> -26.08416 -21.78472 0.00000 0.00000 0.00000 MINI CONSTR> 90.60641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 98.20207 0.00741 0.17726 0.00011 MINI INTERN> 7.76588 30.18349 0.00000 11.50654 6.00051 MINI EXTERN> -26.08407 -21.78587 0.00000 0.00000 0.00000 MINI CONSTR> 90.61559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 98.19436 0.00771 0.19514 0.00011 MINI INTERN> 7.76637 30.17636 0.00000 11.50363 5.99674 MINI EXTERN> -26.08825 -21.78478 0.00000 0.00000 0.00000 MINI CONSTR> 90.62428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 98.18767 0.00669 0.18764 0.00012 MINI INTERN> 7.76926 30.17058 0.00000 11.50021 5.99407 MINI EXTERN> -26.09429 -21.78415 0.00000 0.00000 0.00000 MINI CONSTR> 90.63201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 98.17894 0.00873 0.05713 0.00005 MINI INTERN> 7.79059 30.15583 0.00000 11.49325 5.99203 MINI EXTERN> -26.11057 -21.78220 0.00000 0.00000 0.00000 MINI CONSTR> 90.64001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 98.17622 0.00272 0.20517 0.00013 MINI INTERN> 7.76999 30.16000 0.00000 11.49470 5.98793 MINI EXTERN> -26.10194 -21.78254 0.00000 0.00000 0.00000 MINI CONSTR> 90.64808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 98.16781 0.00841 0.06065 0.00006 MINI INTERN> 7.79351 30.14702 0.00000 11.48644 5.98656 MINI EXTERN> -26.12089 -21.78152 0.00000 0.00000 0.00000 MINI CONSTR> 90.65669 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 98.16363 0.00418 0.04827 0.00006 MINI INTERN> 7.78984 30.14498 0.00000 11.48463 5.98403 MINI EXTERN> -26.12195 -21.78131 0.00000 0.00000 0.00000 MINI CONSTR> 90.66341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 98.15925 0.00438 0.04691 0.00006 MINI INTERN> 7.79049 30.14127 0.00000 11.48168 5.98145 MINI EXTERN> -26.12611 -21.78092 0.00000 0.00000 0.00000 MINI CONSTR> 90.67139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 98.15552 0.00372 0.09557 0.00006 MINI INTERN> 7.80341 30.13411 0.00000 11.47637 5.97947 MINI EXTERN> -26.13796 -21.78029 0.00000 0.00000 0.00000 MINI CONSTR> 90.68040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 98.15179 0.00373 0.05759 0.00006 MINI INTERN> 7.79618 30.13306 0.00000 11.47533 5.97675 MINI EXTERN> -26.13673 -21.77995 0.00000 0.00000 0.00000 MINI CONSTR> 90.68715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 98.14918 0.00261 0.10277 0.00007 MINI INTERN> 7.80864 30.12647 0.00000 11.47072 5.97510 MINI EXTERN> -26.14769 -21.77919 0.00000 0.00000 0.00000 MINI CONSTR> 90.69514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 98.14646 0.00272 0.11215 0.00007 MINI INTERN> 7.81477 30.12133 0.00000 11.46750 5.97312 MINI EXTERN> -26.15470 -21.77822 0.00000 0.00000 0.00000 MINI CONSTR> 90.70267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 98.14409 0.00238 0.10769 0.00007 MINI INTERN> 7.81364 30.11932 0.00000 11.46563 5.97105 MINI EXTERN> -26.15659 -21.77785 0.00000 0.00000 0.00000 MINI CONSTR> 90.70889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 98.14104 0.00304 0.03313 0.00003 MINI INTERN> 7.78271 30.12699 0.00000 11.46843 5.96715 MINI EXTERN> -26.13957 -21.77878 0.00000 0.00000 0.00000 MINI CONSTR> 90.71411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 98.14003 0.00102 0.11789 0.00008 MINI INTERN> 7.82171 30.11132 0.00000 11.46046 5.96743 MINI EXTERN> -26.16708 -21.77594 0.00000 0.00000 0.00000 MINI CONSTR> 90.72213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 98.13825 0.00178 0.12311 0.00008 MINI INTERN> 7.82685 30.10681 0.00000 11.45780 5.96572 MINI EXTERN> -26.17304 -21.77462 0.00000 0.00000 0.00000 MINI CONSTR> 90.72872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 98.13543 0.00281 0.04141 0.00003 MINI INTERN> 7.77459 30.12362 0.00000 11.46347 5.96058 MINI EXTERN> -26.14173 -21.77810 0.00000 0.00000 0.00000 MINI CONSTR> 90.73300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 98.13412 0.00132 0.02653 0.00004 MINI INTERN> 7.78351 30.11862 0.00000 11.46066 5.95966 MINI EXTERN> -26.14953 -21.77689 0.00000 0.00000 0.00000 MINI CONSTR> 90.73809 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 98.13263 0.00149 0.05271 0.00004 MINI INTERN> 7.76752 30.12274 0.00000 11.46078 5.95638 MINI EXTERN> -26.14145 -21.77790 0.00000 0.00000 0.00000 MINI CONSTR> 90.74456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 98.13134 0.00129 0.03462 0.00004 MINI INTERN> 7.77553 30.11797 0.00000 11.45800 5.95527 MINI EXTERN> -26.14881 -21.77662 0.00000 0.00000 0.00000 MINI CONSTR> 90.75001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 98.13042 0.00092 0.05963 0.00004 MINI INTERN> 7.76305 30.12135 0.00000 11.45812 5.95269 MINI EXTERN> -26.14240 -21.77743 0.00000 0.00000 0.00000 MINI CONSTR> 90.75505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 98.12944 0.00098 0.06468 0.00004 MINI INTERN> 7.75951 30.12122 0.00000 11.45696 5.95070 MINI EXTERN> -26.14198 -21.77728 0.00000 0.00000 0.00000 MINI CONSTR> 90.76031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 98.12859 0.00085 0.06254 0.00004 MINI INTERN> 7.76020 30.11961 0.00000 11.45545 5.94929 MINI EXTERN> -26.14417 -21.77671 0.00000 0.00000 0.00000 MINI CONSTR> 90.76492 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 98.12752 0.00107 0.01961 0.00002 MINI INTERN> 7.79005 30.10635 0.00000 11.44983 5.94997 MINI EXTERN> -26.16607 -21.77295 0.00000 0.00000 0.00000 MINI CONSTR> 90.77034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 98.12715 0.00037 0.06939 0.00005 MINI INTERN> 7.75560 30.11889 0.00000 11.45328 5.94598 MINI EXTERN> -26.14448 -21.77613 0.00000 0.00000 0.00000 MINI CONSTR> 90.77400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 98.12650 0.00064 0.07239 0.00005 MINI INTERN> 7.75314 30.11864 0.00000 11.45224 5.94431 MINI EXTERN> -26.14450 -21.77578 0.00000 0.00000 0.00000 MINI CONSTR> 90.77848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 98.12549 0.00101 0.02412 0.00002 MINI INTERN> 7.79623 30.10019 0.00000 11.44484 5.94605 MINI EXTERN> -26.17532 -21.77060 0.00000 0.00000 0.00000 MINI CONSTR> 90.78410 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 98.12501 0.00048 0.01597 0.00002 MINI INTERN> 7.78933 30.10201 0.00000 11.44477 5.94445 MINI EXTERN> -26.17199 -21.77083 0.00000 0.00000 0.00000 MINI CONSTR> 90.78727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 98.12445 0.00056 0.03003 0.00002 MINI INTERN> 7.80105 30.09613 0.00000 11.44166 5.94371 MINI EXTERN> -26.18166 -21.76898 0.00000 0.00000 0.00000 MINI CONSTR> 90.79254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 98.12399 0.00047 0.02104 0.00002 MINI INTERN> 7.79558 30.09735 0.00000 11.44133 5.94212 MINI EXTERN> -26.17939 -21.76898 0.00000 0.00000 0.00000 MINI CONSTR> 90.79599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 98.12364 0.00035 0.03576 0.00002 MINI INTERN> 7.80517 30.09264 0.00000 11.43885 5.94158 MINI EXTERN> -26.18722 -21.76748 0.00000 0.00000 0.00000 MINI CONSTR> 90.80010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 98.12326 0.00038 0.03773 0.00002 MINI INTERN> 7.80683 30.09108 0.00000 11.43752 5.94048 MINI EXTERN> -26.18972 -21.76677 0.00000 0.00000 0.00000 MINI CONSTR> 90.80384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 98.12293 0.00033 0.04173 0.00003 MINI INTERN> 7.80958 30.08915 0.00000 11.43607 5.93950 MINI EXTERN> -26.19289 -21.76595 0.00000 0.00000 0.00000 MINI CONSTR> 90.80748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 98.12264 0.00029 0.03937 0.00003 MINI INTERN> 7.80818 30.08899 0.00000 11.43537 5.93840 MINI EXTERN> -26.19313 -21.76553 0.00000 0.00000 0.00000 MINI CONSTR> 90.81036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 98.12223 0.00041 0.01167 0.00001 MINI INTERN> 7.78479 30.09743 0.00000 11.43764 5.93558 MINI EXTERN> -26.17888 -21.76705 0.00000 0.00000 0.00000 MINI CONSTR> 90.81273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 98.12210 0.00013 0.04286 0.00003 MINI INTERN> 7.81100 30.08642 0.00000 11.43307 5.93646 MINI EXTERN> -26.19746 -21.76420 0.00000 0.00000 0.00000 MINI CONSTR> 90.81682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 98.12171 0.00039 0.01282 0.00001 MINI INTERN> 7.78235 30.09694 0.00000 11.43607 5.93325 MINI EXTERN> -26.17979 -21.76601 0.00000 0.00000 0.00000 MINI CONSTR> 90.81889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 98.12151 0.00020 0.01032 0.00001 MINI INTERN> 7.78509 30.09530 0.00000 11.43493 5.93260 MINI EXTERN> -26.18260 -21.76528 0.00000 0.00000 0.00000 MINI CONSTR> 90.82147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 98.12129 0.00022 0.01000 0.00001 MINI INTERN> 7.78499 30.09470 0.00000 11.43407 5.93159 MINI EXTERN> -26.18373 -21.76467 0.00000 0.00000 0.00000 MINI CONSTR> 90.82435 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> 440 98.12129 0.00022 0.01000 0.00002 STPD INTERN> 7.78499 30.09470 0.00000 11.43407 5.93159 STPD EXTERN> -26.18373 -21.76467 0.00000 0.00000 0.00000 STPD CONSTR> 90.82435 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 9286 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9286 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 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 98.12129 0.00022 0.01000 0.00000 MINI INTERN> 7.78499 30.09470 0.00000 11.43407 5.93159 MINI EXTERN> -26.18373 -21.76467 0.00000 0.00000 0.00000 MINI CONSTR> 90.82435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 2 98.11867 0.00262 0.00779 0.02000 CONJ INTERN> 7.78730 30.07772 0.00000 11.41205 5.90745 CONJ EXTERN> -26.21756 -21.74792 0.00000 0.00000 0.00000 CONJ CONSTR> 90.89963 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 ASP 1 HT1 ) 4.1424 ( PROT ASP 1 HT2 ) 4.1424 ( PROT ASP 1 N ) 5.1780 ( PROT ASP 1 HT3 ) 4.1424 ( PROT ASP 1 CA ) 5.1780 ( PROT ASP 1 CB ) 4.1424 ( PROT ASP 1 CG ) 4.1424 ( PROT ASP 1 OD1 ) 4.1424 ( PROT ASP 1 OD2 ) 4.1424 ( PROT ASP 1 C ) 5.1780 ( PROT ASP 1 O ) 5.1780 ( PROT TYR 2 N ) 5.1780 ( PROT TYR 2 H ) 4.1424 ( PROT TYR 2 CA ) 5.1780 ( PROT TYR 2 CB ) 4.1424 ( PROT TYR 2 CG ) 4.1424 ( PROT TYR 2 CD1 ) 4.1424 ( PROT TYR 2 CE1 ) 4.1424 ( PROT TYR 2 CD2 ) 4.1424 ( PROT TYR 2 CE2 ) 4.1424 ( PROT TYR 2 CZ ) 4.1424 ( PROT TYR 2 OH ) 4.1424 ( PROT TYR 2 HH ) 4.1424 ( PROT TYR 2 C ) 5.1780 ( PROT TYR 2 O ) 5.1780 ( PROT ALA 3 N ) 5.1780 ( PROT ALA 3 H ) 4.1424 ( PROT ALA 3 CA ) 5.1780 ( PROT ALA 3 CB ) 4.1424 ( PROT ALA 3 C ) 5.1780 ( PROT ALA 3 O ) 5.1780 ( PROT PHE 4 N ) 5.1780 ( PROT PHE 4 H ) 4.1424 ( PROT PHE 4 CA ) 5.1780 ( PROT PHE 4 CB ) 4.1424 ( PROT PHE 4 CG ) 4.1424 ( PROT PHE 4 CD1 ) 4.1424 ( PROT PHE 4 CD2 ) 4.1424 ( PROT PHE 4 CE1 ) 4.1424 ( PROT PHE 4 CE2 ) 4.1424 ( PROT PHE 4 CZ ) 4.1424 ( PROT PHE 4 C ) 5.1780 ( PROT PHE 4 O ) 5.1780 ( PROT ILE 5 N ) 5.1780 ( PROT ILE 5 H ) 4.1424 ( PROT ILE 5 CA ) 5.1780 ( PROT ILE 5 CB ) 4.1424 ( PROT ILE 5 CG2 ) 4.1424 ( PROT ILE 5 CG1 ) 4.1424 ( PROT ILE 5 CD ) 4.1424 ( PROT ILE 5 C ) 5.1780 ( PROT ILE 5 O ) 5.1780 ( PROT ALA 6 N ) 5.1780 ( PROT ALA 6 H ) 4.1424 ( PROT ALA 6 CA ) 5.1780 ( PROT ALA 6 CB ) 4.1424 ( PROT ALA 6 C ) 5.1780 ( PROT ALA 6 O ) 5.1780 ( PROT SER 7 N ) 5.1780 ( PROT SER 7 H ) 4.1424 ( PROT SER 7 CA ) 5.1780 ( PROT SER 7 CB ) 4.1424 ( PROT SER 7 OG ) 4.1424 ( PROT SER 7 HG ) 4.1424 ( PROT SER 7 C ) 5.1780 ( PROT SER 7 O ) 5.1780 ( PROT LEU 8 N ) 5.1780 ( PROT LEU 8 H ) 4.1424 ( PROT LEU 8 CA ) 5.1780 ( PROT LEU 8 CB ) 4.1424 ( PROT LEU 8 CG ) 4.1424 ( PROT LEU 8 CD1 ) 4.1424 ( PROT LEU 8 CD2 ) 4.1424 ( PROT LEU 8 C ) 5.1780 ( PROT LEU 8 O ) 5.1780 ( PROT VAL 9 N ) 5.1780 ( PROT VAL 9 H ) 4.1424 ( PROT VAL 9 CA ) 5.1780 ( PROT VAL 9 CB ) 4.1424 ( PROT VAL 9 CG1 ) 4.1424 ( PROT VAL 9 CG2 ) 4.1424 ( PROT VAL 9 C ) 5.1780 ( PROT VAL 9 O ) 5.1780 ( PROT VAL 10 N ) 5.1780 ( PROT VAL 10 H ) 4.1424 ( PROT VAL 10 CA ) 5.1780 ( PROT VAL 10 CB ) 4.1424 ( PROT VAL 10 CG1 ) 4.1424 ( PROT VAL 10 CG2 ) 4.1424 ( PROT VAL 10 C ) 5.1780 ( PROT VAL 10 O ) 5.1780 ( PROT ILE 11 N ) 5.1780 ( PROT ILE 11 H ) 4.1424 ( PROT ILE 11 CA ) 5.1780 ( PROT ILE 11 CB ) 4.1424 ( PROT ILE 11 CG2 ) 4.1424 ( PROT ILE 11 CG1 ) 4.1424 ( PROT ILE 11 CD ) 4.1424 ( PROT ILE 11 C ) 5.1780 ( PROT ILE 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 ASP 13 N ) 5.1780 ( PROT ASP 13 H ) 4.1424 ( PROT ASP 13 CA ) 5.1780 ( PROT ASP 13 CB ) 4.1424 ( PROT ASP 13 CG ) 4.1424 ( PROT ASP 13 OD1 ) 4.1424 ( PROT ASP 13 OD2 ) 4.1424 ( PROT ASP 13 C ) 5.1780 ( PROT ASP 13 O ) 5.1780 ( PROT ASP 14 N ) 5.1780 ( PROT ASP 14 H ) 4.1424 ( PROT ASP 14 CA ) 5.1780 ( PROT ASP 14 CB ) 4.1424 ( PROT ASP 14 CG ) 4.1424 ( PROT ASP 14 OD1 ) 4.1424 ( PROT ASP 14 OD2 ) 4.1424 ( PROT ASP 14 C ) 5.1780 ( PROT ASP 14 O ) 5.1780 ( PROT VAL 15 N ) 5.1780 ( PROT VAL 15 H ) 4.1424 ( PROT VAL 15 CA ) 5.1780 ( PROT VAL 15 CB ) 4.1424 ( PROT VAL 15 CG1 ) 4.1424 ( PROT VAL 15 CG2 ) 4.1424 ( PROT VAL 15 C ) 5.1780 ( PROT VAL 15 O ) 5.1780 ( PROT ASN 16 N ) 5.1780 ( PROT ASN 16 H ) 4.1424 ( PROT ASN 16 CA ) 5.1780 ( PROT ASN 16 CB ) 4.1424 ( PROT ASN 16 CG ) 4.1424 ( PROT ASN 16 OD1 ) 4.1424 ( PROT ASN 16 ND2 ) 4.1424 ( PROT ASN 16 HD21 ) 4.1424 ( PROT ASN 16 HD22 ) 4.1424 ( PROT ASN 16 C ) 5.1780 ( PROT ASN 16 O ) 5.1780 ( PROT ARG 17 N ) 5.1780 ( PROT ARG 17 H ) 4.1424 ( PROT ARG 17 CA ) 5.1780 ( PROT ARG 17 CB ) 4.1424 ( PROT ARG 17 CG ) 4.1424 ( PROT ARG 17 CD ) 4.1424 ( PROT ARG 17 NE ) 4.1424 ( PROT ARG 17 HE ) 4.1424 ( PROT ARG 17 CZ ) 4.1424 ( PROT ARG 17 NH1 ) 4.1424 ( PROT ARG 17 HH11 ) 4.1424 ( PROT ARG 17 HH12 ) 4.1424 ( PROT ARG 17 NH2 ) 4.1424 ( PROT ARG 17 HH21 ) 4.1424 ( PROT ARG 17 HH22 ) 4.1424 ( PROT ARG 17 C ) 5.1780 ( PROT ARG 17 OT1 ) 4.1424 ( PROT ARG 17 OT2 ) 4.1424 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96123 3.71174 -6.80014 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00260 -0.00042 -0.00186 ROTATION MATRIX 1.000000 -0.000170 -0.000187 0.000170 1.000000 0.000484 0.000187 -0.000484 1.000000 AXIS OF ROTATION IS 0.886511 0.341786 -0.311897 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 12.3596 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.274524 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2745" Parameter: A <- "0.2745" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.77716 3.77965 -6.97362 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.00498 0.01205 -0.00362 ROTATION MATRIX 0.999624 0.017875 0.020782 -0.017394 0.999582 -0.023099 -0.021186 0.022728 0.999517 AXIS OF ROTATION IS -0.641366 -0.587366 0.493611 ANGLE IS 2.05 CENTER OF ROTATION 7.667639 3.651934 -7.273644 SHIFT IS -0.005667 TOTAL SQUARE DIFF IS 0.4770 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.167511 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2745" RDCMND substituted energy or value "?RMS" to " 0.1675" Parameter: A <- "0.2745 0.1675" 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 0.2745 0.1675 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 " 90.90" Parameter: H <- "90.90" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 7.21904 90.89963 2.34375 ENER INTERN> 7.78730 30.07772 0.00000 11.41205 5.90745 ENER EXTERN> -26.21756 -21.74792 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 " 7.22" Parameter: B <- "7.22" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -21.75" Parameter: C <- "-21.75" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -26.22" Parameter: C <- " -47.97" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -47.97" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.79" Parameter: D <- "7.79" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 30.08" Parameter: D <- " 37.87" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.41" Parameter: D <- " 49.28" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.91" Parameter: D <- " 55.19" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 55.19" 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= 7.22 GRMS= 2.34 ELEC= -21.75 VDW= -26.22 RDTITL> *EXTERNAL= -47.97 INTERNAL= 55.19 USER= 0.00 HARM= 90.90 RDTITL> *BOND= 7.79 ANGL= 30.08 DIHE= 11.41 IMPR= 5.91 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: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9286 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9285 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 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 80.51514 -73.29610 1.08132 0.02000 MINI INTERN> 7.78730 30.07772 0.00000 11.41205 5.90745 MINI EXTERN> -26.21756 -21.74792 0.00000 0.00000 0.00000 MINI CONSTR> 73.29610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 75.15643 5.35871 1.39602 0.00360 MINI INTERN> 7.50929 27.97768 0.00000 12.22511 6.05387 MINI EXTERN> -33.84837 -20.99162 0.00000 0.00000 0.00000 MINI CONSTR> 76.23047 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9275 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 73.50779 1.64864 1.48611 0.00156 MINI INTERN> 7.64044 28.75296 0.00000 12.41614 5.89334 MINI EXTERN> -36.98653 -20.61498 0.00000 0.00000 0.00000 MINI CONSTR> 76.40641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 72.47744 1.03035 0.69433 0.00067 MINI INTERN> 7.34350 28.65978 0.00000 12.41879 6.02307 MINI EXTERN> -37.72051 -20.57898 0.00000 0.00000 0.00000 MINI CONSTR> 76.33179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9274 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 71.80503 0.67241 0.62324 0.00070 MINI INTERN> 7.25576 28.52781 0.00000 12.44216 5.97909 MINI EXTERN> -38.01177 -20.61547 0.00000 0.00000 0.00000 MINI CONSTR> 76.22745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 71.12803 0.67700 1.07974 0.00072 MINI INTERN> 7.61166 28.18597 0.00000 12.42271 5.97562 MINI EXTERN> -38.55956 -20.60121 0.00000 0.00000 0.00000 MINI CONSTR> 76.09284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9271 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 70.52991 0.59813 0.78238 0.00075 MINI INTERN> 7.38551 28.15823 0.00000 12.44150 5.94913 MINI EXTERN> -38.73813 -20.63921 0.00000 0.00000 0.00000 MINI CONSTR> 75.97289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 69.97085 0.55906 0.85769 0.00078 MINI INTERN> 7.44412 27.99656 0.00000 12.43693 5.93105 MINI EXTERN> -39.02552 -20.65026 0.00000 0.00000 0.00000 MINI CONSTR> 75.83796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9269 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 69.54413 0.42672 1.33275 0.00080 MINI INTERN> 7.76653 27.72028 0.00000 12.42093 5.91526 MINI EXTERN> -39.35641 -20.62718 0.00000 0.00000 0.00000 MINI CONSTR> 75.70472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 69.07304 0.47109 1.40987 0.00083 MINI INTERN> 7.88873 27.54988 0.00000 12.40922 5.89539 MINI EXTERN> -39.60095 -20.63889 0.00000 0.00000 0.00000 MINI CONSTR> 75.56966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9269 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 68.65097 0.42207 1.53010 0.00087 MINI INTERN> 8.01379 27.39230 0.00000 12.39650 5.87527 MINI EXTERN> -39.81758 -20.64836 0.00000 0.00000 0.00000 MINI CONSTR> 75.43905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 68.25686 0.39410 1.45625 0.00090 MINI INTERN> 7.90646 27.34751 0.00000 12.39826 5.85156 MINI EXTERN> -39.91112 -20.66259 0.00000 0.00000 0.00000 MINI CONSTR> 75.32678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9266 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 67.85685 0.40001 1.46103 0.00093 MINI INTERN> 7.94784 27.25735 0.00000 12.37819 5.83682 MINI EXTERN> -40.08258 -20.68708 0.00000 0.00000 0.00000 MINI CONSTR> 75.20631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 67.36401 0.49284 0.46085 0.00040 MINI INTERN> 6.78138 27.81058 0.00000 12.41349 5.81445 MINI EXTERN> -39.78060 -20.79042 0.00000 0.00000 0.00000 MINI CONSTR> 75.11513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9263 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 67.22033 0.14368 1.62026 0.00100 MINI INTERN> 8.04155 27.07453 0.00000 12.35078 5.80212 MINI EXTERN> -40.34414 -20.70038 0.00000 0.00000 0.00000 MINI CONSTR> 74.99588 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 66.90989 0.31044 1.68386 0.00104 MINI INTERN> 8.10958 27.01713 0.00000 12.31582 5.79907 MINI EXTERN> -40.51131 -20.71837 0.00000 0.00000 0.00000 MINI CONSTR> 74.89796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9261 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 66.40517 0.50472 0.53039 0.00045 MINI INTERN> 6.66153 27.65645 0.00000 12.38174 5.75822 MINI EXTERN> -40.04526 -20.81996 0.00000 0.00000 0.00000 MINI CONSTR> 74.81245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 66.15773 0.24744 0.37237 0.00046 MINI INTERN> 6.80812 27.52683 0.00000 12.35210 5.75335 MINI EXTERN> -40.20495 -20.81813 0.00000 0.00000 0.00000 MINI CONSTR> 74.74041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9260 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 65.88089 0.27684 0.36668 0.00048 MINI INTERN> 6.78673 27.47504 0.00000 12.33746 5.73639 MINI EXTERN> -40.28411 -20.82550 0.00000 0.00000 0.00000 MINI CONSTR> 74.65487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 65.63625 0.24464 0.73397 0.00050 MINI INTERN> 6.54230 27.52189 0.00000 12.35921 5.69557 MINI EXTERN> -40.20987 -20.83639 0.00000 0.00000 0.00000 MINI CONSTR> 74.56355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9259 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 65.39118 0.24507 0.44703 0.00052 MINI INTERN> 6.67585 27.41230 0.00000 12.31897 5.69729 MINI EXTERN> -40.37697 -20.83976 0.00000 0.00000 0.00000 MINI CONSTR> 74.50350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 65.17114 0.22004 0.53010 0.00054 MINI INTERN> 6.60753 27.39110 0.00000 12.31227 5.67630 MINI EXTERN> -40.40618 -20.84592 0.00000 0.00000 0.00000 MINI CONSTR> 74.43604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9259 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 65.01721 0.15393 0.81027 0.00056 MINI INTERN> 6.45867 27.41992 0.00000 12.32362 5.64770 MINI EXTERN> -40.35906 -20.85294 0.00000 0.00000 0.00000 MINI CONSTR> 74.37929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 64.83482 0.18239 0.89534 0.00058 MINI INTERN> 6.40041 27.40341 0.00000 12.31721 5.62748 MINI EXTERN> -40.38185 -20.85663 0.00000 0.00000 0.00000 MINI CONSTR> 74.32478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9259 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 64.67432 0.16049 0.86987 0.00060 MINI INTERN> 6.40184 27.36545 0.00000 12.30144 5.61722 MINI EXTERN> -40.43577 -20.85999 0.00000 0.00000 0.00000 MINI CONSTR> 74.28414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 64.46779 0.20654 0.27264 0.00026 MINI INTERN> 6.85772 27.13368 0.00000 12.20810 5.65546 MINI EXTERN> -40.78738 -20.85910 0.00000 0.00000 0.00000 MINI CONSTR> 74.25930 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9259 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 64.39584 0.07195 0.96137 0.00064 MINI INTERN> 6.33808 27.32851 0.00000 12.28293 5.58860 MINI EXTERN> -40.48745 -20.86619 0.00000 0.00000 0.00000 MINI CONSTR> 74.21136 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 64.26614 0.12970 0.99933 0.00067 MINI INTERN> 6.31092 27.30849 0.00000 12.27315 5.57459 MINI EXTERN> -40.51440 -20.86704 0.00000 0.00000 0.00000 MINI CONSTR> 74.18044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9258 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 64.06277 0.20338 0.32143 0.00029 MINI INTERN> 6.92185 27.01208 0.00000 12.15348 5.62998 MINI EXTERN> -40.95650 -20.86830 0.00000 0.00000 0.00000 MINI CONSTR> 74.17018 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 63.96338 0.09939 0.22926 0.00030 MINI INTERN> 6.82227 27.02352 0.00000 12.15684 5.61260 MINI EXTERN> -40.93204 -20.86974 0.00000 0.00000 0.00000 MINI CONSTR> 74.14993 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9258 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 63.85175 0.11163 0.22614 0.00031 MINI INTERN> 6.82734 26.99295 0.00000 12.14190 5.60335 MINI EXTERN> -40.97235 -20.87212 0.00000 0.00000 0.00000 MINI CONSTR> 74.13069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 63.75587 0.09588 0.47333 0.00032 MINI INTERN> 7.03605 26.89185 0.00000 12.09676 5.61230 MINI EXTERN> -41.12316 -20.87604 0.00000 0.00000 0.00000 MINI CONSTR> 74.11810 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9257 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 63.65798 0.09789 0.27886 0.00033 MINI INTERN> 6.88973 26.91846 0.00000 12.10569 5.59110 MINI EXTERN> -41.07400 -20.87689 0.00000 0.00000 0.00000 MINI CONSTR> 74.10389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 63.58584 0.07215 0.52057 0.00034 MINI INTERN> 7.06619 26.83504 0.00000 12.06756 5.59812 MINI EXTERN> -41.19775 -20.88109 0.00000 0.00000 0.00000 MINI CONSTR> 74.09776 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9256 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 63.51068 0.07516 0.55559 0.00036 MINI INTERN> 7.08963 26.80553 0.00000 12.05235 5.59186 MINI EXTERN> -41.23642 -20.88374 0.00000 0.00000 0.00000 MINI CONSTR> 74.09146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 63.44330 0.06738 0.53489 0.00037 MINI INTERN> 7.07317 26.79170 0.00000 12.04405 5.58352 MINI EXTERN> -41.25206 -20.88422 0.00000 0.00000 0.00000 MINI CONSTR> 74.08715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9256 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 63.37821 0.06509 0.55764 0.00038 MINI INTERN> 7.08764 26.76828 0.00000 12.03083 5.57685 MINI EXTERN> -41.28235 -20.88780 0.00000 0.00000 0.00000 MINI CONSTR> 74.08477 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 63.29618 0.08203 0.17576 0.00017 MINI INTERN> 6.71413 26.88042 0.00000 12.07518 5.53592 MINI EXTERN> -41.10614 -20.87965 0.00000 0.00000 0.00000 MINI CONSTR> 74.07631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9256 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 63.27056 0.02562 0.61289 0.00041 MINI INTERN> 7.12244 26.72334 0.00000 12.00599 5.56589 MINI EXTERN> -41.34108 -20.89168 0.00000 0.00000 0.00000 MINI CONSTR> 74.08566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 63.22165 0.04891 0.66765 0.00043 MINI INTERN> 7.10014 26.71264 0.00000 11.99843 5.55996 MINI EXTERN> -41.35384 -20.88487 0.00000 0.00000 0.00000 MINI CONSTR> 74.08919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9256 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 63.14170 0.07995 0.21871 0.00019 MINI INTERN> 6.65622 26.85372 0.00000 12.05437 5.51047 MINI EXTERN> -41.13541 -20.87973 0.00000 0.00000 0.00000 MINI CONSTR> 74.08205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 63.10241 0.03929 0.14397 0.00019 MINI INTERN> 6.72433 26.81458 0.00000 12.03583 5.51225 MINI EXTERN> -41.18963 -20.88250 0.00000 0.00000 0.00000 MINI CONSTR> 74.08755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9256 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 63.05778 0.04463 0.14596 0.00020 MINI INTERN> 6.71107 26.80418 0.00000 12.02809 5.50474 MINI EXTERN> -41.20176 -20.88208 0.00000 0.00000 0.00000 MINI CONSTR> 74.09355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 63.02141 0.03637 0.30615 0.00021 MINI INTERN> 6.59076 26.83758 0.00000 12.03775 5.48607 MINI EXTERN> -41.15152 -20.87762 0.00000 0.00000 0.00000 MINI CONSTR> 74.09840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9257 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 62.98216 0.03925 0.18649 0.00021 MINI INTERN> 6.66931 26.79371 0.00000 12.01694 5.48842 MINI EXTERN> -41.21172 -20.88190 0.00000 0.00000 0.00000 MINI CONSTR> 74.10741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 62.95483 0.02733 0.32443 0.00022 MINI INTERN> 6.57560 26.81897 0.00000 12.02364 5.47388 MINI EXTERN> -41.17460 -20.87676 0.00000 0.00000 0.00000 MINI CONSTR> 74.11411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9257 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 62.92450 0.03033 0.35891 0.00023 MINI INTERN> 6.56949 26.81079 0.00000 12.01694 5.46638 MINI EXTERN> -41.18397 -20.87822 0.00000 0.00000 0.00000 MINI CONSTR> 74.12309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 62.89764 0.02686 0.35028 0.00024 MINI INTERN> 6.56463 26.79989 0.00000 12.00959 5.46340 MINI EXTERN> -41.19903 -20.87373 0.00000 0.00000 0.00000 MINI CONSTR> 74.13289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9257 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 62.86462 0.03302 0.11534 0.00010 MINI INTERN> 6.76122 26.71302 0.00000 11.97149 5.47829 MINI EXTERN> -41.31969 -20.88576 0.00000 0.00000 0.00000 MINI CONSTR> 74.14604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 62.85158 0.01304 0.38082 0.00026 MINI INTERN> 6.53821 26.79188 0.00000 12.00006 5.45128 MINI EXTERN> -41.20796 -20.87359 0.00000 0.00000 0.00000 MINI CONSTR> 74.15170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9256 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 62.82943 0.02214 0.40587 0.00027 MINI INTERN> 6.56191 26.77572 0.00000 11.99032 5.44642 MINI EXTERN> -41.22852 -20.87880 0.00000 0.00000 0.00000 MINI CONSTR> 74.16238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 62.79648 0.03295 0.13168 0.00011 MINI INTERN> 6.78278 26.67580 0.00000 11.94697 5.46686 MINI EXTERN> -41.36824 -20.88682 0.00000 0.00000 0.00000 MINI CONSTR> 74.17913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9255 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 62.77911 0.01738 0.09666 0.00012 MINI INTERN> 6.74635 26.68139 0.00000 11.94692 5.45985 MINI EXTERN> -41.35904 -20.88434 0.00000 0.00000 0.00000 MINI CONSTR> 74.18799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 62.76022 0.01888 0.09886 0.00012 MINI INTERN> 6.75383 26.66989 0.00000 11.93917 5.45624 MINI EXTERN> -41.37413 -20.88480 0.00000 0.00000 0.00000 MINI CONSTR> 74.20003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9255 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 62.74340 0.01683 0.18062 0.00013 MINI INTERN> 6.81735 26.63771 0.00000 11.92256 5.45810 MINI EXTERN> -41.41903 -20.88788 0.00000 0.00000 0.00000 MINI CONSTR> 74.21459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 62.72658 0.01681 0.11470 0.00013 MINI INTERN> 6.77138 26.64685 0.00000 11.92376 5.44991 MINI EXTERN> -41.40477 -20.88541 0.00000 0.00000 0.00000 MINI CONSTR> 74.22485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9255 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 62.71121 0.01537 0.13722 0.00014 MINI INTERN> 6.78204 26.63439 0.00000 11.91561 5.44743 MINI EXTERN> -41.42179 -20.88476 0.00000 0.00000 0.00000 MINI CONSTR> 74.23829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 62.70013 0.01108 0.20749 0.00014 MINI INTERN> 6.83080 26.61014 0.00000 11.90281 5.44841 MINI EXTERN> -41.45559 -20.88753 0.00000 0.00000 0.00000 MINI CONSTR> 74.25109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9255 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 62.68761 0.01252 0.23597 0.00015 MINI INTERN> 6.84064 26.60085 0.00000 11.89592 5.44447 MINI EXTERN> -41.46756 -20.89044 0.00000 0.00000 0.00000 MINI CONSTR> 74.26372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 62.67619 0.01142 0.22376 0.00015 MINI INTERN> 6.83516 26.59479 0.00000 11.89118 5.44220 MINI EXTERN> -41.47607 -20.88658 0.00000 0.00000 0.00000 MINI CONSTR> 74.27552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9255 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 62.66534 0.01086 0.23774 0.00016 MINI INTERN> 6.83280 26.59117 0.00000 11.88694 5.43692 MINI EXTERN> -41.47996 -20.88957 0.00000 0.00000 0.00000 MINI CONSTR> 74.28704 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 62.65196 0.01337 0.07338 0.00007 MINI INTERN> 6.70672 26.62942 0.00000 11.90120 5.42322 MINI EXTERN> -41.42586 -20.87796 0.00000 0.00000 0.00000 MINI CONSTR> 74.29522 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9255 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 62.64713 0.00483 0.25233 0.00017 MINI INTERN> 6.85718 26.56921 0.00000 11.87321 5.43438 MINI EXTERN> -41.51071 -20.88736 0.00000 0.00000 0.00000 MINI CONSTR> 74.31122 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 62.63785 0.00928 0.26188 0.00018 MINI INTERN> 6.86070 26.56188 0.00000 11.86747 5.43153 MINI EXTERN> -41.52061 -20.88741 0.00000 0.00000 0.00000 MINI CONSTR> 74.32428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9255 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 62.62333 0.01452 0.08151 0.00008 MINI INTERN> 6.69193 26.61628 0.00000 11.88822 5.41217 MINI EXTERN> -41.44378 -20.87457 0.00000 0.00000 0.00000 MINI CONSTR> 74.33308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 62.61615 0.00717 0.06156 0.00008 MINI INTERN> 6.70964 26.60482 0.00000 11.88137 5.41150 MINI EXTERN> -41.45969 -20.87543 0.00000 0.00000 0.00000 MINI CONSTR> 74.34394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9254 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 62.60816 0.00800 0.06098 0.00008 MINI INTERN> 6.70726 26.59999 0.00000 11.87695 5.40824 MINI EXTERN> -41.46643 -20.87449 0.00000 0.00000 0.00000 MINI CONSTR> 74.35662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 62.60109 0.00706 0.12369 0.00009 MINI INTERN> 6.66245 26.61083 0.00000 11.87907 5.40053 MINI EXTERN> -41.45176 -20.86938 0.00000 0.00000 0.00000 MINI CONSTR> 74.36936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9254 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 62.59396 0.00713 0.07447 0.00009 MINI INTERN> 6.69122 26.59506 0.00000 11.87031 5.40093 MINI EXTERN> -41.47361 -20.87129 0.00000 0.00000 0.00000 MINI CONSTR> 74.38134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 62.58744 0.00652 0.08781 0.00009 MINI INTERN> 6.68141 26.59318 0.00000 11.86727 5.39724 MINI EXTERN> -41.47660 -20.86905 0.00000 0.00000 0.00000 MINI CONSTR> 74.39400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9254 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 62.58283 0.00462 0.13718 0.00010 MINI INTERN> 6.65343 26.59937 0.00000 11.86788 5.39179 MINI EXTERN> -41.46861 -20.86570 0.00000 0.00000 0.00000 MINI CONSTR> 74.40465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 62.57724 0.00559 0.14867 0.00010 MINI INTERN> 6.64834 26.59618 0.00000 11.86446 5.38847 MINI EXTERN> -41.47332 -20.86394 0.00000 0.00000 0.00000 MINI CONSTR> 74.41705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9252 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 62.57243 0.00481 0.16708 0.00010 MINI INTERN> 6.63871 26.59487 0.00000 11.86190 5.38513 MINI EXTERN> -41.47577 -20.86135 0.00000 0.00000 0.00000 MINI CONSTR> 74.42893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 62.56789 0.00454 0.15610 0.00011 MINI INTERN> 6.64297 26.58963 0.00000 11.85784 5.38344 MINI EXTERN> -41.48344 -20.86152 0.00000 0.00000 0.00000 MINI CONSTR> 74.43897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 62.56143 0.00646 0.04609 0.00005 MINI INTERN> 6.71931 26.55691 0.00000 11.84168 5.38914 MINI EXTERN> -41.52848 -20.86901 0.00000 0.00000 0.00000 MINI CONSTR> 74.45188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 62.55928 0.00214 0.16957 0.00011 MINI INTERN> 6.63695 26.58312 0.00000 11.85135 5.37813 MINI EXTERN> -41.49354 -20.85839 0.00000 0.00000 0.00000 MINI CONSTR> 74.46167 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9252 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 62.55538 0.00390 0.17711 0.00012 MINI INTERN> 6.63361 26.58007 0.00000 11.84827 5.37553 MINI EXTERN> -41.49829 -20.85670 0.00000 0.00000 0.00000 MINI CONSTR> 74.47289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 62.54910 0.00629 0.05779 0.00005 MINI INTERN> 6.72961 26.54083 0.00000 11.82898 5.38357 MINI EXTERN> -41.55238 -20.86754 0.00000 0.00000 0.00000 MINI CONSTR> 74.48603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9252 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 62.54594 0.00315 0.04085 0.00005 MINI INTERN> 6.71554 26.54246 0.00000 11.82841 5.38038 MINI EXTERN> -41.55048 -20.86497 0.00000 0.00000 0.00000 MINI CONSTR> 74.49461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 62.54232 0.00363 0.04026 0.00005 MINI INTERN> 6.71554 26.53846 0.00000 11.82486 5.37825 MINI EXTERN> -41.55664 -20.86400 0.00000 0.00000 0.00000 MINI CONSTR> 74.50584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 62.53894 0.00338 0.08049 0.00006 MINI INTERN> 6.74023 26.52572 0.00000 11.81698 5.37858 MINI EXTERN> -41.57528 -20.86617 0.00000 0.00000 0.00000 MINI CONSTR> 74.51889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 62.53573 0.00321 0.05113 0.00006 MINI INTERN> 6.72415 26.52784 0.00000 11.81660 5.37503 MINI EXTERN> -41.57276 -20.86326 0.00000 0.00000 0.00000 MINI CONSTR> 74.52813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 62.53283 0.00291 0.06403 0.00006 MINI INTERN> 6.72881 26.52239 0.00000 11.81247 5.37381 MINI EXTERN> -41.58118 -20.86254 0.00000 0.00000 0.00000 MINI CONSTR> 74.53906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 62.53064 0.00219 0.09181 0.00006 MINI INTERN> 6.74393 26.51407 0.00000 11.80723 5.37354 MINI EXTERN> -41.59322 -20.86376 0.00000 0.00000 0.00000 MINI CONSTR> 74.54884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 62.52803 0.00261 0.10094 0.00007 MINI INTERN> 6.74630 26.51024 0.00000 11.80387 5.37155 MINI EXTERN> -41.59919 -20.86388 0.00000 0.00000 0.00000 MINI CONSTR> 74.55916 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 62.52581 0.00222 0.10991 0.00007 MINI INTERN> 6.74884 26.50560 0.00000 11.80042 5.37070 MINI EXTERN> -41.60644 -20.86222 0.00000 0.00000 0.00000 MINI CONSTR> 74.56890 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 62.52356 0.00225 0.10301 0.00007 MINI INTERN> 6.74854 26.50290 0.00000 11.79807 5.36880 MINI EXTERN> -41.61041 -20.86169 0.00000 0.00000 0.00000 MINI CONSTR> 74.57735 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 62.52124 0.00232 0.10779 0.00007 MINI INTERN> 6.74579 26.50032 0.00000 11.79539 5.36719 MINI EXTERN> -41.61511 -20.85982 0.00000 0.00000 0.00000 MINI CONSTR> 74.58749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 62.51835 0.00289 0.03492 0.00003 MINI INTERN> 6.69796 26.51377 0.00000 11.80080 5.36045 MINI EXTERN> -41.59694 -20.85227 0.00000 0.00000 0.00000 MINI CONSTR> 74.59458 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 62.51740 0.00096 0.11655 0.00008 MINI INTERN> 6.75246 26.49255 0.00000 11.78946 5.36424 MINI EXTERN> -41.62673 -20.85959 0.00000 0.00000 0.00000 MINI CONSTR> 74.60500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 62.51560 0.00180 0.13271 0.00008 MINI INTERN> 6.73898 26.49330 0.00000 11.78852 5.36243 MINI EXTERN> -41.62723 -20.85487 0.00000 0.00000 0.00000 MINI CONSTR> 74.61448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 62.51248 0.00312 0.03865 0.00004 MINI INTERN> 6.69287 26.50662 0.00000 11.79390 5.35542 MINI EXTERN> -41.60925 -20.84837 0.00000 0.00000 0.00000 MINI CONSTR> 74.62129 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 62.51084 0.00165 0.02962 0.00004 MINI INTERN> 6.69937 26.50184 0.00000 11.79065 5.35488 MINI EXTERN> -41.61653 -20.84845 0.00000 0.00000 0.00000 MINI CONSTR> 74.62908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 62.50895 0.00189 0.02925 0.00004 MINI INTERN> 6.69902 26.49892 0.00000 11.78810 5.35331 MINI EXTERN> -41.62141 -20.84729 0.00000 0.00000 0.00000 MINI CONSTR> 74.63830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 62.50708 0.00187 0.05211 0.00004 MINI INTERN> 6.68427 26.50047 0.00000 11.78765 5.35017 MINI EXTERN> -41.62035 -20.84336 0.00000 0.00000 0.00000 MINI CONSTR> 74.64822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 62.50545 0.00162 0.04119 0.00004 MINI INTERN> 6.69024 26.49600 0.00000 11.78452 5.34939 MINI EXTERN> -41.62725 -20.84363 0.00000 0.00000 0.00000 MINI CONSTR> 74.65618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 62.50393 0.00152 0.04660 0.00004 MINI INTERN> 6.68546 26.49488 0.00000 11.78298 5.34773 MINI EXTERN> -41.62981 -20.84164 0.00000 0.00000 0.00000 MINI CONSTR> 74.66433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 62.50236 0.00157 0.04422 0.00004 MINI INTERN> 6.68627 26.49188 0.00000 11.78056 5.34649 MINI EXTERN> -41.63480 -20.84070 0.00000 0.00000 0.00000 MINI CONSTR> 74.67265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 62.50108 0.00128 0.06668 0.00005 MINI INTERN> 6.67538 26.49298 0.00000 11.78012 5.34414 MINI EXTERN> -41.63441 -20.83771 0.00000 0.00000 0.00000 MINI CONSTR> 74.68059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 62.49954 0.00154 0.06768 0.00005 MINI INTERN> 6.67587 26.49003 0.00000 11.77778 5.34272 MINI EXTERN> -41.63927 -20.83670 0.00000 0.00000 0.00000 MINI CONSTR> 74.68911 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 62.49819 0.00135 0.07997 0.00005 MINI INTERN> 6.67278 26.48791 0.00000 11.77583 5.34165 MINI EXTERN> -41.64343 -20.83417 0.00000 0.00000 0.00000 MINI CONSTR> 74.69762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 62.49819 0.00135 0.07997 0.00002 STPD INTERN> 6.67278 26.48791 0.00000 11.77583 5.34165 STPD EXTERN> -41.64343 -20.83417 0.00000 0.00000 0.00000 STPD CONSTR> 74.69762 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 9253 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9253 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 62.49817 0.00003 0.03843 0.00000 MINI INTERN> 6.70926 26.47659 0.00000 11.77051 5.34535 MINI EXTERN> -41.65811 -20.84156 0.00000 0.00000 0.00000 MINI CONSTR> 74.69613 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 62.44720 0.05097 0.07569 0.00642 MINI INTERN> 6.64449 26.27885 0.00000 11.64772 5.29254 MINI EXTERN> -42.06365 -20.68755 0.00000 0.00000 0.00000 MINI CONSTR> 75.33480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 62.43377 0.01343 0.13994 0.01429 MINI INTERN> 6.65159 26.22262 0.00000 11.60933 5.27030 MINI EXTERN> -42.06568 -20.69221 0.00000 0.00000 0.00000 MINI CONSTR> 75.43782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 62.41123 0.02254 0.08109 0.02160 MINI INTERN> 6.58566 26.06824 0.00000 11.57572 5.28586 MINI EXTERN> -42.24257 -20.54342 0.00000 0.00000 0.00000 MINI CONSTR> 75.68175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 62.40409 0.00714 0.08047 0.00719 MINI INTERN> 6.56166 26.05827 0.00000 11.55373 5.30186 MINI EXTERN> -42.38424 -20.47488 0.00000 0.00000 0.00000 MINI CONSTR> 75.78770 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 62.39612 0.00797 0.07321 0.00918 MINI INTERN> 6.53077 25.98767 0.00000 11.59518 5.31750 MINI EXTERN> -42.44802 -20.45973 0.00000 0.00000 0.00000 MINI CONSTR> 75.87275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 62.39047 0.00565 0.06129 0.00746 MINI INTERN> 6.54895 26.03596 0.00000 11.60271 5.30184 MINI EXTERN> -42.46632 -20.47056 0.00000 0.00000 0.00000 MINI CONSTR> 75.83789 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 62.38743 0.00304 0.04561 0.00533 MINI INTERN> 6.55715 26.06969 0.00000 11.60531 5.30789 MINI EXTERN> -42.39453 -20.48378 0.00000 0.00000 0.00000 MINI CONSTR> 75.72569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 62.38379 0.00364 0.06191 0.00595 MINI INTERN> 6.58563 26.11054 0.00000 11.61559 5.32616 MINI EXTERN> -42.27552 -20.52882 0.00000 0.00000 0.00000 MINI CONSTR> 75.55022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 62.37959 0.00420 0.06038 0.00906 MINI INTERN> 6.57257 26.16418 0.00000 11.65270 5.31146 MINI EXTERN> -42.19644 -20.53903 0.00000 0.00000 0.00000 MINI CONSTR> 75.41416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 62.37549 0.00410 0.05357 0.00661 MINI INTERN> 6.59052 26.17225 0.00000 11.69109 5.35186 MINI EXTERN> -42.20336 -20.57711 0.00000 0.00000 0.00000 MINI CONSTR> 75.35023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 62.37090 0.00458 0.06515 0.01178 MINI INTERN> 6.60630 26.21048 0.00000 11.74272 5.37055 MINI EXTERN> -42.19110 -20.66286 0.00000 0.00000 0.00000 MINI CONSTR> 75.29481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 62.36618 0.00472 0.06486 0.00842 MINI INTERN> 6.61107 26.21549 0.00000 11.76149 5.40357 MINI EXTERN> -42.13410 -20.70613 0.00000 0.00000 0.00000 MINI CONSTR> 75.21481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 62.36283 0.00335 0.04099 0.00703 MINI INTERN> 6.60184 26.15602 0.00000 11.79288 5.39559 MINI EXTERN> -42.01745 -20.73709 0.00000 0.00000 0.00000 MINI CONSTR> 75.17105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 62.36052 0.00231 0.04125 0.00685 MINI INTERN> 6.58895 26.11999 0.00000 11.79817 5.42217 MINI EXTERN> -42.00550 -20.74308 0.00000 0.00000 0.00000 MINI CONSTR> 75.17981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 62.35839 0.00213 0.04416 0.00592 MINI INTERN> 6.59968 26.12400 0.00000 11.81382 5.43418 MINI EXTERN> -42.05687 -20.78014 0.00000 0.00000 0.00000 MINI CONSTR> 75.22373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 62.35620 0.00219 0.03970 0.00639 MINI INTERN> 6.59655 26.07153 0.00000 11.82762 5.45413 MINI EXTERN> -42.09889 -20.76331 0.00000 0.00000 0.00000 MINI CONSTR> 75.26857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 62.35437 0.00183 0.03918 0.00510 MINI INTERN> 6.58715 26.04485 0.00000 11.83575 5.46543 MINI EXTERN> -42.09009 -20.75628 0.00000 0.00000 0.00000 MINI CONSTR> 75.26757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 62.35272 0.00165 0.03406 0.00574 MINI INTERN> 6.56791 26.02975 0.00000 11.84215 5.48292 MINI EXTERN> -42.09438 -20.71970 0.00000 0.00000 0.00000 MINI CONSTR> 75.24407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 62.35146 0.00126 0.02531 0.00382 MINI INTERN> 6.56474 26.01248 0.00000 11.85991 5.48882 MINI EXTERN> -42.10311 -20.69438 0.00000 0.00000 0.00000 MINI CONSTR> 75.22299 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 62.35064 0.00081 0.02498 0.00333 MINI INTERN> 6.56003 26.01462 0.00000 11.87740 5.50661 MINI EXTERN> -42.13199 -20.68060 0.00000 0.00000 0.00000 MINI CONSTR> 75.20457 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 62.35064 0.00081 0.02498 0.02000 CONJ INTERN> 6.56003 26.01462 0.00000 11.87740 5.50661 CONJ EXTERN> -42.13199 -20.68060 0.00000 0.00000 0.00000 CONJ CONSTR> 75.20457 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 ASP 1 HT1 ) 2.6925 ( PROT ASP 1 HT2 ) 2.6925 ( PROT ASP 1 N ) 3.3657 ( PROT ASP 1 HT3 ) 2.6925 ( PROT ASP 1 CA ) 3.3657 ( PROT ASP 1 CB ) 2.6925 ( PROT ASP 1 CG ) 2.6925 ( PROT ASP 1 OD1 ) 2.6925 ( PROT ASP 1 OD2 ) 2.6925 ( PROT ASP 1 C ) 3.3657 ( PROT ASP 1 O ) 3.3657 ( PROT TYR 2 N ) 3.3657 ( PROT TYR 2 H ) 2.6925 ( PROT TYR 2 CA ) 3.3657 ( PROT TYR 2 CB ) 2.6925 ( PROT TYR 2 CG ) 2.6925 ( PROT TYR 2 CD1 ) 2.6925 ( PROT TYR 2 CE1 ) 2.6925 ( PROT TYR 2 CD2 ) 2.6925 ( PROT TYR 2 CE2 ) 2.6925 ( PROT TYR 2 CZ ) 2.6925 ( PROT TYR 2 OH ) 2.6925 ( PROT TYR 2 HH ) 2.6925 ( PROT TYR 2 C ) 3.3657 ( PROT TYR 2 O ) 3.3657 ( PROT ALA 3 N ) 3.3657 ( PROT ALA 3 H ) 2.6925 ( PROT ALA 3 CA ) 3.3657 ( PROT ALA 3 CB ) 2.6925 ( PROT ALA 3 C ) 3.3657 ( PROT ALA 3 O ) 3.3657 ( PROT PHE 4 N ) 3.3657 ( PROT PHE 4 H ) 2.6925 ( PROT PHE 4 CA ) 3.3657 ( PROT PHE 4 CB ) 2.6925 ( PROT PHE 4 CG ) 2.6925 ( PROT PHE 4 CD1 ) 2.6925 ( PROT PHE 4 CD2 ) 2.6925 ( PROT PHE 4 CE1 ) 2.6925 ( PROT PHE 4 CE2 ) 2.6925 ( PROT PHE 4 CZ ) 2.6925 ( PROT PHE 4 C ) 3.3657 ( PROT PHE 4 O ) 3.3657 ( PROT ILE 5 N ) 3.3657 ( PROT ILE 5 H ) 2.6925 ( PROT ILE 5 CA ) 3.3657 ( PROT ILE 5 CB ) 2.6925 ( PROT ILE 5 CG2 ) 2.6925 ( PROT ILE 5 CG1 ) 2.6925 ( PROT ILE 5 CD ) 2.6925 ( PROT ILE 5 C ) 3.3657 ( PROT ILE 5 O ) 3.3657 ( PROT ALA 6 N ) 3.3657 ( PROT ALA 6 H ) 2.6925 ( PROT ALA 6 CA ) 3.3657 ( PROT ALA 6 CB ) 2.6925 ( PROT ALA 6 C ) 3.3657 ( PROT ALA 6 O ) 3.3657 ( PROT SER 7 N ) 3.3657 ( PROT SER 7 H ) 2.6925 ( PROT SER 7 CA ) 3.3657 ( PROT SER 7 CB ) 2.6925 ( PROT SER 7 OG ) 2.6925 ( PROT SER 7 HG ) 2.6925 ( PROT SER 7 C ) 3.3657 ( PROT SER 7 O ) 3.3657 ( PROT LEU 8 N ) 3.3657 ( PROT LEU 8 H ) 2.6925 ( PROT LEU 8 CA ) 3.3657 ( PROT LEU 8 CB ) 2.6925 ( PROT LEU 8 CG ) 2.6925 ( PROT LEU 8 CD1 ) 2.6925 ( PROT LEU 8 CD2 ) 2.6925 ( PROT LEU 8 C ) 3.3657 ( PROT LEU 8 O ) 3.3657 ( PROT VAL 9 N ) 3.3657 ( PROT VAL 9 H ) 2.6925 ( PROT VAL 9 CA ) 3.3657 ( PROT VAL 9 CB ) 2.6925 ( PROT VAL 9 CG1 ) 2.6925 ( PROT VAL 9 CG2 ) 2.6925 ( PROT VAL 9 C ) 3.3657 ( PROT VAL 9 O ) 3.3657 ( PROT VAL 10 N ) 3.3657 ( PROT VAL 10 H ) 2.6925 ( PROT VAL 10 CA ) 3.3657 ( PROT VAL 10 CB ) 2.6925 ( PROT VAL 10 CG1 ) 2.6925 ( PROT VAL 10 CG2 ) 2.6925 ( PROT VAL 10 C ) 3.3657 ( PROT VAL 10 O ) 3.3657 ( PROT ILE 11 N ) 3.3657 ( PROT ILE 11 H ) 2.6925 ( PROT ILE 11 CA ) 3.3657 ( PROT ILE 11 CB ) 2.6925 ( PROT ILE 11 CG2 ) 2.6925 ( PROT ILE 11 CG1 ) 2.6925 ( PROT ILE 11 CD ) 2.6925 ( PROT ILE 11 C ) 3.3657 ( PROT ILE 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 ASP 13 N ) 3.3657 ( PROT ASP 13 H ) 2.6925 ( PROT ASP 13 CA ) 3.3657 ( PROT ASP 13 CB ) 2.6925 ( PROT ASP 13 CG ) 2.6925 ( PROT ASP 13 OD1 ) 2.6925 ( PROT ASP 13 OD2 ) 2.6925 ( PROT ASP 13 C ) 3.3657 ( PROT ASP 13 O ) 3.3657 ( PROT ASP 14 N ) 3.3657 ( PROT ASP 14 H ) 2.6925 ( PROT ASP 14 CA ) 3.3657 ( PROT ASP 14 CB ) 2.6925 ( PROT ASP 14 CG ) 2.6925 ( PROT ASP 14 OD1 ) 2.6925 ( PROT ASP 14 OD2 ) 2.6925 ( PROT ASP 14 C ) 3.3657 ( PROT ASP 14 O ) 3.3657 ( PROT VAL 15 N ) 3.3657 ( PROT VAL 15 H ) 2.6925 ( PROT VAL 15 CA ) 3.3657 ( PROT VAL 15 CB ) 2.6925 ( PROT VAL 15 CG1 ) 2.6925 ( PROT VAL 15 CG2 ) 2.6925 ( PROT VAL 15 C ) 3.3657 ( PROT VAL 15 O ) 3.3657 ( PROT ASN 16 N ) 3.3657 ( PROT ASN 16 H ) 2.6925 ( PROT ASN 16 CA ) 3.3657 ( PROT ASN 16 CB ) 2.6925 ( PROT ASN 16 CG ) 2.6925 ( PROT ASN 16 OD1 ) 2.6925 ( PROT ASN 16 ND2 ) 2.6925 ( PROT ASN 16 HD21 ) 2.6925 ( PROT ASN 16 HD22 ) 2.6925 ( PROT ASN 16 C ) 3.3657 ( PROT ASN 16 O ) 3.3657 ( PROT ARG 17 N ) 3.3657 ( PROT ARG 17 H ) 2.6925 ( PROT ARG 17 CA ) 3.3657 ( PROT ARG 17 CB ) 2.6925 ( PROT ARG 17 CG ) 2.6925 ( PROT ARG 17 CD ) 2.6925 ( PROT ARG 17 NE ) 2.6925 ( PROT ARG 17 HE ) 2.6925 ( PROT ARG 17 CZ ) 2.6925 ( PROT ARG 17 NH1 ) 2.6925 ( PROT ARG 17 HH11 ) 2.6925 ( PROT ARG 17 HH12 ) 2.6925 ( PROT ARG 17 NH2 ) 2.6925 ( PROT ARG 17 HH21 ) 2.6925 ( PROT ARG 17 HH22 ) 2.6925 ( PROT ARG 17 C ) 3.3657 ( PROT ARG 17 OT1 ) 2.6925 ( PROT ARG 17 OT2 ) 2.6925 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96077 3.71138 -6.79934 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00305 -0.00006 -0.00267 ROTATION MATRIX 1.000000 -0.000175 -0.000229 0.000176 1.000000 0.000528 0.000229 -0.000528 1.000000 AXIS OF ROTATION IS 0.877381 0.380958 -0.291674 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 15.8120 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.310507 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3105" Parameter: A <- "0.3105" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.77972 3.78150 -6.97845 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.00754 0.01021 0.00122 ROTATION MATRIX 0.999563 0.019310 0.022386 -0.018744 0.999506 -0.025243 -0.022862 0.024812 0.999431 AXIS OF ROTATION IS -0.646150 -0.584101 0.491239 ANGLE IS 2.22 CENTER OF ROTATION 7.628183 3.711297 -7.261742 SHIFT IS -0.000495 TOTAL SQUARE DIFF IS 0.6960 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.202332 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3105" RDCMND substituted energy or value "?RMS" to " 0.2023" Parameter: A <- "0.3105 0.2023" 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 0.3105 0.2023 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 " 75.20" Parameter: H <- "75.20" 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 -12.85393 75.20457 1.71420 ENER INTERN> 6.56003 26.01462 0.00000 11.87740 5.50661 ENER EXTERN> -42.13199 -20.68060 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 " -12.85" Parameter: B <- "-12.85" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -20.68" Parameter: C <- "-20.68" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -42.13" Parameter: C <- " -62.81" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -62.81" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 6.56" Parameter: D <- "6.56" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 26.01" Parameter: D <- " 32.57" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.88" Parameter: D <- " 44.45" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.51" Parameter: D <- " 49.96" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 49.96" 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= -12.85 GRMS= 1.71 ELEC= -20.68 VDW= -42.13 RDTITL> *EXTERNAL= -62.81 INTERNAL= 49.96 USER= 0.00 HARM= 75.20 RDTITL> *BOND= 6.56 ANGL= 26.01 DIHE= 11.88 IMPR= 5.51 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= -12.85 GRMS= 1.71 ELEC= -20.68 VDW= -42.13 RDTITL> *EXTERNAL= -62.81 INTERNAL= 49.96 USER= 0.00 HARM= 75.20 RDTITL> *BOND= 6.56 ANGL= 26.01 DIHE= 11.88 IMPR= 5.51 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= -12.85 GRMS= 1.71 ELEC= -20.68 VDW= -42.13 RDTITL> *EXTERNAL= -62.81 INTERNAL= 49.96 USER= 0.00 HARM= 75.20 RDTITL> *BOND= 6.56 ANGL= 26.01 DIHE= 11.88 IMPR= 5.51 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 6000 0.3105 0.2023 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "6000" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9253 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9249 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 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 46.80627 -59.66020 0.77800 0.02000 MINI INTERN> 6.56003 26.01462 0.00000 11.87740 5.50661 MINI EXTERN> -42.13199 -20.68060 0.00000 0.00000 0.00000 MINI CONSTR> 59.66020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 63.75383 -16.94756 15.95178 0.00864 MINI INTERN> 28.63028 22.49709 0.00000 13.29165 4.87677 MINI EXTERN> -48.69612 -18.67509 0.00000 0.00000 0.00000 MINI CONSTR> 61.82925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9240 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 42.61481 21.13902 0.58573 0.00156 MINI INTERN> 6.31315 25.27113 0.00000 12.67453 5.54782 MINI EXTERN> -49.75775 -19.57128 0.00000 0.00000 0.00000 MINI CONSTR> 62.13720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 41.83952 0.77529 0.74164 0.00067 MINI INTERN> 6.15228 25.24497 0.00000 12.69507 5.51851 MINI EXTERN> -50.30059 -19.61864 0.00000 0.00000 0.00000 MINI CONSTR> 62.14791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9239 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 41.41384 0.42568 0.82213 0.00070 MINI INTERN> 6.11546 25.15176 0.00000 12.70122 5.50004 MINI EXTERN> -50.54098 -19.64612 0.00000 0.00000 0.00000 MINI CONSTR> 62.13247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 41.08969 0.32415 1.22520 0.00072 MINI INTERN> 6.08585 25.09612 0.00000 12.70715 5.48527 MINI EXTERN> -50.74266 -19.65418 0.00000 0.00000 0.00000 MINI CONSTR> 62.11214 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9238 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 40.71855 0.37114 1.32990 0.00075 MINI INTERN> 6.05894 25.02427 0.00000 12.70717 5.46971 MINI EXTERN> -50.95025 -19.67528 0.00000 0.00000 0.00000 MINI CONSTR> 62.08399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 40.38873 0.32983 1.46579 0.00078 MINI INTERN> 6.06834 24.94895 0.00000 12.70001 5.45788 MINI EXTERN> -51.14639 -19.69272 0.00000 0.00000 0.00000 MINI CONSTR> 62.05265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9238 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 40.07442 0.31430 1.39444 0.00080 MINI INTERN> 6.12374 24.84725 0.00000 12.68163 5.45281 MINI EXTERN> -51.33839 -19.71541 0.00000 0.00000 0.00000 MINI CONSTR> 62.02280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 39.74203 0.33240 1.39611 0.00083 MINI INTERN> 6.10466 24.77927 0.00000 12.67303 5.43937 MINI EXTERN> -51.50314 -19.73509 0.00000 0.00000 0.00000 MINI CONSTR> 61.98393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9236 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 39.32990 0.41213 0.44375 0.00036 MINI INTERN> 6.22062 24.61284 0.00000 12.64700 5.43034 MINI EXTERN> -51.71401 -19.81297 0.00000 0.00000 0.00000 MINI CONSTR> 61.94607 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 39.21600 0.11389 1.55814 0.00090 MINI INTERN> 6.14048 24.64878 0.00000 12.64733 5.41994 MINI EXTERN> -51.78904 -19.76099 0.00000 0.00000 0.00000 MINI CONSTR> 61.90950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9235 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 38.94902 0.26699 1.64266 0.00093 MINI INTERN> 6.12584 24.59970 0.00000 12.63625 5.40741 MINI EXTERN> -51.91384 -19.77282 0.00000 0.00000 0.00000 MINI CONSTR> 61.86648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 38.50754 0.44148 0.53726 0.00040 MINI INTERN> 6.20202 24.43017 0.00000 12.61738 5.38981 MINI EXTERN> -52.08839 -19.86496 0.00000 0.00000 0.00000 MINI CONSTR> 61.82150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9235 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 38.29048 0.21706 0.36849 0.00042 MINI INTERN> 6.13165 24.40558 0.00000 12.61114 5.37946 MINI EXTERN> -52.15963 -19.86526 0.00000 0.00000 0.00000 MINI CONSTR> 61.78755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 38.03969 0.25079 0.37034 0.00043 MINI INTERN> 6.12325 24.35013 0.00000 12.59881 5.36662 MINI EXTERN> -52.26415 -19.87922 0.00000 0.00000 0.00000 MINI CONSTR> 61.74424 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9234 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 37.80959 0.23009 0.72049 0.00045 MINI INTERN> 6.20828 24.26645 0.00000 12.58327 5.35114 MINI EXTERN> -52.38732 -19.90910 0.00000 0.00000 0.00000 MINI CONSTR> 61.69688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 37.58243 0.22716 0.46526 0.00046 MINI INTERN> 6.13217 24.23888 0.00000 12.57290 5.34137 MINI EXTERN> -52.45477 -19.90810 0.00000 0.00000 0.00000 MINI CONSTR> 61.65997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9234 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 37.36620 0.21623 0.51055 0.00048 MINI INTERN> 6.13271 24.18695 0.00000 12.55903 5.32924 MINI EXTERN> -52.54155 -19.91887 0.00000 0.00000 0.00000 MINI CONSTR> 61.61868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 37.19596 0.17024 0.81141 0.00050 MINI INTERN> 6.19460 24.12513 0.00000 12.54504 5.31619 MINI EXTERN> -52.62861 -19.93587 0.00000 0.00000 0.00000 MINI CONSTR> 61.57948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9233 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 36.99980 0.19616 0.82883 0.00052 MINI INTERN> 6.18336 24.08059 0.00000 12.52969 5.30559 MINI EXTERN> -52.70298 -19.93792 0.00000 0.00000 0.00000 MINI CONSTR> 61.54147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 36.81323 0.18657 0.88284 0.00054 MINI INTERN> 6.18108 24.03613 0.00000 12.51326 5.29526 MINI EXTERN> -52.77565 -19.94084 0.00000 0.00000 0.00000 MINI CONSTR> 61.50399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9233 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 36.64351 0.16973 0.96513 0.00056 MINI INTERN> 6.18923 23.99282 0.00000 12.49771 5.28507 MINI EXTERN> -52.84359 -19.94613 0.00000 0.00000 0.00000 MINI CONSTR> 61.46839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 36.48413 0.15937 0.91104 0.00058 MINI INTERN> 6.16241 23.96475 0.00000 12.48753 5.27549 MINI EXTERN> -52.89053 -19.95375 0.00000 0.00000 0.00000 MINI CONSTR> 61.43823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9232 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 36.31777 0.16636 0.93483 0.00060 MINI INTERN> 6.15579 23.92740 0.00000 12.47195 5.26652 MINI EXTERN> -52.95094 -19.95803 0.00000 0.00000 0.00000 MINI CONSTR> 61.40508 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 36.10499 0.21278 0.29003 0.00026 MINI INTERN> 5.99162 23.94930 0.00000 12.47038 5.25852 MINI EXTERN> -52.96415 -19.97488 0.00000 0.00000 0.00000 MINI CONSTR> 61.37419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9232 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 36.03642 0.06856 1.02066 0.00064 MINI INTERN> 6.15748 23.85981 0.00000 12.44561 5.24854 MINI EXTERN> -53.05245 -19.96974 0.00000 0.00000 0.00000 MINI CONSTR> 61.34717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 35.89794 0.13848 1.06267 0.00067 MINI INTERN> 6.16935 23.82082 0.00000 12.43065 5.24043 MINI EXTERN> -53.10745 -19.97489 0.00000 0.00000 0.00000 MINI CONSTR> 61.31904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9232 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 35.67782 0.22012 0.33442 0.00029 MINI INTERN> 5.95738 23.86406 0.00000 12.43339 5.23058 MINI EXTERN> -53.09857 -19.99917 0.00000 0.00000 0.00000 MINI CONSTR> 61.29015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 35.56663 0.11119 0.25185 0.00030 MINI INTERN> 5.97089 23.82666 0.00000 12.42023 5.22429 MINI EXTERN> -53.14276 -20.00282 0.00000 0.00000 0.00000 MINI CONSTR> 61.27014 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9231 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 35.44008 0.12655 0.24790 0.00031 MINI INTERN> 5.96391 23.79879 0.00000 12.40770 5.21573 MINI EXTERN> -53.18272 -20.00975 0.00000 0.00000 0.00000 MINI CONSTR> 61.24642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 35.31738 0.12271 0.46762 0.00032 MINI INTERN> 5.91942 23.79834 0.00000 12.39996 5.20398 MINI EXTERN> -53.20284 -20.02194 0.00000 0.00000 0.00000 MINI CONSTR> 61.22046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9231 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 35.20524 0.11214 0.31263 0.00033 MINI INTERN> 5.93319 23.75807 0.00000 12.38554 5.19810 MINI EXTERN> -53.24740 -20.02499 0.00000 0.00000 0.00000 MINI CONSTR> 61.20272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 35.09654 0.10870 0.32944 0.00034 MINI INTERN> 5.92154 23.73684 0.00000 12.37451 5.18965 MINI EXTERN> -53.27780 -20.03160 0.00000 0.00000 0.00000 MINI CONSTR> 61.18340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9231 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 35.01173 0.08481 0.56287 0.00036 MINI INTERN> 5.88484 23.74185 0.00000 12.36907 5.17930 MINI EXTERN> -53.28671 -20.04165 0.00000 0.00000 0.00000 MINI CONSTR> 61.16502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 34.91604 0.09569 0.57774 0.00037 MINI INTERN> 5.87310 23.72281 0.00000 12.35921 5.17085 MINI EXTERN> -53.31141 -20.04738 0.00000 0.00000 0.00000 MINI CONSTR> 61.14886 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9230 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 34.82636 0.08968 0.62110 0.00038 MINI INTERN> 5.85619 23.70825 0.00000 12.35064 5.16172 MINI EXTERN> -53.33076 -20.05327 0.00000 0.00000 0.00000 MINI CONSTR> 61.13360 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 34.74511 0.08125 0.67554 0.00040 MINI INTERN> 5.84278 23.69520 0.00000 12.34213 5.15337 MINI EXTERN> -53.34920 -20.05918 0.00000 0.00000 0.00000 MINI CONSTR> 61.12001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9228 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 34.66800 0.07712 0.63585 0.00041 MINI INTERN> 5.85250 23.67084 0.00000 12.32998 5.14947 MINI EXTERN> -53.38068 -20.06382 0.00000 0.00000 0.00000 MINI CONSTR> 61.10971 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 34.58651 0.08148 0.64431 0.00043 MINI INTERN> 5.83444 23.65599 0.00000 12.32212 5.14055 MINI EXTERN> -53.39623 -20.06833 0.00000 0.00000 0.00000 MINI CONSTR> 61.09797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9227 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 34.48361 0.10291 0.20226 0.00019 MINI INTERN> 5.96117 23.55943 0.00000 12.28851 5.14921 MINI EXTERN> -53.50226 -20.06435 0.00000 0.00000 0.00000 MINI CONSTR> 61.09189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 34.45130 0.03231 0.70361 0.00046 MINI INTERN> 5.81597 23.63013 0.00000 12.30578 5.12658 MINI EXTERN> -53.42872 -20.07789 0.00000 0.00000 0.00000 MINI CONSTR> 61.07945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9227 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 34.38333 0.06797 0.73091 0.00048 MINI INTERN> 5.79518 23.61826 0.00000 12.29987 5.11736 MINI EXTERN> -53.43735 -20.08081 0.00000 0.00000 0.00000 MINI CONSTR> 61.07082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 34.27530 0.10803 0.23003 0.00021 MINI INTERN> 5.97773 23.50063 0.00000 12.25389 5.13455 MINI EXTERN> -53.58089 -20.07883 0.00000 0.00000 0.00000 MINI CONSTR> 61.06821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9226 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 34.22076 0.05454 0.17259 0.00021 MINI INTERN> 5.94282 23.50003 0.00000 12.25112 5.12660 MINI EXTERN> -53.57968 -20.08258 0.00000 0.00000 0.00000 MINI CONSTR> 61.06246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 34.15867 0.06209 0.16984 0.00022 MINI INTERN> 5.94300 23.48397 0.00000 12.24088 5.12139 MINI EXTERN> -53.60045 -20.08713 0.00000 0.00000 0.00000 MINI CONSTR> 61.05701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9226 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 34.09856 0.06011 0.32013 0.00023 MINI INTERN> 6.02493 23.43902 0.00000 12.21644 5.12396 MINI EXTERN> -53.66553 -20.09358 0.00000 0.00000 0.00000 MINI CONSTR> 61.05332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 34.04352 0.05504 0.21326 0.00024 MINI INTERN> 5.97609 23.44215 0.00000 12.21537 5.11466 MINI EXTERN> -53.65720 -20.09676 0.00000 0.00000 0.00000 MINI CONSTR> 61.04920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9224 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 33.99013 0.05339 0.22387 0.00025 MINI INTERN> 5.98493 23.42515 0.00000 12.20430 5.11065 MINI EXTERN> -53.67984 -20.10146 0.00000 0.00000 0.00000 MINI CONSTR> 61.04640 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 33.94860 0.04153 0.38565 0.00026 MINI INTERN> 6.06658 23.38631 0.00000 12.18227 5.11396 MINI EXTERN> -53.73807 -20.10802 0.00000 0.00000 0.00000 MINI CONSTR> 61.04557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9224 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 33.90189 0.04671 0.39703 0.00027 MINI INTERN> 6.07853 23.36988 0.00000 12.17143 5.11044 MINI EXTERN> -53.75976 -20.11291 0.00000 0.00000 0.00000 MINI CONSTR> 61.04428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 33.85834 0.04356 0.42898 0.00028 MINI INTERN> 6.10086 23.35074 0.00000 12.15904 5.10800 MINI EXTERN> -53.78595 -20.11815 0.00000 0.00000 0.00000 MINI CONSTR> 61.04380 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9224 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 33.81836 0.03997 0.41343 0.00029 MINI INTERN> 6.09362 23.34227 0.00000 12.15242 5.10331 MINI EXTERN> -53.79556 -20.12118 0.00000 0.00000 0.00000 MINI CONSTR> 61.04348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 33.77888 0.03948 0.43210 0.00030 MINI INTERN> 6.10739 23.32695 0.00000 12.14182 5.10047 MINI EXTERN> -53.81612 -20.12570 0.00000 0.00000 0.00000 MINI CONSTR> 61.04406 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9222 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 33.73987 0.03901 0.43731 0.00031 MINI INTERN> 6.11625 23.31286 0.00000 12.13235 5.09653 MINI EXTERN> -53.83255 -20.13049 0.00000 0.00000 0.00000 MINI CONSTR> 61.04491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 33.69139 0.04848 0.14149 0.00013 MINI INTERN> 5.87301 23.38422 0.00000 12.16419 5.06937 MINI EXTERN> -53.72094 -20.12098 0.00000 0.00000 0.00000 MINI CONSTR> 61.04252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9222 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 33.67698 0.01441 0.48559 0.00033 MINI INTERN> 6.14200 23.28701 0.00000 12.11364 5.09186 MINI EXTERN> -53.86863 -20.13728 0.00000 0.00000 0.00000 MINI CONSTR> 61.04838 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 33.64438 0.03259 0.50911 0.00034 MINI INTERN> 6.16026 23.27097 0.00000 12.10305 5.08926 MINI EXTERN> -53.88809 -20.14196 0.00000 0.00000 0.00000 MINI CONSTR> 61.05090 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 33.59208 0.05230 0.16818 0.00015 MINI INTERN> 5.84255 23.36760 0.00000 12.14649 5.05481 MINI EXTERN> -53.74038 -20.12781 0.00000 0.00000 0.00000 MINI CONSTR> 61.04881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 33.56630 0.02578 0.11707 0.00015 MINI INTERN> 5.88446 23.34476 0.00000 12.13326 5.05622 MINI EXTERN> -53.77166 -20.13265 0.00000 0.00000 0.00000 MINI CONSTR> 61.05190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9222 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 33.53638 0.02992 0.11638 0.00016 MINI INTERN> 5.87996 23.33781 0.00000 12.12657 5.05209 MINI EXTERN> -53.78029 -20.13507 0.00000 0.00000 0.00000 MINI CONSTR> 61.05531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 33.50914 0.02724 0.23706 0.00016 MINI INTERN> 5.79778 23.36062 0.00000 12.13312 5.03941 MINI EXTERN> -53.74767 -20.13233 0.00000 0.00000 0.00000 MINI CONSTR> 61.05821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9222 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 33.48224 0.02690 0.14525 0.00017 MINI INTERN> 5.84805 23.33391 0.00000 12.11778 5.04179 MINI EXTERN> -53.78409 -20.13791 0.00000 0.00000 0.00000 MINI CONSTR> 61.06272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 33.45714 0.02510 0.16812 0.00018 MINI INTERN> 5.83507 23.33133 0.00000 12.11326 5.03655 MINI EXTERN> -53.78635 -20.13959 0.00000 0.00000 0.00000 MINI CONSTR> 61.06687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 33.43875 0.01839 0.26626 0.00018 MINI INTERN> 5.77852 23.34743 0.00000 12.11701 5.02778 MINI EXTERN> -53.76504 -20.13734 0.00000 0.00000 0.00000 MINI CONSTR> 61.07039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 33.41639 0.02236 0.28112 0.00019 MINI INTERN> 5.77099 23.34370 0.00000 12.11181 5.02357 MINI EXTERN> -53.77023 -20.13864 0.00000 0.00000 0.00000 MINI CONSTR> 61.07519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 33.39626 0.02013 0.31293 0.00020 MINI INTERN> 5.75470 23.34378 0.00000 12.10821 5.01884 MINI EXTERN> -53.77084 -20.13861 0.00000 0.00000 0.00000 MINI CONSTR> 61.08019 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 33.37775 0.01851 0.29822 0.00020 MINI INTERN> 5.76165 23.33565 0.00000 12.10165 5.01658 MINI EXTERN> -53.78092 -20.14159 0.00000 0.00000 0.00000 MINI CONSTR> 61.08473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 33.35861 0.01913 0.30779 0.00021 MINI INTERN> 5.75681 23.33145 0.00000 12.09603 5.01374 MINI EXTERN> -53.78800 -20.14178 0.00000 0.00000 0.00000 MINI CONSTR> 61.09037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 33.33482 0.02380 0.09959 0.00009 MINI INTERN> 5.91541 23.26421 0.00000 12.06295 5.02712 MINI EXTERN> -53.87476 -20.15762 0.00000 0.00000 0.00000 MINI CONSTR> 61.09751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 33.32738 0.00743 0.33520 0.00023 MINI INTERN> 5.74478 23.32691 0.00000 12.08795 5.00612 MINI EXTERN> -53.79321 -20.14529 0.00000 0.00000 0.00000 MINI CONSTR> 61.10012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 33.31201 0.01537 0.36618 0.00024 MINI INTERN> 5.74445 23.32148 0.00000 12.08157 5.00497 MINI EXTERN> -53.80326 -20.14380 0.00000 0.00000 0.00000 MINI CONSTR> 61.10660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 33.28717 0.02484 0.11923 0.00010 MINI INTERN> 5.93239 23.24282 0.00000 12.04365 5.02061 MINI EXTERN> -53.90257 -20.16413 0.00000 0.00000 0.00000 MINI CONSTR> 61.11440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 33.27435 0.01281 0.08265 0.00011 MINI INTERN> 5.90087 23.25031 0.00000 12.04457 5.01524 MINI EXTERN> -53.89266 -20.16268 0.00000 0.00000 0.00000 MINI CONSTR> 61.11870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 33.25961 0.01474 0.08374 0.00011 MINI INTERN> 5.90332 23.24454 0.00000 12.03861 5.01285 MINI EXTERN> -53.90033 -20.16432 0.00000 0.00000 0.00000 MINI CONSTR> 61.12495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 33.24660 0.01302 0.16322 0.00011 MINI INTERN> 5.95771 23.22021 0.00000 12.02387 5.01535 MINI EXTERN> -53.93215 -20.17078 0.00000 0.00000 0.00000 MINI CONSTR> 61.13239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 33.23343 0.01317 0.10709 0.00012 MINI INTERN> 5.92359 23.22857 0.00000 12.02499 5.00939 MINI EXTERN> -53.92105 -20.16944 0.00000 0.00000 0.00000 MINI CONSTR> 61.13738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 33.22194 0.01149 0.13769 0.00012 MINI INTERN> 5.94361 23.21720 0.00000 12.01658 5.00911 MINI EXTERN> -53.93627 -20.17219 0.00000 0.00000 0.00000 MINI CONSTR> 61.14389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 33.21232 0.00962 0.18587 0.00013 MINI INTERN> 5.97069 23.20399 0.00000 12.00759 5.00928 MINI EXTERN> -53.95352 -20.17583 0.00000 0.00000 0.00000 MINI CONSTR> 61.15012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 33.20098 0.01134 0.19203 0.00013 MINI INTERN> 5.97148 23.19988 0.00000 12.00238 5.00708 MINI EXTERN> -53.95930 -20.17722 0.00000 0.00000 0.00000 MINI CONSTR> 61.15668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 33.19085 0.01013 0.21778 0.00014 MINI INTERN> 5.98194 23.19251 0.00000 11.99626 5.00460 MINI EXTERN> -53.96726 -20.18026 0.00000 0.00000 0.00000 MINI CONSTR> 61.16306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 33.18141 0.00944 0.20561 0.00014 MINI INTERN> 5.97582 23.19151 0.00000 11.99257 5.00310 MINI EXTERN> -53.97085 -20.17973 0.00000 0.00000 0.00000 MINI CONSTR> 61.16898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 33.17209 0.00932 0.21963 0.00015 MINI INTERN> 5.97569 23.18822 0.00000 11.98879 4.99922 MINI EXTERN> -53.97281 -20.18186 0.00000 0.00000 0.00000 MINI CONSTR> 61.17485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 33.16050 0.01159 0.06845 0.00006 MINI INTERN> 5.87225 23.22226 0.00000 12.00163 4.98843 MINI EXTERN> -53.93190 -20.17123 0.00000 0.00000 0.00000 MINI CONSTR> 61.17906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9221 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 33.15610 0.00440 0.23246 0.00016 MINI INTERN> 5.99277 23.17622 0.00000 11.97737 4.99758 MINI EXTERN> -53.99049 -20.18444 0.00000 0.00000 0.00000 MINI CONSTR> 61.18709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 33.14796 0.00814 0.24735 0.00016 MINI INTERN> 5.98224 23.17734 0.00000 11.97416 4.99563 MINI EXTERN> -53.99170 -20.18355 0.00000 0.00000 0.00000 MINI CONSTR> 61.19384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 33.13559 0.01237 0.08101 0.00007 MINI INTERN> 5.85854 23.21831 0.00000 11.99116 4.98059 MINI EXTERN> -53.93881 -20.17189 0.00000 0.00000 0.00000 MINI CONSTR> 61.19769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 33.12893 0.00666 0.06000 0.00007 MINI INTERN> 5.87588 23.20938 0.00000 11.98471 4.98051 MINI EXTERN> -53.95026 -20.17447 0.00000 0.00000 0.00000 MINI CONSTR> 61.20317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 33.12151 0.00742 0.06163 0.00008 MINI INTERN> 5.87154 23.20822 0.00000 11.98127 4.97808 MINI EXTERN> -53.95258 -20.17452 0.00000 0.00000 0.00000 MINI CONSTR> 61.20949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 33.11456 0.00695 0.10708 0.00008 MINI INTERN> 5.84246 23.21642 0.00000 11.98204 4.97278 MINI EXTERN> -53.94324 -20.17175 0.00000 0.00000 0.00000 MINI CONSTR> 61.21585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 33.10778 0.00677 0.07217 0.00008 MINI INTERN> 5.86110 23.20688 0.00000 11.97499 4.97301 MINI EXTERN> -53.95591 -20.17427 0.00000 0.00000 0.00000 MINI CONSTR> 61.22198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 33.10137 0.00642 0.08544 0.00008 MINI INTERN> 5.85689 23.20593 0.00000 11.97194 4.97011 MINI EXTERN> -53.95726 -20.17443 0.00000 0.00000 0.00000 MINI CONSTR> 61.22819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 33.09630 0.00507 0.12857 0.00009 MINI INTERN> 5.83101 23.21363 0.00000 11.97270 4.96580 MINI EXTERN> -53.94914 -20.17156 0.00000 0.00000 0.00000 MINI CONSTR> 61.23385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 33.08972 0.00657 0.08225 0.00009 MINI INTERN> 5.85361 23.20261 0.00000 11.96488 4.96659 MINI EXTERN> -53.96381 -20.17441 0.00000 0.00000 0.00000 MINI CONSTR> 61.24026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 33.08526 0.00446 0.13571 0.00009 MINI INTERN> 5.82614 23.21109 0.00000 11.96613 4.96184 MINI EXTERN> -53.95443 -20.17136 0.00000 0.00000 0.00000 MINI CONSTR> 61.24586 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 33.07999 0.00527 0.15516 0.00010 MINI INTERN> 5.82712 23.20846 0.00000 11.96253 4.95911 MINI EXTERN> -53.95745 -20.17190 0.00000 0.00000 0.00000 MINI CONSTR> 61.25213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 33.07511 0.00488 0.14770 0.00010 MINI INTERN> 5.82125 23.20876 0.00000 11.95971 4.95791 MINI EXTERN> -53.95956 -20.17087 0.00000 0.00000 0.00000 MINI CONSTR> 61.25791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 33.07036 0.00475 0.15743 0.00011 MINI INTERN> 5.83363 23.20207 0.00000 11.95469 4.95601 MINI EXTERN> -53.96654 -20.17319 0.00000 0.00000 0.00000 MINI CONSTR> 61.26369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 33.06442 0.00595 0.04905 0.00005 MINI INTERN> 5.88797 23.17955 0.00000 11.94161 4.96099 MINI EXTERN> -53.99562 -20.17999 0.00000 0.00000 0.00000 MINI CONSTR> 61.26990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 33.06202 0.00240 0.16640 0.00011 MINI INTERN> 5.81118 23.20707 0.00000 11.95156 4.95151 MINI EXTERN> -53.96407 -20.17010 0.00000 0.00000 0.00000 MINI CONSTR> 61.27488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 33.05760 0.00442 0.17217 0.00012 MINI INTERN> 5.81404 23.20397 0.00000 11.94782 4.94939 MINI EXTERN> -53.96802 -20.17052 0.00000 0.00000 0.00000 MINI CONSTR> 61.28092 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 33.05760 0.00442 0.17217 0.00006 STPD INTERN> 5.81404 23.20397 0.00000 11.94782 4.94939 STPD EXTERN> -53.96802 -20.17052 0.00000 0.00000 0.00000 STPD CONSTR> 61.28092 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 9220 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9220 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 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 33.05757 0.00003 0.14429 0.00000 MINI INTERN> 5.93738 23.15852 0.00000 11.92666 4.96273 MINI EXTERN> -54.02340 -20.18629 0.00000 0.00000 0.00000 MINI CONSTR> 61.28197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 32.94917 0.10840 0.05376 0.00156 MINI INTERN> 5.86093 23.07605 0.00000 11.78300 4.88477 MINI EXTERN> -54.20777 -20.14291 0.00000 0.00000 0.00000 MINI CONSTR> 61.69510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 32.93349 0.01568 0.17458 0.01602 MINI INTERN> 5.84808 23.10414 0.00000 11.70522 4.85382 MINI EXTERN> -54.07413 -20.16772 0.00000 0.00000 0.00000 MINI CONSTR> 61.66407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 32.89518 0.03831 0.09860 0.02715 MINI INTERN> 5.80394 23.03069 0.00000 11.60239 4.85772 MINI EXTERN> -54.17078 -20.00810 0.00000 0.00000 0.00000 MINI CONSTR> 61.77932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 32.88926 0.00592 0.04350 0.00325 MINI INTERN> 5.79209 22.99889 0.00000 11.60104 4.86541 MINI EXTERN> -54.28187 -19.97197 0.00000 0.00000 0.00000 MINI CONSTR> 61.88566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 32.88602 0.00324 0.04679 0.00483 MINI INTERN> 5.78903 22.96096 0.00000 11.64279 4.87676 MINI EXTERN> -54.41739 -19.98718 0.00000 0.00000 0.00000 MINI CONSTR> 62.02106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 32.88165 0.00437 0.04963 0.00804 MINI INTERN> 5.80654 22.99457 0.00000 11.66427 4.86972 MINI EXTERN> -54.50554 -20.08475 0.00000 0.00000 0.00000 MINI CONSTR> 62.13685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 32.87953 0.00212 0.03363 0.00333 MINI INTERN> 5.80775 23.00354 0.00000 11.66832 4.86392 MINI EXTERN> -54.42448 -20.15217 0.00000 0.00000 0.00000 MINI CONSTR> 62.11265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 32.87810 0.00143 0.02523 0.00297 MINI INTERN> 5.80241 22.98079 0.00000 11.66107 4.86762 MINI EXTERN> -54.34112 -20.12979 0.00000 0.00000 0.00000 MINI CONSTR> 62.03713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 32.87702 0.00108 0.02735 0.00279 MINI INTERN> 5.79695 22.96845 0.00000 11.66264 4.86186 MINI EXTERN> -54.32835 -20.06577 0.00000 0.00000 0.00000 MINI CONSTR> 61.98123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 32.87621 0.00081 0.02207 0.00223 MINI INTERN> 5.80277 22.96300 0.00000 11.66808 4.87268 MINI EXTERN> -54.34507 -20.03346 0.00000 0.00000 0.00000 MINI CONSTR> 61.94822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 32.87567 0.00054 0.01940 0.00183 MINI INTERN> 5.80926 23.00264 0.00000 11.66241 4.88408 MINI EXTERN> -54.36246 -20.04565 0.00000 0.00000 0.00000 MINI CONSTR> 61.92540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 32.87519 0.00048 0.02004 0.00221 MINI INTERN> 5.81248 23.03050 0.00000 11.65758 4.88107 MINI EXTERN> -54.35107 -20.06189 0.00000 0.00000 0.00000 MINI CONSTR> 61.90652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 32.87477 0.00042 0.01548 0.00173 MINI INTERN> 5.81439 23.03160 0.00000 11.65919 4.87750 MINI EXTERN> -54.33905 -20.06961 0.00000 0.00000 0.00000 MINI CONSTR> 61.90075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 32.87448 0.00029 0.01262 0.00154 MINI INTERN> 5.80790 23.01418 0.00000 11.66096 4.87732 MINI EXTERN> -54.32866 -20.06251 0.00000 0.00000 0.00000 MINI CONSTR> 61.90529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 32.87427 0.00021 0.01172 0.00111 MINI INTERN> 5.80771 23.01332 0.00000 11.66594 4.87265 MINI EXTERN> -54.33677 -20.06055 0.00000 0.00000 0.00000 MINI CONSTR> 61.91197 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> 79 32.87414 0.00013 0.00941 0.02000 CONJ INTERN> 5.80996 23.01304 0.00000 11.66436 4.87321 CONJ EXTERN> -54.32889 -20.06940 0.00000 0.00000 0.00000 CONJ CONSTR> 61.91185 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 ASP 1 HT1 ) 1.7502 ( PROT ASP 1 HT2 ) 1.7502 ( PROT ASP 1 N ) 2.1877 ( PROT ASP 1 HT3 ) 1.7502 ( PROT ASP 1 CA ) 2.1877 ( PROT ASP 1 CB ) 1.7502 ( PROT ASP 1 CG ) 1.7502 ( PROT ASP 1 OD1 ) 1.7502 ( PROT ASP 1 OD2 ) 1.7502 ( PROT ASP 1 C ) 2.1877 ( PROT ASP 1 O ) 2.1877 ( PROT TYR 2 N ) 2.1877 ( PROT TYR 2 H ) 1.7502 ( PROT TYR 2 CA ) 2.1877 ( PROT TYR 2 CB ) 1.7502 ( PROT TYR 2 CG ) 1.7502 ( PROT TYR 2 CD1 ) 1.7502 ( PROT TYR 2 CE1 ) 1.7502 ( PROT TYR 2 CD2 ) 1.7502 ( PROT TYR 2 CE2 ) 1.7502 ( PROT TYR 2 CZ ) 1.7502 ( PROT TYR 2 OH ) 1.7502 ( PROT TYR 2 HH ) 1.7502 ( PROT TYR 2 C ) 2.1877 ( PROT TYR 2 O ) 2.1877 ( PROT ALA 3 N ) 2.1877 ( PROT ALA 3 H ) 1.7502 ( PROT ALA 3 CA ) 2.1877 ( PROT ALA 3 CB ) 1.7502 ( PROT ALA 3 C ) 2.1877 ( PROT ALA 3 O ) 2.1877 ( PROT PHE 4 N ) 2.1877 ( PROT PHE 4 H ) 1.7502 ( PROT PHE 4 CA ) 2.1877 ( PROT PHE 4 CB ) 1.7502 ( PROT PHE 4 CG ) 1.7502 ( PROT PHE 4 CD1 ) 1.7502 ( PROT PHE 4 CD2 ) 1.7502 ( PROT PHE 4 CE1 ) 1.7502 ( PROT PHE 4 CE2 ) 1.7502 ( PROT PHE 4 CZ ) 1.7502 ( PROT PHE 4 C ) 2.1877 ( PROT PHE 4 O ) 2.1877 ( PROT ILE 5 N ) 2.1877 ( PROT ILE 5 H ) 1.7502 ( PROT ILE 5 CA ) 2.1877 ( PROT ILE 5 CB ) 1.7502 ( PROT ILE 5 CG2 ) 1.7502 ( PROT ILE 5 CG1 ) 1.7502 ( PROT ILE 5 CD ) 1.7502 ( PROT ILE 5 C ) 2.1877 ( PROT ILE 5 O ) 2.1877 ( PROT ALA 6 N ) 2.1877 ( PROT ALA 6 H ) 1.7502 ( PROT ALA 6 CA ) 2.1877 ( PROT ALA 6 CB ) 1.7502 ( PROT ALA 6 C ) 2.1877 ( PROT ALA 6 O ) 2.1877 ( PROT SER 7 N ) 2.1877 ( PROT SER 7 H ) 1.7502 ( PROT SER 7 CA ) 2.1877 ( PROT SER 7 CB ) 1.7502 ( PROT SER 7 OG ) 1.7502 ( PROT SER 7 HG ) 1.7502 ( PROT SER 7 C ) 2.1877 ( PROT SER 7 O ) 2.1877 ( PROT LEU 8 N ) 2.1877 ( PROT LEU 8 H ) 1.7502 ( PROT LEU 8 CA ) 2.1877 ( PROT LEU 8 CB ) 1.7502 ( PROT LEU 8 CG ) 1.7502 ( PROT LEU 8 CD1 ) 1.7502 ( PROT LEU 8 CD2 ) 1.7502 ( PROT LEU 8 C ) 2.1877 ( PROT LEU 8 O ) 2.1877 ( PROT VAL 9 N ) 2.1877 ( PROT VAL 9 H ) 1.7502 ( PROT VAL 9 CA ) 2.1877 ( PROT VAL 9 CB ) 1.7502 ( PROT VAL 9 CG1 ) 1.7502 ( PROT VAL 9 CG2 ) 1.7502 ( PROT VAL 9 C ) 2.1877 ( PROT VAL 9 O ) 2.1877 ( PROT VAL 10 N ) 2.1877 ( PROT VAL 10 H ) 1.7502 ( PROT VAL 10 CA ) 2.1877 ( PROT VAL 10 CB ) 1.7502 ( PROT VAL 10 CG1 ) 1.7502 ( PROT VAL 10 CG2 ) 1.7502 ( PROT VAL 10 C ) 2.1877 ( PROT VAL 10 O ) 2.1877 ( PROT ILE 11 N ) 2.1877 ( PROT ILE 11 H ) 1.7502 ( PROT ILE 11 CA ) 2.1877 ( PROT ILE 11 CB ) 1.7502 ( PROT ILE 11 CG2 ) 1.7502 ( PROT ILE 11 CG1 ) 1.7502 ( PROT ILE 11 CD ) 1.7502 ( PROT ILE 11 C ) 2.1877 ( PROT ILE 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 ASP 13 N ) 2.1877 ( PROT ASP 13 H ) 1.7502 ( PROT ASP 13 CA ) 2.1877 ( PROT ASP 13 CB ) 1.7502 ( PROT ASP 13 CG ) 1.7502 ( PROT ASP 13 OD1 ) 1.7502 ( PROT ASP 13 OD2 ) 1.7502 ( PROT ASP 13 C ) 2.1877 ( PROT ASP 13 O ) 2.1877 ( PROT ASP 14 N ) 2.1877 ( PROT ASP 14 H ) 1.7502 ( PROT ASP 14 CA ) 2.1877 ( PROT ASP 14 CB ) 1.7502 ( PROT ASP 14 CG ) 1.7502 ( PROT ASP 14 OD1 ) 1.7502 ( PROT ASP 14 OD2 ) 1.7502 ( PROT ASP 14 C ) 2.1877 ( PROT ASP 14 O ) 2.1877 ( PROT VAL 15 N ) 2.1877 ( PROT VAL 15 H ) 1.7502 ( PROT VAL 15 CA ) 2.1877 ( PROT VAL 15 CB ) 1.7502 ( PROT VAL 15 CG1 ) 1.7502 ( PROT VAL 15 CG2 ) 1.7502 ( PROT VAL 15 C ) 2.1877 ( PROT VAL 15 O ) 2.1877 ( PROT ASN 16 N ) 2.1877 ( PROT ASN 16 H ) 1.7502 ( PROT ASN 16 CA ) 2.1877 ( PROT ASN 16 CB ) 1.7502 ( PROT ASN 16 CG ) 1.7502 ( PROT ASN 16 OD1 ) 1.7502 ( PROT ASN 16 ND2 ) 1.7502 ( PROT ASN 16 HD21 ) 1.7502 ( PROT ASN 16 HD22 ) 1.7502 ( PROT ASN 16 C ) 2.1877 ( PROT ASN 16 O ) 2.1877 ( PROT ARG 17 N ) 2.1877 ( PROT ARG 17 H ) 1.7502 ( PROT ARG 17 CA ) 2.1877 ( PROT ARG 17 CB ) 1.7502 ( PROT ARG 17 CG ) 1.7502 ( PROT ARG 17 CD ) 1.7502 ( PROT ARG 17 NE ) 1.7502 ( PROT ARG 17 HE ) 1.7502 ( PROT ARG 17 CZ ) 1.7502 ( PROT ARG 17 NH1 ) 1.7502 ( PROT ARG 17 HH11 ) 1.7502 ( PROT ARG 17 HH12 ) 1.7502 ( PROT ARG 17 NH2 ) 1.7502 ( PROT ARG 17 HH21 ) 1.7502 ( PROT ARG 17 HH22 ) 1.7502 ( PROT ARG 17 C ) 2.1877 ( PROT ARG 17 OT1 ) 1.7502 ( PROT ARG 17 OT2 ) 1.7502 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96041 3.71075 -6.79881 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00341 0.00058 -0.00319 ROTATION MATRIX 1.000000 -0.000257 -0.000370 0.000257 1.000000 0.000729 0.000370 -0.000729 1.000000 AXIS OF ROTATION IS 0.850773 0.431740 -0.299643 ANGLE IS 0.05 TOTAL SQUARE DIFF IS 20.1338 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.350382 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3504" Parameter: A <- "0.3504" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.78085 3.78552 -6.98189 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.00867 0.00618 0.00466 ROTATION MATRIX 0.999510 0.020376 0.023741 -0.019721 0.999427 -0.027525 -0.024288 0.027044 0.999339 AXIS OF ROTATION IS -0.657301 -0.578527 0.482973 ANGLE IS 2.38 CENTER OF ROTATION 7.639742 3.761415 -7.198282 SHIFT IS 0.004372 TOTAL SQUARE DIFF IS 1.0455 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.247987 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3504" RDCMND substituted energy or value "?RMS" to " 0.2480" Parameter: A <- "0.3504 0.2480" 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 0.3504 0.2480 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 " 61.91" Parameter: H <- "61.91" 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 -29.03771 61.91185 1.25132 ENER INTERN> 5.80996 23.01304 0.00000 11.66436 4.87321 ENER EXTERN> -54.32889 -20.06940 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -29.04" Parameter: B <- "-29.04" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -20.07" Parameter: C <- "-20.07" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -54.33" Parameter: C <- " -74.40" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -74.40" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.81" Parameter: D <- "5.81" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 23.01" Parameter: D <- " 28.82" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.66" Parameter: D <- " 40.48" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.87" Parameter: D <- " 45.35" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 45.35" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 6600 ENER= -29.04 GRMS= 1.25 ELEC= -20.07 VDW= -54.33 RDTITL> *EXTERNAL= -74.40 INTERNAL= 45.35 USER= 0.00 HARM= 61.91 RDTITL> *BOND= 5.81 ANGL= 23.01 DIHE= 11.66 IMPR= 4.87 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9220 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9219 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 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 19.18159 -48.21930 0.55713 0.02000 MINI INTERN> 5.80996 23.01304 0.00000 11.66436 4.87321 MINI EXTERN> -54.32889 -20.06940 0.00000 0.00000 0.00000 MINI CONSTR> 48.21930 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 38.73384 -19.55225 16.49644 0.00864 MINI INTERN> 29.72989 19.44706 0.00000 12.75969 4.30641 MINI EXTERN> -59.30826 -18.15877 0.00000 0.00000 0.00000 MINI CONSTR> 49.95783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9215 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 16.43553 22.29831 0.61835 0.00156 MINI INTERN> 5.86414 22.32869 0.00000 12.27197 4.88505 MINI EXTERN> -60.01346 -19.08104 0.00000 0.00000 0.00000 MINI CONSTR> 50.18018 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 16.10385 0.33168 0.94632 0.00067 MINI INTERN> 5.76222 22.69494 0.00000 12.19032 4.94067 MINI EXTERN> -60.50938 -19.21324 0.00000 0.00000 0.00000 MINI CONSTR> 50.23832 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9215 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 15.83428 0.26957 1.04099 0.00070 MINI INTERN> 6.00475 22.44421 0.00000 12.18265 4.92711 MINI EXTERN> -60.75376 -19.22993 0.00000 0.00000 0.00000 MINI CONSTR> 50.25926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 15.57751 0.25678 1.10977 0.00072 MINI INTERN> 5.86464 22.51358 0.00000 12.16273 4.92899 MINI EXTERN> -60.88513 -19.29302 0.00000 0.00000 0.00000 MINI CONSTR> 50.28573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9214 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 15.32820 0.24931 1.05261 0.00075 MINI INTERN> 5.92040 22.38539 0.00000 12.15556 4.91168 MINI EXTERN> -61.03165 -19.31532 0.00000 0.00000 0.00000 MINI CONSTR> 50.30213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 15.07815 0.25005 1.10592 0.00078 MINI INTERN> 5.78435 22.39544 0.00000 12.15629 4.90028 MINI EXTERN> -61.14048 -19.33949 0.00000 0.00000 0.00000 MINI CONSTR> 50.32176 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9212 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 14.77546 0.30269 0.35498 0.00034 MINI INTERN> 5.66492 22.16724 0.00000 12.19642 4.81232 MINI EXTERN> -61.09218 -19.29845 0.00000 0.00000 0.00000 MINI CONSTR> 50.32519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 14.67420 0.10126 1.25336 0.00083 MINI INTERN> 5.85822 22.25554 0.00000 12.12446 4.88557 MINI EXTERN> -61.41087 -19.38680 0.00000 0.00000 0.00000 MINI CONSTR> 50.34809 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9211 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 14.35212 0.32208 0.39489 0.00036 MINI INTERN> 5.63468 22.05113 0.00000 12.17811 4.78428 MINI EXTERN> -61.31091 -19.33201 0.00000 0.00000 0.00000 MINI CONSTR> 50.34685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 14.29116 0.06097 1.29953 0.00090 MINI INTERN> 5.95027 22.12259 0.00000 12.08409 4.87567 MINI EXTERN> -61.67299 -19.43465 0.00000 0.00000 0.00000 MINI CONSTR> 50.36618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9211 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 13.95959 0.33157 0.45822 0.00039 MINI INTERN> 5.61080 21.93821 0.00000 12.15779 4.75706 MINI EXTERN> -61.50646 -19.35869 0.00000 0.00000 0.00000 MINI CONSTR> 50.36088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 13.79114 0.16846 0.31479 0.00040 MINI INTERN> 5.59326 21.93484 0.00000 12.13810 4.76384 MINI EXTERN> -61.61722 -19.38801 0.00000 0.00000 0.00000 MINI CONSTR> 50.36632 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9211 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 13.61182 0.17931 0.55591 0.00042 MINI INTERN> 5.57474 21.84242 0.00000 12.14091 4.72866 MINI EXTERN> -61.66246 -19.38020 0.00000 0.00000 0.00000 MINI CONSTR> 50.36775 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 13.43399 0.17783 0.41622 0.00043 MINI INTERN> 5.56395 21.82525 0.00000 12.11876 4.73506 MINI EXTERN> -61.77484 -19.40591 0.00000 0.00000 0.00000 MINI CONSTR> 50.37174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9210 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 13.27851 0.15548 0.50737 0.00045 MINI INTERN> 5.52365 21.78805 0.00000 12.11500 4.71808 MINI EXTERN> -61.82660 -19.41189 0.00000 0.00000 0.00000 MINI CONSTR> 50.37221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 13.14104 0.13747 0.66347 0.00046 MINI INTERN> 5.49062 21.74298 0.00000 12.11531 4.69459 MINI EXTERN> -61.86015 -19.41300 0.00000 0.00000 0.00000 MINI CONSTR> 50.37070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9209 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 12.98948 0.15156 0.73341 0.00048 MINI INTERN> 5.49250 21.70156 0.00000 12.09950 4.68971 MINI EXTERN> -61.94113 -19.42414 0.00000 0.00000 0.00000 MINI CONSTR> 50.37147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 12.85320 0.13628 0.76338 0.00050 MINI INTERN> 5.43306 21.68342 0.00000 12.09850 4.67298 MINI EXTERN> -61.97317 -19.43096 0.00000 0.00000 0.00000 MINI CONSTR> 50.36936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9209 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 12.71773 0.13547 0.82222 0.00052 MINI INTERN> 5.43551 21.64272 0.00000 12.08657 4.66177 MINI EXTERN> -62.03332 -19.44257 0.00000 0.00000 0.00000 MINI CONSTR> 50.36704 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 12.58443 0.13330 0.77132 0.00054 MINI INTERN> 5.37629 21.64226 0.00000 12.07786 4.65953 MINI EXTERN> -62.08292 -19.45508 0.00000 0.00000 0.00000 MINI CONSTR> 50.36650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9208 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 12.45445 0.12998 0.84116 0.00056 MINI INTERN> 5.44601 21.57982 0.00000 12.05396 4.65488 MINI EXTERN> -62.17052 -19.47338 0.00000 0.00000 0.00000 MINI CONSTR> 50.36368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 12.29002 0.16443 0.25640 0.00024 MINI INTERN> 5.51604 21.57400 0.00000 12.00155 4.69747 MINI EXTERN> -62.34070 -19.52556 0.00000 0.00000 0.00000 MINI CONSTR> 50.36723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9208 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 12.22549 0.06453 0.88624 0.00060 MINI INTERN> 5.29780 21.58122 0.00000 12.05109 4.63561 MINI EXTERN> -62.21612 -19.48392 0.00000 0.00000 0.00000 MINI CONSTR> 50.35982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 12.11995 0.10554 1.01404 0.00062 MINI INTERN> 5.40445 21.51440 0.00000 12.02339 4.63319 MINI EXTERN> -62.30620 -19.50554 0.00000 0.00000 0.00000 MINI CONSTR> 50.35625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9206 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 11.93492 0.18503 0.28235 0.00027 MINI INTERN> 5.51925 21.47663 0.00000 11.95951 4.68177 MINI EXTERN> -62.50128 -19.56123 0.00000 0.00000 0.00000 MINI CONSTR> 50.36026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 11.83392 0.10101 0.23006 0.00028 MINI INTERN> 5.48884 21.44854 0.00000 11.95529 4.66939 MINI EXTERN> -62.52210 -19.56340 0.00000 0.00000 0.00000 MINI CONSTR> 50.35736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9205 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 11.80303 0.03088 1.05158 0.00069 MINI INTERN> 5.28449 21.46578 0.00000 12.00790 4.60277 MINI EXTERN> -62.38485 -19.52115 0.00000 0.00000 0.00000 MINI CONSTR> 50.34810 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 11.61571 0.18732 0.36902 0.00030 MINI INTERN> 5.54484 21.38491 0.00000 11.91465 4.67075 MINI EXTERN> -62.65366 -19.59931 0.00000 0.00000 0.00000 MINI CONSTR> 50.35354 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9204 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 11.51593 0.09979 0.28492 0.00031 MINI INTERN> 5.50132 21.36291 0.00000 11.91157 4.65848 MINI EXTERN> -62.66811 -19.60109 0.00000 0.00000 0.00000 MINI CONSTR> 50.35085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 11.42110 0.09482 0.33060 0.00032 MINI INTERN> 5.52713 21.32845 0.00000 11.89484 4.65582 MINI EXTERN> -62.71909 -19.61484 0.00000 0.00000 0.00000 MINI CONSTR> 50.34879 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9202 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 11.33250 0.08861 0.37283 0.00033 MINI INTERN> 5.54634 21.29798 0.00000 11.87925 4.65421 MINI EXTERN> -62.76599 -19.62670 0.00000 0.00000 0.00000 MINI CONSTR> 50.34740 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 11.25506 0.07744 0.50574 0.00034 MINI INTERN> 5.60710 21.26066 0.00000 11.85734 4.65677 MINI EXTERN> -62.82865 -19.64440 0.00000 0.00000 0.00000 MINI CONSTR> 50.34624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9202 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 11.16822 0.08684 0.53606 0.00036 MINI INTERN> 5.58477 21.24766 0.00000 11.84822 4.65268 MINI EXTERN> -62.85678 -19.65346 0.00000 0.00000 0.00000 MINI CONSTR> 50.34513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 11.09172 0.07650 0.58099 0.00037 MINI INTERN> 5.63730 21.20334 0.00000 11.83031 4.64951 MINI EXTERN> -62.90568 -19.66648 0.00000 0.00000 0.00000 MINI CONSTR> 50.34343 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9200 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 11.01421 0.07751 0.55398 0.00038 MINI INTERN> 5.62181 21.18310 0.00000 11.82235 4.64435 MINI EXTERN> -62.92837 -19.67168 0.00000 0.00000 0.00000 MINI CONSTR> 50.34265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 10.93992 0.07429 0.61122 0.00040 MINI INTERN> 5.62633 21.15585 0.00000 11.81358 4.63514 MINI EXTERN> -62.95138 -19.68013 0.00000 0.00000 0.00000 MINI CONSTR> 50.34054 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9200 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 10.86542 0.07450 0.58055 0.00041 MINI INTERN> 5.63757 21.13159 0.00000 11.79926 4.63608 MINI EXTERN> -62.99021 -19.68993 0.00000 0.00000 0.00000 MINI CONSTR> 50.34106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 10.77221 0.09321 0.19573 0.00018 MINI INTERN> 5.40107 21.16281 0.00000 11.83408 4.59893 MINI EXTERN> -62.89780 -19.66402 0.00000 0.00000 0.00000 MINI CONSTR> 50.33713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9200 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 10.73526 0.03695 0.65510 0.00044 MINI INTERN> 5.67782 21.07801 0.00000 11.77377 4.63083 MINI EXTERN> -63.05620 -19.70958 0.00000 0.00000 0.00000 MINI CONSTR> 50.34061 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 10.67036 0.06489 0.71853 0.00046 MINI INTERN> 5.67105 21.05752 0.00000 11.76809 4.62017 MINI EXTERN> -63.06865 -19.71690 0.00000 0.00000 0.00000 MINI CONSTR> 50.33908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9200 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 10.56871 0.10165 0.21937 0.00020 MINI INTERN> 5.37096 21.11345 0.00000 11.80960 4.58403 MINI EXTERN> -62.96010 -19.68594 0.00000 0.00000 0.00000 MINI CONSTR> 50.33670 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 10.55067 0.01804 0.73060 0.00050 MINI INTERN> 5.72338 21.00294 0.00000 11.74028 4.61913 MINI EXTERN> -63.13831 -19.73736 0.00000 0.00000 0.00000 MINI CONSTR> 50.34062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9200 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 10.44630 0.10437 0.26123 0.00021 MINI INTERN> 5.34456 21.08653 0.00000 11.79594 4.57355 MINI EXTERN> -62.99275 -19.69891 0.00000 0.00000 0.00000 MINI CONSTR> 50.33738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 10.39400 0.05230 0.17425 0.00022 MINI INTERN> 5.38421 21.06197 0.00000 11.77914 4.57801 MINI EXTERN> -63.03476 -19.71341 0.00000 0.00000 0.00000 MINI CONSTR> 50.33885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9201 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 10.33600 0.05800 0.31875 0.00023 MINI INTERN> 5.30812 21.06890 0.00000 11.78475 4.56396 MINI EXTERN> -63.01808 -19.71070 0.00000 0.00000 0.00000 MINI CONSTR> 50.33905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 10.27903 0.05696 0.21920 0.00024 MINI INTERN> 5.35398 21.03718 0.00000 11.76700 4.56672 MINI EXTERN> -63.06120 -19.72532 0.00000 0.00000 0.00000 MINI CONSTR> 50.34069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9201 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 10.22667 0.05236 0.26322 0.00025 MINI INTERN> 5.32159 21.03420 0.00000 11.76401 4.56076 MINI EXTERN> -63.06651 -19.72943 0.00000 0.00000 0.00000 MINI CONSTR> 50.34205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 10.18160 0.04507 0.37817 0.00026 MINI INTERN> 5.27589 21.03662 0.00000 11.76537 4.55138 MINI EXTERN> -63.06046 -19.73024 0.00000 0.00000 0.00000 MINI CONSTR> 50.34304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9201 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 10.12990 0.05170 0.38230 0.00027 MINI INTERN> 5.27513 21.02246 0.00000 11.75628 4.54962 MINI EXTERN> -63.08102 -19.73796 0.00000 0.00000 0.00000 MINI CONSTR> 50.34538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 10.08562 0.04427 0.44522 0.00028 MINI INTERN> 5.28011 21.00542 0.00000 11.74940 4.54380 MINI EXTERN> -63.09501 -19.74478 0.00000 0.00000 0.00000 MINI CONSTR> 50.34668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9200 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 10.04069 0.04493 0.40974 0.00029 MINI INTERN> 5.25191 21.00597 0.00000 11.74520 4.54182 MINI EXTERN> -63.10319 -19.75022 0.00000 0.00000 0.00000 MINI CONSTR> 50.34920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 9.99587 0.04482 0.47486 0.00030 MINI INTERN> 5.25452 20.98849 0.00000 11.73836 4.53592 MINI EXTERN> -63.11689 -19.75586 0.00000 0.00000 0.00000 MINI CONSTR> 50.35132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9200 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 9.95367 0.04220 0.44608 0.00031 MINI INTERN> 5.23584 20.98643 0.00000 11.73277 4.53495 MINI EXTERN> -63.12818 -19.76237 0.00000 0.00000 0.00000 MINI CONSTR> 50.35423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 9.91053 0.04314 0.47201 0.00032 MINI INTERN> 5.25961 20.96209 0.00000 11.72222 4.53173 MINI EXTERN> -63.15079 -19.77107 0.00000 0.00000 0.00000 MINI CONSTR> 50.35674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9197 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 9.85693 0.05360 0.14843 0.00014 MINI INTERN> 5.40508 20.89912 0.00000 11.68414 4.55068 MINI EXTERN> -63.24151 -19.80235 0.00000 0.00000 0.00000 MINI CONSTR> 50.36176 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 9.83723 0.01970 0.50232 0.00034 MINI INTERN> 5.21361 20.96100 0.00000 11.71585 4.52472 MINI EXTERN> -63.16023 -19.78026 0.00000 0.00000 0.00000 MINI CONSTR> 50.36254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9198 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 9.79952 0.03771 0.54132 0.00035 MINI INTERN> 5.21483 20.95165 0.00000 11.70727 4.52507 MINI EXTERN> -63.17852 -19.78757 0.00000 0.00000 0.00000 MINI CONSTR> 50.36678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 9.74127 0.05825 0.17504 0.00015 MINI INTERN> 5.42088 20.85952 0.00000 11.65970 4.54553 MINI EXTERN> -63.29011 -19.82615 0.00000 0.00000 0.00000 MINI CONSTR> 50.37190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9198 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 9.73255 0.00872 0.55982 0.00038 MINI INTERN> 5.19366 20.93800 0.00000 11.69973 4.51570 MINI EXTERN> -63.18966 -19.79728 0.00000 0.00000 0.00000 MINI CONSTR> 50.37239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 9.67157 0.06099 0.20156 0.00016 MINI INTERN> 5.43394 20.83386 0.00000 11.64406 4.54233 MINI EXTERN> -63.32040 -19.84150 0.00000 0.00000 0.00000 MINI CONSTR> 50.37928 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9196 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 9.64160 0.02996 0.12815 0.00017 MINI INTERN> 5.38651 20.84015 0.00000 11.64720 4.53558 MINI EXTERN> -63.30993 -19.83987 0.00000 0.00000 0.00000 MINI CONSTR> 50.38196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 9.60740 0.03420 0.24652 0.00018 MINI INTERN> 5.45296 20.80808 0.00000 11.62788 4.54021 MINI EXTERN> -63.35153 -19.85749 0.00000 0.00000 0.00000 MINI CONSTR> 50.38729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9195 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 9.57429 0.03311 0.15648 0.00018 MINI INTERN> 5.40759 20.81279 0.00000 11.62991 4.53358 MINI EXTERN> -63.34313 -19.85710 0.00000 0.00000 0.00000 MINI CONSTR> 50.39066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 9.54125 0.03304 0.15692 0.00019 MINI INTERN> 5.40362 20.80478 0.00000 11.62373 4.53154 MINI EXTERN> -63.35367 -19.86400 0.00000 0.00000 0.00000 MINI CONSTR> 50.39525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9195 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 9.51107 0.03019 0.20740 0.00020 MINI INTERN> 5.42600 20.78772 0.00000 11.61363 4.53112 MINI EXTERN> -63.37326 -19.87408 0.00000 0.00000 0.00000 MINI CONSTR> 50.39995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 9.48824 0.02283 0.29588 0.00020 MINI INTERN> 5.46778 20.76684 0.00000 11.60091 4.53358 MINI EXTERN> -63.39948 -19.88595 0.00000 0.00000 0.00000 MINI CONSTR> 50.40458 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9194 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 9.46212 0.02612 0.34151 0.00021 MINI INTERN> 5.45965 20.76412 0.00000 11.59571 4.53296 MINI EXTERN> -63.40783 -19.89216 0.00000 0.00000 0.00000 MINI CONSTR> 50.40967 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 9.43671 0.02541 0.31592 0.00022 MINI INTERN> 5.47579 20.74755 0.00000 11.58866 4.53065 MINI EXTERN> -63.42066 -19.89874 0.00000 0.00000 0.00000 MINI CONSTR> 50.41346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9194 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 9.41308 0.02363 0.38516 0.00023 MINI INTERN> 5.47375 20.74421 0.00000 11.58242 4.53089 MINI EXTERN> -63.43113 -19.90607 0.00000 0.00000 0.00000 MINI CONSTR> 50.41902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 9.38940 0.02368 0.35132 0.00024 MINI INTERN> 5.47814 20.73280 0.00000 11.57732 4.52865 MINI EXTERN> -63.43976 -19.91072 0.00000 0.00000 0.00000 MINI CONSTR> 50.42296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9194 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 9.35767 0.03173 0.11430 0.00010 MINI INTERN> 5.34436 20.76584 0.00000 11.59648 4.51257 MINI EXTERN> -63.39271 -19.89452 0.00000 0.00000 0.00000 MINI CONSTR> 50.42566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 9.34573 0.01194 0.37591 0.00025 MINI INTERN> 5.50000 20.70864 0.00000 11.56479 4.52524 MINI EXTERN> -63.46141 -19.92336 0.00000 0.00000 0.00000 MINI CONSTR> 50.43184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9194 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 9.32509 0.02064 0.42294 0.00026 MINI INTERN> 5.46106 20.71964 0.00000 11.56525 4.52336 MINI EXTERN> -63.45685 -19.92473 0.00000 0.00000 0.00000 MINI CONSTR> 50.43736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 9.29109 0.03400 0.12162 0.00011 MINI INTERN> 5.33445 20.74811 0.00000 11.58334 4.50701 MINI EXTERN> -63.41255 -19.90930 0.00000 0.00000 0.00000 MINI CONSTR> 50.44003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9194 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 9.27209 0.01899 0.10079 0.00012 MINI INTERN> 5.34736 20.73779 0.00000 11.57650 4.50731 MINI EXTERN> -63.42503 -19.91643 0.00000 0.00000 0.00000 MINI CONSTR> 50.44459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 9.25142 0.02067 0.10258 0.00012 MINI INTERN> 5.34418 20.73206 0.00000 11.57235 4.50538 MINI EXTERN> -63.43099 -19.92118 0.00000 0.00000 0.00000 MINI CONSTR> 50.44961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9194 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 9.23213 0.01929 0.10573 0.00013 MINI INTERN> 5.33861 20.72795 0.00000 11.56874 4.50361 MINI EXTERN> -63.43585 -19.92548 0.00000 0.00000 0.00000 MINI CONSTR> 50.45455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 9.21283 0.01930 0.17356 0.00013 MINI INTERN> 5.30599 20.73312 0.00000 11.57005 4.49860 MINI EXTERN> -63.42939 -19.92536 0.00000 0.00000 0.00000 MINI CONSTR> 50.45982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9194 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 9.19385 0.01898 0.11912 0.00014 MINI INTERN> 5.32810 20.71911 0.00000 11.56144 4.49984 MINI EXTERN> -63.44556 -19.93406 0.00000 0.00000 0.00000 MINI CONSTR> 50.46498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 9.17706 0.01679 0.09791 0.00014 MINI INTERN> 5.34066 20.70901 0.00000 11.55515 4.49981 MINI EXTERN> -63.45660 -19.94075 0.00000 0.00000 0.00000 MINI CONSTR> 50.46979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9194 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 9.16077 0.01629 0.21718 0.00015 MINI INTERN> 5.29025 20.72149 0.00000 11.56018 4.49284 MINI EXTERN> -63.44190 -19.93721 0.00000 0.00000 0.00000 MINI CONSTR> 50.47513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 9.14425 0.01652 0.22844 0.00015 MINI INTERN> 5.28765 20.71812 0.00000 11.55584 4.49261 MINI EXTERN> -63.44851 -19.94217 0.00000 0.00000 0.00000 MINI CONSTR> 50.48071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9193 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 9.12929 0.01496 0.24272 0.00016 MINI INTERN> 5.28039 20.71472 0.00000 11.55390 4.48945 MINI EXTERN> -63.44965 -19.94492 0.00000 0.00000 0.00000 MINI CONSTR> 50.48539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 9.11438 0.01491 0.26099 0.00016 MINI INTERN> 5.27209 20.71398 0.00000 11.55087 4.48867 MINI EXTERN> -63.45334 -19.94878 0.00000 0.00000 0.00000 MINI CONSTR> 50.49089 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9193 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 9.09984 0.01453 0.24393 0.00017 MINI INTERN> 5.27685 20.70642 0.00000 11.54680 4.48713 MINI EXTERN> -63.45936 -19.95347 0.00000 0.00000 0.00000 MINI CONSTR> 50.49547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 9.08546 0.01438 0.26740 0.00018 MINI INTERN> 5.27379 20.70405 0.00000 11.54273 4.48711 MINI EXTERN> -63.46543 -19.95811 0.00000 0.00000 0.00000 MINI CONSTR> 50.50132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9192 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 9.06735 0.01811 0.08543 0.00008 MINI INTERN> 5.35994 20.66545 0.00000 11.52336 4.49377 MINI EXTERN> -63.50470 -19.97701 0.00000 0.00000 0.00000 MINI CONSTR> 50.50654 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 9.05957 0.00778 0.27916 0.00019 MINI INTERN> 5.26129 20.69954 0.00000 11.53815 4.48339 MINI EXTERN> -63.46963 -19.96432 0.00000 0.00000 0.00000 MINI CONSTR> 50.51115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9192 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 9.04068 0.01890 0.08950 0.00008 MINI INTERN> 5.36305 20.65514 0.00000 11.51551 4.49204 MINI EXTERN> -63.51586 -19.98623 0.00000 0.00000 0.00000 MINI CONSTR> 50.51703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 9.03556 0.00512 0.30921 0.00020 MINI INTERN> 5.27203 20.68554 0.00000 11.53047 4.48030 MINI EXTERN> -63.48062 -19.97309 0.00000 0.00000 0.00000 MINI CONSTR> 50.52092 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9192 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 9.01621 0.01935 0.09916 0.00009 MINI INTERN> 5.36927 20.64420 0.00000 11.50759 4.49056 MINI EXTERN> -63.52728 -19.99545 0.00000 0.00000 0.00000 MINI CONSTR> 50.52732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 9.01290 0.00331 0.31865 0.00022 MINI INTERN> 5.24468 20.68978 0.00000 11.52784 4.47788 MINI EXTERN> -63.48083 -19.97775 0.00000 0.00000 0.00000 MINI CONSTR> 50.53128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9191 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 8.99240 0.02049 0.11082 0.00009 MINI INTERN> 5.37415 20.63406 0.00000 11.49985 4.48909 MINI EXTERN> -63.53809 -20.00468 0.00000 0.00000 0.00000 MINI CONSTR> 50.53802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 8.98225 0.01015 0.07334 0.00010 MINI INTERN> 5.35212 20.63821 0.00000 11.50103 4.48623 MINI EXTERN> -63.53331 -20.00425 0.00000 0.00000 0.00000 MINI CONSTR> 50.54221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9191 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 8.97024 0.01201 0.07459 0.00010 MINI INTERN> 5.35325 20.63357 0.00000 11.49724 4.48543 MINI EXTERN> -63.53835 -20.00887 0.00000 0.00000 0.00000 MINI CONSTR> 50.54799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 8.95959 0.01065 0.15063 0.00011 MINI INTERN> 5.38829 20.61731 0.00000 11.48742 4.48760 MINI EXTERN> -63.55585 -20.01954 0.00000 0.00000 0.00000 MINI CONSTR> 50.55435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9191 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 8.94850 0.01109 0.09243 0.00011 MINI INTERN> 5.36418 20.62162 0.00000 11.48874 4.48442 MINI EXTERN> -63.55056 -20.01897 0.00000 0.00000 0.00000 MINI CONSTR> 50.55907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 8.93836 0.01013 0.11862 0.00011 MINI INTERN> 5.37074 20.61608 0.00000 11.48410 4.48458 MINI EXTERN> -63.55744 -20.02453 0.00000 0.00000 0.00000 MINI CONSTR> 50.56483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9190 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 8.93053 0.00784 0.16901 0.00012 MINI INTERN> 5.39262 20.60521 0.00000 11.47757 4.48554 MINI EXTERN> -63.56860 -20.03176 0.00000 0.00000 0.00000 MINI CONSTR> 50.56994 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 8.93053 0.00784 0.16901 0.00014 STPD INTERN> 5.39262 20.60521 0.00000 11.47757 4.48554 STPD EXTERN> -63.56860 -20.03176 0.00000 0.00000 0.00000 STPD CONSTR> 50.56994 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 9190 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9190 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 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 8.93053 0.00784 0.16901 0.00000 MINI INTERN> 5.39262 20.60521 0.00000 11.47757 4.48554 MINI EXTERN> -63.56860 -20.03176 0.00000 0.00000 0.00000 MINI CONSTR> 50.56994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 8.64271 0.28782 0.01393 0.00293 MINI INTERN> 5.32395 20.43347 0.00000 11.31921 4.43376 MINI EXTERN> -63.79544 -20.23579 0.00000 0.00000 0.00000 MINI CONSTR> 51.16355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 8.64202 0.00069 0.02779 0.00240 MINI INTERN> 5.31565 20.41133 0.00000 11.31477 4.42337 MINI EXTERN> -63.63614 -20.26667 0.00000 0.00000 0.00000 MINI CONSTR> 51.07971 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 8.64119 0.00083 0.01628 0.00236 MINI INTERN> 5.31673 20.46019 0.00000 11.32161 4.43310 MINI EXTERN> -63.62078 -20.25340 0.00000 0.00000 0.00000 MINI CONSTR> 50.98373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 8.64088 0.00031 0.01021 0.00101 MINI INTERN> 5.33178 20.48573 0.00000 11.32942 4.43906 MINI EXTERN> -63.64837 -20.25872 0.00000 0.00000 0.00000 MINI CONSTR> 50.96198 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> 21 8.64085 0.00003 0.00826 0.02000 CONJ INTERN> 5.33455 20.48701 0.00000 11.32937 4.43930 CONJ EXTERN> -63.65388 -20.25690 0.00000 0.00000 0.00000 CONJ CONSTR> 50.96139 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 ASP 1 HT1 ) 1.1376 ( PROT ASP 1 HT2 ) 1.1376 ( PROT ASP 1 N ) 1.4220 ( PROT ASP 1 HT3 ) 1.1376 ( PROT ASP 1 CA ) 1.4220 ( PROT ASP 1 CB ) 1.1376 ( PROT ASP 1 CG ) 1.1376 ( PROT ASP 1 OD1 ) 1.1376 ( PROT ASP 1 OD2 ) 1.1376 ( PROT ASP 1 C ) 1.4220 ( PROT ASP 1 O ) 1.4220 ( PROT TYR 2 N ) 1.4220 ( PROT TYR 2 H ) 1.1376 ( PROT TYR 2 CA ) 1.4220 ( PROT TYR 2 CB ) 1.1376 ( PROT TYR 2 CG ) 1.1376 ( PROT TYR 2 CD1 ) 1.1376 ( PROT TYR 2 CE1 ) 1.1376 ( PROT TYR 2 CD2 ) 1.1376 ( PROT TYR 2 CE2 ) 1.1376 ( PROT TYR 2 CZ ) 1.1376 ( PROT TYR 2 OH ) 1.1376 ( PROT TYR 2 HH ) 1.1376 ( PROT TYR 2 C ) 1.4220 ( PROT TYR 2 O ) 1.4220 ( PROT ALA 3 N ) 1.4220 ( PROT ALA 3 H ) 1.1376 ( PROT ALA 3 CA ) 1.4220 ( PROT ALA 3 CB ) 1.1376 ( PROT ALA 3 C ) 1.4220 ( PROT ALA 3 O ) 1.4220 ( PROT PHE 4 N ) 1.4220 ( PROT PHE 4 H ) 1.1376 ( PROT PHE 4 CA ) 1.4220 ( PROT PHE 4 CB ) 1.1376 ( PROT PHE 4 CG ) 1.1376 ( PROT PHE 4 CD1 ) 1.1376 ( PROT PHE 4 CD2 ) 1.1376 ( PROT PHE 4 CE1 ) 1.1376 ( PROT PHE 4 CE2 ) 1.1376 ( PROT PHE 4 CZ ) 1.1376 ( PROT PHE 4 C ) 1.4220 ( PROT PHE 4 O ) 1.4220 ( PROT ILE 5 N ) 1.4220 ( PROT ILE 5 H ) 1.1376 ( PROT ILE 5 CA ) 1.4220 ( PROT ILE 5 CB ) 1.1376 ( PROT ILE 5 CG2 ) 1.1376 ( PROT ILE 5 CG1 ) 1.1376 ( PROT ILE 5 CD ) 1.1376 ( PROT ILE 5 C ) 1.4220 ( PROT ILE 5 O ) 1.4220 ( PROT ALA 6 N ) 1.4220 ( PROT ALA 6 H ) 1.1376 ( PROT ALA 6 CA ) 1.4220 ( PROT ALA 6 CB ) 1.1376 ( PROT ALA 6 C ) 1.4220 ( PROT ALA 6 O ) 1.4220 ( PROT SER 7 N ) 1.4220 ( PROT SER 7 H ) 1.1376 ( PROT SER 7 CA ) 1.4220 ( PROT SER 7 CB ) 1.1376 ( PROT SER 7 OG ) 1.1376 ( PROT SER 7 HG ) 1.1376 ( PROT SER 7 C ) 1.4220 ( PROT SER 7 O ) 1.4220 ( PROT LEU 8 N ) 1.4220 ( PROT LEU 8 H ) 1.1376 ( PROT LEU 8 CA ) 1.4220 ( PROT LEU 8 CB ) 1.1376 ( PROT LEU 8 CG ) 1.1376 ( PROT LEU 8 CD1 ) 1.1376 ( PROT LEU 8 CD2 ) 1.1376 ( PROT LEU 8 C ) 1.4220 ( PROT LEU 8 O ) 1.4220 ( PROT VAL 9 N ) 1.4220 ( PROT VAL 9 H ) 1.1376 ( PROT VAL 9 CA ) 1.4220 ( PROT VAL 9 CB ) 1.1376 ( PROT VAL 9 CG1 ) 1.1376 ( PROT VAL 9 CG2 ) 1.1376 ( PROT VAL 9 C ) 1.4220 ( PROT VAL 9 O ) 1.4220 ( PROT VAL 10 N ) 1.4220 ( PROT VAL 10 H ) 1.1376 ( PROT VAL 10 CA ) 1.4220 ( PROT VAL 10 CB ) 1.1376 ( PROT VAL 10 CG1 ) 1.1376 ( PROT VAL 10 CG2 ) 1.1376 ( PROT VAL 10 C ) 1.4220 ( PROT VAL 10 O ) 1.4220 ( PROT ILE 11 N ) 1.4220 ( PROT ILE 11 H ) 1.1376 ( PROT ILE 11 CA ) 1.4220 ( PROT ILE 11 CB ) 1.1376 ( PROT ILE 11 CG2 ) 1.1376 ( PROT ILE 11 CG1 ) 1.1376 ( PROT ILE 11 CD ) 1.1376 ( PROT ILE 11 C ) 1.4220 ( PROT ILE 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 ASP 13 N ) 1.4220 ( PROT ASP 13 H ) 1.1376 ( PROT ASP 13 CA ) 1.4220 ( PROT ASP 13 CB ) 1.1376 ( PROT ASP 13 CG ) 1.1376 ( PROT ASP 13 OD1 ) 1.1376 ( PROT ASP 13 OD2 ) 1.1376 ( PROT ASP 13 C ) 1.4220 ( PROT ASP 13 O ) 1.4220 ( PROT ASP 14 N ) 1.4220 ( PROT ASP 14 H ) 1.1376 ( PROT ASP 14 CA ) 1.4220 ( PROT ASP 14 CB ) 1.1376 ( PROT ASP 14 CG ) 1.1376 ( PROT ASP 14 OD1 ) 1.1376 ( PROT ASP 14 OD2 ) 1.1376 ( PROT ASP 14 C ) 1.4220 ( PROT ASP 14 O ) 1.4220 ( PROT VAL 15 N ) 1.4220 ( PROT VAL 15 H ) 1.1376 ( PROT VAL 15 CA ) 1.4220 ( PROT VAL 15 CB ) 1.1376 ( PROT VAL 15 CG1 ) 1.1376 ( PROT VAL 15 CG2 ) 1.1376 ( PROT VAL 15 C ) 1.4220 ( PROT VAL 15 O ) 1.4220 ( PROT ASN 16 N ) 1.4220 ( PROT ASN 16 H ) 1.1376 ( PROT ASN 16 CA ) 1.4220 ( PROT ASN 16 CB ) 1.1376 ( PROT ASN 16 CG ) 1.1376 ( PROT ASN 16 OD1 ) 1.1376 ( PROT ASN 16 ND2 ) 1.1376 ( PROT ASN 16 HD21 ) 1.1376 ( PROT ASN 16 HD22 ) 1.1376 ( PROT ASN 16 C ) 1.4220 ( PROT ASN 16 O ) 1.4220 ( PROT ARG 17 N ) 1.4220 ( PROT ARG 17 H ) 1.1376 ( PROT ARG 17 CA ) 1.4220 ( PROT ARG 17 CB ) 1.1376 ( PROT ARG 17 CG ) 1.1376 ( PROT ARG 17 CD ) 1.1376 ( PROT ARG 17 NE ) 1.1376 ( PROT ARG 17 HE ) 1.1376 ( PROT ARG 17 CZ ) 1.1376 ( PROT ARG 17 NH1 ) 1.1376 ( PROT ARG 17 HH11 ) 1.1376 ( PROT ARG 17 HH12 ) 1.1376 ( PROT ARG 17 NH2 ) 1.1376 ( PROT ARG 17 HH21 ) 1.1376 ( PROT ARG 17 HH22 ) 1.1376 ( PROT ARG 17 C ) 1.4220 ( PROT ARG 17 OT1 ) 1.1376 ( PROT ARG 17 OT2 ) 1.1376 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96005 3.71011 -6.79836 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00377 0.00122 -0.00364 ROTATION MATRIX 1.000000 -0.000233 -0.000361 0.000234 1.000000 0.000779 0.000361 -0.000779 1.000000 AXIS OF ROTATION IS 0.875468 0.405910 -0.262283 ANGLE IS 0.05 TOTAL SQUARE DIFF IS 25.6436 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.395428 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3954" Parameter: A <- "0.3954" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.78267 3.78845 -6.98585 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.01050 0.00326 0.00861 ROTATION MATRIX 0.999461 0.021535 0.024759 -0.020796 0.999342 -0.029724 -0.025382 0.029193 0.999251 AXIS OF ROTATION IS -0.668082 -0.568563 0.480003 ANGLE IS 2.53 CENTER OF ROTATION 7.630996 3.806297 -7.166134 SHIFT IS 0.009296 TOTAL SQUARE DIFF IS 1.5561 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.302553 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3954" RDCMND substituted energy or value "?RMS" to " 0.3026" Parameter: A <- "0.3954 0.3026" 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 0.3954 0.3026 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 " 50.96" Parameter: H <- "50.96" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -42.32053 50.96139 0.91354 ENER INTERN> 5.33455 20.48701 0.00000 11.32937 4.43930 ENER EXTERN> -63.65388 -20.25690 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 " -42.32" Parameter: B <- "-42.32" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -20.26" Parameter: C <- "-20.26" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -63.65" Parameter: C <- " -83.91" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -83.91" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.33" Parameter: D <- "5.33" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 20.49" Parameter: D <- " 25.82" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.33" Parameter: D <- " 37.15" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.44" Parameter: D <- " 41.59" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 41.59" 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= 7200 ENER= -42.32 GRMS= 0.91 ELEC= -20.26 VDW= -63.65 RDTITL> *EXTERNAL= -83.91 INTERNAL= 41.59 USER= 0.00 HARM= 50.96 RDTITL> *BOND= 5.33 ANGL= 20.49 DIHE= 11.33 IMPR= 4.44 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= -42.32 GRMS= 0.91 ELEC= -20.26 VDW= -63.65 RDTITL> *EXTERNAL= -83.91 INTERNAL= 41.59 USER= 0.00 HARM= 50.96 RDTITL> *BOND= 5.33 ANGL= 20.49 DIHE= 11.33 IMPR= 4.44 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= -42.32 GRMS= 0.91 ELEC= -20.26 VDW= -63.65 RDTITL> *EXTERNAL= -83.91 INTERNAL= 41.59 USER= 0.00 HARM= 50.96 RDTITL> *BOND= 5.33 ANGL= 20.49 DIHE= 11.33 IMPR= 4.44 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 7200 0.3954 0.3026 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "7200" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9190 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9186 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 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 -3.40324 -38.91729 0.39842 0.02000 MINI INTERN> 5.33455 20.48701 0.00000 11.32937 4.43930 MINI EXTERN> -63.65388 -20.25690 0.00000 0.00000 0.00000 MINI CONSTR> 38.91729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 18.84984 -22.25309 17.25701 0.00864 MINI INTERN> 31.04102 17.60729 0.00000 12.17059 3.98149 MINI EXTERN> -67.70572 -18.58055 0.00000 0.00000 0.00000 MINI CONSTR> 40.33572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9184 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -5.15300 24.00284 1.00492 0.00156 MINI INTERN> 5.71735 19.82475 0.00000 11.80628 4.43693 MINI EXTERN> -67.99218 -19.42480 0.00000 0.00000 0.00000 MINI CONSTR> 40.47867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -5.40099 0.24799 0.58535 0.00067 MINI INTERN> 5.39634 20.27298 0.00000 11.73990 4.48161 MINI EXTERN> -68.27980 -19.54114 0.00000 0.00000 0.00000 MINI CONSTR> 40.52913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9183 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -5.48814 0.08715 1.02496 0.00070 MINI INTERN> 5.51691 20.25595 0.00000 11.70372 4.49617 MINI EXTERN> -68.41049 -19.61203 0.00000 0.00000 0.00000 MINI CONSTR> 40.56164 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -5.61643 0.12829 1.19353 0.00072 MINI INTERN> 5.42462 20.25206 0.00000 11.69994 4.48371 MINI EXTERN> -68.44774 -19.62520 0.00000 0.00000 0.00000 MINI CONSTR> 40.59618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9184 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -5.85934 0.24291 0.31852 0.00031 MINI INTERN> 5.33053 20.06989 0.00000 11.72469 4.41558 MINI EXTERN> -68.40012 -19.62108 0.00000 0.00000 0.00000 MINI CONSTR> 40.62116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -5.98678 0.12744 0.27160 0.00032 MINI INTERN> 5.31441 20.05248 0.00000 11.71089 4.41243 MINI EXTERN> -68.47468 -19.65372 0.00000 0.00000 0.00000 MINI CONSTR> 40.65143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9182 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -6.11609 0.12931 0.27923 0.00034 MINI INTERN> 5.29495 20.02029 0.00000 11.70136 4.40271 MINI EXTERN> -68.54110 -19.67730 0.00000 0.00000 0.00000 MINI CONSTR> 40.68300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -6.24711 0.13102 0.44966 0.00035 MINI INTERN> 5.27336 19.96162 0.00000 11.69943 4.37992 MINI EXTERN> -68.59103 -19.68761 0.00000 0.00000 0.00000 MINI CONSTR> 40.71720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9182 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -6.37066 0.12355 0.37340 0.00036 MINI INTERN> 5.26467 19.94006 0.00000 11.68485 4.37799 MINI EXTERN> -68.67207 -19.71233 0.00000 0.00000 0.00000 MINI CONSTR> 40.74617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -6.48642 0.11576 0.41230 0.00037 MINI INTERN> 5.22906 19.91732 0.00000 11.67945 4.36739 MINI EXTERN> -68.72717 -19.72742 0.00000 0.00000 0.00000 MINI CONSTR> 40.77495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9181 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -6.60799 0.12157 0.38383 0.00039 MINI INTERN> 5.22182 19.88564 0.00000 11.66642 4.36201 MINI EXTERN> -68.80304 -19.74471 0.00000 0.00000 0.00000 MINI CONSTR> 40.80388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -6.70790 0.09991 0.57896 0.00040 MINI INTERN> 5.18917 19.84840 0.00000 11.66814 4.34112 MINI EXTERN> -68.83594 -19.74935 0.00000 0.00000 0.00000 MINI CONSTR> 40.83056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9181 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -6.82199 0.11409 0.61277 0.00042 MINI INTERN> 5.18781 19.81144 0.00000 11.65498 4.33462 MINI EXTERN> -68.90812 -19.76099 0.00000 0.00000 0.00000 MINI CONSTR> 40.85827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -6.92124 0.09925 0.67487 0.00043 MINI INTERN> 5.17253 19.78108 0.00000 11.64991 4.32189 MINI EXTERN> -68.95544 -19.77279 0.00000 0.00000 0.00000 MINI CONSTR> 40.88159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9180 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -7.02295 0.10171 0.64524 0.00045 MINI INTERN> 5.13357 19.77670 0.00000 11.64036 4.32030 MINI EXTERN> -69.01065 -19.78762 0.00000 0.00000 0.00000 MINI CONSTR> 40.90438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -7.11948 0.09653 0.70790 0.00046 MINI INTERN> 5.17118 19.73167 0.00000 11.62408 4.31501 MINI EXTERN> -69.08342 -19.80392 0.00000 0.00000 0.00000 MINI CONSTR> 40.92593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9179 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -7.21658 0.09710 0.67205 0.00048 MINI INTERN> 5.09763 19.73288 0.00000 11.62396 4.30539 MINI EXTERN> -69.11007 -19.81298 0.00000 0.00000 0.00000 MINI CONSTR> 40.94661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -7.34097 0.12439 0.22698 0.00021 MINI INTERN> 5.22898 19.69122 0.00000 11.56915 4.34094 MINI EXTERN> -69.27999 -19.85956 0.00000 0.00000 0.00000 MINI CONSTR> 40.96829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9179 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -7.39047 0.04950 0.76366 0.00052 MINI INTERN> 5.05109 19.69957 0.00000 11.61045 4.29017 MINI EXTERN> -69.19297 -19.83398 0.00000 0.00000 0.00000 MINI CONSTR> 40.98521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -7.47535 0.08488 0.85769 0.00054 MINI INTERN> 5.06086 19.68400 0.00000 11.59256 4.29415 MINI EXTERN> -69.26244 -19.85057 0.00000 0.00000 0.00000 MINI CONSTR> 41.00609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9178 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -7.61567 0.14032 0.24574 0.00023 MINI INTERN> 5.22930 19.60546 0.00000 11.53339 4.32596 MINI EXTERN> -69.43668 -19.89774 0.00000 0.00000 0.00000 MINI CONSTR> 41.02464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -7.69469 0.07902 0.20679 0.00024 MINI INTERN> 5.20468 19.58303 0.00000 11.52888 4.31639 MINI EXTERN> -69.46387 -19.90339 0.00000 0.00000 0.00000 MINI CONSTR> 41.03959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9176 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -7.77953 0.08484 0.21144 0.00025 MINI INTERN> 5.20874 19.55462 0.00000 11.51667 4.31184 MINI EXTERN> -69.51183 -19.91569 0.00000 0.00000 0.00000 MINI CONSTR> 41.05611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -7.86166 0.08213 0.20993 0.00026 MINI INTERN> 5.20410 19.53004 0.00000 11.50622 4.30666 MINI EXTERN> -69.55366 -19.92685 0.00000 0.00000 0.00000 MINI CONSTR> 41.07183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9176 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -7.94411 0.08245 0.35557 0.00027 MINI INTERN> 5.26973 19.49062 0.00000 11.48021 4.31214 MINI EXTERN> -69.63589 -19.95041 0.00000 0.00000 0.00000 MINI CONSTR> 41.08948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -8.02382 0.07971 0.25402 0.00028 MINI INTERN> 5.21750 19.47793 0.00000 11.47981 4.30045 MINI EXTERN> -69.64826 -19.95409 0.00000 0.00000 0.00000 MINI CONSTR> 41.10284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9174 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -8.09972 0.07589 0.29616 0.00029 MINI INTERN> 5.24176 19.44501 0.00000 11.46463 4.29778 MINI EXTERN> -69.69822 -19.96782 0.00000 0.00000 0.00000 MINI CONSTR> 41.11715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -8.17178 0.07206 0.33142 0.00030 MINI INTERN> 5.25485 19.41904 0.00000 11.45116 4.29565 MINI EXTERN> -69.74253 -19.98083 0.00000 0.00000 0.00000 MINI CONSTR> 41.13089 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9173 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -8.23456 0.06278 0.45435 0.00031 MINI INTERN> 5.31262 19.38076 0.00000 11.43097 4.29718 MINI EXTERN> -69.80249 -19.99761 0.00000 0.00000 0.00000 MINI CONSTR> 41.14401 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -8.30698 0.07242 0.47238 0.00032 MINI INTERN> 5.29510 19.36772 0.00000 11.42226 4.29316 MINI EXTERN> -69.83305 -20.00958 0.00000 0.00000 0.00000 MINI CONSTR> 41.15741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9173 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -8.37069 0.06371 0.52622 0.00033 MINI INTERN> 5.33436 19.32842 0.00000 11.40723 4.28912 MINI EXTERN> -69.87768 -20.02117 0.00000 0.00000 0.00000 MINI CONSTR> 41.16905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -8.43390 0.06321 0.53991 0.00034 MINI INTERN> 5.34754 19.30497 0.00000 11.39442 4.28774 MINI EXTERN> -69.91624 -20.03326 0.00000 0.00000 0.00000 MINI CONSTR> 41.18093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9173 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -8.49792 0.06401 0.51353 0.00036 MINI INTERN> 5.34110 19.28298 0.00000 11.38677 4.28148 MINI EXTERN> -69.94072 -20.04085 0.00000 0.00000 0.00000 MINI CONSTR> 41.19133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -8.56229 0.06437 0.55437 0.00037 MINI INTERN> 5.33363 19.27041 0.00000 11.37657 4.27915 MINI EXTERN> -69.97141 -20.05416 0.00000 0.00000 0.00000 MINI CONSTR> 41.20352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9173 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -8.64399 0.08170 0.18112 0.00016 MINI INTERN> 5.11673 19.30701 0.00000 11.40765 4.24783 MINI EXTERN> -69.89907 -20.03541 0.00000 0.00000 0.00000 MINI CONSTR> 41.21127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -8.67912 0.03513 0.58439 0.00040 MINI INTERN> 5.36922 19.21630 0.00000 11.35285 4.27228 MINI EXTERN> -70.03818 -20.07562 0.00000 0.00000 0.00000 MINI CONSTR> 41.22402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9172 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -8.76744 0.08832 0.17604 0.00017 MINI INTERN> 5.11185 19.27048 0.00000 11.38849 4.24005 MINI EXTERN> -69.95467 -20.05612 0.00000 0.00000 0.00000 MINI CONSTR> 41.23247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -8.79529 0.02784 0.63763 0.00043 MINI INTERN> 5.38287 19.17456 0.00000 11.33187 4.26479 MINI EXTERN> -70.09573 -20.09834 0.00000 0.00000 0.00000 MINI CONSTR> 41.24469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9172 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -8.88448 0.08920 0.19936 0.00019 MINI INTERN> 5.08861 19.24189 0.00000 11.37361 4.23005 MINI EXTERN> -69.99752 -20.07363 0.00000 0.00000 0.00000 MINI CONSTR> 41.25251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -8.93452 0.05004 0.16611 0.00019 MINI INTERN> 5.10860 19.22058 0.00000 11.36114 4.22997 MINI EXTERN> -70.02995 -20.08588 0.00000 0.00000 0.00000 MINI CONSTR> 41.26104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9172 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -8.98851 0.05398 0.16967 0.00020 MINI INTERN> 5.09871 19.20794 0.00000 11.35366 4.22590 MINI EXTERN> -70.05017 -20.09485 0.00000 0.00000 0.00000 MINI CONSTR> 41.27030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -9.04139 0.05288 0.16625 0.00021 MINI INTERN> 5.09864 19.19162 0.00000 11.34464 4.22263 MINI EXTERN> -70.07366 -20.10462 0.00000 0.00000 0.00000 MINI CONSTR> 41.27935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9171 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -9.09554 0.05415 0.28257 0.00021 MINI INTERN> 5.03648 19.19646 0.00000 11.34712 4.21130 MINI EXTERN> -70.06951 -20.10648 0.00000 0.00000 0.00000 MINI CONSTR> 41.28908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -9.14671 0.05117 0.20498 0.00022 MINI INTERN> 5.07195 19.16794 0.00000 11.33156 4.21253 MINI EXTERN> -70.10761 -20.12058 0.00000 0.00000 0.00000 MINI CONSTR> 41.29750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9170 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -9.19567 0.04896 0.23636 0.00023 MINI INTERN> 5.04873 19.16296 0.00000 11.32671 4.20781 MINI EXTERN> -70.12007 -20.12808 0.00000 0.00000 0.00000 MINI CONSTR> 41.30627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -9.24262 0.04694 0.26182 0.00024 MINI INTERN> 5.03715 19.15216 0.00000 11.32079 4.20289 MINI EXTERN> -70.13465 -20.13541 0.00000 0.00000 0.00000 MINI CONSTR> 41.31444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9170 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -9.28335 0.04073 0.36343 0.00025 MINI INTERN> 4.99113 19.15862 0.00000 11.32144 4.19549 MINI EXTERN> -70.13355 -20.13893 0.00000 0.00000 0.00000 MINI CONSTR> 41.32245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -9.33063 0.04728 0.37451 0.00026 MINI INTERN> 5.00273 19.13725 0.00000 11.31163 4.19193 MINI EXTERN> -70.15684 -20.14797 0.00000 0.00000 0.00000 MINI CONSTR> 41.33065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9169 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -9.37226 0.04163 0.41997 0.00027 MINI INTERN> 4.97381 19.14045 0.00000 11.30762 4.18898 MINI EXTERN> -70.16623 -20.15593 0.00000 0.00000 0.00000 MINI CONSTR> 41.33904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -9.41348 0.04122 0.43010 0.00028 MINI INTERN> 4.96065 19.13149 0.00000 11.30302 4.18366 MINI EXTERN> -70.17651 -20.16204 0.00000 0.00000 0.00000 MINI CONSTR> 41.34625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9169 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -9.45539 0.04191 0.40908 0.00029 MINI INTERN> 4.96263 19.11915 0.00000 11.29445 4.18230 MINI EXTERN> -70.19591 -20.17170 0.00000 0.00000 0.00000 MINI CONSTR> 41.35370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -9.49762 0.04224 0.44205 0.00030 MINI INTERN> 4.95957 19.10586 0.00000 11.28761 4.17775 MINI EXTERN> -70.21139 -20.17865 0.00000 0.00000 0.00000 MINI CONSTR> 41.36163 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -9.53439 0.03677 0.51667 0.00031 MINI INTERN> 4.93488 19.10924 0.00000 11.28341 4.17503 MINI EXTERN> -70.22037 -20.18655 0.00000 0.00000 0.00000 MINI CONSTR> 41.36996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -9.57351 0.03912 0.47246 0.00032 MINI INTERN> 4.93592 19.09645 0.00000 11.27598 4.17290 MINI EXTERN> -70.23626 -20.19500 0.00000 0.00000 0.00000 MINI CONSTR> 41.37649 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -9.62875 0.05524 0.15156 0.00014 MINI INTERN> 5.12144 19.00637 0.00000 11.23236 4.18997 MINI EXTERN> -70.33517 -20.22835 0.00000 0.00000 0.00000 MINI CONSTR> 41.38463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -9.64580 0.01705 0.51718 0.00034 MINI INTERN> 4.94561 19.06767 0.00000 11.26144 4.16607 MINI EXTERN> -70.26711 -20.20977 0.00000 0.00000 0.00000 MINI CONSTR> 41.39029 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -9.70309 0.05729 0.16204 0.00015 MINI INTERN> 5.12811 18.98136 0.00000 11.21658 4.18583 MINI EXTERN> -70.36819 -20.24579 0.00000 0.00000 0.00000 MINI CONSTR> 41.39901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -9.71548 0.01239 0.53757 0.00037 MINI INTERN> 4.91117 19.06272 0.00000 11.25301 4.15947 MINI EXTERN> -70.28331 -20.22295 0.00000 0.00000 0.00000 MINI CONSTR> 41.40441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -9.77678 0.06130 0.17653 0.00016 MINI INTERN> 5.13479 18.95682 0.00000 11.20061 4.18180 MINI EXTERN> -70.40073 -20.26373 0.00000 0.00000 0.00000 MINI CONSTR> 41.41366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -9.80839 0.03161 0.13055 0.00016 MINI INTERN> 5.10062 18.95956 0.00000 11.20064 4.17635 MINI EXTERN> -70.39909 -20.26598 0.00000 0.00000 0.00000 MINI CONSTR> 41.41950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -9.84466 0.03627 0.13579 0.00017 MINI INTERN> 5.10486 18.94741 0.00000 11.19235 4.17465 MINI EXTERN> -70.41560 -20.27531 0.00000 0.00000 0.00000 MINI CONSTR> 41.42698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -9.87842 0.03375 0.24436 0.00018 MINI INTERN> 5.16661 18.91449 0.00000 11.17401 4.17795 MINI EXTERN> -70.45421 -20.29236 0.00000 0.00000 0.00000 MINI CONSTR> 41.43508 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -9.90901 0.03059 0.12685 0.00018 MINI INTERN> 5.09679 18.93084 0.00000 11.18063 4.16959 MINI EXTERN> -70.43775 -20.28934 0.00000 0.00000 0.00000 MINI CONSTR> 41.44022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -9.94358 0.03457 0.27609 0.00019 MINI INTERN> 5.17870 18.89058 0.00000 11.15815 4.17469 MINI EXTERN> -70.48465 -20.31028 0.00000 0.00000 0.00000 MINI CONSTR> 41.44923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -9.97854 0.03497 0.16442 0.00020 MINI INTERN> 5.12241 18.90070 0.00000 11.16122 4.16758 MINI EXTERN> -70.47555 -20.31040 0.00000 0.00000 0.00000 MINI CONSTR> 41.45549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -10.01188 0.03334 0.18741 0.00020 MINI INTERN> 5.13326 18.88678 0.00000 11.15211 4.16634 MINI EXTERN> -70.49287 -20.32051 0.00000 0.00000 0.00000 MINI CONSTR> 41.46301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -10.03722 0.02534 0.30714 0.00021 MINI INTERN> 5.18697 18.86017 0.00000 11.13646 4.16937 MINI EXTERN> -70.52456 -20.33583 0.00000 0.00000 0.00000 MINI CONSTR> 41.47021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -10.06815 0.03093 0.32052 0.00022 MINI INTERN> 5.19097 18.84911 0.00000 11.12916 4.16725 MINI EXTERN> -70.53748 -20.34448 0.00000 0.00000 0.00000 MINI CONSTR> 41.47731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -10.09555 0.02741 0.37127 0.00023 MINI INTERN> 5.18928 18.84495 0.00000 11.12226 4.16687 MINI EXTERN> -70.54954 -20.35404 0.00000 0.00000 0.00000 MINI CONSTR> 41.48467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -10.12254 0.02698 0.34094 0.00024 MINI INTERN> 5.19795 18.83064 0.00000 11.11572 4.16441 MINI EXTERN> -70.56148 -20.36013 0.00000 0.00000 0.00000 MINI CONSTR> 41.49035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -10.15059 0.02805 0.36250 0.00025 MINI INTERN> 5.20453 18.82035 0.00000 11.10811 4.16308 MINI EXTERN> -70.57477 -20.36926 0.00000 0.00000 0.00000 MINI CONSTR> 41.49737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -10.17578 0.02519 0.42130 0.00025 MINI INTERN> 5.22419 18.80717 0.00000 11.09827 4.16337 MINI EXTERN> -70.59261 -20.38087 0.00000 0.00000 0.00000 MINI CONSTR> 41.50471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -10.20141 0.02564 0.38715 0.00026 MINI INTERN> 5.21323 18.80185 0.00000 11.09500 4.16023 MINI EXTERN> -70.59746 -20.38452 0.00000 0.00000 0.00000 MINI CONSTR> 41.51025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -10.23984 0.03842 0.11457 0.00011 MINI INTERN> 5.05459 18.84707 0.00000 11.11622 4.14353 MINI EXTERN> -70.55020 -20.36681 0.00000 0.00000 0.00000 MINI CONSTR> 41.51577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -10.25163 0.01180 0.41908 0.00028 MINI INTERN> 5.21477 18.78819 0.00000 11.08252 4.15760 MINI EXTERN> -70.61800 -20.40036 0.00000 0.00000 0.00000 MINI CONSTR> 41.52365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -10.29039 0.03876 0.13079 0.00012 MINI INTERN> 5.04146 18.83656 0.00000 11.10697 4.13862 MINI EXTERN> -70.56455 -20.37817 0.00000 0.00000 0.00000 MINI CONSTR> 41.52872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -10.31179 0.02140 0.10955 0.00013 MINI INTERN> 5.05346 18.82619 0.00000 11.09962 4.13875 MINI EXTERN> -70.57760 -20.38656 0.00000 0.00000 0.00000 MINI CONSTR> 41.53435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -10.33475 0.02296 0.11220 0.00013 MINI INTERN> 5.04918 18.82076 0.00000 11.09503 4.13665 MINI EXTERN> -70.58466 -20.39215 0.00000 0.00000 0.00000 MINI CONSTR> 41.54045 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9168 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -10.35743 0.02269 0.10817 0.00014 MINI INTERN> 5.05069 18.81345 0.00000 11.08933 4.13532 MINI EXTERN> -70.59396 -20.39887 0.00000 0.00000 0.00000 MINI CONSTR> 41.54661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -10.38130 0.02386 0.18454 0.00014 MINI INTERN> 5.01357 18.81983 0.00000 11.09037 4.12941 MINI EXTERN> -70.58896 -20.39900 0.00000 0.00000 0.00000 MINI CONSTR> 41.55349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9167 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -10.40340 0.02210 0.13530 0.00015 MINI INTERN> 5.03252 18.80670 0.00000 11.08141 4.13046 MINI EXTERN> -70.60494 -20.40906 0.00000 0.00000 0.00000 MINI CONSTR> 41.55952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -10.42455 0.02115 0.15712 0.00015 MINI INTERN> 5.02390 18.80279 0.00000 11.07805 4.12750 MINI EXTERN> -70.60924 -20.41312 0.00000 0.00000 0.00000 MINI CONSTR> 41.56557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9167 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -10.44468 0.02013 0.17567 0.00016 MINI INTERN> 5.01214 18.80210 0.00000 11.07488 4.12544 MINI EXTERN> -70.61314 -20.41774 0.00000 0.00000 0.00000 MINI CONSTR> 41.57165 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -10.46237 0.01769 0.24012 0.00016 MINI INTERN> 4.98989 18.80488 0.00000 11.07452 4.12126 MINI EXTERN> -70.61137 -20.41893 0.00000 0.00000 0.00000 MINI CONSTR> 41.57738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9167 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -10.48286 0.02049 0.24810 0.00017 MINI INTERN> 4.98833 18.80075 0.00000 11.06912 4.12064 MINI EXTERN> -70.61969 -20.42586 0.00000 0.00000 0.00000 MINI CONSTR> 41.58384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -10.50090 0.01804 0.27770 0.00018 MINI INTERN> 4.98633 18.79369 0.00000 11.06571 4.11724 MINI EXTERN> -70.62415 -20.42913 0.00000 0.00000 0.00000 MINI CONSTR> 41.58941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9166 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -10.51882 0.01792 0.28393 0.00018 MINI INTERN> 4.97069 18.79619 0.00000 11.06327 4.11564 MINI EXTERN> -70.62644 -20.43348 0.00000 0.00000 0.00000 MINI CONSTR> 41.59531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -10.53706 0.01824 0.27010 0.00019 MINI INTERN> 4.97551 18.78832 0.00000 11.05794 4.11462 MINI EXTERN> -70.63475 -20.43952 0.00000 0.00000 0.00000 MINI CONSTR> 41.60084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9166 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -10.55542 0.01837 0.29239 0.00020 MINI INTERN> 4.96829 18.78677 0.00000 11.05394 4.11326 MINI EXTERN> -70.64017 -20.44477 0.00000 0.00000 0.00000 MINI CONSTR> 41.60725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -10.57136 0.01594 0.33916 0.00020 MINI INTERN> 4.96869 18.77919 0.00000 11.05049 4.10983 MINI EXTERN> -70.64455 -20.44789 0.00000 0.00000 0.00000 MINI CONSTR> 41.61288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9166 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -10.58845 0.01709 0.31081 0.00021 MINI INTERN> 4.96443 18.77668 0.00000 11.04649 4.10921 MINI EXTERN> -70.65006 -20.45345 0.00000 0.00000 0.00000 MINI CONSTR> 41.61824 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -10.61280 0.02435 0.09906 0.00009 MINI INTERN> 5.07065 18.72851 0.00000 11.02144 4.11908 MINI EXTERN> -70.69769 -20.47940 0.00000 0.00000 0.00000 MINI CONSTR> 41.62461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9165 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -10.62062 0.00782 0.33524 0.00023 MINI INTERN> 4.95258 18.77401 0.00000 11.03904 4.10714 MINI EXTERN> -70.65976 -20.46362 0.00000 0.00000 0.00000 MINI CONSTR> 41.62998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -10.63511 0.01449 0.38711 0.00023 MINI INTERN> 4.99147 18.74946 0.00000 11.02984 4.10570 MINI EXTERN> -70.67578 -20.47114 0.00000 0.00000 0.00000 MINI CONSTR> 41.63533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9164 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -10.66142 0.02630 0.10957 0.00010 MINI INTERN> 5.07672 18.71125 0.00000 11.00724 4.11597 MINI EXTERN> -70.71805 -20.49633 0.00000 0.00000 0.00000 MINI CONSTR> 41.64179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -10.67565 0.01423 0.08743 0.00011 MINI INTERN> 5.06062 18.71297 0.00000 11.00627 4.11352 MINI EXTERN> -70.71766 -20.49811 0.00000 0.00000 0.00000 MINI CONSTR> 41.64674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9164 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -10.69164 0.01599 0.08954 0.00011 MINI INTERN> 5.06318 18.70683 0.00000 11.00147 4.11239 MINI EXTERN> -70.72440 -20.50374 0.00000 0.00000 0.00000 MINI CONSTR> 41.65263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -10.70722 0.01558 0.14772 0.00011 MINI INTERN> 5.09291 18.69118 0.00000 10.99154 4.11393 MINI EXTERN> -70.74099 -20.51496 0.00000 0.00000 0.00000 MINI CONSTR> 41.65917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9163 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -10.72066 0.01344 0.08503 0.00012 MINI INTERN> 5.05942 18.69928 0.00000 10.99404 4.10986 MINI EXTERN> -70.73394 -20.51291 0.00000 0.00000 0.00000 MINI CONSTR> 41.66358 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 -10.72066 0.01344 0.08503 0.00014 STPD INTERN> 5.05942 18.69928 0.00000 10.99404 4.10986 STPD EXTERN> -70.73394 -20.51291 0.00000 0.00000 0.00000 STPD CONSTR> 41.66358 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 9163 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9163 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 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 -10.72066 0.01344 0.08503 0.00000 MINI INTERN> 5.05942 18.69928 0.00000 10.99404 4.10986 MINI EXTERN> -70.73394 -20.51291 0.00000 0.00000 0.00000 MINI CONSTR> 41.66358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -11.39481 0.67415 0.03041 0.00117 MINI INTERN> 5.02426 18.34655 0.00000 10.65187 4.01490 MINI EXTERN> -71.34271 -20.92443 0.00000 0.00000 0.00000 MINI CONSTR> 42.83476 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -11.39758 0.00277 0.05249 0.00319 MINI INTERN> 4.98551 18.29080 0.00000 10.63401 3.99159 MINI EXTERN> -71.03720 -20.98534 0.00000 0.00000 0.00000 MINI CONSTR> 42.72304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -11.40200 0.00442 0.04781 0.00583 MINI INTERN> 4.97577 18.35082 0.00000 10.62832 3.99929 MINI EXTERN> -70.92321 -20.94194 0.00000 0.00000 0.00000 MINI CONSTR> 42.50895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -11.40508 0.00308 0.03398 0.00445 MINI INTERN> 5.02075 18.42458 0.00000 10.64080 4.01268 MINI EXTERN> -70.92824 -20.94857 0.00000 0.00000 0.00000 MINI CONSTR> 42.37293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -11.40620 0.00112 0.02126 0.00217 MINI INTERN> 5.02598 18.43600 0.00000 10.65607 4.02629 MINI EXTERN> -70.95474 -20.93267 0.00000 0.00000 0.00000 MINI CONSTR> 42.33687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -11.40688 0.00068 0.02050 0.00199 MINI INTERN> 5.02574 18.45744 0.00000 10.66927 4.02137 MINI EXTERN> -70.97440 -20.93256 0.00000 0.00000 0.00000 MINI CONSTR> 42.32626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -11.40734 0.00045 0.01737 0.00171 MINI INTERN> 5.02529 18.45954 0.00000 10.67179 4.02975 MINI EXTERN> -70.97749 -20.94191 0.00000 0.00000 0.00000 MINI CONSTR> 42.32568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -11.40778 0.00044 0.01607 0.00187 MINI INTERN> 5.02651 18.47230 0.00000 10.67730 4.02886 MINI EXTERN> -70.98916 -20.95862 0.00000 0.00000 0.00000 MINI CONSTR> 42.33502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -11.40813 0.00034 0.01525 0.00167 MINI INTERN> 5.02519 18.45767 0.00000 10.67933 4.02525 MINI EXTERN> -70.97792 -20.96652 0.00000 0.00000 0.00000 MINI CONSTR> 42.34888 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -11.40838 0.00025 0.01091 0.00131 MINI INTERN> 5.02234 18.44882 0.00000 10.68022 4.02551 MINI EXTERN> -70.97593 -20.97145 0.00000 0.00000 0.00000 MINI CONSTR> 42.36211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -11.40854 0.00017 0.01046 0.00104 MINI INTERN> 5.02231 18.45424 0.00000 10.67831 4.02330 MINI EXTERN> -70.98298 -20.97573 0.00000 0.00000 0.00000 MINI CONSTR> 42.37200 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> 56 -11.40858 0.00003 0.00949 0.02000 CONJ INTERN> 5.02265 18.45028 0.00000 10.67855 4.02368 CONJ EXTERN> -70.97956 -20.97805 0.00000 0.00000 0.00000 CONJ CONSTR> 42.37388 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 ASP 1 HT1 ) 0.73944 ( PROT ASP 1 HT2 ) 0.73944 ( PROT ASP 1 N ) 0.92430 ( PROT ASP 1 HT3 ) 0.73944 ( PROT ASP 1 CA ) 0.92430 ( PROT ASP 1 CB ) 0.73944 ( PROT ASP 1 CG ) 0.73944 ( PROT ASP 1 OD1 ) 0.73944 ( PROT ASP 1 OD2 ) 0.73944 ( PROT ASP 1 C ) 0.92430 ( PROT ASP 1 O ) 0.92430 ( PROT TYR 2 N ) 0.92430 ( PROT TYR 2 H ) 0.73944 ( PROT TYR 2 CA ) 0.92430 ( PROT TYR 2 CB ) 0.73944 ( PROT TYR 2 CG ) 0.73944 ( PROT TYR 2 CD1 ) 0.73944 ( PROT TYR 2 CE1 ) 0.73944 ( PROT TYR 2 CD2 ) 0.73944 ( PROT TYR 2 CE2 ) 0.73944 ( PROT TYR 2 CZ ) 0.73944 ( PROT TYR 2 OH ) 0.73944 ( PROT TYR 2 HH ) 0.73944 ( PROT TYR 2 C ) 0.92430 ( PROT TYR 2 O ) 0.92430 ( PROT ALA 3 N ) 0.92430 ( PROT ALA 3 H ) 0.73944 ( PROT ALA 3 CA ) 0.92430 ( PROT ALA 3 CB ) 0.73944 ( PROT ALA 3 C ) 0.92430 ( PROT ALA 3 O ) 0.92430 ( PROT PHE 4 N ) 0.92430 ( PROT PHE 4 H ) 0.73944 ( PROT PHE 4 CA ) 0.92430 ( PROT PHE 4 CB ) 0.73944 ( PROT PHE 4 CG ) 0.73944 ( PROT PHE 4 CD1 ) 0.73944 ( PROT PHE 4 CD2 ) 0.73944 ( PROT PHE 4 CE1 ) 0.73944 ( PROT PHE 4 CE2 ) 0.73944 ( PROT PHE 4 CZ ) 0.73944 ( PROT PHE 4 C ) 0.92430 ( PROT PHE 4 O ) 0.92430 ( PROT ILE 5 N ) 0.92430 ( PROT ILE 5 H ) 0.73944 ( PROT ILE 5 CA ) 0.92430 ( PROT ILE 5 CB ) 0.73944 ( PROT ILE 5 CG2 ) 0.73944 ( PROT ILE 5 CG1 ) 0.73944 ( PROT ILE 5 CD ) 0.73944 ( PROT ILE 5 C ) 0.92430 ( PROT ILE 5 O ) 0.92430 ( PROT ALA 6 N ) 0.92430 ( PROT ALA 6 H ) 0.73944 ( PROT ALA 6 CA ) 0.92430 ( PROT ALA 6 CB ) 0.73944 ( PROT ALA 6 C ) 0.92430 ( PROT ALA 6 O ) 0.92430 ( PROT SER 7 N ) 0.92430 ( PROT SER 7 H ) 0.73944 ( PROT SER 7 CA ) 0.92430 ( PROT SER 7 CB ) 0.73944 ( PROT SER 7 OG ) 0.73944 ( PROT SER 7 HG ) 0.73944 ( PROT SER 7 C ) 0.92430 ( PROT SER 7 O ) 0.92430 ( PROT LEU 8 N ) 0.92430 ( PROT LEU 8 H ) 0.73944 ( PROT LEU 8 CA ) 0.92430 ( PROT LEU 8 CB ) 0.73944 ( PROT LEU 8 CG ) 0.73944 ( PROT LEU 8 CD1 ) 0.73944 ( PROT LEU 8 CD2 ) 0.73944 ( PROT LEU 8 C ) 0.92430 ( PROT LEU 8 O ) 0.92430 ( PROT VAL 9 N ) 0.92430 ( PROT VAL 9 H ) 0.73944 ( PROT VAL 9 CA ) 0.92430 ( PROT VAL 9 CB ) 0.73944 ( PROT VAL 9 CG1 ) 0.73944 ( PROT VAL 9 CG2 ) 0.73944 ( PROT VAL 9 C ) 0.92430 ( PROT VAL 9 O ) 0.92430 ( PROT VAL 10 N ) 0.92430 ( PROT VAL 10 H ) 0.73944 ( PROT VAL 10 CA ) 0.92430 ( PROT VAL 10 CB ) 0.73944 ( PROT VAL 10 CG1 ) 0.73944 ( PROT VAL 10 CG2 ) 0.73944 ( PROT VAL 10 C ) 0.92430 ( PROT VAL 10 O ) 0.92430 ( PROT ILE 11 N ) 0.92430 ( PROT ILE 11 H ) 0.73944 ( PROT ILE 11 CA ) 0.92430 ( PROT ILE 11 CB ) 0.73944 ( PROT ILE 11 CG2 ) 0.73944 ( PROT ILE 11 CG1 ) 0.73944 ( PROT ILE 11 CD ) 0.73944 ( PROT ILE 11 C ) 0.92430 ( PROT ILE 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 ASP 13 N ) 0.92430 ( PROT ASP 13 H ) 0.73944 ( PROT ASP 13 CA ) 0.92430 ( PROT ASP 13 CB ) 0.73944 ( PROT ASP 13 CG ) 0.73944 ( PROT ASP 13 OD1 ) 0.73944 ( PROT ASP 13 OD2 ) 0.73944 ( PROT ASP 13 C ) 0.92430 ( PROT ASP 13 O ) 0.92430 ( PROT ASP 14 N ) 0.92430 ( PROT ASP 14 H ) 0.73944 ( PROT ASP 14 CA ) 0.92430 ( PROT ASP 14 CB ) 0.73944 ( PROT ASP 14 CG ) 0.73944 ( PROT ASP 14 OD1 ) 0.73944 ( PROT ASP 14 OD2 ) 0.73944 ( PROT ASP 14 C ) 0.92430 ( PROT ASP 14 O ) 0.92430 ( PROT VAL 15 N ) 0.92430 ( PROT VAL 15 H ) 0.73944 ( PROT VAL 15 CA ) 0.92430 ( PROT VAL 15 CB ) 0.73944 ( PROT VAL 15 CG1 ) 0.73944 ( PROT VAL 15 CG2 ) 0.73944 ( PROT VAL 15 C ) 0.92430 ( PROT VAL 15 O ) 0.92430 ( PROT ASN 16 N ) 0.92430 ( PROT ASN 16 H ) 0.73944 ( PROT ASN 16 CA ) 0.92430 ( PROT ASN 16 CB ) 0.73944 ( PROT ASN 16 CG ) 0.73944 ( PROT ASN 16 OD1 ) 0.73944 ( PROT ASN 16 ND2 ) 0.73944 ( PROT ASN 16 HD21 ) 0.73944 ( PROT ASN 16 HD22 ) 0.73944 ( PROT ASN 16 C ) 0.92430 ( PROT ASN 16 O ) 0.92430 ( PROT ARG 17 N ) 0.92430 ( PROT ARG 17 H ) 0.73944 ( PROT ARG 17 CA ) 0.92430 ( PROT ARG 17 CB ) 0.73944 ( PROT ARG 17 CG ) 0.73944 ( PROT ARG 17 CD ) 0.73944 ( PROT ARG 17 NE ) 0.73944 ( PROT ARG 17 HE ) 0.73944 ( PROT ARG 17 CZ ) 0.73944 ( PROT ARG 17 NH1 ) 0.73944 ( PROT ARG 17 HH11 ) 0.73944 ( PROT ARG 17 HH12 ) 0.73944 ( PROT ARG 17 NH2 ) 0.73944 ( PROT ARG 17 HH21 ) 0.73944 ( PROT ARG 17 HH22 ) 0.73944 ( PROT ARG 17 C ) 0.92430 ( PROT ARG 17 OT1 ) 0.73944 ( PROT ARG 17 OT2 ) 0.73944 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.95975 3.70942 -6.79790 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00407 0.00191 -0.00410 ROTATION MATRIX 1.000000 -0.000204 -0.000343 0.000205 1.000000 0.000845 0.000342 -0.000845 1.000000 AXIS OF ROTATION IS 0.904371 0.366358 -0.218850 ANGLE IS 0.05 TOTAL SQUARE DIFF IS 32.9775 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.448422 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4484" Parameter: A <- "0.4484" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.78398 3.79073 -6.99024 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.01180 0.00098 0.01300 ROTATION MATRIX 0.999414 0.022709 0.025630 -0.021887 0.999251 -0.031909 -0.026336 0.031330 0.999162 AXIS OF ROTATION IS -0.678443 -0.557507 0.478436 ANGLE IS 2.67 CENTER OF ROTATION 7.612572 3.859264 -7.139137 SHIFT IS 0.013683 TOTAL SQUARE DIFF IS 2.3058 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.368287 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4484" RDCMND substituted energy or value "?RMS" to " 0.3683" Parameter: A <- "0.4484 0.3683" 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 0.4484 0.3683 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 42.37" Parameter: H <- "42.37" 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 -53.78246 42.37388 0.66926 ENER INTERN> 5.02265 18.45028 0.00000 10.67855 4.02368 ENER EXTERN> -70.97956 -20.97805 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 " -53.78" Parameter: B <- "-53.78" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -20.98" Parameter: C <- "-20.98" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -70.98" Parameter: C <- " -91.96" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -91.96" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.02" Parameter: D <- "5.02" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 18.45" Parameter: D <- " 23.47" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.68" Parameter: D <- " 34.15" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.02" Parameter: D <- " 38.17" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 38.17" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 7800 ENER= -53.78 GRMS= 0.67 ELEC= -20.98 VDW= -70.98 RDTITL> *EXTERNAL= -91.96 INTERNAL= 38.17 USER= 0.00 HARM= 42.37 RDTITL> *BOND= 5.02 ANGL= 18.45 DIHE= 10.68 IMPR= 4.02 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9163 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9156 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 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 -22.06923 -31.71322 0.28506 0.02000 MINI INTERN> 5.02265 18.45028 0.00000 10.67855 4.02368 MINI EXTERN> -70.97956 -20.97805 0.00000 0.00000 0.00000 MINI CONSTR> 31.71322 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1.27652 -23.34575 17.42814 0.00864 MINI INTERN> 30.32886 16.66038 0.00000 11.36468 3.60310 MINI EXTERN> -74.03005 -19.51465 0.00000 0.00000 0.00000 MINI CONSTR> 32.86420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9154 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -23.18431 24.46083 1.19048 0.00156 MINI INTERN> 5.49570 17.94537 0.00000 11.03688 4.01295 MINI EXTERN> -74.34528 -20.28950 0.00000 0.00000 0.00000 MINI CONSTR> 32.95955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -23.32206 0.13775 1.00219 0.00067 MINI INTERN> 5.03478 18.57605 0.00000 10.95885 4.09576 MINI EXTERN> -74.54336 -20.44573 0.00000 0.00000 0.00000 MINI CONSTR> 33.00159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9154 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -23.49514 0.17308 0.30282 0.00029 MINI INTERN> 5.13043 18.26226 0.00000 10.97266 4.02358 MINI EXTERN> -74.49611 -20.41184 0.00000 0.00000 0.00000 MINI CONSTR> 33.02387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -23.58259 0.08745 0.27656 0.00030 MINI INTERN> 5.10079 18.26101 0.00000 10.95376 4.02060 MINI EXTERN> -74.51309 -20.45981 0.00000 0.00000 0.00000 MINI CONSTR> 33.05415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9154 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -23.66037 0.07777 0.33121 0.00031 MINI INTERN> 5.09472 18.23059 0.00000 10.93991 4.01057 MINI EXTERN> -74.53094 -20.49009 0.00000 0.00000 0.00000 MINI CONSTR> 33.08488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -23.72986 0.06949 0.45402 0.00032 MINI INTERN> 5.13907 18.15640 0.00000 10.92966 3.99728 MINI EXTERN> -74.56368 -20.50470 0.00000 0.00000 0.00000 MINI CONSTR> 33.11611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9154 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -23.80217 0.07231 0.46508 0.00034 MINI INTERN> 5.14970 18.11288 0.00000 10.91908 3.98666 MINI EXTERN> -74.59627 -20.52073 0.00000 0.00000 0.00000 MINI CONSTR> 33.14652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -23.86921 0.06704 0.56285 0.00035 MINI INTERN> 5.12306 18.11551 0.00000 10.90759 3.98697 MINI EXTERN> -74.63720 -20.54423 0.00000 0.00000 0.00000 MINI CONSTR> 33.17910 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9153 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -23.94270 0.07348 0.47913 0.00036 MINI INTERN> 5.13923 18.06140 0.00000 10.89869 3.97440 MINI EXTERN> -74.67327 -20.55128 0.00000 0.00000 0.00000 MINI CONSTR> 33.20815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -24.00877 0.06607 0.62296 0.00037 MINI INTERN> 5.15863 18.04188 0.00000 10.88365 3.97555 MINI EXTERN> -74.73227 -20.57929 0.00000 0.00000 0.00000 MINI CONSTR> 33.24309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9153 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -24.07818 0.06941 0.54735 0.00039 MINI INTERN> 5.16707 18.00165 0.00000 10.87456 3.96714 MINI EXTERN> -74.77192 -20.58765 0.00000 0.00000 0.00000 MINI CONSTR> 33.27098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -24.16116 0.08298 0.18872 0.00017 MINI INTERN> 4.98938 18.13247 0.00000 10.86913 3.99029 MINI EXTERN> -74.80916 -20.63159 0.00000 0.00000 0.00000 MINI CONSTR> 33.29834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9152 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -24.19649 0.03533 0.66285 0.00042 MINI INTERN> 5.12709 17.99163 0.00000 10.85751 3.96312 MINI EXTERN> -74.85416 -20.61033 0.00000 0.00000 0.00000 MINI CONSTR> 33.32864 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -24.26074 0.06425 0.63140 0.00043 MINI INTERN> 5.18518 17.90928 0.00000 10.84659 3.94691 MINI EXTERN> -74.89901 -20.60520 0.00000 0.00000 0.00000 MINI CONSTR> 33.35551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9151 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -24.30740 0.04666 0.78811 0.00045 MINI INTERN> 5.07938 18.00120 0.00000 10.84197 3.96320 MINI EXTERN> -74.93339 -20.64364 0.00000 0.00000 0.00000 MINI CONSTR> 33.38389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -24.40573 0.09833 0.22579 0.00019 MINI INTERN> 4.96212 18.06073 0.00000 10.83516 3.97511 MINI EXTERN> -74.97242 -20.67424 0.00000 0.00000 0.00000 MINI CONSTR> 33.40781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9151 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -24.45489 0.04916 0.17410 0.00020 MINI INTERN> 4.98209 18.01884 0.00000 10.82780 3.96708 MINI EXTERN> -75.00426 -20.67490 0.00000 0.00000 0.00000 MINI CONSTR> 33.42845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -24.51229 0.05739 0.30023 0.00021 MINI INTERN> 4.96922 18.01486 0.00000 10.81843 3.96667 MINI EXTERN> -75.04773 -20.68948 0.00000 0.00000 0.00000 MINI CONSTR> 33.45574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9150 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -24.56325 0.05097 0.23022 0.00022 MINI INTERN> 4.98193 17.97788 0.00000 10.81127 3.95917 MINI EXTERN> -75.07875 -20.69124 0.00000 0.00000 0.00000 MINI CONSTR> 33.47649 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -24.61377 0.05052 0.24538 0.00022 MINI INTERN> 4.98532 17.95431 0.00000 10.80356 3.95443 MINI EXTERN> -75.11254 -20.69739 0.00000 0.00000 0.00000 MINI CONSTR> 33.49854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9150 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -24.65441 0.04063 0.41154 0.00023 MINI INTERN> 4.99932 17.93065 0.00000 10.79553 3.94994 MINI EXTERN> -75.14620 -20.70302 0.00000 0.00000 0.00000 MINI CONSTR> 33.51936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -24.70247 0.04806 0.41418 0.00024 MINI INTERN> 4.99870 17.91114 0.00000 10.78839 3.94572 MINI EXTERN> -75.17717 -20.70924 0.00000 0.00000 0.00000 MINI CONSTR> 33.53998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9150 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -24.75065 0.04818 0.42843 0.00025 MINI INTERN> 4.99805 17.89257 0.00000 10.78092 3.94180 MINI EXTERN> -75.20884 -20.71601 0.00000 0.00000 0.00000 MINI CONSTR> 33.56085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -24.79741 0.04676 0.46091 0.00026 MINI INTERN> 4.99889 17.87411 0.00000 10.77331 3.93793 MINI EXTERN> -75.24041 -20.72276 0.00000 0.00000 0.00000 MINI CONSTR> 33.58152 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9149 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -24.84035 0.04294 0.51385 0.00027 MINI INTERN> 5.00143 17.85632 0.00000 10.76601 3.93407 MINI EXTERN> -75.27026 -20.72905 0.00000 0.00000 0.00000 MINI CONSTR> 33.60113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -24.88145 0.04110 0.48640 0.00028 MINI INTERN> 4.99443 17.84405 0.00000 10.76037 3.93099 MINI EXTERN> -75.29355 -20.73520 0.00000 0.00000 0.00000 MINI CONSTR> 33.61745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9148 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -24.92538 0.04392 0.50553 0.00029 MINI INTERN> 4.99361 17.82792 0.00000 10.75313 3.92756 MINI EXTERN> -75.32197 -20.74190 0.00000 0.00000 0.00000 MINI CONSTR> 33.63627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -24.96971 0.04433 0.51210 0.00030 MINI INTERN> 4.99142 17.81238 0.00000 10.74593 3.92423 MINI EXTERN> -75.34976 -20.74870 0.00000 0.00000 0.00000 MINI CONSTR> 33.65478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9148 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -25.02640 0.05669 0.16440 0.00013 MINI INTERN> 4.95118 17.81594 0.00000 10.74137 3.92392 MINI EXTERN> -75.36922 -20.76102 0.00000 0.00000 0.00000 MINI CONSTR> 33.67144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -25.04516 0.01877 0.56505 0.00032 MINI INTERN> 4.99135 17.78449 0.00000 10.73298 3.91803 MINI EXTERN> -75.39843 -20.76093 0.00000 0.00000 0.00000 MINI CONSTR> 33.68735 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9146 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -25.08595 0.04078 0.58419 0.00033 MINI INTERN> 4.99071 17.76970 0.00000 10.72592 3.91484 MINI EXTERN> -75.42433 -20.76734 0.00000 0.00000 0.00000 MINI CONSTR> 33.70456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -25.12569 0.03974 0.61345 0.00034 MINI INTERN> 4.99132 17.75471 0.00000 10.71874 3.91160 MINI EXTERN> -75.45012 -20.77359 0.00000 0.00000 0.00000 MINI CONSTR> 33.72164 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9145 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -25.19070 0.06501 0.19815 0.00015 MINI INTERN> 4.94092 17.76190 0.00000 10.71389 3.91219 MINI EXTERN> -75.46855 -20.78945 0.00000 0.00000 0.00000 MINI CONSTR> 33.73839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -25.22425 0.03355 0.14713 0.00015 MINI INTERN> 4.94128 17.74778 0.00000 10.70811 3.90939 MINI EXTERN> -75.48845 -20.79348 0.00000 0.00000 0.00000 MINI CONSTR> 33.75113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9145 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -25.26397 0.03972 0.14581 0.00016 MINI INTERN> 4.93908 17.73442 0.00000 10.70125 3.90648 MINI EXTERN> -75.51182 -20.80028 0.00000 0.00000 0.00000 MINI CONSTR> 33.76690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -25.30371 0.03974 0.14694 0.00017 MINI INTERN> 4.93668 17.72134 0.00000 10.69434 3.90360 MINI EXTERN> -75.53499 -20.80730 0.00000 0.00000 0.00000 MINI CONSTR> 33.78263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9144 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -25.34253 0.03882 0.28604 0.00017 MINI INTERN> 4.93171 17.71405 0.00000 10.68726 3.90134 MINI EXTERN> -75.55840 -20.81840 0.00000 0.00000 0.00000 MINI CONSTR> 33.79993 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -25.37963 0.03710 0.18583 0.00018 MINI INTERN> 4.93104 17.69823 0.00000 10.68092 3.89831 MINI EXTERN> -75.57877 -20.82224 0.00000 0.00000 0.00000 MINI CONSTR> 33.81288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9144 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -25.41716 0.03752 0.18656 0.00019 MINI INTERN> 4.92916 17.68580 0.00000 10.67417 3.89555 MINI EXTERN> -75.60016 -20.82917 0.00000 0.00000 0.00000 MINI CONSTR> 33.82750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -25.45430 0.03714 0.20251 0.00019 MINI INTERN> 4.92706 17.67412 0.00000 10.66740 3.89287 MINI EXTERN> -75.62124 -20.83662 0.00000 0.00000 0.00000 MINI CONSTR> 33.84210 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9144 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -25.48378 0.02949 0.35350 0.00020 MINI INTERN> 4.92576 17.66867 0.00000 10.66130 3.89101 MINI EXTERN> -75.63975 -20.84690 0.00000 0.00000 0.00000 MINI CONSTR> 33.85613 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -25.51851 0.03473 0.35806 0.00021 MINI INTERN> 4.92417 17.65746 0.00000 10.65488 3.88842 MINI EXTERN> -75.65912 -20.85388 0.00000 0.00000 0.00000 MINI CONSTR> 33.86956 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9144 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -25.55307 0.03456 0.37421 0.00021 MINI INTERN> 4.92296 17.64668 0.00000 10.64836 3.88582 MINI EXTERN> -75.67838 -20.86165 0.00000 0.00000 0.00000 MINI CONSTR> 33.88313 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -25.58617 0.03310 0.40677 0.00022 MINI INTERN> 4.92234 17.63678 0.00000 10.64192 3.88331 MINI EXTERN> -75.69702 -20.86998 0.00000 0.00000 0.00000 MINI CONSTR> 33.89650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9144 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -25.61743 0.03126 0.39388 0.00023 MINI INTERN> 4.92061 17.62605 0.00000 10.63608 3.88100 MINI EXTERN> -75.71401 -20.87522 0.00000 0.00000 0.00000 MINI CONSTR> 33.90805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -25.64889 0.03146 0.41655 0.00024 MINI INTERN> 4.92015 17.61627 0.00000 10.62988 3.87861 MINI EXTERN> -75.73141 -20.88288 0.00000 0.00000 0.00000 MINI CONSTR> 33.92048 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9144 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -25.68119 0.03230 0.43240 0.00025 MINI INTERN> 4.91986 17.60623 0.00000 10.62353 3.87610 MINI EXTERN> -75.74879 -20.89116 0.00000 0.00000 0.00000 MINI CONSTR> 33.93304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -25.71384 0.03266 0.43789 0.00026 MINI INTERN> 4.91944 17.59590 0.00000 10.61715 3.87355 MINI EXTERN> -75.76595 -20.89935 0.00000 0.00000 0.00000 MINI CONSTR> 33.94542 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9144 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -25.75573 0.04189 0.13984 0.00011 MINI INTERN> 4.91547 17.56797 0.00000 10.61001 3.86996 MINI EXTERN> -75.78925 -20.88573 0.00000 0.00000 0.00000 MINI CONSTR> 33.95583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -25.76994 0.01420 0.48226 0.00028 MINI INTERN> 4.91890 17.57822 0.00000 10.60566 3.86927 MINI EXTERN> -75.79693 -20.91264 0.00000 0.00000 0.00000 MINI CONSTR> 33.96758 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9143 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -25.80015 0.03021 0.49677 0.00029 MINI INTERN> 4.91932 17.56901 0.00000 10.59954 3.86679 MINI EXTERN> -75.81254 -20.92148 0.00000 0.00000 0.00000 MINI CONSTR> 33.97921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -25.82991 0.02976 0.51806 0.00030 MINI INTERN> 4.92073 17.56020 0.00000 10.59337 3.86423 MINI EXTERN> -75.82766 -20.93161 0.00000 0.00000 0.00000 MINI CONSTR> 33.99084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9143 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -25.87821 0.04830 0.15982 0.00013 MINI INTERN> 4.90955 17.52627 0.00000 10.58527 3.86093 MINI EXTERN> -75.85597 -20.90584 0.00000 0.00000 0.00000 MINI CONSTR> 34.00157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -25.90369 0.02548 0.12701 0.00013 MINI INTERN> 4.90726 17.52091 0.00000 10.58047 3.85913 MINI EXTERN> -75.86725 -20.91494 0.00000 0.00000 0.00000 MINI CONSTR> 34.01072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9143 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -25.93326 0.02957 0.12535 0.00014 MINI INTERN> 4.90564 17.51150 0.00000 10.57444 3.85695 MINI EXTERN> -75.88265 -20.92077 0.00000 0.00000 0.00000 MINI CONSTR> 34.02162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -25.96329 0.03003 0.12491 0.00014 MINI INTERN> 4.90405 17.50178 0.00000 10.56825 3.85474 MINI EXTERN> -75.89833 -20.92645 0.00000 0.00000 0.00000 MINI CONSTR> 34.03267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9143 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -25.99315 0.02987 0.12674 0.00015 MINI INTERN> 4.90250 17.49183 0.00000 10.56203 3.85254 MINI EXTERN> -75.91407 -20.93165 0.00000 0.00000 0.00000 MINI CONSTR> 34.04366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -26.02192 0.02876 0.24573 0.00015 MINI INTERN> 4.90195 17.47489 0.00000 10.55485 3.85056 MINI EXTERN> -75.93628 -20.92350 0.00000 0.00000 0.00000 MINI CONSTR> 34.05561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9142 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -26.05024 0.02832 0.15751 0.00016 MINI INTERN> 4.89964 17.47077 0.00000 10.54976 3.84841 MINI EXTERN> -75.94576 -20.93793 0.00000 0.00000 0.00000 MINI CONSTR> 34.06487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -26.07899 0.02875 0.15643 0.00016 MINI INTERN> 4.89855 17.46126 0.00000 10.54369 3.84628 MINI EXTERN> -75.96044 -20.94370 0.00000 0.00000 0.00000 MINI CONSTR> 34.07536 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9142 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -26.10773 0.02874 0.16514 0.00017 MINI INTERN> 4.89776 17.45092 0.00000 10.53750 3.84414 MINI EXTERN> -75.97566 -20.94832 0.00000 0.00000 0.00000 MINI CONSTR> 34.08594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -26.13517 0.02744 0.19672 0.00018 MINI INTERN> 4.89744 17.43947 0.00000 10.53134 3.84212 MINI EXTERN> -75.99150 -20.95033 0.00000 0.00000 0.00000 MINI CONSTR> 34.09629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9142 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -26.15617 0.02100 0.30365 0.00018 MINI INTERN> 4.89921 17.42587 0.00000 10.52569 3.84062 MINI EXTERN> -76.00848 -20.94467 0.00000 0.00000 0.00000 MINI CONSTR> 34.10559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -26.18278 0.02660 0.31492 0.00019 MINI INTERN> 4.89968 17.41525 0.00000 10.51983 3.83853 MINI EXTERN> -76.02266 -20.94886 0.00000 0.00000 0.00000 MINI CONSTR> 34.11545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9142 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -26.20855 0.02577 0.33941 0.00020 MINI INTERN> 4.90109 17.40368 0.00000 10.51394 3.83647 MINI EXTERN> -76.03727 -20.95173 0.00000 0.00000 0.00000 MINI CONSTR> 34.12527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -26.23246 0.02391 0.37415 0.00020 MINI INTERN> 4.90283 17.39234 0.00000 10.50824 3.83453 MINI EXTERN> -76.05157 -20.95351 0.00000 0.00000 0.00000 MINI CONSTR> 34.13468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9142 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -26.25555 0.02310 0.35288 0.00021 MINI INTERN> 4.90016 17.38725 0.00000 10.50338 3.83285 MINI EXTERN> -76.06148 -20.96030 0.00000 0.00000 0.00000 MINI CONSTR> 34.14259 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -26.28021 0.02465 0.36815 0.00022 MINI INTERN> 4.90184 17.37628 0.00000 10.49769 3.83085 MINI EXTERN> -76.07492 -20.96380 0.00000 0.00000 0.00000 MINI CONSTR> 34.15184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9141 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -26.30523 0.02502 0.37564 0.00023 MINI INTERN> 4.90343 17.36551 0.00000 10.49198 3.82880 MINI EXTERN> -76.08800 -20.96800 0.00000 0.00000 0.00000 MINI CONSTR> 34.16104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -26.33772 0.03249 0.11797 0.00010 MINI INTERN> 4.88582 17.38876 0.00000 10.48698 3.82635 MINI EXTERN> -76.08292 -21.01165 0.00000 0.00000 0.00000 MINI CONSTR> 34.16895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9141 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -26.34892 0.01120 0.41087 0.00025 MINI INTERN> 4.90552 17.34705 0.00000 10.48156 3.82529 MINI EXTERN> -76.11200 -20.97401 0.00000 0.00000 0.00000 MINI CONSTR> 34.17767 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -26.37199 0.02307 0.42324 0.00025 MINI INTERN> 4.90753 17.33651 0.00000 10.47612 3.82335 MINI EXTERN> -76.12432 -20.97749 0.00000 0.00000 0.00000 MINI CONSTR> 34.18631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9141 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -26.39478 0.02279 0.44160 0.00026 MINI INTERN> 4.91067 17.32488 0.00000 10.47060 3.82136 MINI EXTERN> -76.13695 -20.98035 0.00000 0.00000 0.00000 MINI CONSTR> 34.19501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -26.43171 0.03692 0.13572 0.00011 MINI INTERN> 4.87958 17.36397 0.00000 10.46516 3.81915 MINI EXTERN> -76.12691 -21.03582 0.00000 0.00000 0.00000 MINI CONSTR> 34.20317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9140 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -26.45112 0.01942 0.10875 0.00012 MINI INTERN> 4.88066 17.35249 0.00000 10.46073 3.81770 MINI EXTERN> -76.13820 -21.03454 0.00000 0.00000 0.00000 MINI CONSTR> 34.21003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -26.47358 0.02246 0.10738 0.00012 MINI INTERN> 4.87963 17.34540 0.00000 10.45544 3.81597 MINI EXTERN> -76.14901 -21.03919 0.00000 0.00000 0.00000 MINI CONSTR> 34.21818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9139 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -26.49632 0.02274 0.10729 0.00013 MINI INTERN> 4.87838 17.33868 0.00000 10.45005 3.81422 MINI EXTERN> -76.15976 -21.04434 0.00000 0.00000 0.00000 MINI CONSTR> 34.22645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -26.51876 0.02244 0.10987 0.00013 MINI INTERN> 4.87677 17.33288 0.00000 10.44469 3.81249 MINI EXTERN> -76.17005 -21.05018 0.00000 0.00000 0.00000 MINI CONSTR> 34.23464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9138 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -26.53972 0.02096 0.21863 0.00014 MINI INTERN> 4.86861 17.34382 0.00000 10.43906 3.81080 MINI EXTERN> -76.17510 -21.07029 0.00000 0.00000 0.00000 MINI CONSTR> 34.24339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -26.56128 0.02156 0.13583 0.00014 MINI INTERN> 4.87194 17.32564 0.00000 10.43437 3.80922 MINI EXTERN> -76.18844 -21.06436 0.00000 0.00000 0.00000 MINI CONSTR> 34.25036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9138 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -26.58289 0.02161 0.13913 0.00015 MINI INTERN> 4.87049 17.31955 0.00000 10.42915 3.80756 MINI EXTERN> -76.19864 -21.06929 0.00000 0.00000 0.00000 MINI CONSTR> 34.25829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -26.60409 0.02120 0.15511 0.00015 MINI INTERN> 4.86831 17.31533 0.00000 10.42396 3.80593 MINI EXTERN> -76.20821 -21.07562 0.00000 0.00000 0.00000 MINI CONSTR> 34.26621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9137 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -26.62089 0.01680 0.25715 0.00016 MINI INTERN> 4.86208 17.32347 0.00000 10.41923 3.80457 MINI EXTERN> -76.21354 -21.09039 0.00000 0.00000 0.00000 MINI CONSTR> 34.27370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -26.64116 0.02027 0.25953 0.00016 MINI INTERN> 4.86149 17.31622 0.00000 10.41436 3.80300 MINI EXTERN> -76.22378 -21.09364 0.00000 0.00000 0.00000 MINI CONSTR> 34.28119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9137 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -26.66147 0.02031 0.26893 0.00017 MINI INTERN> 4.86152 17.30832 0.00000 10.40946 3.80140 MINI EXTERN> -76.23444 -21.09656 0.00000 0.00000 0.00000 MINI CONSTR> 34.28883 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -26.68120 0.01973 0.28889 0.00018 MINI INTERN> 4.86213 17.30059 0.00000 10.40458 3.79980 MINI EXTERN> -76.24501 -21.09976 0.00000 0.00000 0.00000 MINI CONSTR> 34.29646 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9137 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -26.69965 0.01844 0.31736 0.00018 MINI INTERN> 4.86250 17.29463 0.00000 10.39984 3.79826 MINI EXTERN> -76.25461 -21.10408 0.00000 0.00000 0.00000 MINI CONSTR> 34.30382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -26.71744 0.01780 0.29990 0.00019 MINI INTERN> 4.86191 17.28796 0.00000 10.39547 3.79686 MINI EXTERN> -76.26266 -21.10704 0.00000 0.00000 0.00000 MINI CONSTR> 34.31006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9137 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -26.73633 0.01889 0.31331 0.00020 MINI INTERN> 4.86299 17.27978 0.00000 10.39072 3.79530 MINI EXTERN> -76.27271 -21.10972 0.00000 0.00000 0.00000 MINI CONSTR> 34.31732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -26.75555 0.01922 0.32132 0.00020 MINI INTERN> 4.86407 17.27129 0.00000 10.38585 3.79372 MINI EXTERN> -76.28273 -21.11235 0.00000 0.00000 0.00000 MINI CONSTR> 34.32461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9137 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -26.78074 0.02519 0.09929 0.00009 MINI INTERN> 4.86961 17.24520 0.00000 10.37922 3.79168 MINI EXTERN> -76.29372 -21.10370 0.00000 0.00000 0.00000 MINI CONSTR> 34.33097 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -26.78979 0.00905 0.35025 0.00022 MINI INTERN> 4.86416 17.26008 0.00000 10.37683 3.79087 MINI EXTERN> -76.29962 -21.12011 0.00000 0.00000 0.00000 MINI CONSTR> 34.33800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9137 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -26.80746 0.01768 0.35998 0.00023 MINI INTERN> 4.86446 17.25374 0.00000 10.37212 3.78943 MINI EXTERN> -76.30830 -21.12374 0.00000 0.00000 0.00000 MINI CONSTR> 34.34484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -26.82503 0.01756 0.37450 0.00023 MINI INTERN> 4.86475 17.24768 0.00000 10.36731 3.78801 MINI EXTERN> -76.31701 -21.12754 0.00000 0.00000 0.00000 MINI CONSTR> 34.35177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9136 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -26.85335 0.02832 0.11236 0.00010 MINI INTERN> 4.86747 17.22196 0.00000 10.36001 3.78568 MINI EXTERN> -76.32684 -21.11995 0.00000 0.00000 0.00000 MINI CONSTR> 34.35833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -26.86843 0.01508 0.09343 0.00011 MINI INTERN> 4.86555 17.21893 0.00000 10.35631 3.78458 MINI EXTERN> -76.33340 -21.12432 0.00000 0.00000 0.00000 MINI CONSTR> 34.36391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9136 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -26.88563 0.01720 0.09200 0.00011 MINI INTERN> 4.86477 17.21379 0.00000 10.35175 3.78317 MINI EXTERN> -76.34114 -21.12842 0.00000 0.00000 0.00000 MINI CONSTR> 34.37043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -26.90313 0.01750 0.09152 0.00011 MINI INTERN> 4.86410 17.20843 0.00000 10.34706 3.78173 MINI EXTERN> -76.34902 -21.13253 0.00000 0.00000 0.00000 MINI CONSTR> 34.37710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9136 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -26.92054 0.01741 0.09287 0.00012 MINI INTERN> 4.86362 17.20288 0.00000 10.34234 3.78027 MINI EXTERN> -76.35687 -21.13654 0.00000 0.00000 0.00000 MINI CONSTR> 34.38376 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 -26.92054 0.01741 0.09287 0.00014 STPD INTERN> 4.86362 17.20288 0.00000 10.34234 3.78027 STPD EXTERN> -76.35687 -21.13654 0.00000 0.00000 0.00000 STPD CONSTR> 34.38376 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 9136 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9136 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 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 -26.92054 0.01741 0.09287 0.00000 MINI INTERN> 4.86362 17.20288 0.00000 10.34234 3.78027 MINI EXTERN> -76.35687 -21.13654 0.00000 0.00000 0.00000 MINI CONSTR> 34.38376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -28.05125 1.13071 0.07371 0.00576 MINI INTERN> 4.81272 16.62748 0.00000 9.80408 3.63298 MINI EXTERN> -77.65157 -21.52921 0.00000 0.00000 0.00000 MINI CONSTR> 36.25226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -28.06311 0.01186 0.10307 0.00640 MINI INTERN> 4.75393 16.48522 0.00000 9.76049 3.58941 MINI EXTERN> -77.10141 -21.64198 0.00000 0.00000 0.00000 MINI CONSTR> 36.09122 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -28.08227 0.01915 0.11092 0.01219 MINI INTERN> 4.72373 16.56660 0.00000 9.73157 3.59126 MINI EXTERN> -76.88699 -21.54349 0.00000 0.00000 0.00000 MINI CONSTR> 35.73506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -28.09827 0.01601 0.08103 0.01124 MINI INTERN> 4.78761 16.70864 0.00000 9.73622 3.60308 MINI EXTERN> -76.82189 -21.54394 0.00000 0.00000 0.00000 MINI CONSTR> 35.43202 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -28.10493 0.00666 0.05302 0.00623 MINI INTERN> 4.79734 16.72217 0.00000 9.76571 3.62647 MINI EXTERN> -76.85560 -21.47753 0.00000 0.00000 0.00000 MINI CONSTR> 35.31651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -28.10862 0.00369 0.04318 0.00424 MINI INTERN> 4.79851 16.76419 0.00000 9.79226 3.61399 MINI EXTERN> -76.87605 -21.46084 0.00000 0.00000 0.00000 MINI CONSTR> 35.25932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -28.11080 0.00218 0.03702 0.00332 MINI INTERN> 4.80309 16.77845 0.00000 9.79793 3.62804 MINI EXTERN> -76.87489 -21.47401 0.00000 0.00000 0.00000 MINI CONSTR> 35.23058 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -28.11271 0.00191 0.03066 0.00307 MINI INTERN> 4.81389 16.81463 0.00000 9.81601 3.63154 MINI EXTERN> -76.90345 -21.50383 0.00000 0.00000 0.00000 MINI CONSTR> 35.21849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -28.11402 0.00131 0.02955 0.00334 MINI INTERN> 4.81141 16.80116 0.00000 9.82625 3.63440 MINI EXTERN> -76.89692 -21.51059 0.00000 0.00000 0.00000 MINI CONSTR> 35.22026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -28.11507 0.00105 0.02184 0.00227 MINI INTERN> 4.80365 16.79146 0.00000 9.83585 3.63593 MINI EXTERN> -76.88849 -21.51964 0.00000 0.00000 0.00000 MINI CONSTR> 35.22617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -28.11576 0.00069 0.01960 0.00225 MINI INTERN> 4.80288 16.79763 0.00000 9.83913 3.62940 MINI EXTERN> -76.89532 -21.52187 0.00000 0.00000 0.00000 MINI CONSTR> 35.23239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -28.11635 0.00058 0.02002 0.00247 MINI INTERN> 4.80106 16.78196 0.00000 9.84319 3.62789 MINI EXTERN> -76.88924 -21.51902 0.00000 0.00000 0.00000 MINI CONSTR> 35.23781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -28.11682 0.00047 0.01784 0.00187 MINI INTERN> 4.80006 16.77624 0.00000 9.84264 3.62591 MINI EXTERN> -76.89622 -21.50840 0.00000 0.00000 0.00000 MINI CONSTR> 35.24296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -28.11733 0.00051 0.01744 0.00255 MINI INTERN> 4.80627 16.77357 0.00000 9.83803 3.62738 MINI EXTERN> -76.90390 -21.50792 0.00000 0.00000 0.00000 MINI CONSTR> 35.24925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -28.11776 0.00043 0.01677 0.00237 MINI INTERN> 4.80365 16.76087 0.00000 9.84083 3.62389 MINI EXTERN> -76.88625 -21.51500 0.00000 0.00000 0.00000 MINI CONSTR> 35.25425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -28.11815 0.00039 0.01381 0.00236 MINI INTERN> 4.80031 16.76444 0.00000 9.84390 3.62650 MINI EXTERN> -76.89472 -21.51961 0.00000 0.00000 0.00000 MINI CONSTR> 35.26104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -28.11843 0.00028 0.01244 0.00172 MINI INTERN> 4.80160 16.76295 0.00000 9.84533 3.62843 MINI EXTERN> -76.89607 -21.52974 0.00000 0.00000 0.00000 MINI CONSTR> 35.26907 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> 88 -28.11855 0.00012 0.00993 0.02000 CONJ INTERN> 4.80072 16.76261 0.00000 9.84460 3.62889 CONJ EXTERN> -76.90004 -21.52947 0.00000 0.00000 0.00000 CONJ CONSTR> 35.27414 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 ASP 1 HT1 ) 0.48064 ( PROT ASP 1 HT2 ) 0.48064 ( PROT ASP 1 N ) 0.60080 ( PROT ASP 1 HT3 ) 0.48064 ( PROT ASP 1 CA ) 0.60080 ( PROT ASP 1 CB ) 0.48064 ( PROT ASP 1 CG ) 0.48064 ( PROT ASP 1 OD1 ) 0.48064 ( PROT ASP 1 OD2 ) 0.48064 ( PROT ASP 1 C ) 0.60080 ( PROT ASP 1 O ) 0.60080 ( PROT TYR 2 N ) 0.60080 ( PROT TYR 2 H ) 0.48064 ( PROT TYR 2 CA ) 0.60080 ( PROT TYR 2 CB ) 0.48064 ( PROT TYR 2 CG ) 0.48064 ( PROT TYR 2 CD1 ) 0.48064 ( PROT TYR 2 CE1 ) 0.48064 ( PROT TYR 2 CD2 ) 0.48064 ( PROT TYR 2 CE2 ) 0.48064 ( PROT TYR 2 CZ ) 0.48064 ( PROT TYR 2 OH ) 0.48064 ( PROT TYR 2 HH ) 0.48064 ( PROT TYR 2 C ) 0.60080 ( PROT TYR 2 O ) 0.60080 ( PROT ALA 3 N ) 0.60080 ( PROT ALA 3 H ) 0.48064 ( PROT ALA 3 CA ) 0.60080 ( PROT ALA 3 CB ) 0.48064 ( PROT ALA 3 C ) 0.60080 ( PROT ALA 3 O ) 0.60080 ( PROT PHE 4 N ) 0.60080 ( PROT PHE 4 H ) 0.48064 ( PROT PHE 4 CA ) 0.60080 ( PROT PHE 4 CB ) 0.48064 ( PROT PHE 4 CG ) 0.48064 ( PROT PHE 4 CD1 ) 0.48064 ( PROT PHE 4 CD2 ) 0.48064 ( PROT PHE 4 CE1 ) 0.48064 ( PROT PHE 4 CE2 ) 0.48064 ( PROT PHE 4 CZ ) 0.48064 ( PROT PHE 4 C ) 0.60080 ( PROT PHE 4 O ) 0.60080 ( PROT ILE 5 N ) 0.60080 ( PROT ILE 5 H ) 0.48064 ( PROT ILE 5 CA ) 0.60080 ( PROT ILE 5 CB ) 0.48064 ( PROT ILE 5 CG2 ) 0.48064 ( PROT ILE 5 CG1 ) 0.48064 ( PROT ILE 5 CD ) 0.48064 ( PROT ILE 5 C ) 0.60080 ( PROT ILE 5 O ) 0.60080 ( PROT ALA 6 N ) 0.60080 ( PROT ALA 6 H ) 0.48064 ( PROT ALA 6 CA ) 0.60080 ( PROT ALA 6 CB ) 0.48064 ( PROT ALA 6 C ) 0.60080 ( PROT ALA 6 O ) 0.60080 ( PROT SER 7 N ) 0.60080 ( PROT SER 7 H ) 0.48064 ( PROT SER 7 CA ) 0.60080 ( PROT SER 7 CB ) 0.48064 ( PROT SER 7 OG ) 0.48064 ( PROT SER 7 HG ) 0.48064 ( PROT SER 7 C ) 0.60080 ( PROT SER 7 O ) 0.60080 ( PROT LEU 8 N ) 0.60080 ( PROT LEU 8 H ) 0.48064 ( PROT LEU 8 CA ) 0.60080 ( PROT LEU 8 CB ) 0.48064 ( PROT LEU 8 CG ) 0.48064 ( PROT LEU 8 CD1 ) 0.48064 ( PROT LEU 8 CD2 ) 0.48064 ( PROT LEU 8 C ) 0.60080 ( PROT LEU 8 O ) 0.60080 ( PROT VAL 9 N ) 0.60080 ( PROT VAL 9 H ) 0.48064 ( PROT VAL 9 CA ) 0.60080 ( PROT VAL 9 CB ) 0.48064 ( PROT VAL 9 CG1 ) 0.48064 ( PROT VAL 9 CG2 ) 0.48064 ( PROT VAL 9 C ) 0.60080 ( PROT VAL 9 O ) 0.60080 ( PROT VAL 10 N ) 0.60080 ( PROT VAL 10 H ) 0.48064 ( PROT VAL 10 CA ) 0.60080 ( PROT VAL 10 CB ) 0.48064 ( PROT VAL 10 CG1 ) 0.48064 ( PROT VAL 10 CG2 ) 0.48064 ( PROT VAL 10 C ) 0.60080 ( PROT VAL 10 O ) 0.60080 ( PROT ILE 11 N ) 0.60080 ( PROT ILE 11 H ) 0.48064 ( PROT ILE 11 CA ) 0.60080 ( PROT ILE 11 CB ) 0.48064 ( PROT ILE 11 CG2 ) 0.48064 ( PROT ILE 11 CG1 ) 0.48064 ( PROT ILE 11 CD ) 0.48064 ( PROT ILE 11 C ) 0.60080 ( PROT ILE 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 ASP 13 N ) 0.60080 ( PROT ASP 13 H ) 0.48064 ( PROT ASP 13 CA ) 0.60080 ( PROT ASP 13 CB ) 0.48064 ( PROT ASP 13 CG ) 0.48064 ( PROT ASP 13 OD1 ) 0.48064 ( PROT ASP 13 OD2 ) 0.48064 ( PROT ASP 13 C ) 0.60080 ( PROT ASP 13 O ) 0.60080 ( PROT ASP 14 N ) 0.60080 ( PROT ASP 14 H ) 0.48064 ( PROT ASP 14 CA ) 0.60080 ( PROT ASP 14 CB ) 0.48064 ( PROT ASP 14 CG ) 0.48064 ( PROT ASP 14 OD1 ) 0.48064 ( PROT ASP 14 OD2 ) 0.48064 ( PROT ASP 14 C ) 0.60080 ( PROT ASP 14 O ) 0.60080 ( PROT VAL 15 N ) 0.60080 ( PROT VAL 15 H ) 0.48064 ( PROT VAL 15 CA ) 0.60080 ( PROT VAL 15 CB ) 0.48064 ( PROT VAL 15 CG1 ) 0.48064 ( PROT VAL 15 CG2 ) 0.48064 ( PROT VAL 15 C ) 0.60080 ( PROT VAL 15 O ) 0.60080 ( PROT ASN 16 N ) 0.60080 ( PROT ASN 16 H ) 0.48064 ( PROT ASN 16 CA ) 0.60080 ( PROT ASN 16 CB ) 0.48064 ( PROT ASN 16 CG ) 0.48064 ( PROT ASN 16 OD1 ) 0.48064 ( PROT ASN 16 ND2 ) 0.48064 ( PROT ASN 16 HD21 ) 0.48064 ( PROT ASN 16 HD22 ) 0.48064 ( PROT ASN 16 C ) 0.60080 ( PROT ASN 16 O ) 0.60080 ( PROT ARG 17 N ) 0.60080 ( PROT ARG 17 H ) 0.48064 ( PROT ARG 17 CA ) 0.60080 ( PROT ARG 17 CB ) 0.48064 ( PROT ARG 17 CG ) 0.48064 ( PROT ARG 17 CD ) 0.48064 ( PROT ARG 17 NE ) 0.48064 ( PROT ARG 17 HE ) 0.48064 ( PROT ARG 17 CZ ) 0.48064 ( PROT ARG 17 NH1 ) 0.48064 ( PROT ARG 17 HH11 ) 0.48064 ( PROT ARG 17 HH12 ) 0.48064 ( PROT ARG 17 NH2 ) 0.48064 ( PROT ARG 17 HH21 ) 0.48064 ( PROT ARG 17 HH22 ) 0.48064 ( PROT ARG 17 C ) 0.60080 ( PROT ARG 17 OT1 ) 0.48064 ( PROT ARG 17 OT2 ) 0.48064 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.95942 3.70860 -6.79757 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00440 0.00273 -0.00443 ROTATION MATRIX 1.000000 -0.000180 -0.000313 0.000180 1.000000 0.000900 0.000313 -0.000900 1.000000 AXIS OF ROTATION IS 0.928211 0.322520 -0.185485 ANGLE IS 0.06 TOTAL SQUARE DIFF IS 42.4423 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.508718 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.5087" Parameter: A <- "0.5087" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.78530 3.79292 -6.99435 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.01312 -0.00121 0.01711 ROTATION MATRIX 0.999369 0.023765 0.026384 -0.022867 0.999167 -0.033800 -0.027165 0.033175 0.999080 AXIS OF ROTATION IS -0.686151 -0.548599 0.477740 ANGLE IS 2.80 CENTER OF ROTATION 7.598341 3.904363 -7.116215 SHIFT IS 0.017845 TOTAL SQUARE DIFF IS 3.3085 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.441152 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.5087" RDCMND substituted energy or value "?RMS" to " 0.4412" Parameter: A <- "0.5087 0.4412" 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 0.5087 0.4412 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 " 35.27" Parameter: H <- "35.27" 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 -63.39269 35.27414 0.49155 ENER INTERN> 4.80072 16.76261 0.00000 9.84460 3.62889 ENER EXTERN> -76.90004 -21.52947 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 " -63.39" Parameter: B <- "-63.39" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -21.53" Parameter: C <- "-21.53" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -76.90" Parameter: C <- " -98.43" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -98.43" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.80" Parameter: D <- "4.80" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 16.76" Parameter: D <- " 21.56" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 9.84" Parameter: D <- " 31.40" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.63" Parameter: D <- " 35.03" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 35.03" 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= -63.39 GRMS= 0.49 ELEC= -21.53 VDW= -76.90 RDTITL> *EXTERNAL= -98.43 INTERNAL= 35.03 USER= 0.00 HARM= 35.27 RDTITL> *BOND= 4.80 ANGL= 16.76 DIHE= 9.84 IMPR= 3.63 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= -63.39 GRMS= 0.49 ELEC= -21.53 VDW= -76.90 RDTITL> *EXTERNAL= -98.43 INTERNAL= 35.03 USER= 0.00 HARM= 35.27 RDTITL> *BOND= 4.80 ANGL= 16.76 DIHE= 9.84 IMPR= 3.63 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= -63.39 GRMS= 0.49 ELEC= -21.53 VDW= -76.90 RDTITL> *EXTERNAL= -98.43 INTERNAL= 35.03 USER= 0.00 HARM= 35.27 RDTITL> *BOND= 4.80 ANGL= 16.76 DIHE= 9.84 IMPR= 3.63 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 8400 0.5087 0.4412 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "8400" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9136 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9122 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 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 -37.50797 -25.88472 0.20479 0.02000 MINI INTERN> 4.80072 16.76261 0.00000 9.84460 3.62889 MINI EXTERN> -76.90004 -21.52947 0.00000 0.00000 0.00000 MINI CONSTR> 25.88472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -12.67995 -24.82802 17.99415 0.00864 MINI INTERN> 30.04596 16.48583 0.00000 10.52792 3.30133 MINI EXTERN> -79.32433 -20.53967 0.00000 0.00000 0.00000 MINI CONSTR> 26.82301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9118 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -38.18154 25.50159 1.39338 0.00156 MINI INTERN> 5.27510 16.47536 0.00000 10.13154 3.61687 MINI EXTERN> -79.63316 -20.92503 0.00000 0.00000 0.00000 MINI CONSTR> 26.87777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -38.22199 0.04046 1.44578 0.00067 MINI INTERN> 4.87721 17.05023 0.00000 10.02466 3.69814 MINI EXTERN> -79.72426 -21.05186 0.00000 0.00000 0.00000 MINI CONSTR> 26.90387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9116 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -38.41938 0.19739 0.46492 0.00029 MINI INTERN> 4.93384 16.69681 0.00000 10.07222 3.62890 MINI EXTERN> -79.65138 -21.01237 0.00000 0.00000 0.00000 MINI CONSTR> 26.91261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -38.46457 0.04518 0.43874 0.00030 MINI INTERN> 4.88749 16.70965 0.00000 10.05793 3.62676 MINI EXTERN> -79.61706 -21.06019 0.00000 0.00000 0.00000 MINI CONSTR> 26.93085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9116 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -38.50954 0.04498 0.45167 0.00031 MINI INTERN> 4.82212 16.73943 0.00000 10.04415 3.62376 MINI EXTERN> -79.58181 -21.11022 0.00000 0.00000 0.00000 MINI CONSTR> 26.95302 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -38.55442 0.04488 0.46153 0.00032 MINI INTERN> 4.84128 16.68756 0.00000 10.03499 3.61647 MINI EXTERN> -79.58302 -21.12822 0.00000 0.00000 0.00000 MINI CONSTR> 26.97651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9116 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -38.61119 0.05677 0.14958 0.00014 MINI INTERN> 4.85653 16.68882 0.00000 10.00616 3.63532 MINI EXTERN> -79.63860 -21.15882 0.00000 0.00000 0.00000 MINI CONSTR> 26.99939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -38.63221 0.02102 0.51516 0.00035 MINI INTERN> 4.78828 16.68554 0.00000 10.01772 3.61006 MINI EXTERN> -79.58632 -21.17122 0.00000 0.00000 0.00000 MINI CONSTR> 27.02373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9116 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -38.66876 0.03655 0.58119 0.00036 MINI INTERN> 4.82105 16.64507 0.00000 10.00823 3.60617 MINI EXTERN> -79.61488 -21.18233 0.00000 0.00000 0.00000 MINI CONSTR> 27.04794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -38.73154 0.06278 0.16332 0.00016 MINI INTERN> 4.84626 16.63871 0.00000 9.97885 3.62847 MINI EXTERN> -79.69293 -21.20304 0.00000 0.00000 0.00000 MINI CONSTR> 27.07214 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9115 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -38.76683 0.03529 0.13649 0.00016 MINI INTERN> 4.83656 16.62235 0.00000 9.97451 3.62312 MINI EXTERN> -79.70714 -21.21002 0.00000 0.00000 0.00000 MINI CONSTR> 27.09381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -38.77743 0.01061 0.63347 0.00040 MINI INTERN> 4.75163 16.63905 0.00000 9.99141 3.59873 MINI EXTERN> -79.66463 -21.21469 0.00000 0.00000 0.00000 MINI CONSTR> 27.12106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9114 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -38.84434 0.06691 0.19974 0.00017 MINI INTERN> 4.84950 16.58798 0.00000 9.95486 3.62303 MINI EXTERN> -79.77587 -21.22899 0.00000 0.00000 0.00000 MINI CONSTR> 27.14515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -38.87726 0.03292 0.13274 0.00018 MINI INTERN> 4.82738 16.57594 0.00000 9.95463 3.61522 MINI EXTERN> -79.78408 -21.23139 0.00000 0.00000 0.00000 MINI CONSTR> 27.16505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9113 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -38.91615 0.03889 0.14117 0.00019 MINI INTERN> 4.82917 16.55883 0.00000 9.94674 3.61353 MINI EXTERN> -79.81716 -21.23793 0.00000 0.00000 0.00000 MINI CONSTR> 27.19065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -38.95065 0.03450 0.27340 0.00019 MINI INTERN> 4.86422 16.53820 0.00000 9.93122 3.61969 MINI EXTERN> -79.87270 -21.24823 0.00000 0.00000 0.00000 MINI CONSTR> 27.21695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9113 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -38.98815 0.03750 0.16889 0.00020 MINI INTERN> 4.83334 16.52850 0.00000 9.93186 3.61114 MINI EXTERN> -79.88184 -21.24972 0.00000 0.00000 0.00000 MINI CONSTR> 27.23857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -39.02512 0.03697 0.18089 0.00021 MINI INTERN> 4.82916 16.51690 0.00000 9.92515 3.60975 MINI EXTERN> -79.91335 -21.25592 0.00000 0.00000 0.00000 MINI CONSTR> 27.26319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9113 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -39.05502 0.02990 0.31961 0.00022 MINI INTERN> 4.85824 16.49988 0.00000 9.91220 3.61441 MINI EXTERN> -79.96179 -21.26503 0.00000 0.00000 0.00000 MINI CONSTR> 27.28708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -39.08577 0.03075 0.34273 0.00022 MINI INTERN> 4.86161 16.48774 0.00000 9.90517 3.61407 MINI EXTERN> -79.99239 -21.27034 0.00000 0.00000 0.00000 MINI CONSTR> 27.30837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9113 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -39.11601 0.03024 0.35835 0.00023 MINI INTERN> 4.88218 16.46099 0.00000 9.89734 3.61166 MINI EXTERN> -80.02507 -21.27177 0.00000 0.00000 0.00000 MINI CONSTR> 27.32866 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -39.14609 0.03008 0.38104 0.00024 MINI INTERN> 4.88436 16.44894 0.00000 9.89085 3.61073 MINI EXTERN> -80.05394 -21.27642 0.00000 0.00000 0.00000 MINI CONSTR> 27.34939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9112 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -39.17631 0.03021 0.35831 0.00025 MINI INTERN> 4.89234 16.42614 0.00000 9.88568 3.60650 MINI EXTERN> -80.07841 -21.27641 0.00000 0.00000 0.00000 MINI CONSTR> 27.36785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -39.20664 0.03033 0.39081 0.00026 MINI INTERN> 4.87669 16.42477 0.00000 9.88148 3.60504 MINI EXTERN> -80.10097 -21.28246 0.00000 0.00000 0.00000 MINI CONSTR> 27.38881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9111 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -39.24525 0.03861 0.12431 0.00011 MINI INTERN> 4.78702 16.42722 0.00000 9.89596 3.58428 MINI EXTERN> -80.07275 -21.27218 0.00000 0.00000 0.00000 MINI CONSTR> 27.40519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -39.26233 0.01708 0.41505 0.00028 MINI INTERN> 4.90353 16.38601 0.00000 9.86721 3.60207 MINI EXTERN> -80.15952 -21.28755 0.00000 0.00000 0.00000 MINI CONSTR> 27.42592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9111 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -39.30313 0.04080 0.13236 0.00012 MINI INTERN> 4.77586 16.40769 0.00000 9.88702 3.57926 MINI EXTERN> -80.11757 -21.27776 0.00000 0.00000 0.00000 MINI CONSTR> 27.44237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -39.31551 0.01239 0.45260 0.00030 MINI INTERN> 4.92694 16.34401 0.00000 9.85561 3.59547 MINI EXTERN> -80.20981 -21.28879 0.00000 0.00000 0.00000 MINI CONSTR> 27.46105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9108 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -39.35889 0.04338 0.14154 0.00013 MINI INTERN> 4.76547 16.38899 0.00000 9.87815 3.57448 MINI EXTERN> -80.16073 -21.28313 0.00000 0.00000 0.00000 MINI CONSTR> 27.47788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -39.36831 0.00941 0.46886 0.00032 MINI INTERN> 4.94777 16.31353 0.00000 9.84145 3.59415 MINI EXTERN> -80.26540 -21.29563 0.00000 0.00000 0.00000 MINI CONSTR> 27.49583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9107 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -39.41530 0.04699 0.15155 0.00014 MINI INTERN> 4.75663 16.36918 0.00000 9.86876 3.56963 MINI EXTERN> -80.20468 -21.28829 0.00000 0.00000 0.00000 MINI CONSTR> 27.51348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -39.43973 0.02444 0.11577 0.00014 MINI INTERN> 4.77405 16.35315 0.00000 9.86043 3.57093 MINI EXTERN> -80.23401 -21.29251 0.00000 0.00000 0.00000 MINI CONSTR> 27.52824 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9106 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -39.46727 0.02754 0.12168 0.00015 MINI INTERN> 4.76600 16.34539 0.00000 9.85633 3.56824 MINI EXTERN> -80.25363 -21.29500 0.00000 0.00000 0.00000 MINI CONSTR> 27.54540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -39.49428 0.02701 0.20508 0.00015 MINI INTERN> 4.72991 16.34774 0.00000 9.85787 3.56082 MINI EXTERN> -80.25947 -21.29458 0.00000 0.00000 0.00000 MINI CONSTR> 27.56343 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9104 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -39.52090 0.02662 0.14320 0.00016 MINI INTERN> 4.75091 16.32966 0.00000 9.84823 3.56275 MINI EXTERN> -80.29165 -21.29949 0.00000 0.00000 0.00000 MINI CONSTR> 27.57869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -39.54706 0.02616 0.16500 0.00017 MINI INTERN> 4.74564 16.31977 0.00000 9.84424 3.55949 MINI EXTERN> -80.31019 -21.30090 0.00000 0.00000 0.00000 MINI CONSTR> 27.59489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9104 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -39.57085 0.02379 0.19544 0.00017 MINI INTERN> 4.72726 16.31878 0.00000 9.84237 3.55606 MINI EXTERN> -80.32247 -21.30277 0.00000 0.00000 0.00000 MINI CONSTR> 27.60992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -39.59246 0.02161 0.26265 0.00018 MINI INTERN> 4.69829 16.32397 0.00000 9.84254 3.55160 MINI EXTERN> -80.32935 -21.30415 0.00000 0.00000 0.00000 MINI CONSTR> 27.62464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9103 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -39.61997 0.02751 0.17686 0.00019 MINI INTERN> 4.73368 16.29645 0.00000 9.83088 3.55373 MINI EXTERN> -80.36555 -21.30825 0.00000 0.00000 0.00000 MINI CONSTR> 27.63909 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -39.63956 0.01959 0.27889 0.00019 MINI INTERN> 4.69320 16.30664 0.00000 9.83367 3.54741 MINI EXTERN> -80.36547 -21.30817 0.00000 0.00000 0.00000 MINI CONSTR> 27.65316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9102 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -39.66199 0.02243 0.32301 0.00020 MINI INTERN> 4.68152 16.30678 0.00000 9.82968 3.54636 MINI EXTERN> -80.38215 -21.31213 0.00000 0.00000 0.00000 MINI CONSTR> 27.66795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -39.68481 0.02282 0.29598 0.00021 MINI INTERN> 4.67744 16.29750 0.00000 9.82613 3.54356 MINI EXTERN> -80.39692 -21.31308 0.00000 0.00000 0.00000 MINI CONSTR> 27.68056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9102 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -39.70913 0.02432 0.32779 0.00021 MINI INTERN> 4.66610 16.29231 0.00000 9.82288 3.54012 MINI EXTERN> -80.41237 -21.31403 0.00000 0.00000 0.00000 MINI CONSTR> 27.69586 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -39.73192 0.02280 0.31739 0.00022 MINI INTERN> 4.66734 16.28303 0.00000 9.81760 3.53899 MINI EXTERN> -80.43115 -21.31655 0.00000 0.00000 0.00000 MINI CONSTR> 27.70881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9101 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -39.75532 0.02340 0.33097 0.00023 MINI INTERN> 4.66175 16.27601 0.00000 9.81343 3.53654 MINI EXTERN> -80.44783 -21.31805 0.00000 0.00000 0.00000 MINI CONSTR> 27.72284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -39.77903 0.02371 0.33728 0.00024 MINI INTERN> 4.65901 16.26739 0.00000 9.80873 3.53434 MINI EXTERN> -80.46567 -21.31954 0.00000 0.00000 0.00000 MINI CONSTR> 27.73672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9101 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -39.80948 0.03045 0.10938 0.00010 MINI INTERN> 4.77974 16.20367 0.00000 9.78077 3.54721 MINI EXTERN> -80.53755 -21.33257 0.00000 0.00000 0.00000 MINI CONSTR> 27.74925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -39.82037 0.01089 0.37462 0.00026 MINI INTERN> 4.64299 16.25907 0.00000 9.80189 3.52977 MINI EXTERN> -80.49298 -21.32280 0.00000 0.00000 0.00000 MINI CONSTR> 27.76170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9101 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -39.84285 0.02248 0.38479 0.00027 MINI INTERN> 4.63928 16.25153 0.00000 9.79746 3.52753 MINI EXTERN> -80.50949 -21.32401 0.00000 0.00000 0.00000 MINI CONSTR> 27.77484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -39.86520 0.02235 0.40220 0.00028 MINI INTERN> 4.64090 16.23954 0.00000 9.79268 3.52468 MINI EXTERN> -80.52696 -21.32401 0.00000 0.00000 0.00000 MINI CONSTR> 27.78796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9101 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -39.90022 0.03503 0.12976 0.00012 MINI INTERN> 4.78732 16.16640 0.00000 9.75830 3.54221 MINI EXTERN> -80.61153 -21.34376 0.00000 0.00000 0.00000 MINI CONSTR> 27.80083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -39.91883 0.01860 0.10072 0.00012 MINI INTERN> 4.76866 16.16577 0.00000 9.75770 3.53831 MINI EXTERN> -80.61708 -21.34294 0.00000 0.00000 0.00000 MINI CONSTR> 27.81075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9101 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -39.93985 0.02103 0.10498 0.00013 MINI INTERN> 4.77193 16.15662 0.00000 9.75209 3.53731 MINI EXTERN> -80.63461 -21.34566 0.00000 0.00000 0.00000 MINI CONSTR> 27.82247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -39.96062 0.02076 0.17387 0.00013 MINI INTERN> 4.80706 16.13458 0.00000 9.74060 3.53967 MINI EXTERN> -80.66563 -21.35186 0.00000 0.00000 0.00000 MINI CONSTR> 27.83496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9101 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -39.97867 0.01805 0.10086 0.00014 MINI INTERN> 4.76711 16.14358 0.00000 9.74380 3.53395 MINI EXTERN> -80.66183 -21.34902 0.00000 0.00000 0.00000 MINI CONSTR> 27.84374 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -39.99844 0.01977 0.20582 0.00014 MINI INTERN> 4.81812 16.11590 0.00000 9.72939 3.53812 MINI EXTERN> -80.69905 -21.35721 0.00000 0.00000 0.00000 MINI CONSTR> 27.85628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9101 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -40.01850 0.02006 0.14787 0.00015 MINI INTERN> 4.79320 16.11649 0.00000 9.72977 3.53324 MINI EXTERN> -80.70200 -21.35514 0.00000 0.00000 0.00000 MINI CONSTR> 27.86594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -40.03512 0.01662 0.22410 0.00015 MINI INTERN> 4.82869 16.09626 0.00000 9.71893 3.53581 MINI EXTERN> -80.73012 -21.36116 0.00000 0.00000 0.00000 MINI CONSTR> 27.87646 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9100 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -40.05666 0.02154 0.13473 0.00016 MINI INTERN> 4.78774 16.10462 0.00000 9.72139 3.53011 MINI EXTERN> -80.72808 -21.35872 0.00000 0.00000 0.00000 MINI CONSTR> 27.88628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -40.07318 0.01651 0.24424 0.00016 MINI INTERN> 4.83180 16.08155 0.00000 9.70873 3.53369 MINI EXTERN> -80.76001 -21.36623 0.00000 0.00000 0.00000 MINI CONSTR> 27.89728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9099 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -40.09091 0.01773 0.27043 0.00017 MINI INTERN> 4.83962 16.06871 0.00000 9.70373 3.53150 MINI EXTERN> -80.77470 -21.36682 0.00000 0.00000 0.00000 MINI CONSTR> 27.90705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -40.10796 0.01705 0.27566 0.00018 MINI INTERN> 4.84981 16.05901 0.00000 9.69733 3.53175 MINI EXTERN> -80.79202 -21.37025 0.00000 0.00000 0.00000 MINI CONSTR> 27.91641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9098 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -40.12556 0.01760 0.26238 0.00018 MINI INTERN> 4.84340 16.05517 0.00000 9.69409 3.52996 MINI EXTERN> -80.80211 -21.37136 0.00000 0.00000 0.00000 MINI CONSTR> 27.92530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -40.14370 0.01815 0.30006 0.00019 MINI INTERN> 4.85670 16.04193 0.00000 9.68730 3.52915 MINI EXTERN> -80.82022 -21.37422 0.00000 0.00000 0.00000 MINI CONSTR> 27.93565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9098 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -40.16083 0.01713 0.28675 0.00020 MINI INTERN> 4.84968 16.04002 0.00000 9.68381 3.52809 MINI EXTERN> -80.83053 -21.37620 0.00000 0.00000 0.00000 MINI CONSTR> 27.94430 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -40.17851 0.01768 0.30422 0.00020 MINI INTERN> 4.84645 16.03162 0.00000 9.68079 3.52465 MINI EXTERN> -80.84012 -21.37537 0.00000 0.00000 0.00000 MINI CONSTR> 27.95346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9098 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -40.20081 0.02230 0.09517 0.00009 MINI INTERN> 4.73305 16.07362 0.00000 9.69512 3.51398 MINI EXTERN> -80.81119 -21.36646 0.00000 0.00000 0.00000 MINI CONSTR> 27.96107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -40.20992 0.00911 0.32234 0.00022 MINI INTERN> 4.86798 16.01223 0.00000 9.66838 3.52494 MINI EXTERN> -80.87227 -21.38163 0.00000 0.00000 0.00000 MINI CONSTR> 27.97044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9098 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -40.22719 0.01727 0.33458 0.00023 MINI INTERN> 4.86094 16.01144 0.00000 9.66440 3.52412 MINI EXTERN> -80.88310 -21.38462 0.00000 0.00000 0.00000 MINI CONSTR> 27.97963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -40.25169 0.02450 0.10348 0.00010 MINI INTERN> 4.72357 16.05904 0.00000 9.68360 3.50933 MINI EXTERN> -80.84404 -21.37013 0.00000 0.00000 0.00000 MINI CONSTR> 27.98694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9098 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -40.25732 0.00563 0.36274 0.00025 MINI INTERN> 4.87932 15.98805 0.00000 9.65445 3.52104 MINI EXTERN> -80.90959 -21.38601 0.00000 0.00000 0.00000 MINI CONSTR> 27.99542 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -40.28400 0.02668 0.12522 0.00011 MINI INTERN> 4.71079 16.05257 0.00000 9.67739 3.50552 MINI EXTERN> -80.86215 -21.37139 0.00000 0.00000 0.00000 MINI CONSTR> 28.00328 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9098 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -40.29815 0.01415 0.09063 0.00011 MINI INTERN> 4.73056 16.03918 0.00000 9.67014 3.50674 MINI EXTERN> -80.87949 -21.37533 0.00000 0.00000 0.00000 MINI CONSTR> 28.01005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -40.31382 0.01568 0.09536 0.00011 MINI INTERN> 4.72491 16.03590 0.00000 9.66697 3.50500 MINI EXTERN> -80.88836 -21.37608 0.00000 0.00000 0.00000 MINI CONSTR> 28.01782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9097 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -40.32977 0.01594 0.15461 0.00012 MINI INTERN> 4.69460 16.04336 0.00000 9.66791 3.50061 MINI EXTERN> -80.88862 -21.37386 0.00000 0.00000 0.00000 MINI CONSTR> 28.02623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -40.34390 0.01414 0.08876 0.00012 MINI INTERN> 4.72913 16.02317 0.00000 9.65821 3.50322 MINI EXTERN> -80.91091 -21.37926 0.00000 0.00000 0.00000 MINI CONSTR> 28.03254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9097 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -40.35944 0.01554 0.18365 0.00013 MINI INTERN> 4.68084 16.03965 0.00000 9.66198 3.49742 MINI EXTERN> -80.90500 -21.37547 0.00000 0.00000 0.00000 MINI CONSTR> 28.04116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -40.37522 0.01578 0.13106 0.00013 MINI INTERN> 4.70685 16.02094 0.00000 9.65377 3.49824 MINI EXTERN> -80.92424 -21.37881 0.00000 0.00000 0.00000 MINI CONSTR> 28.04803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9097 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -40.38816 0.01295 0.19920 0.00014 MINI INTERN> 4.67300 16.03246 0.00000 9.65560 3.49427 MINI EXTERN> -80.92197 -21.37677 0.00000 0.00000 0.00000 MINI CONSTR> 28.05524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -40.40515 0.01698 0.11777 0.00014 MINI INTERN> 4.70668 16.01088 0.00000 9.64549 3.49638 MINI EXTERN> -80.94512 -21.38179 0.00000 0.00000 0.00000 MINI CONSTR> 28.06234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -40.41838 0.01324 0.21742 0.00015 MINI INTERN> 4.66538 16.02500 0.00000 9.64858 3.49117 MINI EXTERN> -80.94046 -21.37807 0.00000 0.00000 0.00000 MINI CONSTR> 28.07000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -40.43356 0.01518 0.22262 0.00015 MINI INTERN> 4.66397 16.01980 0.00000 9.64474 3.48968 MINI EXTERN> -80.95034 -21.37869 0.00000 0.00000 0.00000 MINI CONSTR> 28.07728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -40.44830 0.01474 0.23958 0.00016 MINI INTERN> 4.65776 16.01833 0.00000 9.64136 3.48839 MINI EXTERN> -80.95909 -21.37965 0.00000 0.00000 0.00000 MINI CONSTR> 28.08461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -40.46155 0.01325 0.26555 0.00016 MINI INTERN> 4.65712 16.01166 0.00000 9.63836 3.48597 MINI EXTERN> -80.96704 -21.37879 0.00000 0.00000 0.00000 MINI CONSTR> 28.09117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -40.47511 0.01356 0.24467 0.00017 MINI INTERN> 4.65379 16.00990 0.00000 9.63477 3.48561 MINI EXTERN> -80.97550 -21.38088 0.00000 0.00000 0.00000 MINI CONSTR> 28.09721 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -40.48944 0.01433 0.25964 0.00018 MINI INTERN> 4.64834 16.00740 0.00000 9.63156 3.48397 MINI EXTERN> -80.98381 -21.38109 0.00000 0.00000 0.00000 MINI CONSTR> 28.10419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -40.50239 0.01295 0.30183 0.00018 MINI INTERN> 4.63726 16.00690 0.00000 9.62991 3.48112 MINI EXTERN> -80.98900 -21.37964 0.00000 0.00000 0.00000 MINI CONSTR> 28.11107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -40.51572 0.01333 0.27705 0.00019 MINI INTERN> 4.64215 16.00058 0.00000 9.62524 3.48110 MINI EXTERN> -80.99942 -21.38204 0.00000 0.00000 0.00000 MINI CONSTR> 28.11666 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -40.53567 0.01995 0.08281 0.00008 MINI INTERN> 4.74311 15.94829 0.00000 9.60290 3.48986 MINI EXTERN> -81.04606 -21.39692 0.00000 0.00000 0.00000 MINI CONSTR> 28.12313 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -40.54213 0.00646 0.30396 0.00020 MINI INTERN> 4.64261 15.98967 0.00000 9.61797 3.47816 MINI EXTERN> -81.01723 -21.38250 0.00000 0.00000 0.00000 MINI CONSTR> 28.12919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -40.55371 0.01158 0.34422 0.00021 MINI INTERN> 4.64670 15.98972 0.00000 9.61197 3.48019 MINI EXTERN> -81.02985 -21.38805 0.00000 0.00000 0.00000 MINI CONSTR> 28.13560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -40.57484 0.02112 0.09736 0.00009 MINI INTERN> 4.75287 15.93027 0.00000 9.59000 3.48766 MINI EXTERN> -81.07541 -21.40124 0.00000 0.00000 0.00000 MINI CONSTR> 28.14102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -40.58646 0.01162 0.07870 0.00009 MINI INTERN> 4.73851 15.93234 0.00000 9.58922 3.48543 MINI EXTERN> -81.07793 -21.40009 0.00000 0.00000 0.00000 MINI CONSTR> 28.14606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -40.59039 0.00393 0.35870 0.00023 MINI INTERN> 4.62233 15.98692 0.00000 9.60570 3.47446 MINI EXTERN> -81.04579 -21.38657 0.00000 0.00000 0.00000 MINI CONSTR> 28.15255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -40.61274 0.02235 0.12379 0.00010 MINI INTERN> 4.76497 15.91190 0.00000 9.57685 3.48574 MINI EXTERN> -81.10462 -21.40582 0.00000 0.00000 0.00000 MINI CONSTR> 28.15823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -40.62392 0.01117 0.07843 0.00011 MINI INTERN> 4.73784 15.91947 0.00000 9.57851 3.48238 MINI EXTERN> -81.10216 -21.40269 0.00000 0.00000 0.00000 MINI CONSTR> 28.16272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9096 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -40.63702 0.01310 0.15031 0.00011 MINI INTERN> 4.77628 15.89847 0.00000 9.56777 3.48467 MINI EXTERN> -81.12438 -21.40910 0.00000 0.00000 0.00000 MINI CONSTR> 28.16926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -40.64982 0.01280 0.09631 0.00011 MINI INTERN> 4.75027 15.90529 0.00000 9.56867 3.48151 MINI EXTERN> -81.12337 -21.40648 0.00000 0.00000 0.00000 MINI CONSTR> 28.17428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9095 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -40.66132 0.01150 0.07882 0.00012 MINI INTERN> 4.73813 15.90652 0.00000 9.56746 3.47952 MINI EXTERN> -81.12657 -21.40554 0.00000 0.00000 0.00000 MINI CONSTR> 28.17915 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 -40.66132 0.01150 0.07882 0.00014 STPD INTERN> 4.73813 15.90652 0.00000 9.56746 3.47952 STPD EXTERN> -81.12657 -21.40554 0.00000 0.00000 0.00000 STPD CONSTR> 28.17915 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 9095 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9095 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 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 -40.66132 0.01150 0.07882 0.00000 MINI INTERN> 4.73813 15.90652 0.00000 9.56746 3.47952 MINI EXTERN> -81.12657 -21.40554 0.00000 0.00000 0.00000 MINI CONSTR> 28.17915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -41.76717 1.10584 0.07996 0.00932 MINI INTERN> 4.74315 15.33070 0.00000 9.00984 3.35077 MINI EXTERN> -82.79137 -21.42458 0.00000 0.00000 0.00000 MINI CONSTR> 30.01433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -41.78503 0.01787 0.13061 0.01004 MINI INTERN> 4.59444 15.18748 0.00000 8.98087 3.29441 MINI EXTERN> -82.20337 -21.52436 0.00000 0.00000 0.00000 MINI CONSTR> 29.88551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -41.82209 0.03706 0.16755 0.02199 MINI INTERN> 4.53476 15.20469 0.00000 8.95640 3.29247 MINI EXTERN> -81.88514 -21.41142 0.00000 0.00000 0.00000 MINI CONSTR> 29.48615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -41.85900 0.03691 0.12623 0.02118 MINI INTERN> 4.64690 15.39565 0.00000 8.96049 3.31977 MINI EXTERN> -81.75341 -21.49435 0.00000 0.00000 0.00000 MINI CONSTR> 29.06596 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -41.87319 0.01419 0.07705 0.00854 MINI INTERN> 4.67004 15.45502 0.00000 8.97225 3.32758 MINI EXTERN> -81.81618 -21.39114 0.00000 0.00000 0.00000 MINI CONSTR> 28.90925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -41.88069 0.00750 0.06490 0.00578 MINI INTERN> 4.67472 15.48848 0.00000 9.00383 3.31600 MINI EXTERN> -81.84286 -21.35231 0.00000 0.00000 0.00000 MINI CONSTR> 28.83145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -41.88464 0.00395 0.04562 0.00412 MINI INTERN> 4.67470 15.51868 0.00000 9.01144 3.32495 MINI EXTERN> -81.85381 -21.35391 0.00000 0.00000 0.00000 MINI CONSTR> 28.79331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -41.88778 0.00314 0.04362 0.00413 MINI INTERN> 4.68441 15.57043 0.00000 9.03373 3.33642 MINI EXTERN> -81.92068 -21.36266 0.00000 0.00000 0.00000 MINI CONSTR> 28.77058 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -41.89007 0.00229 0.03519 0.00307 MINI INTERN> 4.68971 15.54265 0.00000 9.05017 3.33850 MINI EXTERN> -81.90291 -21.36757 0.00000 0.00000 0.00000 MINI CONSTR> 28.75938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -41.89161 0.00154 0.02721 0.00325 MINI INTERN> 4.68399 15.55077 0.00000 9.05962 3.33297 MINI EXTERN> -81.90647 -21.36796 0.00000 0.00000 0.00000 MINI CONSTR> 28.75546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -41.89253 0.00092 0.02086 0.00211 MINI INTERN> 4.68035 15.56003 0.00000 9.06597 3.33361 MINI EXTERN> -81.91232 -21.37318 0.00000 0.00000 0.00000 MINI CONSTR> 28.75301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -41.89313 0.00061 0.01888 0.00189 MINI INTERN> 4.68084 15.54628 0.00000 9.07634 3.33219 MINI EXTERN> -81.89861 -21.38000 0.00000 0.00000 0.00000 MINI CONSTR> 28.74982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -41.89353 0.00039 0.01346 0.00118 MINI INTERN> 4.67932 15.54425 0.00000 9.07907 3.33090 MINI EXTERN> -81.90715 -21.36707 0.00000 0.00000 0.00000 MINI CONSTR> 28.74715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -41.89379 0.00027 0.01319 0.00138 MINI INTERN> 4.68162 15.54190 0.00000 9.07992 3.33169 MINI EXTERN> -81.91959 -21.35390 0.00000 0.00000 0.00000 MINI CONSTR> 28.74456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -41.89403 0.00024 0.01155 0.00161 MINI INTERN> 4.67972 15.53494 0.00000 9.08438 3.33021 MINI EXTERN> -81.91070 -21.35284 0.00000 0.00000 0.00000 MINI CONSTR> 28.74025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -41.89422 0.00019 0.01092 0.00118 MINI INTERN> 4.67784 15.53189 0.00000 9.08707 3.33388 MINI EXTERN> -81.91921 -21.34130 0.00000 0.00000 0.00000 MINI CONSTR> 28.73560 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> 82 -41.89430 0.00007 0.00969 0.02000 CONJ INTERN> 4.67936 15.52974 0.00000 9.09036 3.33371 CONJ EXTERN> -81.91793 -21.34324 0.00000 0.00000 0.00000 CONJ CONSTR> 28.73370 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 ASP 1 HT1 ) 0.31241 ( PROT ASP 1 HT2 ) 0.31241 ( PROT ASP 1 N ) 0.39052 ( PROT ASP 1 HT3 ) 0.31241 ( PROT ASP 1 CA ) 0.39052 ( PROT ASP 1 CB ) 0.31241 ( PROT ASP 1 CG ) 0.31241 ( PROT ASP 1 OD1 ) 0.31241 ( PROT ASP 1 OD2 ) 0.31241 ( PROT ASP 1 C ) 0.39052 ( PROT ASP 1 O ) 0.39052 ( PROT TYR 2 N ) 0.39052 ( PROT TYR 2 H ) 0.31241 ( PROT TYR 2 CA ) 0.39052 ( PROT TYR 2 CB ) 0.31241 ( PROT TYR 2 CG ) 0.31241 ( PROT TYR 2 CD1 ) 0.31241 ( PROT TYR 2 CE1 ) 0.31241 ( PROT TYR 2 CD2 ) 0.31241 ( PROT TYR 2 CE2 ) 0.31241 ( PROT TYR 2 CZ ) 0.31241 ( PROT TYR 2 OH ) 0.31241 ( PROT TYR 2 HH ) 0.31241 ( PROT TYR 2 C ) 0.39052 ( PROT TYR 2 O ) 0.39052 ( PROT ALA 3 N ) 0.39052 ( PROT ALA 3 H ) 0.31241 ( PROT ALA 3 CA ) 0.39052 ( PROT ALA 3 CB ) 0.31241 ( PROT ALA 3 C ) 0.39052 ( PROT ALA 3 O ) 0.39052 ( PROT PHE 4 N ) 0.39052 ( PROT PHE 4 H ) 0.31241 ( PROT PHE 4 CA ) 0.39052 ( PROT PHE 4 CB ) 0.31241 ( PROT PHE 4 CG ) 0.31241 ( PROT PHE 4 CD1 ) 0.31241 ( PROT PHE 4 CD2 ) 0.31241 ( PROT PHE 4 CE1 ) 0.31241 ( PROT PHE 4 CE2 ) 0.31241 ( PROT PHE 4 CZ ) 0.31241 ( PROT PHE 4 C ) 0.39052 ( PROT PHE 4 O ) 0.39052 ( PROT ILE 5 N ) 0.39052 ( PROT ILE 5 H ) 0.31241 ( PROT ILE 5 CA ) 0.39052 ( PROT ILE 5 CB ) 0.31241 ( PROT ILE 5 CG2 ) 0.31241 ( PROT ILE 5 CG1 ) 0.31241 ( PROT ILE 5 CD ) 0.31241 ( PROT ILE 5 C ) 0.39052 ( PROT ILE 5 O ) 0.39052 ( PROT ALA 6 N ) 0.39052 ( PROT ALA 6 H ) 0.31241 ( PROT ALA 6 CA ) 0.39052 ( PROT ALA 6 CB ) 0.31241 ( PROT ALA 6 C ) 0.39052 ( PROT ALA 6 O ) 0.39052 ( PROT SER 7 N ) 0.39052 ( PROT SER 7 H ) 0.31241 ( PROT SER 7 CA ) 0.39052 ( PROT SER 7 CB ) 0.31241 ( PROT SER 7 OG ) 0.31241 ( PROT SER 7 HG ) 0.31241 ( PROT SER 7 C ) 0.39052 ( PROT SER 7 O ) 0.39052 ( PROT LEU 8 N ) 0.39052 ( PROT LEU 8 H ) 0.31241 ( PROT LEU 8 CA ) 0.39052 ( PROT LEU 8 CB ) 0.31241 ( PROT LEU 8 CG ) 0.31241 ( PROT LEU 8 CD1 ) 0.31241 ( PROT LEU 8 CD2 ) 0.31241 ( PROT LEU 8 C ) 0.39052 ( PROT LEU 8 O ) 0.39052 ( PROT VAL 9 N ) 0.39052 ( PROT VAL 9 H ) 0.31241 ( PROT VAL 9 CA ) 0.39052 ( PROT VAL 9 CB ) 0.31241 ( PROT VAL 9 CG1 ) 0.31241 ( PROT VAL 9 CG2 ) 0.31241 ( PROT VAL 9 C ) 0.39052 ( PROT VAL 9 O ) 0.39052 ( PROT VAL 10 N ) 0.39052 ( PROT VAL 10 H ) 0.31241 ( PROT VAL 10 CA ) 0.39052 ( PROT VAL 10 CB ) 0.31241 ( PROT VAL 10 CG1 ) 0.31241 ( PROT VAL 10 CG2 ) 0.31241 ( PROT VAL 10 C ) 0.39052 ( PROT VAL 10 O ) 0.39052 ( PROT ILE 11 N ) 0.39052 ( PROT ILE 11 H ) 0.31241 ( PROT ILE 11 CA ) 0.39052 ( PROT ILE 11 CB ) 0.31241 ( PROT ILE 11 CG2 ) 0.31241 ( PROT ILE 11 CG1 ) 0.31241 ( PROT ILE 11 CD ) 0.31241 ( PROT ILE 11 C ) 0.39052 ( PROT ILE 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 ASP 13 N ) 0.39052 ( PROT ASP 13 H ) 0.31241 ( PROT ASP 13 CA ) 0.39052 ( PROT ASP 13 CB ) 0.31241 ( PROT ASP 13 CG ) 0.31241 ( PROT ASP 13 OD1 ) 0.31241 ( PROT ASP 13 OD2 ) 0.31241 ( PROT ASP 13 C ) 0.39052 ( PROT ASP 13 O ) 0.39052 ( PROT ASP 14 N ) 0.39052 ( PROT ASP 14 H ) 0.31241 ( PROT ASP 14 CA ) 0.39052 ( PROT ASP 14 CB ) 0.31241 ( PROT ASP 14 CG ) 0.31241 ( PROT ASP 14 OD1 ) 0.31241 ( PROT ASP 14 OD2 ) 0.31241 ( PROT ASP 14 C ) 0.39052 ( PROT ASP 14 O ) 0.39052 ( PROT VAL 15 N ) 0.39052 ( PROT VAL 15 H ) 0.31241 ( PROT VAL 15 CA ) 0.39052 ( PROT VAL 15 CB ) 0.31241 ( PROT VAL 15 CG1 ) 0.31241 ( PROT VAL 15 CG2 ) 0.31241 ( PROT VAL 15 C ) 0.39052 ( PROT VAL 15 O ) 0.39052 ( PROT ASN 16 N ) 0.39052 ( PROT ASN 16 H ) 0.31241 ( PROT ASN 16 CA ) 0.39052 ( PROT ASN 16 CB ) 0.31241 ( PROT ASN 16 CG ) 0.31241 ( PROT ASN 16 OD1 ) 0.31241 ( PROT ASN 16 ND2 ) 0.31241 ( PROT ASN 16 HD21 ) 0.31241 ( PROT ASN 16 HD22 ) 0.31241 ( PROT ASN 16 C ) 0.39052 ( PROT ASN 16 O ) 0.39052 ( PROT ARG 17 N ) 0.39052 ( PROT ARG 17 H ) 0.31241 ( PROT ARG 17 CA ) 0.39052 ( PROT ARG 17 CB ) 0.31241 ( PROT ARG 17 CG ) 0.31241 ( PROT ARG 17 CD ) 0.31241 ( PROT ARG 17 NE ) 0.31241 ( PROT ARG 17 HE ) 0.31241 ( PROT ARG 17 CZ ) 0.31241 ( PROT ARG 17 NH1 ) 0.31241 ( PROT ARG 17 HH11 ) 0.31241 ( PROT ARG 17 HH12 ) 0.31241 ( PROT ARG 17 NH2 ) 0.31241 ( PROT ARG 17 HH21 ) 0.31241 ( PROT ARG 17 HH22 ) 0.31241 ( PROT ARG 17 C ) 0.39052 ( PROT ARG 17 OT1 ) 0.31241 ( PROT ARG 17 OT2 ) 0.31241 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.95919 3.70783 -6.79715 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00463 0.00350 -0.00485 ROTATION MATRIX 1.000000 -0.000243 -0.000399 0.000243 0.999999 0.001040 0.000398 -0.001041 0.999999 AXIS OF ROTATION IS 0.912420 0.349531 -0.212880 ANGLE IS 0.07 TOTAL SQUARE DIFF IS 53.4652 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.570970 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.5710" Parameter: A <- "0.5710" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.78782 3.79737 -6.99919 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.01564 -0.00566 0.02195 ROTATION MATRIX 0.999346 0.024381 0.026720 -0.023439 0.999112 -0.035014 -0.027550 0.034364 0.999030 AXIS OF ROTATION IS -0.692209 -0.541481 0.477122 ANGLE IS 2.87 CENTER OF ROTATION 7.596813 3.948745 -7.078966 SHIFT IS 0.024368 TOTAL SQUARE DIFF IS 4.4175 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.509758 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.5710" RDCMND substituted energy or value "?RMS" to " 0.5098" Parameter: A <- "0.5710 0.5098" 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 0.5710 0.5098 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 " 28.73" Parameter: H <- "28.73" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -70.62800 28.73370 0.35681 ENER INTERN> 4.67936 15.52974 0.00000 9.09036 3.33371 ENER EXTERN> -81.91793 -21.34324 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 " -70.63" Parameter: B <- "-70.63" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -21.34" Parameter: C <- "-21.34" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -81.92" Parameter: C <- " -103.26" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -103.26" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.68" Parameter: D <- "4.68" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 15.53" Parameter: D <- " 20.21" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 9.09" Parameter: D <- " 29.30" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.33" Parameter: D <- " 32.63" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 32.63" 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= -70.63 GRMS= 0.36 ELEC= -21.34 VDW= -81.92 RDTITL> *EXTERNAL= -103.26 INTERNAL= 32.63 USER= 0.00 HARM= 28.73 RDTITL> *BOND= 4.68 ANGL= 15.53 DIHE= 9.09 IMPR= 3.33 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9095 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9076 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 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 -49.92795 -20.70005 0.14544 0.02000 MINI INTERN> 4.67936 15.52974 0.00000 9.09036 3.33371 MINI EXTERN> -81.91793 -21.34324 0.00000 0.00000 0.00000 MINI CONSTR> 20.70005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -50.38650 0.45855 0.36397 0.00150 MINI INTERN> 4.89376 15.94319 0.00000 9.37214 3.34329 MINI EXTERN> -85.08386 -20.33881 0.00000 0.00000 0.00000 MINI CONSTR> 21.48378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9070 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -50.36266 -0.02384 1.21404 0.00065 MINI INTERN> 5.12596 15.47917 0.00000 9.28725 3.29508 MINI EXTERN> -84.27776 -20.74681 0.00000 0.00000 0.00000 MINI CONSTR> 21.47443 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -50.50682 0.14416 0.46182 0.00028 MINI INTERN> 4.79768 15.65317 0.00000 9.26870 3.35912 MINI EXTERN> -84.19976 -20.86851 0.00000 0.00000 0.00000 MINI CONSTR> 21.48279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9070 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -50.53585 0.02903 0.41854 0.00029 MINI INTERN> 4.75543 15.65387 0.00000 9.25541 3.35982 MINI EXTERN> -84.12241 -20.93063 0.00000 0.00000 0.00000 MINI CONSTR> 21.49266 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -50.57294 0.03709 0.13011 0.00013 MINI INTERN> 4.78999 15.57230 0.00000 9.24069 3.34706 MINI EXTERN> -84.08337 -20.94236 0.00000 0.00000 0.00000 MINI CONSTR> 21.50274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9070 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -50.59570 0.02276 0.11540 0.00013 MINI INTERN> 4.77596 15.56028 0.00000 9.23013 3.34671 MINI EXTERN> -84.05147 -20.97195 0.00000 0.00000 0.00000 MINI CONSTR> 21.51465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -50.61703 0.02133 0.11166 0.00013 MINI INTERN> 4.76789 15.54655 0.00000 9.22111 3.34570 MINI EXTERN> -84.03093 -20.99460 0.00000 0.00000 0.00000 MINI CONSTR> 21.52725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9069 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -50.63880 0.02177 0.18231 0.00014 MINI INTERN> 4.78196 15.51235 0.00000 9.21083 3.34115 MINI EXTERN> -84.01959 -21.00802 0.00000 0.00000 0.00000 MINI CONSTR> 21.54252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -50.65903 0.02024 0.14804 0.00014 MINI INTERN> 4.76670 15.50979 0.00000 9.20453 3.34177 MINI EXTERN> -84.01388 -21.02370 0.00000 0.00000 0.00000 MINI CONSTR> 21.55575 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9069 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -50.67826 0.01923 0.17124 0.00015 MINI INTERN> 4.76044 15.49988 0.00000 9.19786 3.34111 MINI EXTERN> -84.01366 -21.03391 0.00000 0.00000 0.00000 MINI CONSTR> 21.57003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -50.69300 0.01474 0.26694 0.00016 MINI INTERN> 4.75503 15.49289 0.00000 9.19164 3.34086 MINI EXTERN> -84.01733 -21.03959 0.00000 0.00000 0.00000 MINI CONSTR> 21.58349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9067 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -50.71042 0.01742 0.29176 0.00016 MINI INTERN> 4.74731 15.48687 0.00000 9.18642 3.34064 MINI EXTERN> -84.02317 -21.04614 0.00000 0.00000 0.00000 MINI CONSTR> 21.59765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -50.72664 0.01622 0.31978 0.00017 MINI INTERN> 4.74036 15.48170 0.00000 9.18175 3.34042 MINI EXTERN> -84.03080 -21.05145 0.00000 0.00000 0.00000 MINI CONSTR> 21.61139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9065 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -50.74247 0.01583 0.30092 0.00017 MINI INTERN> 4.73372 15.47787 0.00000 9.17834 3.34013 MINI EXTERN> -84.03796 -21.05781 0.00000 0.00000 0.00000 MINI CONSTR> 21.62323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -50.75947 0.01700 0.31199 0.00018 MINI INTERN> 4.73147 15.46815 0.00000 9.17400 3.33908 MINI EXTERN> -84.04914 -21.06037 0.00000 0.00000 0.00000 MINI CONSTR> 21.63733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9065 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -50.77667 0.01720 0.31571 0.00019 MINI INTERN> 4.72957 15.45821 0.00000 9.16992 3.33796 MINI EXTERN> -84.06151 -21.06229 0.00000 0.00000 0.00000 MINI CONSTR> 21.65148 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -50.79874 0.02207 0.10098 0.00008 MINI INTERN> 4.72835 15.45195 0.00000 9.16939 3.33636 MINI EXTERN> -84.06847 -21.07997 0.00000 0.00000 0.00000 MINI CONSTR> 21.66365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9065 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -50.80637 0.00762 0.34778 0.00020 MINI INTERN> 4.72688 15.44227 0.00000 9.16266 3.33605 MINI EXTERN> -84.08603 -21.06548 0.00000 0.00000 0.00000 MINI CONSTR> 21.67729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -50.82242 0.01605 0.35731 0.00021 MINI INTERN> 4.72607 15.43237 0.00000 9.15906 3.33486 MINI EXTERN> -84.10053 -21.06532 0.00000 0.00000 0.00000 MINI CONSTR> 21.69107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9063 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -50.83838 0.01596 0.37094 0.00022 MINI INTERN> 4.72579 15.42176 0.00000 9.15553 3.33359 MINI EXTERN> -84.11607 -21.06404 0.00000 0.00000 0.00000 MINI CONSTR> 21.70506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -50.86413 0.02575 0.11069 0.00009 MINI INTERN> 4.72367 15.42011 0.00000 9.15542 3.33214 MINI EXTERN> -84.12325 -21.09037 0.00000 0.00000 0.00000 MINI CONSTR> 21.71815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9063 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -50.87793 0.01380 0.09257 0.00010 MINI INTERN> 4.72206 15.41232 0.00000 9.15240 3.33125 MINI EXTERN> -84.13649 -21.08897 0.00000 0.00000 0.00000 MINI CONSTR> 21.72950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -50.89368 0.01575 0.09110 0.00010 MINI INTERN> 4.72095 15.40471 0.00000 9.14915 3.33022 MINI EXTERN> -84.15130 -21.09012 0.00000 0.00000 0.00000 MINI CONSTR> 21.74271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9063 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -50.90982 0.01613 0.09035 0.00010 MINI INTERN> 4.71989 15.39709 0.00000 9.14585 3.32917 MINI EXTERN> -84.16673 -21.09135 0.00000 0.00000 0.00000 MINI CONSTR> 21.75627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -50.92609 0.01627 0.09063 0.00011 MINI INTERN> 4.71888 15.38964 0.00000 9.14255 3.32810 MINI EXTERN> -84.18247 -21.09276 0.00000 0.00000 0.00000 MINI CONSTR> 21.76996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9062 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -50.94279 0.01670 0.16755 0.00011 MINI INTERN> 4.71850 15.38805 0.00000 9.13910 3.32713 MINI EXTERN> -84.19720 -21.10366 0.00000 0.00000 0.00000 MINI CONSTR> 21.78529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -50.95768 0.01489 0.11869 0.00012 MINI INTERN> 4.71707 15.37817 0.00000 9.13617 3.32611 MINI EXTERN> -84.21264 -21.09945 0.00000 0.00000 0.00000 MINI CONSTR> 21.79689 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9061 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -50.97289 0.01521 0.11829 0.00012 MINI INTERN> 4.71604 15.37149 0.00000 9.13306 3.32512 MINI EXTERN> -84.22787 -21.10039 0.00000 0.00000 0.00000 MINI CONSTR> 21.80966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -50.98806 0.01518 0.12630 0.00012 MINI INTERN> 4.71502 15.36559 0.00000 9.12993 3.32414 MINI EXTERN> -84.24299 -21.10229 0.00000 0.00000 0.00000 MINI CONSTR> 21.82252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9061 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -51.00043 0.01237 0.21975 0.00013 MINI INTERN> 4.71473 15.36683 0.00000 9.12693 3.32342 MINI EXTERN> -84.25486 -21.11250 0.00000 0.00000 0.00000 MINI CONSTR> 21.83501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -51.01490 0.01446 0.21889 0.00013 MINI INTERN> 4.71336 15.36104 0.00000 9.12394 3.32247 MINI EXTERN> -84.26948 -21.11331 0.00000 0.00000 0.00000 MINI CONSTR> 21.84708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9060 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -51.03074 0.01584 0.14573 0.00014 MINI INTERN> 4.71223 15.34895 0.00000 9.12110 3.32137 MINI EXTERN> -84.28610 -21.10683 0.00000 0.00000 0.00000 MINI CONSTR> 21.85854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -51.04139 0.01065 0.23555 0.00014 MINI INTERN> 4.71212 15.35070 0.00000 9.11834 3.32075 MINI EXTERN> -84.29670 -21.11625 0.00000 0.00000 0.00000 MINI CONSTR> 21.86965 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9060 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -51.05539 0.01399 0.25825 0.00015 MINI INTERN> 4.71033 15.34757 0.00000 9.11516 3.31983 MINI EXTERN> -84.31096 -21.11933 0.00000 0.00000 0.00000 MINI CONSTR> 21.88202 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -51.06819 0.01280 0.28628 0.00015 MINI INTERN> 4.70925 15.34477 0.00000 9.11218 3.31898 MINI EXTERN> -84.32428 -21.12271 0.00000 0.00000 0.00000 MINI CONSTR> 21.89362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9060 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -51.08077 0.01259 0.26818 0.00016 MINI INTERN> 4.70920 15.33741 0.00000 9.10976 3.31817 MINI EXTERN> -84.33718 -21.12148 0.00000 0.00000 0.00000 MINI CONSTR> 21.90335 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -51.09447 0.01370 0.27681 0.00017 MINI INTERN> 4.70736 15.33354 0.00000 9.10669 3.31727 MINI EXTERN> -84.35116 -21.12312 0.00000 0.00000 0.00000 MINI CONSTR> 21.91495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9060 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -51.10828 0.01381 0.27825 0.00017 MINI INTERN> 4.70555 15.32901 0.00000 9.10366 3.31635 MINI EXTERN> -84.36522 -21.12398 0.00000 0.00000 0.00000 MINI CONSTR> 21.92635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -51.12582 0.01753 0.09034 0.00007 MINI INTERN> 4.71274 15.29382 0.00000 9.10160 3.31474 MINI EXTERN> -84.38862 -21.09628 0.00000 0.00000 0.00000 MINI CONSTR> 21.93617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9058 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -51.13164 0.00582 0.30944 0.00019 MINI INTERN> 4.70446 15.32185 0.00000 9.09826 3.31482 MINI EXTERN> -84.38962 -21.12804 0.00000 0.00000 0.00000 MINI CONSTR> 21.94662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -51.14456 0.01291 0.31959 0.00019 MINI INTERN> 4.70220 15.31896 0.00000 9.09524 3.31394 MINI EXTERN> -84.40277 -21.12967 0.00000 0.00000 0.00000 MINI CONSTR> 21.95755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -51.15726 0.01270 0.33456 0.00020 MINI INTERN> 4.69955 15.31690 0.00000 9.09215 3.31305 MINI EXTERN> -84.41578 -21.13162 0.00000 0.00000 0.00000 MINI CONSTR> 21.96849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -51.17801 0.02075 0.10533 0.00009 MINI INTERN> 4.71389 15.26745 0.00000 9.09033 3.31120 MINI EXTERN> -84.44387 -21.09572 0.00000 0.00000 0.00000 MINI CONSTR> 21.97870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -51.18889 0.01088 0.08154 0.00009 MINI INTERN> 4.71024 15.26838 0.00000 9.08788 3.31059 MINI EXTERN> -84.45290 -21.10023 0.00000 0.00000 0.00000 MINI CONSTR> 21.98717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -51.20168 0.01279 0.08073 0.00009 MINI INTERN> 4.70985 15.26310 0.00000 9.08503 3.30974 MINI EXTERN> -84.46594 -21.10087 0.00000 0.00000 0.00000 MINI CONSTR> 21.99741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -51.21468 0.01300 0.08075 0.00010 MINI INTERN> 4.70967 15.25745 0.00000 9.08212 3.30887 MINI EXTERN> -84.47928 -21.10130 0.00000 0.00000 0.00000 MINI CONSTR> 22.00778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -51.22760 0.01292 0.08249 0.00010 MINI INTERN> 4.70989 15.25126 0.00000 9.07922 3.30801 MINI EXTERN> -84.49270 -21.10135 0.00000 0.00000 0.00000 MINI CONSTR> 22.01807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -51.23995 0.01235 0.16109 0.00010 MINI INTERN> 4.72019 15.23184 0.00000 9.07646 3.30702 MINI EXTERN> -84.51078 -21.09374 0.00000 0.00000 0.00000 MINI CONSTR> 22.02907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -51.25232 0.01236 0.10287 0.00011 MINI INTERN> 4.71283 15.23624 0.00000 9.07364 3.30634 MINI EXTERN> -84.51939 -21.09982 0.00000 0.00000 0.00000 MINI CONSTR> 22.03784 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9056 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -51.26488 0.01256 0.10307 0.00011 MINI INTERN> 4.71239 15.23162 0.00000 9.07071 3.30555 MINI EXTERN> -84.53184 -21.10103 0.00000 0.00000 0.00000 MINI CONSTR> 22.04771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -51.27749 0.01261 0.10898 0.00011 MINI INTERN> 4.71238 15.22646 0.00000 9.06773 3.30477 MINI EXTERN> -84.54453 -21.10196 0.00000 0.00000 0.00000 MINI CONSTR> 22.05765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9055 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -51.28972 0.01222 0.12589 0.00012 MINI INTERN> 4.71351 15.22012 0.00000 9.06481 3.30402 MINI EXTERN> -84.55736 -21.10224 0.00000 0.00000 0.00000 MINI CONSTR> 22.06742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -51.29939 0.00967 0.19578 0.00012 MINI INTERN> 4.72060 15.20865 0.00000 9.06228 3.30344 MINI EXTERN> -84.57046 -21.10025 0.00000 0.00000 0.00000 MINI CONSTR> 22.07635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9055 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -51.31146 0.01207 0.19855 0.00013 MINI INTERN> 4.71888 15.20616 0.00000 9.05927 3.30275 MINI EXTERN> -84.58181 -21.10247 0.00000 0.00000 0.00000 MINI CONSTR> 22.08575 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -51.32360 0.01214 0.20637 0.00013 MINI INTERN> 4.71727 15.20338 0.00000 9.05616 3.30204 MINI EXTERN> -84.59347 -21.10427 0.00000 0.00000 0.00000 MINI CONSTR> 22.09529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9055 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -51.33541 0.01181 0.22268 0.00014 MINI INTERN> 4.71666 15.19941 0.00000 9.05306 3.30133 MINI EXTERN> -84.60546 -21.10519 0.00000 0.00000 0.00000 MINI CONSTR> 22.10477 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -51.34638 0.01097 0.24643 0.00014 MINI INTERN> 4.71738 15.19442 0.00000 9.05011 3.30064 MINI EXTERN> -84.61726 -21.10551 0.00000 0.00000 0.00000 MINI CONSTR> 22.11383 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -51.35700 0.01063 0.23268 0.00015 MINI INTERN> 4.71628 15.19078 0.00000 9.04765 3.29988 MINI EXTERN> -84.62718 -21.10586 0.00000 0.00000 0.00000 MINI CONSTR> 22.12145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -51.36838 0.01138 0.24274 0.00015 MINI INTERN> 4.71548 15.18673 0.00000 9.04468 3.29913 MINI EXTERN> -84.63865 -21.10608 0.00000 0.00000 0.00000 MINI CONSTR> 22.13033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -51.37998 0.01160 0.24827 0.00016 MINI INTERN> 4.71430 15.18276 0.00000 9.04168 3.29833 MINI EXTERN> -84.65016 -21.10611 0.00000 0.00000 0.00000 MINI CONSTR> 22.13921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -51.39516 0.01518 0.07739 0.00007 MINI INTERN> 4.70234 15.18718 0.00000 9.03906 3.29640 MINI EXTERN> -84.65946 -21.10768 0.00000 0.00000 0.00000 MINI CONSTR> 22.14700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -51.40066 0.00550 0.27102 0.00017 MINI INTERN> 4.71429 15.17409 0.00000 9.03620 3.29692 MINI EXTERN> -84.67139 -21.10612 0.00000 0.00000 0.00000 MINI CONSTR> 22.15534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -51.41152 0.01087 0.27788 0.00018 MINI INTERN> 4.71361 15.17004 0.00000 9.03331 3.29615 MINI EXTERN> -84.68227 -21.10597 0.00000 0.00000 0.00000 MINI CONSTR> 22.16362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -51.42248 0.01095 0.28747 0.00018 MINI INTERN> 4.71266 15.16614 0.00000 9.03031 3.29536 MINI EXTERN> -84.69332 -21.10565 0.00000 0.00000 0.00000 MINI CONSTR> 22.17201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -51.43317 0.01070 0.30192 0.00019 MINI INTERN> 4.71184 15.16232 0.00000 9.02727 3.29458 MINI EXTERN> -84.70434 -21.10522 0.00000 0.00000 0.00000 MINI CONSTR> 22.18038 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -51.45077 0.01760 0.09746 0.00008 MINI INTERN> 4.70153 15.16532 0.00000 9.02486 3.29234 MINI EXTERN> -84.71384 -21.10909 0.00000 0.00000 0.00000 MINI CONSTR> 22.18811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -51.45993 0.00916 0.07260 0.00009 MINI INTERN> 4.70133 15.16091 0.00000 9.02250 3.29190 MINI EXTERN> -84.72241 -21.10863 0.00000 0.00000 0.00000 MINI CONSTR> 22.19448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -51.47082 0.01090 0.07203 0.00009 MINI INTERN> 4.70118 15.15652 0.00000 9.01965 3.29113 MINI EXTERN> -84.73289 -21.10875 0.00000 0.00000 0.00000 MINI CONSTR> 22.20233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -51.48185 0.01103 0.07228 0.00009 MINI INTERN> 4.70105 15.15212 0.00000 9.01676 3.29035 MINI EXTERN> -84.74347 -21.10889 0.00000 0.00000 0.00000 MINI CONSTR> 22.21024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -51.49274 0.01089 0.07445 0.00010 MINI INTERN> 4.70098 15.14783 0.00000 9.01388 3.28955 MINI EXTERN> -84.75390 -21.10910 0.00000 0.00000 0.00000 MINI CONSTR> 22.21802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -51.50286 0.01012 0.14933 0.00010 MINI INTERN> 4.70319 15.14396 0.00000 9.01106 3.28839 MINI EXTERN> -84.76494 -21.11074 0.00000 0.00000 0.00000 MINI CONSTR> 22.22622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -51.51344 0.01058 0.09173 0.00010 MINI INTERN> 4.70132 15.13965 0.00000 9.00839 3.28795 MINI EXTERN> -84.77384 -21.10976 0.00000 0.00000 0.00000 MINI CONSTR> 22.23284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -51.52410 0.01066 0.09351 0.00011 MINI INTERN> 4.70139 15.13528 0.00000 9.00554 3.28719 MINI EXTERN> -84.78396 -21.10987 0.00000 0.00000 0.00000 MINI CONSTR> 22.24034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -51.53463 0.01054 0.10332 0.00011 MINI INTERN> 4.70174 15.13093 0.00000 9.00271 3.28639 MINI EXTERN> -84.79408 -21.11013 0.00000 0.00000 0.00000 MINI CONSTR> 22.24781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -51.54299 0.00836 0.17664 0.00011 MINI INTERN> 4.70482 15.12683 0.00000 9.00026 3.28543 MINI EXTERN> -84.80370 -21.11148 0.00000 0.00000 0.00000 MINI CONSTR> 22.25484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -51.55305 0.01006 0.17832 0.00012 MINI INTERN> 4.70510 15.12251 0.00000 8.99754 3.28471 MINI EXTERN> -84.81322 -21.11151 0.00000 0.00000 0.00000 MINI CONSTR> 22.26182 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -51.56319 0.01014 0.18455 0.00012 MINI INTERN> 4.70570 15.11798 0.00000 8.99476 3.28397 MINI EXTERN> -84.82295 -21.11157 0.00000 0.00000 0.00000 MINI CONSTR> 22.26892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -51.57312 0.00993 0.19791 0.00013 MINI INTERN> 4.70672 15.11338 0.00000 8.99199 3.28320 MINI EXTERN> -84.83269 -21.11172 0.00000 0.00000 0.00000 MINI CONSTR> 22.27601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -51.58239 0.00927 0.21909 0.00013 MINI INTERN> 4.70813 15.10900 0.00000 8.98931 3.28244 MINI EXTERN> -84.84210 -21.11199 0.00000 0.00000 0.00000 MINI CONSTR> 22.28282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9051 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -51.59131 0.00892 0.20786 0.00014 MINI INTERN> 4.70713 15.10598 0.00000 8.98688 3.28184 MINI EXTERN> -84.84990 -21.11180 0.00000 0.00000 0.00000 MINI CONSTR> 22.28856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -51.60079 0.00948 0.21766 0.00014 MINI INTERN> 4.70785 15.10177 0.00000 8.98419 3.28112 MINI EXTERN> -84.85902 -21.11187 0.00000 0.00000 0.00000 MINI CONSTR> 22.29518 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9051 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -51.61049 0.00970 0.22393 0.00015 MINI INTERN> 4.70845 15.09747 0.00000 8.98144 3.28039 MINI EXTERN> -84.86818 -21.11187 0.00000 0.00000 0.00000 MINI CONSTR> 22.30181 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -51.62329 0.01281 0.06882 0.00006 MINI INTERN> 4.69686 15.09825 0.00000 8.97780 3.28022 MINI EXTERN> -84.87554 -21.10857 0.00000 0.00000 0.00000 MINI CONSTR> 22.30770 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9050 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -51.62807 0.00478 0.24404 0.00016 MINI INTERN> 4.70978 15.08985 0.00000 8.97634 3.27902 MINI EXTERN> -84.88504 -21.11201 0.00000 0.00000 0.00000 MINI CONSTR> 22.31400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -51.63713 0.00906 0.25009 0.00016 MINI INTERN> 4.71042 15.08587 0.00000 8.97370 3.27833 MINI EXTERN> -84.89357 -21.11201 0.00000 0.00000 0.00000 MINI CONSTR> 22.32012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9050 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -51.64628 0.00915 0.25872 0.00017 MINI INTERN> 4.71152 15.08156 0.00000 8.97099 3.27764 MINI EXTERN> -84.90229 -21.11205 0.00000 0.00000 0.00000 MINI CONSTR> 22.32635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -51.65526 0.00897 0.27157 0.00018 MINI INTERN> 4.71314 15.07704 0.00000 8.96826 3.27694 MINI EXTERN> -84.91104 -21.11216 0.00000 0.00000 0.00000 MINI CONSTR> 22.33256 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9050 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -51.66998 0.01473 0.08706 0.00008 MINI INTERN> 4.69396 15.08230 0.00000 8.96417 3.27678 MINI EXTERN> -84.91782 -21.10772 0.00000 0.00000 0.00000 MINI CONSTR> 22.33836 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -51.67767 0.00768 0.06573 0.00008 MINI INTERN> 4.69569 15.07804 0.00000 8.96219 3.27617 MINI EXTERN> -84.92465 -21.10821 0.00000 0.00000 0.00000 MINI CONSTR> 22.34310 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9049 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -51.68679 0.00912 0.06516 0.00008 MINI INTERN> 4.69549 15.07469 0.00000 8.95954 3.27548 MINI EXTERN> -84.93279 -21.10812 0.00000 0.00000 0.00000 MINI CONSTR> 22.34892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -51.69604 0.00926 0.06529 0.00008 MINI INTERN> 4.69514 15.07142 0.00000 8.95682 3.27479 MINI EXTERN> -84.94102 -21.10799 0.00000 0.00000 0.00000 MINI CONSTR> 22.35480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9047 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -51.70522 0.00917 0.06703 0.00009 MINI INTERN> 4.69452 15.06838 0.00000 8.95410 3.27410 MINI EXTERN> -84.94915 -21.10777 0.00000 0.00000 0.00000 MINI CONSTR> 22.36061 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -51.71379 0.00858 0.13484 0.00009 MINI INTERN> 4.68898 15.06962 0.00000 8.95092 3.27343 MINI EXTERN> -84.95725 -21.10624 0.00000 0.00000 0.00000 MINI CONSTR> 22.36675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9047 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -51.72265 0.00886 0.08316 0.00009 MINI INTERN> 4.69202 15.06368 0.00000 8.94881 3.27278 MINI EXTERN> -84.96453 -21.10705 0.00000 0.00000 0.00000 MINI CONSTR> 22.37165 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -51.73158 0.00893 0.08454 0.00010 MINI INTERN> 4.69130 15.06087 0.00000 8.94617 3.27209 MINI EXTERN> -84.97236 -21.10686 0.00000 0.00000 0.00000 MINI CONSTR> 22.37721 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9047 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -51.74044 0.00886 0.09282 0.00010 MINI INTERN> 4.68990 15.05864 0.00000 8.94350 3.27139 MINI EXTERN> -84.98012 -21.10651 0.00000 0.00000 0.00000 MINI CONSTR> 22.38275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -51.74752 0.00708 0.16019 0.00011 MINI INTERN> 4.68418 15.06084 0.00000 8.94084 3.27072 MINI EXTERN> -84.98702 -21.10510 0.00000 0.00000 0.00000 MINI CONSTR> 22.38802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9047 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -51.75597 0.00845 0.16112 0.00011 MINI INTERN> 4.68314 15.05851 0.00000 8.93838 3.27004 MINI EXTERN> -84.99433 -21.10490 0.00000 0.00000 0.00000 MINI CONSTR> 22.39319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -51.76452 0.00855 0.16584 0.00011 MINI INTERN> 4.68149 15.05668 0.00000 8.93588 3.26932 MINI EXTERN> -85.00173 -21.10463 0.00000 0.00000 0.00000 MINI CONSTR> 22.39846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9047 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -51.77297 0.00845 0.17619 0.00012 MINI INTERN> 4.67929 15.05542 0.00000 8.93338 3.26858 MINI EXTERN> -85.00910 -21.10430 0.00000 0.00000 0.00000 MINI CONSTR> 22.40375 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 -51.77297 0.00845 0.17619 0.00014 STPD INTERN> 4.67929 15.05542 0.00000 8.93338 3.26858 STPD EXTERN> -85.00910 -21.10430 0.00000 0.00000 0.00000 STPD CONSTR> 22.40375 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 9047 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9047 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 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 -51.77297 0.00845 0.17619 0.00000 MINI INTERN> 4.67929 15.05542 0.00000 8.93338 3.26858 MINI EXTERN> -85.00910 -21.10430 0.00000 0.00000 0.00000 MINI CONSTR> 22.40375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -52.76506 0.99209 0.09937 0.01802 MINI INTERN> 4.80566 14.51562 0.00000 8.40371 3.17629 MINI EXTERN> -86.91208 -21.00385 0.00000 0.00000 0.00000 MINI CONSTR> 24.24959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -52.78870 0.02364 0.14244 0.01461 MINI INTERN> 4.63039 14.38448 0.00000 8.38688 3.09306 MINI EXTERN> -86.43387 -21.03943 0.00000 0.00000 0.00000 MINI CONSTR> 24.18979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -52.84565 0.05694 0.21641 0.03852 MINI INTERN> 4.48258 14.29334 0.00000 8.35820 3.09150 MINI EXTERN> -86.04400 -20.92119 0.00000 0.00000 0.00000 MINI CONSTR> 23.89392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -52.92583 0.08018 0.20994 0.04707 MINI INTERN> 4.59437 14.51045 0.00000 8.33669 3.13615 MINI EXTERN> -85.84963 -21.09102 0.00000 0.00000 0.00000 MINI CONSTR> 23.43716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -52.96364 0.03782 0.11960 0.01869 MINI INTERN> 4.66129 14.61891 0.00000 8.30266 3.12101 MINI EXTERN> -85.88429 -21.00322 0.00000 0.00000 0.00000 MINI CONSTR> 23.22000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -52.98137 0.01773 0.09238 0.01001 MINI INTERN> 4.68008 14.66837 0.00000 8.33648 3.11327 MINI EXTERN> -85.90753 -20.99349 0.00000 0.00000 0.00000 MINI CONSTR> 23.12145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -52.98998 0.00861 0.06732 0.00710 MINI INTERN> 4.67001 14.71340 0.00000 8.33454 3.12192 MINI EXTERN> -85.92199 -20.98613 0.00000 0.00000 0.00000 MINI CONSTR> 23.07827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -52.99717 0.00719 0.06936 0.00832 MINI INTERN> 4.68206 14.78328 0.00000 8.37878 3.13114 MINI EXTERN> -86.04588 -20.97912 0.00000 0.00000 0.00000 MINI CONSTR> 23.05258 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -53.00327 0.00610 0.05706 0.00597 MINI INTERN> 4.69101 14.73235 0.00000 8.40641 3.12722 MINI EXTERN> -86.02303 -20.97459 0.00000 0.00000 0.00000 MINI CONSTR> 23.03736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -53.00763 0.00435 0.05031 0.00601 MINI INTERN> 4.68096 14.76528 0.00000 8.43191 3.11307 MINI EXTERN> -86.03470 -20.99562 0.00000 0.00000 0.00000 MINI CONSTR> 23.03146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -53.01065 0.00302 0.04100 0.00482 MINI INTERN> 4.68537 14.78003 0.00000 8.44839 3.11959 MINI EXTERN> -86.04934 -21.02322 0.00000 0.00000 0.00000 MINI CONSTR> 23.02854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -53.01288 0.00222 0.03174 0.00413 MINI INTERN> 4.68326 14.76115 0.00000 8.47145 3.11934 MINI EXTERN> -86.01654 -21.05752 0.00000 0.00000 0.00000 MINI CONSTR> 23.02599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -53.01475 0.00188 0.03518 0.00342 MINI INTERN> 4.67498 14.76117 0.00000 8.48763 3.11842 MINI EXTERN> -86.05266 -21.02923 0.00000 0.00000 0.00000 MINI CONSTR> 23.02495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -53.01651 0.00176 0.03555 0.00431 MINI INTERN> 4.67624 14.75178 0.00000 8.50187 3.12030 MINI EXTERN> -86.08028 -21.00926 0.00000 0.00000 0.00000 MINI CONSTR> 23.02283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -53.01894 0.00242 0.03900 0.00779 MINI INTERN> 4.67336 14.73514 0.00000 8.52731 3.11935 MINI EXTERN> -86.08811 -21.00000 0.00000 0.00000 0.00000 MINI CONSTR> 23.01402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -53.02185 0.00291 0.04665 0.00823 MINI INTERN> 4.66864 14.70287 0.00000 8.54373 3.13046 MINI EXTERN> -86.10595 -20.96039 0.00000 0.00000 0.00000 MINI CONSTR> 22.99881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -53.02539 0.00355 0.05304 0.01254 MINI INTERN> 4.68459 14.68228 0.00000 8.59185 3.13317 MINI EXTERN> -86.07285 -21.02524 0.00000 0.00000 0.00000 MINI CONSTR> 22.98079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -53.02913 0.00374 0.04596 0.01143 MINI INTERN> 4.67603 14.68925 0.00000 8.61622 3.14347 MINI EXTERN> -86.09683 -21.02521 0.00000 0.00000 0.00000 MINI CONSTR> 22.96793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -53.03294 0.00381 0.05385 0.01248 MINI INTERN> 4.68190 14.71065 0.00000 8.65318 3.12854 MINI EXTERN> -86.12938 -21.04177 0.00000 0.00000 0.00000 MINI CONSTR> 22.96394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -53.03802 0.00508 0.06840 0.01951 MINI INTERN> 4.69949 14.69835 0.00000 8.70878 3.12836 MINI EXTERN> -86.16076 -21.08331 0.00000 0.00000 0.00000 MINI CONSTR> 22.97106 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 -53.03802 0.00508 0.06840 0.02000 CONJ INTERN> 4.69949 14.69835 0.00000 8.70878 3.12836 CONJ EXTERN> -86.16076 -21.08331 0.00000 0.00000 0.00000 CONJ CONSTR> 22.97106 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 ASP 1 HT1 ) 0.20307 ( PROT ASP 1 HT2 ) 0.20307 ( PROT ASP 1 N ) 0.25384 ( PROT ASP 1 HT3 ) 0.20307 ( PROT ASP 1 CA ) 0.25384 ( PROT ASP 1 CB ) 0.20307 ( PROT ASP 1 CG ) 0.20307 ( PROT ASP 1 OD1 ) 0.20307 ( PROT ASP 1 OD2 ) 0.20307 ( PROT ASP 1 C ) 0.25384 ( PROT ASP 1 O ) 0.25384 ( PROT TYR 2 N ) 0.25384 ( PROT TYR 2 H ) 0.20307 ( PROT TYR 2 CA ) 0.25384 ( PROT TYR 2 CB ) 0.20307 ( PROT TYR 2 CG ) 0.20307 ( PROT TYR 2 CD1 ) 0.20307 ( PROT TYR 2 CE1 ) 0.20307 ( PROT TYR 2 CD2 ) 0.20307 ( PROT TYR 2 CE2 ) 0.20307 ( PROT TYR 2 CZ ) 0.20307 ( PROT TYR 2 OH ) 0.20307 ( PROT TYR 2 HH ) 0.20307 ( PROT TYR 2 C ) 0.25384 ( PROT TYR 2 O ) 0.25384 ( PROT ALA 3 N ) 0.25384 ( PROT ALA 3 H ) 0.20307 ( PROT ALA 3 CA ) 0.25384 ( PROT ALA 3 CB ) 0.20307 ( PROT ALA 3 C ) 0.25384 ( PROT ALA 3 O ) 0.25384 ( PROT PHE 4 N ) 0.25384 ( PROT PHE 4 H ) 0.20307 ( PROT PHE 4 CA ) 0.25384 ( PROT PHE 4 CB ) 0.20307 ( PROT PHE 4 CG ) 0.20307 ( PROT PHE 4 CD1 ) 0.20307 ( PROT PHE 4 CD2 ) 0.20307 ( PROT PHE 4 CE1 ) 0.20307 ( PROT PHE 4 CE2 ) 0.20307 ( PROT PHE 4 CZ ) 0.20307 ( PROT PHE 4 C ) 0.25384 ( PROT PHE 4 O ) 0.25384 ( PROT ILE 5 N ) 0.25384 ( PROT ILE 5 H ) 0.20307 ( PROT ILE 5 CA ) 0.25384 ( PROT ILE 5 CB ) 0.20307 ( PROT ILE 5 CG2 ) 0.20307 ( PROT ILE 5 CG1 ) 0.20307 ( PROT ILE 5 CD ) 0.20307 ( PROT ILE 5 C ) 0.25384 ( PROT ILE 5 O ) 0.25384 ( PROT ALA 6 N ) 0.25384 ( PROT ALA 6 H ) 0.20307 ( PROT ALA 6 CA ) 0.25384 ( PROT ALA 6 CB ) 0.20307 ( PROT ALA 6 C ) 0.25384 ( PROT ALA 6 O ) 0.25384 ( PROT SER 7 N ) 0.25384 ( PROT SER 7 H ) 0.20307 ( PROT SER 7 CA ) 0.25384 ( PROT SER 7 CB ) 0.20307 ( PROT SER 7 OG ) 0.20307 ( PROT SER 7 HG ) 0.20307 ( PROT SER 7 C ) 0.25384 ( PROT SER 7 O ) 0.25384 ( PROT LEU 8 N ) 0.25384 ( PROT LEU 8 H ) 0.20307 ( PROT LEU 8 CA ) 0.25384 ( PROT LEU 8 CB ) 0.20307 ( PROT LEU 8 CG ) 0.20307 ( PROT LEU 8 CD1 ) 0.20307 ( PROT LEU 8 CD2 ) 0.20307 ( PROT LEU 8 C ) 0.25384 ( PROT LEU 8 O ) 0.25384 ( PROT VAL 9 N ) 0.25384 ( PROT VAL 9 H ) 0.20307 ( PROT VAL 9 CA ) 0.25384 ( PROT VAL 9 CB ) 0.20307 ( PROT VAL 9 CG1 ) 0.20307 ( PROT VAL 9 CG2 ) 0.20307 ( PROT VAL 9 C ) 0.25384 ( PROT VAL 9 O ) 0.25384 ( PROT VAL 10 N ) 0.25384 ( PROT VAL 10 H ) 0.20307 ( PROT VAL 10 CA ) 0.25384 ( PROT VAL 10 CB ) 0.20307 ( PROT VAL 10 CG1 ) 0.20307 ( PROT VAL 10 CG2 ) 0.20307 ( PROT VAL 10 C ) 0.25384 ( PROT VAL 10 O ) 0.25384 ( PROT ILE 11 N ) 0.25384 ( PROT ILE 11 H ) 0.20307 ( PROT ILE 11 CA ) 0.25384 ( PROT ILE 11 CB ) 0.20307 ( PROT ILE 11 CG2 ) 0.20307 ( PROT ILE 11 CG1 ) 0.20307 ( PROT ILE 11 CD ) 0.20307 ( PROT ILE 11 C ) 0.25384 ( PROT ILE 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 ASP 13 N ) 0.25384 ( PROT ASP 13 H ) 0.20307 ( PROT ASP 13 CA ) 0.25384 ( PROT ASP 13 CB ) 0.20307 ( PROT ASP 13 CG ) 0.20307 ( PROT ASP 13 OD1 ) 0.20307 ( PROT ASP 13 OD2 ) 0.20307 ( PROT ASP 13 C ) 0.25384 ( PROT ASP 13 O ) 0.25384 ( PROT ASP 14 N ) 0.25384 ( PROT ASP 14 H ) 0.20307 ( PROT ASP 14 CA ) 0.25384 ( PROT ASP 14 CB ) 0.20307 ( PROT ASP 14 CG ) 0.20307 ( PROT ASP 14 OD1 ) 0.20307 ( PROT ASP 14 OD2 ) 0.20307 ( PROT ASP 14 C ) 0.25384 ( PROT ASP 14 O ) 0.25384 ( PROT VAL 15 N ) 0.25384 ( PROT VAL 15 H ) 0.20307 ( PROT VAL 15 CA ) 0.25384 ( PROT VAL 15 CB ) 0.20307 ( PROT VAL 15 CG1 ) 0.20307 ( PROT VAL 15 CG2 ) 0.20307 ( PROT VAL 15 C ) 0.25384 ( PROT VAL 15 O ) 0.25384 ( PROT ASN 16 N ) 0.25384 ( PROT ASN 16 H ) 0.20307 ( PROT ASN 16 CA ) 0.25384 ( PROT ASN 16 CB ) 0.20307 ( PROT ASN 16 CG ) 0.20307 ( PROT ASN 16 OD1 ) 0.20307 ( PROT ASN 16 ND2 ) 0.20307 ( PROT ASN 16 HD21 ) 0.20307 ( PROT ASN 16 HD22 ) 0.20307 ( PROT ASN 16 C ) 0.25384 ( PROT ASN 16 O ) 0.25384 ( PROT ARG 17 N ) 0.25384 ( PROT ARG 17 H ) 0.20307 ( PROT ARG 17 CA ) 0.25384 ( PROT ARG 17 CB ) 0.20307 ( PROT ARG 17 CG ) 0.20307 ( PROT ARG 17 CD ) 0.20307 ( PROT ARG 17 NE ) 0.20307 ( PROT ARG 17 HE ) 0.20307 ( PROT ARG 17 CZ ) 0.20307 ( PROT ARG 17 NH1 ) 0.20307 ( PROT ARG 17 HH11 ) 0.20307 ( PROT ARG 17 HH12 ) 0.20307 ( PROT ARG 17 NH2 ) 0.20307 ( PROT ARG 17 HH21 ) 0.20307 ( PROT ARG 17 HH22 ) 0.20307 ( PROT ARG 17 C ) 0.25384 ( PROT ARG 17 OT1 ) 0.20307 ( PROT ARG 17 OT2 ) 0.20307 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.95854 3.70607 -6.79661 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00528 0.00526 -0.00539 ROTATION MATRIX 1.000000 0.000335 0.000363 -0.000335 1.000000 0.000304 -0.000363 -0.000304 1.000000 AXIS OF ROTATION IS 0.524588 -0.625995 0.577007 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 66.1179 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.634947 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.6349" Parameter: A <- "0.6349" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.79257 3.80186 -7.00225 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.02039 -0.01015 0.02502 ROTATION MATRIX 0.999283 0.025499 0.027998 -0.024451 0.999010 -0.037171 -0.028918 0.036460 0.998917 AXIS OF ROTATION IS -0.697116 -0.538869 0.472916 ANGLE IS 3.03 CENTER OF ROTATION 7.618143 3.944316 -7.063724 SHIFT IS 0.031519 TOTAL SQUARE DIFF IS 5.5431 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.571020 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.6349" RDCMND substituted energy or value "?RMS" to " 0.5710" Parameter: A <- "0.6349 0.5710" 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 0.6349 0.5710 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 " 22.97" Parameter: H <- "22.97" 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 -76.00908 22.97106 0.26667 ENER INTERN> 4.69949 14.69835 0.00000 8.70878 3.12836 ENER EXTERN> -86.16076 -21.08331 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 " -76.01" Parameter: B <- "-76.01" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -21.08" Parameter: C <- "-21.08" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -86.16" Parameter: C <- " -107.24" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -107.24" 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 " 14.70" Parameter: D <- " 19.40" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 8.71" Parameter: D <- " 28.11" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.13" Parameter: D <- " 31.24" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 31.24" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 9600 ENER= -76.01 GRMS= 0.27 ELEC= -21.08 VDW= -86.16 RDTITL> *EXTERNAL= -107.24 INTERNAL= 31.24 USER= 0.00 HARM= 22.97 RDTITL> *BOND= 4.70 ANGL= 14.70 DIHE= 8.71 IMPR= 3.13 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= -76.01 GRMS= 0.27 ELEC= -21.08 VDW= -86.16 RDTITL> *EXTERNAL= -107.24 INTERNAL= 31.24 USER= 0.00 HARM= 22.97 RDTITL> *BOND= 4.70 ANGL= 14.70 DIHE= 8.71 IMPR= 3.13 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= -76.01 GRMS= 0.27 ELEC= -21.08 VDW= -86.16 RDTITL> *EXTERNAL= -107.24 INTERNAL= 31.24 USER= 0.00 HARM= 22.97 RDTITL> *BOND= 4.70 ANGL= 14.70 DIHE= 8.71 IMPR= 3.13 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 9600 0.6349 0.5710 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "9600" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9047 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9032 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 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 -59.61259 -16.39649 0.12483 0.02000 MINI INTERN> 4.69949 14.69835 0.00000 8.70878 3.12836 MINI EXTERN> -86.16076 -21.08331 0.00000 0.00000 0.00000 MINI CONSTR> 16.39649 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -56.54626 -3.06633 6.41003 0.00360 MINI INTERN> 7.72965 15.50140 0.00000 8.82973 3.12041 MINI EXTERN> -88.47486 -20.14442 0.00000 0.00000 0.00000 MINI CONSTR> 16.89183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9023 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -59.29527 2.74901 2.80349 0.00156 MINI INTERN> 5.40260 15.12715 0.00000 8.80073 3.15521 MINI EXTERN> -88.15985 -20.51233 0.00000 0.00000 0.00000 MINI CONSTR> 16.89121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -59.96355 0.66828 0.11605 0.00028 MINI INTERN> 4.81672 14.93081 0.00000 8.79852 3.14116 MINI EXTERN> -87.97337 -20.57076 0.00000 0.00000 0.00000 MINI CONSTR> 16.89339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9024 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -59.98874 0.02519 0.12830 0.00012 MINI INTERN> 4.80238 14.86403 0.00000 8.78362 3.13872 MINI EXTERN> -87.80669 -20.67121 0.00000 0.00000 0.00000 MINI CONSTR> 16.90041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -60.00497 0.01623 0.11820 0.00013 MINI INTERN> 4.78853 14.83663 0.00000 8.77406 3.13821 MINI EXTERN> -87.73782 -20.71239 0.00000 0.00000 0.00000 MINI CONSTR> 16.90781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9024 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -60.01971 0.01473 0.13312 0.00013 MINI INTERN> 4.77912 14.81608 0.00000 8.76584 3.13708 MINI EXTERN> -87.69098 -20.74327 0.00000 0.00000 0.00000 MINI CONSTR> 16.91642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -60.03188 0.01217 0.19635 0.00013 MINI INTERN> 4.77162 14.80244 0.00000 8.75849 3.13573 MINI EXTERN> -87.65969 -20.76622 0.00000 0.00000 0.00000 MINI CONSTR> 16.92576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9024 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -60.04499 0.01311 0.20768 0.00014 MINI INTERN> 4.76908 14.78664 0.00000 8.75216 3.13436 MINI EXTERN> -87.64036 -20.78240 0.00000 0.00000 0.00000 MINI CONSTR> 16.93551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -60.05693 0.01194 0.22390 0.00014 MINI INTERN> 4.75709 14.78262 0.00000 8.74669 3.13432 MINI EXTERN> -87.62833 -20.79475 0.00000 0.00000 0.00000 MINI CONSTR> 16.94543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9024 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -60.06877 0.01184 0.23808 0.00015 MINI INTERN> 4.75340 14.77303 0.00000 8.74199 3.13315 MINI EXTERN> -87.62216 -20.80375 0.00000 0.00000 0.00000 MINI CONSTR> 16.95555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -60.08058 0.01180 0.22575 0.00016 MINI INTERN> 4.74352 14.77018 0.00000 8.73785 3.13345 MINI EXTERN> -87.62025 -20.81052 0.00000 0.00000 0.00000 MINI CONSTR> 16.96520 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9024 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -60.09259 0.01201 0.23941 0.00016 MINI INTERN> 4.74545 14.75755 0.00000 8.73332 3.13183 MINI EXTERN> -87.62103 -20.81581 0.00000 0.00000 0.00000 MINI CONSTR> 16.97609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -60.10785 0.01526 0.07813 0.00007 MINI INTERN> 4.74390 14.74449 0.00000 8.72803 3.13469 MINI EXTERN> -87.62893 -20.81578 0.00000 0.00000 0.00000 MINI CONSTR> 16.98574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9024 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -60.11449 0.00664 0.25915 0.00017 MINI INTERN> 4.73531 14.74901 0.00000 8.72643 3.13065 MINI EXTERN> -87.62877 -20.82381 0.00000 0.00000 0.00000 MINI CONSTR> 16.99668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -60.13060 0.01611 0.08197 0.00007 MINI INTERN> 4.74250 14.72931 0.00000 8.72072 3.13331 MINI EXTERN> -87.64124 -20.82182 0.00000 0.00000 0.00000 MINI CONSTR> 17.00664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9024 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -60.13561 0.00502 0.27933 0.00019 MINI INTERN> 4.72097 14.74728 0.00000 8.72045 3.13057 MINI EXTERN> -87.64200 -20.83015 0.00000 0.00000 0.00000 MINI CONSTR> 17.01726 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -60.14563 0.01001 0.31488 0.00019 MINI INTERN> 4.73348 14.72871 0.00000 8.71691 3.12824 MINI EXTERN> -87.65198 -20.82880 0.00000 0.00000 0.00000 MINI CONSTR> 17.02781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9023 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -60.16346 0.01783 0.09040 0.00008 MINI INTERN> 4.74274 14.70854 0.00000 8.71105 3.13117 MINI EXTERN> -87.66790 -20.82677 0.00000 0.00000 0.00000 MINI CONSTR> 17.03771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -60.17322 0.00976 0.07242 0.00009 MINI INTERN> 4.73978 14.70538 0.00000 8.70884 3.13013 MINI EXTERN> -87.67574 -20.82838 0.00000 0.00000 0.00000 MINI CONSTR> 17.04676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9023 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -60.17680 0.00358 0.32163 0.00022 MINI INTERN> 4.71168 14.72945 0.00000 8.70985 3.12693 MINI EXTERN> -87.67830 -20.83507 0.00000 0.00000 0.00000 MINI CONSTR> 17.05865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -60.19595 0.01915 0.11436 0.00009 MINI INTERN> 4.74476 14.68917 0.00000 8.70199 3.12919 MINI EXTERN> -87.70166 -20.82869 0.00000 0.00000 0.00000 MINI CONSTR> 17.06930 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9022 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -60.20537 0.00942 0.07132 0.00010 MINI INTERN> 4.73844 14.68913 0.00000 8.70052 3.12792 MINI EXTERN> -87.70867 -20.83039 0.00000 0.00000 0.00000 MINI CONSTR> 17.07768 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -60.21664 0.01126 0.07573 0.00010 MINI INTERN> 4.73944 14.68261 0.00000 8.69754 3.12718 MINI EXTERN> -87.72156 -20.83048 0.00000 0.00000 0.00000 MINI CONSTR> 17.08863 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9022 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -60.22671 0.01008 0.14813 0.00010 MINI INTERN> 4.74918 14.67067 0.00000 8.69347 3.12721 MINI EXTERN> -87.73816 -20.82893 0.00000 0.00000 0.00000 MINI CONSTR> 17.09985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -60.23767 0.01095 0.09119 0.00011 MINI INTERN> 4.74092 14.67148 0.00000 8.69193 3.12602 MINI EXTERN> -87.74685 -20.83042 0.00000 0.00000 0.00000 MINI CONSTR> 17.10926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9021 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -60.24855 0.01088 0.09729 0.00011 MINI INTERN> 4.74067 14.66667 0.00000 8.68925 3.12527 MINI EXTERN> -87.76001 -20.83031 0.00000 0.00000 0.00000 MINI CONSTR> 17.11991 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -60.25842 0.00987 0.12911 0.00012 MINI INTERN> 4.74303 14.66093 0.00000 8.68618 3.12506 MINI EXTERN> -87.77396 -20.82980 0.00000 0.00000 0.00000 MINI CONSTR> 17.13015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9021 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -60.26674 0.00832 0.17291 0.00012 MINI INTERN> 4.75074 14.65166 0.00000 8.68313 3.12444 MINI EXTERN> -87.78765 -20.82845 0.00000 0.00000 0.00000 MINI CONSTR> 17.13939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -60.27692 0.01017 0.18052 0.00012 MINI INTERN> 4.74613 14.65147 0.00000 8.68079 3.12420 MINI EXTERN> -87.80008 -20.82892 0.00000 0.00000 0.00000 MINI CONSTR> 17.14950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9021 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -60.28575 0.00884 0.20951 0.00013 MINI INTERN> 4.75262 14.64198 0.00000 8.67823 3.12265 MINI EXTERN> -87.81278 -20.82731 0.00000 0.00000 0.00000 MINI CONSTR> 17.15886 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -60.29498 0.00923 0.19072 0.00013 MINI INTERN> 4.75261 14.63843 0.00000 8.67578 3.12240 MINI EXTERN> -87.82381 -20.82771 0.00000 0.00000 0.00000 MINI CONSTR> 17.16732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9020 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -60.30469 0.00970 0.21372 0.00014 MINI INTERN> 4.74970 14.63741 0.00000 8.67328 3.12213 MINI EXTERN> -87.83742 -20.82734 0.00000 0.00000 0.00000 MINI CONSTR> 17.17755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -60.31389 0.00920 0.20557 0.00014 MINI INTERN> 4.75162 14.63164 0.00000 8.67107 3.12104 MINI EXTERN> -87.84831 -20.82703 0.00000 0.00000 0.00000 MINI CONSTR> 17.18608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9019 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -60.32332 0.00944 0.21873 0.00015 MINI INTERN> 4.74393 14.63433 0.00000 8.66902 3.12110 MINI EXTERN> -87.85928 -20.82800 0.00000 0.00000 0.00000 MINI CONSTR> 17.19559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -60.33521 0.01189 0.06973 0.00006 MINI INTERN> 4.73516 14.63220 0.00000 8.66864 3.11850 MINI EXTERN> -87.86176 -20.83122 0.00000 0.00000 0.00000 MINI CONSTR> 17.20326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9019 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -60.34008 0.00487 0.23527 0.00016 MINI INTERN> 4.75142 14.62212 0.00000 8.66402 3.11952 MINI EXTERN> -87.88308 -20.82650 0.00000 0.00000 0.00000 MINI CONSTR> 17.21242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -60.34830 0.00822 0.26723 0.00017 MINI INTERN> 4.75605 14.61353 0.00000 8.66221 3.11720 MINI EXTERN> -87.89310 -20.82521 0.00000 0.00000 0.00000 MINI CONSTR> 17.22101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9018 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -60.35708 0.00878 0.25588 0.00017 MINI INTERN> 4.75490 14.61311 0.00000 8.65922 3.11808 MINI EXTERN> -87.90671 -20.82528 0.00000 0.00000 0.00000 MINI CONSTR> 17.22960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -60.37121 0.01413 0.07913 0.00007 MINI INTERN> 4.73482 14.61769 0.00000 8.65953 3.11596 MINI EXTERN> -87.90640 -20.83064 0.00000 0.00000 0.00000 MINI CONSTR> 17.23781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9017 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -60.37913 0.00792 0.06634 0.00008 MINI INTERN> 4.73485 14.61482 0.00000 8.65739 3.11569 MINI EXTERN> -87.91698 -20.83008 0.00000 0.00000 0.00000 MINI CONSTR> 17.24518 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -60.38765 0.00852 0.06845 0.00008 MINI INTERN> 4.73458 14.61155 0.00000 8.65523 3.11507 MINI EXTERN> -87.92744 -20.82993 0.00000 0.00000 0.00000 MINI CONSTR> 17.25329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9017 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -60.39622 0.00857 0.06591 0.00008 MINI INTERN> 4.73505 14.60784 0.00000 8.65294 3.11450 MINI EXTERN> -87.93842 -20.82950 0.00000 0.00000 0.00000 MINI CONSTR> 17.26137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -60.40509 0.00886 0.06739 0.00009 MINI INTERN> 4.73477 14.60465 0.00000 8.65062 3.11394 MINI EXTERN> -87.94946 -20.82937 0.00000 0.00000 0.00000 MINI CONSTR> 17.26976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9016 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -60.41371 0.00863 0.12024 0.00009 MINI INTERN> 4.73369 14.60178 0.00000 8.64851 3.11293 MINI EXTERN> -87.95903 -20.83032 0.00000 0.00000 0.00000 MINI CONSTR> 17.27872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -60.42149 0.00778 0.06512 0.00009 MINI INTERN> 4.73498 14.59820 0.00000 8.64624 3.11287 MINI EXTERN> -87.97019 -20.82873 0.00000 0.00000 0.00000 MINI CONSTR> 17.28515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9016 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -60.42989 0.00840 0.13744 0.00010 MINI INTERN> 4.73270 14.59664 0.00000 8.64416 3.11200 MINI EXTERN> -87.97931 -20.83036 0.00000 0.00000 0.00000 MINI CONSTR> 17.29427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -60.43858 0.00869 0.09888 0.00010 MINI INTERN> 4.73559 14.59069 0.00000 8.64173 3.11129 MINI EXTERN> -87.99093 -20.82850 0.00000 0.00000 0.00000 MINI CONSTR> 17.30154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9016 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -60.44550 0.00692 0.14817 0.00010 MINI INTERN> 4.73333 14.58996 0.00000 8.63994 3.11076 MINI EXTERN> -87.99888 -20.82968 0.00000 0.00000 0.00000 MINI CONSTR> 17.30906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -60.45440 0.00889 0.10746 0.00011 MINI INTERN> 4.73286 14.58749 0.00000 8.63747 3.11071 MINI EXTERN> -88.01045 -20.82891 0.00000 0.00000 0.00000 MINI CONSTR> 17.31643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9017 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -60.46082 0.00642 0.16015 0.00011 MINI INTERN> 4.73079 14.58687 0.00000 8.63576 3.11021 MINI EXTERN> -88.01803 -20.82998 0.00000 0.00000 0.00000 MINI CONSTR> 17.32356 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -60.46810 0.00728 0.18347 0.00011 MINI INTERN> 4.73500 14.58000 0.00000 8.63359 3.10890 MINI EXTERN> -88.02782 -20.82858 0.00000 0.00000 0.00000 MINI CONSTR> 17.33081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9016 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -60.47575 0.00765 0.16889 0.00012 MINI INTERN> 4.73050 14.58132 0.00000 8.63171 3.10910 MINI EXTERN> -88.03637 -20.82957 0.00000 0.00000 0.00000 MINI CONSTR> 17.33757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -60.48305 0.00731 0.20593 0.00012 MINI INTERN> 4.73680 14.57314 0.00000 8.62921 3.10769 MINI EXTERN> -88.04727 -20.82778 0.00000 0.00000 0.00000 MINI CONSTR> 17.34517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9016 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -60.49058 0.00752 0.18624 0.00013 MINI INTERN> 4.73346 14.57308 0.00000 8.62741 3.10760 MINI EXTERN> -88.05537 -20.82832 0.00000 0.00000 0.00000 MINI CONSTR> 17.35156 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -60.49802 0.00744 0.20140 0.00013 MINI INTERN> 4.72967 14.57523 0.00000 8.62504 3.10825 MINI EXTERN> -88.06575 -20.82918 0.00000 0.00000 0.00000 MINI CONSTR> 17.35871 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9014 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -60.50758 0.00956 0.06334 0.00006 MINI INTERN> 4.73708 14.56450 0.00000 8.62239 3.10704 MINI EXTERN> -88.07863 -20.82450 0.00000 0.00000 0.00000 MINI CONSTR> 17.36454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -60.51184 0.00426 0.21035 0.00014 MINI INTERN> 4.73303 14.56570 0.00000 8.62137 3.10610 MINI EXTERN> -88.08181 -20.82788 0.00000 0.00000 0.00000 MINI CONSTR> 17.37164 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9014 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -60.52235 0.01051 0.06789 0.00006 MINI INTERN> 4.73791 14.55847 0.00000 8.61813 3.10596 MINI EXTERN> -88.09718 -20.82358 0.00000 0.00000 0.00000 MINI CONSTR> 17.37793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -60.52541 0.00306 0.23522 0.00015 MINI INTERN> 4.72757 14.56707 0.00000 8.61730 3.10640 MINI EXTERN> -88.09922 -20.82922 0.00000 0.00000 0.00000 MINI CONSTR> 17.38469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9014 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -60.53672 0.01131 0.07254 0.00007 MINI INTERN> 4.73849 14.55289 0.00000 8.61394 3.10496 MINI EXTERN> -88.11513 -20.82275 0.00000 0.00000 0.00000 MINI CONSTR> 17.39088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -60.53919 0.00247 0.24182 0.00016 MINI INTERN> 4.72746 14.56172 0.00000 8.61345 3.10518 MINI EXTERN> -88.11542 -20.82899 0.00000 0.00000 0.00000 MINI CONSTR> 17.39741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9014 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -60.55109 0.01190 0.08401 0.00007 MINI INTERN> 4.73894 14.54762 0.00000 8.60968 3.10401 MINI EXTERN> -88.13327 -20.82191 0.00000 0.00000 0.00000 MINI CONSTR> 17.40384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -60.55748 0.00639 0.06161 0.00007 MINI INTERN> 4.73791 14.54564 0.00000 8.60808 3.10350 MINI EXTERN> -88.13965 -20.82219 0.00000 0.00000 0.00000 MINI CONSTR> 17.40923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9014 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -60.56448 0.00700 0.06450 0.00008 MINI INTERN> 4.73831 14.54292 0.00000 8.60597 3.10302 MINI EXTERN> -88.14845 -20.82171 0.00000 0.00000 0.00000 MINI CONSTR> 17.41545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -60.57177 0.00729 0.10138 0.00008 MINI INTERN> 4.74035 14.53941 0.00000 8.60343 3.10254 MINI EXTERN> -88.15941 -20.82047 0.00000 0.00000 0.00000 MINI CONSTR> 17.42239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9014 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -60.57880 0.00703 0.08052 0.00008 MINI INTERN> 4.73994 14.53658 0.00000 8.60163 3.10186 MINI EXTERN> -88.16659 -20.82043 0.00000 0.00000 0.00000 MINI CONSTR> 17.42822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -60.58557 0.00678 0.08843 0.00009 MINI INTERN> 4.74027 14.53427 0.00000 8.59949 3.10149 MINI EXTERN> -88.17542 -20.81994 0.00000 0.00000 0.00000 MINI CONSTR> 17.43428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9014 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -60.59281 0.00724 0.08120 0.00009 MINI INTERN> 4.73920 14.53249 0.00000 8.59747 3.10107 MINI EXTERN> -88.18355 -20.81998 0.00000 0.00000 0.00000 MINI CONSTR> 17.44049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -60.59992 0.00711 0.09328 0.00009 MINI INTERN> 4.74079 14.52856 0.00000 8.59527 3.10032 MINI EXTERN> -88.19258 -20.81909 0.00000 0.00000 0.00000 MINI CONSTR> 17.44680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -60.60583 0.00591 0.13652 0.00010 MINI INTERN> 4.74254 14.52611 0.00000 8.59300 3.09999 MINI EXTERN> -88.20219 -20.81803 0.00000 0.00000 0.00000 MINI CONSTR> 17.45275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -60.61365 0.00783 0.08745 0.00010 MINI INTERN> 4.74023 14.52411 0.00000 8.59126 3.09938 MINI EXTERN> -88.20858 -20.81865 0.00000 0.00000 0.00000 MINI CONSTR> 17.45859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -60.61937 0.00571 0.14497 0.00010 MINI INTERN> 4.74279 14.52117 0.00000 8.58893 3.09896 MINI EXTERN> -88.21857 -20.81724 0.00000 0.00000 0.00000 MINI CONSTR> 17.46459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -60.62669 0.00732 0.14818 0.00011 MINI INTERN> 4.74234 14.51882 0.00000 8.58683 3.09839 MINI EXTERN> -88.22700 -20.81700 0.00000 0.00000 0.00000 MINI CONSTR> 17.47093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -60.63387 0.00718 0.15997 0.00011 MINI INTERN> 4.74058 14.51811 0.00000 8.58467 3.09817 MINI EXTERN> -88.23549 -20.81723 0.00000 0.00000 0.00000 MINI CONSTR> 17.47733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -60.63984 0.00597 0.18811 0.00011 MINI INTERN> 4.74520 14.51170 0.00000 8.58269 3.09683 MINI EXTERN> -88.24367 -20.81559 0.00000 0.00000 0.00000 MINI CONSTR> 17.48299 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -60.64627 0.00643 0.16957 0.00012 MINI INTERN> 4.74345 14.51118 0.00000 8.58081 3.09677 MINI EXTERN> -88.25084 -20.81568 0.00000 0.00000 0.00000 MINI CONSTR> 17.48806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -60.65274 0.00646 0.18724 0.00012 MINI INTERN> 4.73875 14.51390 0.00000 8.57873 3.09727 MINI EXTERN> -88.25810 -20.81718 0.00000 0.00000 0.00000 MINI CONSTR> 17.49389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -60.66108 0.00834 0.05761 0.00005 MINI INTERN> 4.73772 14.50952 0.00000 8.57718 3.09629 MINI EXTERN> -88.26243 -20.81791 0.00000 0.00000 0.00000 MINI CONSTR> 17.49855 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -60.66483 0.00375 0.19273 0.00013 MINI INTERN> 4.74498 14.50377 0.00000 8.57494 3.09522 MINI EXTERN> -88.27367 -20.81432 0.00000 0.00000 0.00000 MINI CONSTR> 17.50425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -60.67386 0.00903 0.06291 0.00006 MINI INTERN> 4.73800 14.50493 0.00000 8.57323 3.09534 MINI EXTERN> -88.27730 -20.81734 0.00000 0.00000 0.00000 MINI CONSTR> 17.50927 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -60.67637 0.00250 0.22072 0.00014 MINI INTERN> 4.73999 14.50567 0.00000 8.57105 3.09559 MINI EXTERN> -88.28759 -20.81568 0.00000 0.00000 0.00000 MINI CONSTR> 17.51460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -60.68208 0.00571 0.23388 0.00015 MINI INTERN> 4.74891 14.49474 0.00000 8.56926 3.09331 MINI EXTERN> -88.29533 -20.81257 0.00000 0.00000 0.00000 MINI CONSTR> 17.51960 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -60.69223 0.01016 0.06669 0.00006 MINI INTERN> 4.73789 14.49893 0.00000 8.56753 3.09409 MINI EXTERN> -88.29860 -20.81659 0.00000 0.00000 0.00000 MINI CONSTR> 17.52451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -60.69794 0.00571 0.05556 0.00007 MINI INTERN> 4.73839 14.49651 0.00000 8.56579 3.09361 MINI EXTERN> -88.30542 -20.81591 0.00000 0.00000 0.00000 MINI CONSTR> 17.52909 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -60.70418 0.00624 0.05771 0.00007 MINI INTERN> 4.73818 14.49467 0.00000 8.56384 3.09321 MINI EXTERN> -88.31255 -20.81575 0.00000 0.00000 0.00000 MINI CONSTR> 17.53422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -60.71036 0.00618 0.05666 0.00007 MINI INTERN> 4.73850 14.49231 0.00000 8.56191 3.09272 MINI EXTERN> -88.31972 -20.81533 0.00000 0.00000 0.00000 MINI CONSTR> 17.53924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -60.71683 0.00647 0.09413 0.00007 MINI INTERN> 4.73797 14.49100 0.00000 8.55971 3.09241 MINI EXTERN> -88.32705 -20.81581 0.00000 0.00000 0.00000 MINI CONSTR> 17.54493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -60.72284 0.00600 0.07521 0.00008 MINI INTERN> 4.73915 14.48765 0.00000 8.55794 3.09172 MINI EXTERN> -88.33399 -20.81482 0.00000 0.00000 0.00000 MINI CONSTR> 17.54952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -60.72863 0.00580 0.08166 0.00008 MINI INTERN> 4.73859 14.48640 0.00000 8.55608 3.09144 MINI EXTERN> -88.34053 -20.81489 0.00000 0.00000 0.00000 MINI CONSTR> 17.55428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -60.73483 0.00620 0.07577 0.00008 MINI INTERN> 4.73826 14.48474 0.00000 8.55414 3.09109 MINI EXTERN> -88.34766 -20.81460 0.00000 0.00000 0.00000 MINI CONSTR> 17.55919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -60.74077 0.00593 0.09099 0.00008 MINI INTERN> 4.73946 14.48170 0.00000 8.55220 3.09044 MINI EXTERN> -88.35452 -20.81415 0.00000 0.00000 0.00000 MINI CONSTR> 17.56410 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -60.74590 0.00513 0.12656 0.00009 MINI INTERN> 4.73861 14.48141 0.00000 8.55033 3.09033 MINI EXTERN> -88.36062 -20.81474 0.00000 0.00000 0.00000 MINI CONSTR> 17.56878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -60.75236 0.00646 0.09266 0.00009 MINI INTERN> 4.74012 14.47733 0.00000 8.54853 3.08950 MINI EXTERN> -88.36780 -20.81336 0.00000 0.00000 0.00000 MINI CONSTR> 17.57331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -60.75705 0.00469 0.13683 0.00009 MINI INTERN> 4.74087 14.47562 0.00000 8.54675 3.08909 MINI EXTERN> -88.37353 -20.81359 0.00000 0.00000 0.00000 MINI CONSTR> 17.57774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -60.76240 0.00535 0.15393 0.00010 MINI INTERN> 4.73801 14.47726 0.00000 8.54487 3.08938 MINI EXTERN> -88.37979 -20.81449 0.00000 0.00000 0.00000 MINI CONSTR> 17.58236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -60.76799 0.00559 0.14488 0.00010 MINI INTERN> 4.74078 14.47237 0.00000 8.54321 3.08836 MINI EXTERN> -88.38593 -20.81330 0.00000 0.00000 0.00000 MINI CONSTR> 17.58652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -60.77310 0.00510 0.17583 0.00011 MINI INTERN> 4.73765 14.47471 0.00000 8.54127 3.08878 MINI EXTERN> -88.39240 -20.81432 0.00000 0.00000 0.00000 MINI CONSTR> 17.59121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -60.77863 0.00554 0.15877 0.00011 MINI INTERN> 4.73843 14.47177 0.00000 8.53968 3.08815 MINI EXTERN> -88.39805 -20.81378 0.00000 0.00000 0.00000 MINI CONSTR> 17.59516 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -60.78409 0.00545 0.17149 0.00011 MINI INTERN> 4.74387 14.46453 0.00000 8.53792 3.08664 MINI EXTERN> -88.40492 -20.81158 0.00000 0.00000 0.00000 MINI CONSTR> 17.59945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -60.79112 0.00703 0.05422 0.00005 MINI INTERN> 4.73970 14.46535 0.00000 8.53641 3.08680 MINI EXTERN> -88.41175 -20.81085 0.00000 0.00000 0.00000 MINI CONSTR> 17.60323 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 -60.79112 0.00703 0.05422 0.00006 STPD INTERN> 4.73970 14.46535 0.00000 8.53641 3.08680 STPD EXTERN> -88.41175 -20.81085 0.00000 0.00000 0.00000 STPD CONSTR> 17.60323 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 9012 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9012 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 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 -60.79112 0.00703 0.05422 0.00000 MINI INTERN> 4.73970 14.46535 0.00000 8.53641 3.08680 MINI EXTERN> -88.41175 -20.81085 0.00000 0.00000 0.00000 MINI CONSTR> 17.60323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -61.66966 0.87854 0.12337 0.03165 MINI INTERN> 4.94370 14.12968 0.00000 8.07529 3.02867 MINI EXTERN> -90.55808 -20.70685 0.00000 0.00000 0.00000 MINI CONSTR> 19.41793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -61.69723 0.02758 0.14614 0.01355 MINI INTERN> 4.73896 14.03005 0.00000 8.05847 2.95710 MINI EXTERN> -90.25005 -20.66065 0.00000 0.00000 0.00000 MINI CONSTR> 19.42889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -61.73675 0.03952 0.20206 0.02331 MINI INTERN> 4.66314 13.84310 0.00000 8.03577 2.97617 MINI EXTERN> -89.96560 -20.65033 0.00000 0.00000 0.00000 MINI CONSTR> 19.36101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -61.80761 0.07086 0.24858 0.03782 MINI INTERN> 4.71271 13.97413 0.00000 8.02670 2.97916 MINI EXTERN> -89.86870 -20.81204 0.00000 0.00000 0.00000 MINI CONSTR> 19.18043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -61.88159 0.07399 0.23471 0.04300 MINI INTERN> 4.74791 14.11452 0.00000 7.95838 2.96501 MINI EXTERN> -89.73290 -20.89809 0.00000 0.00000 0.00000 MINI CONSTR> 18.96358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -61.95399 0.07239 0.23544 0.04379 MINI INTERN> 4.81391 14.27441 0.00000 7.99925 3.02487 MINI EXTERN> -89.71690 -21.09467 0.00000 0.00000 0.00000 MINI CONSTR> 18.74514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -62.01015 0.05616 0.18621 0.03003 MINI INTERN> 4.74803 14.38086 0.00000 7.98915 2.97635 MINI EXTERN> -89.57517 -21.10799 0.00000 0.00000 0.00000 MINI CONSTR> 18.57862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -62.04286 0.03271 0.14789 0.01934 MINI INTERN> 4.74955 14.36529 0.00000 8.00854 2.94738 MINI EXTERN> -89.50622 -21.09645 0.00000 0.00000 0.00000 MINI CONSTR> 18.48905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -62.06951 0.02665 0.14719 0.01517 MINI INTERN> 4.76799 14.39824 0.00000 8.05143 2.96939 MINI EXTERN> -89.57508 -21.11233 0.00000 0.00000 0.00000 MINI CONSTR> 18.43084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -62.09180 0.02229 0.13177 0.01818 MINI INTERN> 4.76469 14.30230 0.00000 8.09516 2.99141 MINI EXTERN> -89.49101 -21.15108 0.00000 0.00000 0.00000 MINI CONSTR> 18.39673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -62.11744 0.02564 0.15091 0.02116 MINI INTERN> 4.76529 14.37135 0.00000 8.13386 2.94470 MINI EXTERN> -89.50643 -21.20271 0.00000 0.00000 0.00000 MINI CONSTR> 18.37651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -62.14521 0.02777 0.15898 0.02594 MINI INTERN> 4.76395 14.38604 0.00000 8.18734 2.96674 MINI EXTERN> -89.51806 -21.30268 0.00000 0.00000 0.00000 MINI CONSTR> 18.37147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -62.17037 0.02516 0.12313 0.02495 MINI INTERN> 4.76729 14.45779 0.00000 8.25069 2.97076 MINI EXTERN> -89.51900 -21.47956 0.00000 0.00000 0.00000 MINI CONSTR> 18.38166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -62.18831 0.01794 0.11089 0.01626 MINI INTERN> 4.76936 14.47616 0.00000 8.27347 2.96665 MINI EXTERN> -89.62598 -21.45003 0.00000 0.00000 0.00000 MINI CONSTR> 18.40206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -62.20398 0.01567 0.11448 0.01455 MINI INTERN> 4.76313 14.42142 0.00000 8.28553 2.97654 MINI EXTERN> -89.66930 -21.41202 0.00000 0.00000 0.00000 MINI CONSTR> 18.43073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -62.22314 0.01916 0.13462 0.02003 MINI INTERN> 4.76563 14.38960 0.00000 8.32710 2.99216 MINI EXTERN> -89.69738 -21.47103 0.00000 0.00000 0.00000 MINI CONSTR> 18.47079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -62.24551 0.02237 0.14360 0.02930 MINI INTERN> 4.72623 14.31228 0.00000 8.33098 2.99253 MINI EXTERN> -89.70995 -21.41690 0.00000 0.00000 0.00000 MINI CONSTR> 18.51930 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -62.26759 0.02208 0.12246 0.02509 MINI INTERN> 4.73557 14.22929 0.00000 8.35088 2.98423 MINI EXTERN> -89.59350 -21.54626 0.00000 0.00000 0.00000 MINI CONSTR> 18.57221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -62.28511 0.01752 0.11190 0.02174 MINI INTERN> 4.74948 14.21128 0.00000 8.39237 3.00733 MINI EXTERN> -89.59161 -21.67857 0.00000 0.00000 0.00000 MINI CONSTR> 18.62461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -62.30121 0.01610 0.10902 0.01832 MINI INTERN> 4.74599 14.24776 0.00000 8.38221 3.02564 MINI EXTERN> -89.68032 -21.70707 0.00000 0.00000 0.00000 MINI CONSTR> 18.68458 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 -62.30121 0.01610 0.10902 0.02000 CONJ INTERN> 4.74599 14.24776 0.00000 8.38221 3.02564 CONJ EXTERN> -89.68032 -21.70707 0.00000 0.00000 0.00000 CONJ CONSTR> 18.68458 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 ASP 1 HT1 ) 0.13199 ( PROT ASP 1 HT2 ) 0.13199 ( PROT ASP 1 N ) 0.16499 ( PROT ASP 1 HT3 ) 0.13199 ( PROT ASP 1 CA ) 0.16499 ( PROT ASP 1 CB ) 0.13199 ( PROT ASP 1 CG ) 0.13199 ( PROT ASP 1 OD1 ) 0.13199 ( PROT ASP 1 OD2 ) 0.13199 ( PROT ASP 1 C ) 0.16499 ( PROT ASP 1 O ) 0.16499 ( PROT TYR 2 N ) 0.16499 ( PROT TYR 2 H ) 0.13199 ( PROT TYR 2 CA ) 0.16499 ( PROT TYR 2 CB ) 0.13199 ( PROT TYR 2 CG ) 0.13199 ( PROT TYR 2 CD1 ) 0.13199 ( PROT TYR 2 CE1 ) 0.13199 ( PROT TYR 2 CD2 ) 0.13199 ( PROT TYR 2 CE2 ) 0.13199 ( PROT TYR 2 CZ ) 0.13199 ( PROT TYR 2 OH ) 0.13199 ( PROT TYR 2 HH ) 0.13199 ( PROT TYR 2 C ) 0.16499 ( PROT TYR 2 O ) 0.16499 ( PROT ALA 3 N ) 0.16499 ( PROT ALA 3 H ) 0.13199 ( PROT ALA 3 CA ) 0.16499 ( PROT ALA 3 CB ) 0.13199 ( PROT ALA 3 C ) 0.16499 ( PROT ALA 3 O ) 0.16499 ( PROT PHE 4 N ) 0.16499 ( PROT PHE 4 H ) 0.13199 ( PROT PHE 4 CA ) 0.16499 ( PROT PHE 4 CB ) 0.13199 ( PROT PHE 4 CG ) 0.13199 ( PROT PHE 4 CD1 ) 0.13199 ( PROT PHE 4 CD2 ) 0.13199 ( PROT PHE 4 CE1 ) 0.13199 ( PROT PHE 4 CE2 ) 0.13199 ( PROT PHE 4 CZ ) 0.13199 ( PROT PHE 4 C ) 0.16499 ( PROT PHE 4 O ) 0.16499 ( PROT ILE 5 N ) 0.16499 ( PROT ILE 5 H ) 0.13199 ( PROT ILE 5 CA ) 0.16499 ( PROT ILE 5 CB ) 0.13199 ( PROT ILE 5 CG2 ) 0.13199 ( PROT ILE 5 CG1 ) 0.13199 ( PROT ILE 5 CD ) 0.13199 ( PROT ILE 5 C ) 0.16499 ( PROT ILE 5 O ) 0.16499 ( PROT ALA 6 N ) 0.16499 ( PROT ALA 6 H ) 0.13199 ( PROT ALA 6 CA ) 0.16499 ( PROT ALA 6 CB ) 0.13199 ( PROT ALA 6 C ) 0.16499 ( PROT ALA 6 O ) 0.16499 ( PROT SER 7 N ) 0.16499 ( PROT SER 7 H ) 0.13199 ( PROT SER 7 CA ) 0.16499 ( PROT SER 7 CB ) 0.13199 ( PROT SER 7 OG ) 0.13199 ( PROT SER 7 HG ) 0.13199 ( PROT SER 7 C ) 0.16499 ( PROT SER 7 O ) 0.16499 ( PROT LEU 8 N ) 0.16499 ( PROT LEU 8 H ) 0.13199 ( PROT LEU 8 CA ) 0.16499 ( PROT LEU 8 CB ) 0.13199 ( PROT LEU 8 CG ) 0.13199 ( PROT LEU 8 CD1 ) 0.13199 ( PROT LEU 8 CD2 ) 0.13199 ( PROT LEU 8 C ) 0.16499 ( PROT LEU 8 O ) 0.16499 ( PROT VAL 9 N ) 0.16499 ( PROT VAL 9 H ) 0.13199 ( PROT VAL 9 CA ) 0.16499 ( PROT VAL 9 CB ) 0.13199 ( PROT VAL 9 CG1 ) 0.13199 ( PROT VAL 9 CG2 ) 0.13199 ( PROT VAL 9 C ) 0.16499 ( PROT VAL 9 O ) 0.16499 ( PROT VAL 10 N ) 0.16499 ( PROT VAL 10 H ) 0.13199 ( PROT VAL 10 CA ) 0.16499 ( PROT VAL 10 CB ) 0.13199 ( PROT VAL 10 CG1 ) 0.13199 ( PROT VAL 10 CG2 ) 0.13199 ( PROT VAL 10 C ) 0.16499 ( PROT VAL 10 O ) 0.16499 ( PROT ILE 11 N ) 0.16499 ( PROT ILE 11 H ) 0.13199 ( PROT ILE 11 CA ) 0.16499 ( PROT ILE 11 CB ) 0.13199 ( PROT ILE 11 CG2 ) 0.13199 ( PROT ILE 11 CG1 ) 0.13199 ( PROT ILE 11 CD ) 0.13199 ( PROT ILE 11 C ) 0.16499 ( PROT ILE 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 ASP 13 N ) 0.16499 ( PROT ASP 13 H ) 0.13199 ( PROT ASP 13 CA ) 0.16499 ( PROT ASP 13 CB ) 0.13199 ( PROT ASP 13 CG ) 0.13199 ( PROT ASP 13 OD1 ) 0.13199 ( PROT ASP 13 OD2 ) 0.13199 ( PROT ASP 13 C ) 0.16499 ( PROT ASP 13 O ) 0.16499 ( PROT ASP 14 N ) 0.16499 ( PROT ASP 14 H ) 0.13199 ( PROT ASP 14 CA ) 0.16499 ( PROT ASP 14 CB ) 0.13199 ( PROT ASP 14 CG ) 0.13199 ( PROT ASP 14 OD1 ) 0.13199 ( PROT ASP 14 OD2 ) 0.13199 ( PROT ASP 14 C ) 0.16499 ( PROT ASP 14 O ) 0.16499 ( PROT VAL 15 N ) 0.16499 ( PROT VAL 15 H ) 0.13199 ( PROT VAL 15 CA ) 0.16499 ( PROT VAL 15 CB ) 0.13199 ( PROT VAL 15 CG1 ) 0.13199 ( PROT VAL 15 CG2 ) 0.13199 ( PROT VAL 15 C ) 0.16499 ( PROT VAL 15 O ) 0.16499 ( PROT ASN 16 N ) 0.16499 ( PROT ASN 16 H ) 0.13199 ( PROT ASN 16 CA ) 0.16499 ( PROT ASN 16 CB ) 0.13199 ( PROT ASN 16 CG ) 0.13199 ( PROT ASN 16 OD1 ) 0.13199 ( PROT ASN 16 ND2 ) 0.13199 ( PROT ASN 16 HD21 ) 0.13199 ( PROT ASN 16 HD22 ) 0.13199 ( PROT ASN 16 C ) 0.16499 ( PROT ASN 16 O ) 0.16499 ( PROT ARG 17 N ) 0.16499 ( PROT ARG 17 H ) 0.13199 ( PROT ARG 17 CA ) 0.16499 ( PROT ARG 17 CB ) 0.13199 ( PROT ARG 17 CG ) 0.13199 ( PROT ARG 17 CD ) 0.13199 ( PROT ARG 17 NE ) 0.13199 ( PROT ARG 17 HE ) 0.13199 ( PROT ARG 17 CZ ) 0.13199 ( PROT ARG 17 NH1 ) 0.13199 ( PROT ARG 17 HH11 ) 0.13199 ( PROT ARG 17 HH12 ) 0.13199 ( PROT ARG 17 NH2 ) 0.13199 ( PROT ARG 17 HH21 ) 0.13199 ( PROT ARG 17 HH22 ) 0.13199 ( PROT ARG 17 C ) 0.16499 ( PROT ARG 17 OT1 ) 0.13199 ( PROT ARG 17 OT2 ) 0.13199 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.96094 3.70493 -6.80109 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00288 0.00640 -0.00091 ROTATION MATRIX 0.999982 0.004085 0.004376 -0.004064 0.999980 -0.004802 -0.004395 0.004785 0.999979 AXIS OF ROTATION IS -0.625052 -0.571824 0.531344 ANGLE IS 0.44 TOTAL SQUARE DIFF IS 83.1803 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.712178 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.7122" Parameter: A <- "0.7122" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.80207 3.79995 -7.00096 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.02989 -0.00824 0.02373 ROTATION MATRIX 0.999066 0.028257 0.032697 -0.026807 0.998674 -0.043959 -0.033896 0.043041 0.998498 AXIS OF ROTATION IS -0.709507 -0.543085 0.449064 ANGLE IS 3.52 CENTER OF ROTATION 7.637480 3.851401 -7.158321 SHIFT IS 0.036342 TOTAL SQUARE DIFF IS 6.5942 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.622813 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.7122" RDCMND substituted energy or value "?RMS" to " 0.6228" Parameter: A <- "0.7122 0.6228" 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 0.7122 0.6228 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 " 18.68" Parameter: H <- "18.68" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -80.98579 18.68458 0.21663 ENER INTERN> 4.74599 14.24776 0.00000 8.38221 3.02564 ENER EXTERN> -89.68032 -21.70707 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 " -80.99" Parameter: B <- "-80.99" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -21.71" Parameter: C <- "-21.71" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -89.68" Parameter: C <- " -111.39" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -111.39" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.75" Parameter: D <- "4.75" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.25" Parameter: D <- " 19.00" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 8.38" Parameter: D <- " 27.38" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.03" Parameter: D <- " 30.41" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 30.41" 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= 10200 ENER= -80.99 GRMS= 0.22 ELEC= -21.71 VDW= -89.68 RDTITL> *EXTERNAL= -111.39 INTERNAL= 30.41 USER= 0.00 HARM= 18.68 RDTITL> *BOND= 4.75 ANGL= 14.25 DIHE= 8.38 IMPR= 3.03 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 9012 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9016 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 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 -67.55819 -13.42761 0.13345 0.02000 MINI INTERN> 4.74599 14.24776 0.00000 8.38221 3.02564 MINI EXTERN> -89.68032 -21.70707 0.00000 0.00000 0.00000 MINI CONSTR> 13.42761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -63.05771 -4.50048 7.13896 0.00360 MINI INTERN> 8.38640 15.25939 0.00000 8.66451 2.90436 MINI EXTERN> -91.01055 -20.93996 0.00000 0.00000 0.00000 MINI CONSTR> 13.67814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9011 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -67.67281 4.61510 0.94474 0.00065 MINI INTERN> 4.85530 14.46900 0.00000 8.51079 2.95225 MINI EXTERN> -90.85727 -21.28507 0.00000 0.00000 0.00000 MINI CONSTR> 13.68219 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -67.77191 0.09910 0.36872 0.00028 MINI INTERN> 4.88993 14.37504 0.00000 8.47058 2.97343 MINI EXTERN> -90.80131 -21.36691 0.00000 0.00000 0.00000 MINI CONSTR> 13.68733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9011 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -67.79982 0.02791 0.09673 0.00012 MINI INTERN> 4.83162 14.37584 0.00000 8.46036 2.97458 MINI EXTERN> -90.74340 -21.39300 0.00000 0.00000 0.00000 MINI CONSTR> 13.69418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -67.81187 0.01205 0.09110 0.00013 MINI INTERN> 4.82261 14.37097 0.00000 8.45101 2.97879 MINI EXTERN> -90.71759 -21.41873 0.00000 0.00000 0.00000 MINI CONSTR> 13.70107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9009 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -67.82206 0.01019 0.16403 0.00013 MINI INTERN> 4.82475 14.36113 0.00000 8.44224 2.98189 MINI EXTERN> -90.70101 -21.44024 0.00000 0.00000 0.00000 MINI CONSTR> 13.70919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -67.83193 0.00987 0.21558 0.00013 MINI INTERN> 4.82602 14.35212 0.00000 8.43455 2.98308 MINI EXTERN> -90.69210 -21.45285 0.00000 0.00000 0.00000 MINI CONSTR> 13.71725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9008 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -67.84210 0.01017 0.18537 0.00014 MINI INTERN> 4.81917 14.35226 0.00000 8.43086 2.98598 MINI EXTERN> -90.68927 -21.46574 0.00000 0.00000 0.00000 MINI CONSTR> 13.72465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -67.84999 0.00789 0.23463 0.00014 MINI INTERN> 4.82175 14.34263 0.00000 8.42631 2.98503 MINI EXTERN> -90.68647 -21.47099 0.00000 0.00000 0.00000 MINI CONSTR> 13.73175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9008 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -67.86143 0.01145 0.07340 0.00006 MINI INTERN> 4.80986 14.34874 0.00000 8.42364 2.98693 MINI EXTERN> -90.68766 -21.48092 0.00000 0.00000 0.00000 MINI CONSTR> 13.73797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -67.86410 0.00266 0.27331 0.00016 MINI INTERN> 4.82097 14.33618 0.00000 8.41976 2.98552 MINI EXTERN> -90.68975 -21.48131 0.00000 0.00000 0.00000 MINI CONSTR> 13.74452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9008 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -67.87703 0.01293 0.08822 0.00007 MINI INTERN> 4.80910 14.34217 0.00000 8.41750 2.98784 MINI EXTERN> -90.69474 -21.49021 0.00000 0.00000 0.00000 MINI CONSTR> 13.75132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -67.88353 0.00650 0.06467 0.00007 MINI INTERN> 4.80940 14.33812 0.00000 8.41519 2.98767 MINI EXTERN> -90.69849 -21.49209 0.00000 0.00000 0.00000 MINI CONSTR> 13.75668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9007 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -67.89126 0.00773 0.06491 0.00007 MINI INTERN> 4.80918 14.33495 0.00000 8.41255 2.98772 MINI EXTERN> -90.70417 -21.49491 0.00000 0.00000 0.00000 MINI CONSTR> 13.76342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -67.89921 0.00795 0.11688 0.00007 MINI INTERN> 4.80861 14.33365 0.00000 8.40992 2.98818 MINI EXTERN> -90.71203 -21.49862 0.00000 0.00000 0.00000 MINI CONSTR> 13.77107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9008 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -67.90643 0.00721 0.08251 0.00008 MINI INTERN> 4.80869 14.32980 0.00000 8.40776 2.98779 MINI EXTERN> -90.71784 -21.49961 0.00000 0.00000 0.00000 MINI CONSTR> 13.77698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -67.91298 0.00656 0.06490 0.00008 MINI INTERN> 4.80890 14.32650 0.00000 8.40578 2.98744 MINI EXTERN> -90.72377 -21.50046 0.00000 0.00000 0.00000 MINI CONSTR> 13.78263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9006 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -67.91997 0.00699 0.14769 0.00008 MINI INTERN> 4.80839 14.32666 0.00000 8.40367 2.98791 MINI EXTERN> -90.73324 -21.50348 0.00000 0.00000 0.00000 MINI CONSTR> 13.79012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -67.92774 0.00777 0.08571 0.00009 MINI INTERN> 4.80866 14.32206 0.00000 8.40159 2.98724 MINI EXTERN> -90.73994 -21.50343 0.00000 0.00000 0.00000 MINI CONSTR> 13.79608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9005 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -67.93502 0.00728 0.10398 0.00009 MINI INTERN> 4.80871 14.32006 0.00000 8.39959 2.98711 MINI EXTERN> -90.74868 -21.50469 0.00000 0.00000 0.00000 MINI CONSTR> 13.80288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -67.94058 0.00557 0.16054 0.00009 MINI INTERN> 4.80869 14.31973 0.00000 8.39799 2.98723 MINI EXTERN> -90.75689 -21.50629 0.00000 0.00000 0.00000 MINI CONSTR> 13.80896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9003 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -67.94769 0.00711 0.16665 0.00010 MINI INTERN> 4.80916 14.31743 0.00000 8.39609 2.98695 MINI EXTERN> -90.76580 -21.50705 0.00000 0.00000 0.00000 MINI CONSTR> 13.81553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -67.95462 0.00693 0.17905 0.00010 MINI INTERN> 4.80982 14.31536 0.00000 8.39423 2.98669 MINI EXTERN> -90.77503 -21.50780 0.00000 0.00000 0.00000 MINI CONSTR> 13.82211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9001 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -67.96114 0.00652 0.19607 0.00010 MINI INTERN> 4.81044 14.31361 0.00000 8.39249 2.98645 MINI EXTERN> -90.78408 -21.50853 0.00000 0.00000 0.00000 MINI CONSTR> 13.82849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -67.96749 0.00634 0.18557 0.00011 MINI INTERN> 4.81007 14.31144 0.00000 8.39095 2.98611 MINI EXTERN> -90.79129 -21.50873 0.00000 0.00000 0.00000 MINI CONSTR> 13.83396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9001 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -67.97422 0.00674 0.19415 0.00011 MINI INTERN> 4.81091 14.30941 0.00000 8.38919 2.98579 MINI EXTERN> -90.80061 -21.50923 0.00000 0.00000 0.00000 MINI CONSTR> 13.84032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -67.98114 0.00692 0.19951 0.00012 MINI INTERN> 4.81206 14.30717 0.00000 8.38740 2.98541 MINI EXTERN> -90.81033 -21.50962 0.00000 0.00000 0.00000 MINI CONSTR> 13.84678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9000 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -67.98816 0.00701 0.20004 0.00012 MINI INTERN> 4.81328 14.30474 0.00000 8.38557 2.98497 MINI EXTERN> -90.82005 -21.50985 0.00000 0.00000 0.00000 MINI CONSTR> 13.85319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -67.99713 0.00897 0.06413 0.00005 MINI INTERN> 4.81027 14.29740 0.00000 8.38338 2.98373 MINI EXTERN> -90.82378 -21.50689 0.00000 0.00000 0.00000 MINI CONSTR> 13.85877 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9000 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -68.00034 0.00322 0.22040 0.00013 MINI INTERN> 4.81482 14.30138 0.00000 8.38242 2.98433 MINI EXTERN> -90.83759 -21.51061 0.00000 0.00000 0.00000 MINI CONSTR> 13.86490 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -68.00703 0.00669 0.22432 0.00013 MINI INTERN> 4.81673 14.29889 0.00000 8.38058 2.98383 MINI EXTERN> -90.84754 -21.51065 0.00000 0.00000 0.00000 MINI CONSTR> 13.87114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9000 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -68.01382 0.00679 0.22929 0.00014 MINI INTERN> 4.81938 14.29584 0.00000 8.37853 2.98321 MINI EXTERN> -90.85795 -21.51034 0.00000 0.00000 0.00000 MINI CONSTR> 13.87751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -68.02055 0.00673 0.23789 0.00014 MINI INTERN> 4.82188 14.29266 0.00000 8.37634 2.98261 MINI EXTERN> -90.86822 -21.50976 0.00000 0.00000 0.00000 MINI CONSTR> 13.88395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9000 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -68.03147 0.01092 0.07261 0.00006 MINI INTERN> 4.81048 14.28774 0.00000 8.37489 2.98201 MINI EXTERN> -90.86871 -21.50799 0.00000 0.00000 0.00000 MINI CONSTR> 13.89012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -68.03731 0.00585 0.05922 0.00006 MINI INTERN> 4.81149 14.28622 0.00000 8.37338 2.98174 MINI EXTERN> -90.87722 -21.50822 0.00000 0.00000 0.00000 MINI CONSTR> 13.89530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9000 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -68.03937 0.00206 0.26392 0.00016 MINI INTERN> 4.82493 14.28659 0.00000 8.37075 2.98159 MINI EXTERN> -90.89587 -21.50938 0.00000 0.00000 0.00000 MINI CONSTR> 13.90203 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -68.05108 0.01171 0.09578 0.00007 MINI INTERN> 4.81046 14.28223 0.00000 8.37002 2.98091 MINI EXTERN> -90.89442 -21.50851 0.00000 0.00000 0.00000 MINI CONSTR> 13.90823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9000 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -68.05678 0.00570 0.05836 0.00007 MINI INTERN> 4.81227 14.28085 0.00000 8.36845 2.98073 MINI EXTERN> -90.90337 -21.50868 0.00000 0.00000 0.00000 MINI CONSTR> 13.91297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -68.06374 0.00696 0.06021 0.00007 MINI INTERN> 4.81237 14.27896 0.00000 8.36670 2.98035 MINI EXTERN> -90.91255 -21.50886 0.00000 0.00000 0.00000 MINI CONSTR> 13.91929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9000 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -68.07014 0.00640 0.12353 0.00008 MINI INTERN> 4.81069 14.27710 0.00000 8.36524 2.97978 MINI EXTERN> -90.91972 -21.50919 0.00000 0.00000 0.00000 MINI CONSTR> 13.92596 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -68.07686 0.00673 0.07507 0.00008 MINI INTERN> 4.81215 14.27549 0.00000 8.36344 2.97958 MINI EXTERN> -90.92956 -21.50930 0.00000 0.00000 0.00000 MINI CONSTR> 13.93133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9001 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -68.08360 0.00674 0.07784 0.00008 MINI INTERN> 4.81231 14.27384 0.00000 8.36173 2.97920 MINI EXTERN> -90.93857 -21.50957 0.00000 0.00000 0.00000 MINI CONSTR> 13.93745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -68.09021 0.00660 0.08837 0.00009 MINI INTERN> 4.81223 14.27227 0.00000 8.36008 2.97880 MINI EXTERN> -90.94724 -21.50990 0.00000 0.00000 0.00000 MINI CONSTR> 13.94355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9001 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -68.09541 0.00520 0.14400 0.00009 MINI INTERN> 4.81136 14.27116 0.00000 8.35883 2.97829 MINI EXTERN> -90.95379 -21.51047 0.00000 0.00000 0.00000 MINI CONSTR> 13.94920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -68.10185 0.00644 0.14564 0.00009 MINI INTERN> 4.81161 14.26981 0.00000 8.35719 2.97791 MINI EXTERN> -90.96253 -21.51087 0.00000 0.00000 0.00000 MINI CONSTR> 13.95504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9000 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -68.10835 0.00651 0.15065 0.00010 MINI INTERN> 4.81179 14.26861 0.00000 8.35552 2.97751 MINI EXTERN> -90.97142 -21.51138 0.00000 0.00000 0.00000 MINI CONSTR> 13.96101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -68.11475 0.00640 0.16129 0.00010 MINI INTERN> 4.81189 14.26757 0.00000 8.35386 2.97709 MINI EXTERN> -90.98022 -21.51195 0.00000 0.00000 0.00000 MINI CONSTR> 13.96701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8999 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -68.12074 0.00598 0.17903 0.00010 MINI INTERN> 4.81194 14.26662 0.00000 8.35228 2.97667 MINI EXTERN> -90.98853 -21.51255 0.00000 0.00000 0.00000 MINI CONSTR> 13.97284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -68.12648 0.00574 0.17037 0.00011 MINI INTERN> 4.81230 14.26495 0.00000 8.35075 2.97642 MINI EXTERN> -90.99604 -21.51261 0.00000 0.00000 0.00000 MINI CONSTR> 13.97776 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8999 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -68.13257 0.00609 0.17841 0.00011 MINI INTERN> 4.81238 14.26394 0.00000 8.34913 2.97604 MINI EXTERN> -91.00439 -21.51309 0.00000 0.00000 0.00000 MINI CONSTR> 13.98342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -68.13881 0.00624 0.18366 0.00011 MINI INTERN> 4.81245 14.26292 0.00000 8.34746 2.97567 MINI EXTERN> -91.01291 -21.51355 0.00000 0.00000 0.00000 MINI CONSTR> 13.98915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8999 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -68.14707 0.00825 0.05655 0.00005 MINI INTERN> 4.81724 14.25643 0.00000 8.34448 2.97615 MINI EXTERN> -91.02483 -21.51078 0.00000 0.00000 0.00000 MINI CONSTR> 13.99425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -68.15019 0.00313 0.20035 0.00012 MINI INTERN> 4.81268 14.26084 0.00000 8.34436 2.97496 MINI EXTERN> -91.02842 -21.51439 0.00000 0.00000 0.00000 MINI CONSTR> 13.99978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8999 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -68.15607 0.00588 0.20504 0.00013 MINI INTERN> 4.81284 14.25972 0.00000 8.34275 2.97461 MINI EXTERN> -91.03636 -21.51480 0.00000 0.00000 0.00000 MINI CONSTR> 14.00516 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -68.16205 0.00598 0.21157 0.00013 MINI INTERN> 4.81295 14.25875 0.00000 8.34109 2.97425 MINI EXTERN> -91.04450 -21.51527 0.00000 0.00000 0.00000 MINI CONSTR> 14.01068 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8998 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -68.16800 0.00594 0.22091 0.00014 MINI INTERN> 4.81302 14.25791 0.00000 8.33943 2.97386 MINI EXTERN> -91.05267 -21.51580 0.00000 0.00000 0.00000 MINI CONSTR> 14.01626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -68.17768 0.00968 0.06722 0.00006 MINI INTERN> 4.81958 14.24765 0.00000 8.33586 2.97467 MINI EXTERN> -91.06557 -21.51144 0.00000 0.00000 0.00000 MINI CONSTR> 14.02157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8998 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -68.18276 0.00508 0.05470 0.00006 MINI INTERN> 4.81871 14.24725 0.00000 8.33467 2.97430 MINI EXTERN> -91.07154 -21.51210 0.00000 0.00000 0.00000 MINI CONSTR> 14.02596 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -68.18865 0.00589 0.05423 0.00006 MINI INTERN> 4.81894 14.24577 0.00000 8.33303 2.97399 MINI EXTERN> -91.07917 -21.51236 0.00000 0.00000 0.00000 MINI CONSTR> 14.03116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8998 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -68.19464 0.00599 0.05438 0.00007 MINI INTERN> 4.81926 14.24418 0.00000 8.33134 2.97368 MINI EXTERN> -91.08697 -21.51259 0.00000 0.00000 0.00000 MINI CONSTR> 14.03645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -68.20059 0.00595 0.05580 0.00007 MINI INTERN> 4.81973 14.24248 0.00000 8.32963 2.97340 MINI EXTERN> -91.09477 -21.51276 0.00000 0.00000 0.00000 MINI CONSTR> 14.04171 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8996 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -68.20622 0.00563 0.11061 0.00007 MINI INTERN> 4.82378 14.23793 0.00000 8.32726 2.97343 MINI EXTERN> -91.10434 -21.51159 0.00000 0.00000 0.00000 MINI CONSTR> 14.04732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -68.21201 0.00579 0.06870 0.00007 MINI INTERN> 4.82134 14.23858 0.00000 8.32617 2.97292 MINI EXTERN> -91.11007 -21.51280 0.00000 0.00000 0.00000 MINI CONSTR> 14.05186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8994 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -68.21790 0.00589 0.06851 0.00008 MINI INTERN> 4.82161 14.23705 0.00000 8.32449 2.97262 MINI EXTERN> -91.11761 -21.51308 0.00000 0.00000 0.00000 MINI CONSTR> 14.05702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -68.22383 0.00593 0.07224 0.00008 MINI INTERN> 4.82215 14.23528 0.00000 8.32274 2.97234 MINI EXTERN> -91.12534 -21.51326 0.00000 0.00000 0.00000 MINI CONSTR> 14.06226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8994 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -68.22956 0.00573 0.08542 0.00008 MINI INTERN> 4.82327 14.23307 0.00000 8.32093 2.97212 MINI EXTERN> -91.13313 -21.51322 0.00000 0.00000 0.00000 MINI CONSTR> 14.06741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -68.23397 0.00442 0.13497 0.00009 MINI INTERN> 4.82649 14.22953 0.00000 8.31900 2.97211 MINI EXTERN> -91.14080 -21.51236 0.00000 0.00000 0.00000 MINI CONSTR> 14.07206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8994 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -68.23958 0.00561 0.13862 0.00009 MINI INTERN> 4.82703 14.22784 0.00000 8.31733 2.97184 MINI EXTERN> -91.14803 -21.51260 0.00000 0.00000 0.00000 MINI CONSTR> 14.07702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -68.24514 0.00556 0.14677 0.00009 MINI INTERN> 4.82787 14.22595 0.00000 8.31561 2.97159 MINI EXTERN> -91.15538 -21.51279 0.00000 0.00000 0.00000 MINI CONSTR> 14.08202 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8993 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -68.25043 0.00529 0.16101 0.00010 MINI INTERN> 4.82907 14.22386 0.00000 8.31387 2.97137 MINI EXTERN> -91.16268 -21.51287 0.00000 0.00000 0.00000 MINI CONSTR> 14.08694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -68.25549 0.00506 0.15441 0.00010 MINI INTERN> 4.82869 14.22299 0.00000 8.31249 2.97108 MINI EXTERN> -91.16873 -21.51319 0.00000 0.00000 0.00000 MINI CONSTR> 14.09117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8991 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -68.26075 0.00525 0.16290 0.00010 MINI INTERN> 4.82941 14.22128 0.00000 8.31084 2.97084 MINI EXTERN> -91.17566 -21.51338 0.00000 0.00000 0.00000 MINI CONSTR> 14.09591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -68.26617 0.00542 0.16946 0.00011 MINI INTERN> 4.83004 14.21963 0.00000 8.30918 2.97059 MINI EXTERN> -91.18265 -21.51371 0.00000 0.00000 0.00000 MINI CONSTR> 14.10076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8991 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -68.27171 0.00554 0.17292 0.00011 MINI INTERN> 4.83048 14.21814 0.00000 8.30753 2.97031 MINI EXTERN> -91.18959 -21.51422 0.00000 0.00000 0.00000 MINI CONSTR> 14.10563 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -68.27901 0.00730 0.05319 0.00005 MINI INTERN> 4.82138 14.22454 0.00000 8.30712 2.96915 MINI EXTERN> -91.19378 -21.51738 0.00000 0.00000 0.00000 MINI CONSTR> 14.10997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8991 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -68.28167 0.00265 0.18764 0.00012 MINI INTERN> 4.83155 14.21522 0.00000 8.30441 2.96983 MINI EXTERN> -91.20251 -21.51475 0.00000 0.00000 0.00000 MINI CONSTR> 14.11458 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -68.28687 0.00520 0.19208 0.00012 MINI INTERN> 4.83205 14.21387 0.00000 8.30284 2.96956 MINI EXTERN> -91.20904 -21.51532 0.00000 0.00000 0.00000 MINI CONSTR> 14.11917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8991 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -68.29214 0.00527 0.19806 0.00013 MINI INTERN> 4.83278 14.21251 0.00000 8.30124 2.96930 MINI EXTERN> -91.21567 -21.51618 0.00000 0.00000 0.00000 MINI CONSTR> 14.12387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -68.29735 0.00521 0.20671 0.00013 MINI INTERN> 4.83391 14.21112 0.00000 8.29963 2.96904 MINI EXTERN> -91.22234 -21.51730 0.00000 0.00000 0.00000 MINI CONSTR> 14.12859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -68.30587 0.00852 0.06437 0.00006 MINI INTERN> 4.82127 14.21878 0.00000 8.29909 2.96765 MINI EXTERN> -91.22705 -21.51867 0.00000 0.00000 0.00000 MINI CONSTR> 14.13306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -68.31040 0.00454 0.05079 0.00006 MINI INTERN> 4.82278 14.21657 0.00000 8.29766 2.96755 MINI EXTERN> -91.23264 -21.51912 0.00000 0.00000 0.00000 MINI CONSTR> 14.13680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -68.31200 0.00160 0.22762 0.00015 MINI INTERN> 4.83674 14.20738 0.00000 8.29507 2.96831 MINI EXTERN> -91.24111 -21.52013 0.00000 0.00000 0.00000 MINI CONSTR> 14.14176 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -68.32121 0.00921 0.08197 0.00006 MINI INTERN> 4.82042 14.21593 0.00000 8.29443 2.96673 MINI EXTERN> -91.24595 -21.51905 0.00000 0.00000 0.00000 MINI CONSTR> 14.14628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8988 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -68.32570 0.00449 0.05027 0.00007 MINI INTERN> 4.82332 14.21283 0.00000 8.29300 2.96676 MINI EXTERN> -91.25131 -21.52008 0.00000 0.00000 0.00000 MINI CONSTR> 14.14977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -68.33118 0.00548 0.05187 0.00007 MINI INTERN> 4.82311 14.21174 0.00000 8.29134 2.96645 MINI EXTERN> -91.25794 -21.52030 0.00000 0.00000 0.00000 MINI CONSTR> 14.15442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -68.33629 0.00510 0.10469 0.00007 MINI INTERN> 4.81861 14.21350 0.00000 8.28976 2.96578 MINI EXTERN> -91.26445 -21.51882 0.00000 0.00000 0.00000 MINI CONSTR> 14.15934 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -68.34160 0.00531 0.06456 0.00007 MINI INTERN> 4.82150 14.21035 0.00000 8.28817 2.96578 MINI EXTERN> -91.27046 -21.52024 0.00000 0.00000 0.00000 MINI CONSTR> 14.16330 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -68.34696 0.00536 0.06587 0.00008 MINI INTERN> 4.82104 14.20936 0.00000 8.28653 2.96547 MINI EXTERN> -91.27686 -21.52033 0.00000 0.00000 0.00000 MINI CONSTR> 14.16782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -68.35229 0.00533 0.07222 0.00008 MINI INTERN> 4.82003 14.20872 0.00000 8.28490 2.96513 MINI EXTERN> -91.28321 -21.52023 0.00000 0.00000 0.00000 MINI CONSTR> 14.17235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -68.35659 0.00429 0.12382 0.00008 MINI INTERN> 4.81463 14.21088 0.00000 8.28350 2.96452 MINI EXTERN> -91.28874 -21.51807 0.00000 0.00000 0.00000 MINI CONSTR> 14.17670 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -68.36173 0.00514 0.12383 0.00008 MINI INTERN> 4.81410 14.20999 0.00000 8.28192 2.96424 MINI EXTERN> -91.29479 -21.51818 0.00000 0.00000 0.00000 MINI CONSTR> 14.18099 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -68.36737 0.00564 0.08311 0.00009 MINI INTERN> 4.81843 14.20628 0.00000 8.28025 2.96425 MINI EXTERN> -91.30112 -21.52053 0.00000 0.00000 0.00000 MINI CONSTR> 14.18506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -68.37118 0.00382 0.13340 0.00009 MINI INTERN> 4.81303 14.20855 0.00000 8.27896 2.96367 MINI EXTERN> -91.30610 -21.51833 0.00000 0.00000 0.00000 MINI CONSTR> 14.18904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -68.37623 0.00505 0.14586 0.00009 MINI INTERN> 4.81109 14.20857 0.00000 8.27737 2.96330 MINI EXTERN> -91.31220 -21.51785 0.00000 0.00000 0.00000 MINI CONSTR> 14.19349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -68.38089 0.00466 0.16157 0.00010 MINI INTERN> 4.80927 14.20867 0.00000 8.27586 2.96293 MINI EXTERN> -91.31796 -21.51736 0.00000 0.00000 0.00000 MINI CONSTR> 14.19770 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -68.38548 0.00458 0.15153 0.00010 MINI INTERN> 4.81067 14.20685 0.00000 8.27446 2.96278 MINI EXTERN> -91.32317 -21.51831 0.00000 0.00000 0.00000 MINI CONSTR> 14.20125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -68.39046 0.00498 0.15733 0.00011 MINI INTERN> 4.80959 14.20645 0.00000 8.27291 2.96247 MINI EXTERN> -91.32907 -21.51831 0.00000 0.00000 0.00000 MINI CONSTR> 14.20549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -68.39553 0.00507 0.15983 0.00011 MINI INTERN> 4.80900 14.20576 0.00000 8.27134 2.96219 MINI EXTERN> -91.33502 -21.51852 0.00000 0.00000 0.00000 MINI CONSTR> 14.20972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -68.40210 0.00657 0.05088 0.00005 MINI INTERN> 4.83063 14.19246 0.00000 8.26914 2.96302 MINI EXTERN> -91.34269 -21.52809 0.00000 0.00000 0.00000 MINI CONSTR> 14.21342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -68.40440 0.00230 0.17557 0.00012 MINI INTERN> 4.80729 14.20498 0.00000 8.26850 2.96161 MINI EXTERN> -91.34564 -21.51853 0.00000 0.00000 0.00000 MINI CONSTR> 14.21738 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 -68.40440 0.00230 0.17557 0.00006 STPD INTERN> 4.80729 14.20498 0.00000 8.26850 2.96161 STPD EXTERN> -91.34564 -21.51853 0.00000 0.00000 0.00000 STPD CONSTR> 14.21738 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 8989 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8989 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 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 -68.40444 0.00004 0.14455 0.00000 MINI INTERN> 4.84768 14.18377 0.00000 8.26736 2.96353 MINI EXTERN> -91.34891 -21.53454 0.00000 0.00000 0.00000 MINI CONSTR> 14.21667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -69.21278 0.80834 0.24169 0.10300 MINI INTERN> 5.17574 14.06773 0.00000 7.84492 2.93807 MINI EXTERN> -93.22599 -21.81272 0.00000 0.00000 0.00000 MINI CONSTR> 15.79947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -69.25205 0.03927 0.19826 0.01609 MINI INTERN> 4.90634 14.01844 0.00000 7.81135 2.90513 MINI EXTERN> -93.12963 -21.62941 0.00000 0.00000 0.00000 MINI CONSTR> 15.86573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -69.28237 0.03032 0.18269 0.01390 MINI INTERN> 4.86896 13.81082 0.00000 7.77838 2.90460 MINI EXTERN> -92.91280 -21.61302 0.00000 0.00000 0.00000 MINI CONSTR> 15.88068 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -69.36993 0.08756 0.36374 0.06080 MINI INTERN> 4.83470 13.99520 0.00000 7.72955 2.87211 MINI EXTERN> -92.94654 -21.70143 0.00000 0.00000 0.00000 MINI CONSTR> 15.84647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -69.50528 0.13535 0.29050 0.06725 MINI INTERN> 4.90996 13.98009 0.00000 7.65192 2.86240 MINI EXTERN> -92.62080 -22.08267 0.00000 0.00000 0.00000 MINI CONSTR> 15.79381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -69.58823 0.08294 0.24930 0.04509 MINI INTERN> 4.82890 13.96667 0.00000 7.60644 2.89143 MINI EXTERN> -92.56877 -22.07559 0.00000 0.00000 0.00000 MINI CONSTR> 15.76270 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -69.64688 0.05865 0.19300 0.03453 MINI INTERN> 4.89885 13.92703 0.00000 7.64871 2.92626 MINI EXTERN> -92.62705 -22.15488 0.00000 0.00000 0.00000 MINI CONSTR> 15.73421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -69.68658 0.03970 0.20352 0.02549 MINI INTERN> 4.91948 13.92883 0.00000 7.65233 2.93032 MINI EXTERN> -92.62173 -22.20140 0.00000 0.00000 0.00000 MINI CONSTR> 15.70560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -69.72643 0.03985 0.18335 0.02210 MINI INTERN> 4.86560 13.98978 0.00000 7.72249 2.89742 MINI EXTERN> -92.65401 -22.21720 0.00000 0.00000 0.00000 MINI CONSTR> 15.66950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -69.75076 0.02433 0.14500 0.01421 MINI INTERN> 4.90372 13.96535 0.00000 7.73486 2.86590 MINI EXTERN> -92.57730 -22.28553 0.00000 0.00000 0.00000 MINI CONSTR> 15.64225 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -69.76974 0.01898 0.12593 0.01475 MINI INTERN> 4.85949 13.97129 0.00000 7.76248 2.89670 MINI EXTERN> -92.50054 -22.37276 0.00000 0.00000 0.00000 MINI CONSTR> 15.61360 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -69.78693 0.01719 0.11793 0.01509 MINI INTERN> 4.88777 14.01785 0.00000 7.76190 2.86998 MINI EXTERN> -92.56911 -22.33763 0.00000 0.00000 0.00000 MINI CONSTR> 15.58231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -69.80297 0.01604 0.10695 0.01723 MINI INTERN> 4.87848 14.01735 0.00000 7.78762 2.86630 MINI EXTERN> -92.54972 -22.35151 0.00000 0.00000 0.00000 MINI CONSTR> 15.54850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -69.81222 0.00925 0.08118 0.00660 MINI INTERN> 4.86065 14.03593 0.00000 7.82115 2.86496 MINI EXTERN> -92.48806 -22.43210 0.00000 0.00000 0.00000 MINI CONSTR> 15.52525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -69.81974 0.00752 0.07221 0.00800 MINI INTERN> 4.84026 14.01688 0.00000 7.85117 2.86093 MINI EXTERN> -92.47778 -22.41402 0.00000 0.00000 0.00000 MINI CONSTR> 15.50282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -69.82491 0.00517 0.06471 0.00524 MINI INTERN> 4.85285 14.02210 0.00000 7.86577 2.86319 MINI EXTERN> -92.49905 -22.41616 0.00000 0.00000 0.00000 MINI CONSTR> 15.48637 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -69.82879 0.00388 0.06135 0.00479 MINI INTERN> 4.85685 14.03879 0.00000 7.89023 2.86802 MINI EXTERN> -92.50254 -22.45264 0.00000 0.00000 0.00000 MINI CONSTR> 15.47249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -69.83259 0.00379 0.06240 0.00515 MINI INTERN> 4.85304 14.02366 0.00000 7.89147 2.86250 MINI EXTERN> -92.50149 -22.41890 0.00000 0.00000 0.00000 MINI CONSTR> 15.45713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -69.83643 0.00384 0.05764 0.00608 MINI INTERN> 4.84186 14.02973 0.00000 7.88984 2.85319 MINI EXTERN> -92.47042 -22.41908 0.00000 0.00000 0.00000 MINI CONSTR> 15.43844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -69.83963 0.00320 0.05161 0.00524 MINI INTERN> 4.84657 14.04441 0.00000 7.88605 2.86538 MINI EXTERN> -92.43564 -22.46715 0.00000 0.00000 0.00000 MINI CONSTR> 15.42076 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 -69.83963 0.00320 0.05161 0.02000 CONJ INTERN> 4.84657 14.04441 0.00000 7.88605 2.86538 CONJ EXTERN> -92.43564 -22.46715 0.00000 0.00000 0.00000 CONJ CONSTR> 15.42076 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 ASP 1 HT1 ) 0.85797E-01 ( PROT ASP 1 HT2 ) 0.85797E-01 ( PROT ASP 1 N ) 0.10725 ( PROT ASP 1 HT3 ) 0.85797E-01 ( PROT ASP 1 CA ) 0.10725 ( PROT ASP 1 CB ) 0.85797E-01 ( PROT ASP 1 CG ) 0.85797E-01 ( PROT ASP 1 OD1 ) 0.85797E-01 ( PROT ASP 1 OD2 ) 0.85797E-01 ( PROT ASP 1 C ) 0.10725 ( PROT ASP 1 O ) 0.10725 ( PROT TYR 2 N ) 0.10725 ( PROT TYR 2 H ) 0.85797E-01 ( PROT TYR 2 CA ) 0.10725 ( PROT TYR 2 CB ) 0.85797E-01 ( PROT TYR 2 CG ) 0.85797E-01 ( PROT TYR 2 CD1 ) 0.85797E-01 ( PROT TYR 2 CE1 ) 0.85797E-01 ( PROT TYR 2 CD2 ) 0.85797E-01 ( PROT TYR 2 CE2 ) 0.85797E-01 ( PROT TYR 2 CZ ) 0.85797E-01 ( PROT TYR 2 OH ) 0.85797E-01 ( PROT TYR 2 HH ) 0.85797E-01 ( PROT TYR 2 C ) 0.10725 ( PROT TYR 2 O ) 0.10725 ( PROT ALA 3 N ) 0.10725 ( PROT ALA 3 H ) 0.85797E-01 ( PROT ALA 3 CA ) 0.10725 ( PROT ALA 3 CB ) 0.85797E-01 ( PROT ALA 3 C ) 0.10725 ( PROT ALA 3 O ) 0.10725 ( PROT PHE 4 N ) 0.10725 ( PROT PHE 4 H ) 0.85797E-01 ( PROT PHE 4 CA ) 0.10725 ( PROT PHE 4 CB ) 0.85797E-01 ( PROT PHE 4 CG ) 0.85797E-01 ( PROT PHE 4 CD1 ) 0.85797E-01 ( PROT PHE 4 CD2 ) 0.85797E-01 ( PROT PHE 4 CE1 ) 0.85797E-01 ( PROT PHE 4 CE2 ) 0.85797E-01 ( PROT PHE 4 CZ ) 0.85797E-01 ( PROT PHE 4 C ) 0.10725 ( PROT PHE 4 O ) 0.10725 ( PROT ILE 5 N ) 0.10725 ( PROT ILE 5 H ) 0.85797E-01 ( PROT ILE 5 CA ) 0.10725 ( PROT ILE 5 CB ) 0.85797E-01 ( PROT ILE 5 CG2 ) 0.85797E-01 ( PROT ILE 5 CG1 ) 0.85797E-01 ( PROT ILE 5 CD ) 0.85797E-01 ( PROT ILE 5 C ) 0.10725 ( PROT ILE 5 O ) 0.10725 ( PROT ALA 6 N ) 0.10725 ( PROT ALA 6 H ) 0.85797E-01 ( PROT ALA 6 CA ) 0.10725 ( PROT ALA 6 CB ) 0.85797E-01 ( PROT ALA 6 C ) 0.10725 ( PROT ALA 6 O ) 0.10725 ( PROT SER 7 N ) 0.10725 ( PROT SER 7 H ) 0.85797E-01 ( PROT SER 7 CA ) 0.10725 ( PROT SER 7 CB ) 0.85797E-01 ( PROT SER 7 OG ) 0.85797E-01 ( PROT SER 7 HG ) 0.85797E-01 ( PROT SER 7 C ) 0.10725 ( PROT SER 7 O ) 0.10725 ( PROT LEU 8 N ) 0.10725 ( PROT LEU 8 H ) 0.85797E-01 ( PROT LEU 8 CA ) 0.10725 ( PROT LEU 8 CB ) 0.85797E-01 ( PROT LEU 8 CG ) 0.85797E-01 ( PROT LEU 8 CD1 ) 0.85797E-01 ( PROT LEU 8 CD2 ) 0.85797E-01 ( PROT LEU 8 C ) 0.10725 ( PROT LEU 8 O ) 0.10725 ( PROT VAL 9 N ) 0.10725 ( PROT VAL 9 H ) 0.85797E-01 ( PROT VAL 9 CA ) 0.10725 ( PROT VAL 9 CB ) 0.85797E-01 ( PROT VAL 9 CG1 ) 0.85797E-01 ( PROT VAL 9 CG2 ) 0.85797E-01 ( PROT VAL 9 C ) 0.10725 ( PROT VAL 9 O ) 0.10725 ( PROT VAL 10 N ) 0.10725 ( PROT VAL 10 H ) 0.85797E-01 ( PROT VAL 10 CA ) 0.10725 ( PROT VAL 10 CB ) 0.85797E-01 ( PROT VAL 10 CG1 ) 0.85797E-01 ( PROT VAL 10 CG2 ) 0.85797E-01 ( PROT VAL 10 C ) 0.10725 ( PROT VAL 10 O ) 0.10725 ( PROT ILE 11 N ) 0.10725 ( PROT ILE 11 H ) 0.85797E-01 ( PROT ILE 11 CA ) 0.10725 ( PROT ILE 11 CB ) 0.85797E-01 ( PROT ILE 11 CG2 ) 0.85797E-01 ( PROT ILE 11 CG1 ) 0.85797E-01 ( PROT ILE 11 CD ) 0.85797E-01 ( PROT ILE 11 C ) 0.10725 ( PROT ILE 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 ASP 13 N ) 0.10725 ( PROT ASP 13 H ) 0.85797E-01 ( PROT ASP 13 CA ) 0.10725 ( PROT ASP 13 CB ) 0.85797E-01 ( PROT ASP 13 CG ) 0.85797E-01 ( PROT ASP 13 OD1 ) 0.85797E-01 ( PROT ASP 13 OD2 ) 0.85797E-01 ( PROT ASP 13 C ) 0.10725 ( PROT ASP 13 O ) 0.10725 ( PROT ASP 14 N ) 0.10725 ( PROT ASP 14 H ) 0.85797E-01 ( PROT ASP 14 CA ) 0.10725 ( PROT ASP 14 CB ) 0.85797E-01 ( PROT ASP 14 CG ) 0.85797E-01 ( PROT ASP 14 OD1 ) 0.85797E-01 ( PROT ASP 14 OD2 ) 0.85797E-01 ( PROT ASP 14 C ) 0.10725 ( PROT ASP 14 O ) 0.10725 ( PROT VAL 15 N ) 0.10725 ( PROT VAL 15 H ) 0.85797E-01 ( PROT VAL 15 CA ) 0.10725 ( PROT VAL 15 CB ) 0.85797E-01 ( PROT VAL 15 CG1 ) 0.85797E-01 ( PROT VAL 15 CG2 ) 0.85797E-01 ( PROT VAL 15 C ) 0.10725 ( PROT VAL 15 O ) 0.10725 ( PROT ASN 16 N ) 0.10725 ( PROT ASN 16 H ) 0.85797E-01 ( PROT ASN 16 CA ) 0.10725 ( PROT ASN 16 CB ) 0.85797E-01 ( PROT ASN 16 CG ) 0.85797E-01 ( PROT ASN 16 OD1 ) 0.85797E-01 ( PROT ASN 16 ND2 ) 0.85797E-01 ( PROT ASN 16 HD21 ) 0.85797E-01 ( PROT ASN 16 HD22 ) 0.85797E-01 ( PROT ASN 16 C ) 0.10725 ( PROT ASN 16 O ) 0.10725 ( PROT ARG 17 N ) 0.10725 ( PROT ARG 17 H ) 0.85797E-01 ( PROT ARG 17 CA ) 0.10725 ( PROT ARG 17 CB ) 0.85797E-01 ( PROT ARG 17 CG ) 0.85797E-01 ( PROT ARG 17 CD ) 0.85797E-01 ( PROT ARG 17 NE ) 0.85797E-01 ( PROT ARG 17 HE ) 0.85797E-01 ( PROT ARG 17 CZ ) 0.85797E-01 ( PROT ARG 17 NH1 ) 0.85797E-01 ( PROT ARG 17 HH11 ) 0.85797E-01 ( PROT ARG 17 HH12 ) 0.85797E-01 ( PROT ARG 17 NH2 ) 0.85797E-01 ( PROT ARG 17 HH21 ) 0.85797E-01 ( PROT ARG 17 HH22 ) 0.85797E-01 ( PROT ARG 17 C ) 0.10725 ( PROT ARG 17 OT1 ) 0.85797E-01 ( PROT ARG 17 OT2 ) 0.85797E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.95648 3.70680 -6.79619 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00734 0.00453 -0.00581 ROTATION MATRIX 0.999997 -0.001291 -0.002126 0.001298 0.999994 0.003253 0.002122 -0.003256 0.999992 AXIS OF ROTATION IS 0.794458 0.518584 -0.316082 ANGLE IS 0.23 TOTAL SQUARE DIFF IS 106.7658 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.806852 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.8069" Parameter: A <- "0.8069" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.81272 3.80311 -7.00235 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.04055 -0.01140 0.02512 ROTATION MATRIX 0.998931 0.029967 0.035205 -0.028254 0.998439 -0.048187 -0.036594 0.047140 0.998218 AXIS OF ROTATION IS -0.717899 -0.540717 0.438458 ANGLE IS 3.81 CENTER OF ROTATION 7.663326 3.801210 -7.196519 SHIFT IS 0.046284 TOTAL SQUARE DIFF IS 7.7546 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.675389 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.8069" RDCMND substituted energy or value "?RMS" to " 0.6754" Parameter: A <- "0.8069 0.6754" 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 0.8069 0.6754 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 " 15.42" Parameter: H <- "15.42" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -85.26039 15.42076 0.14348 ENER INTERN> 4.84657 14.04441 0.00000 7.88605 2.86538 ENER EXTERN> -92.43564 -22.46715 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 " -85.26" Parameter: B <- "-85.26" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -22.47" Parameter: C <- "-22.47" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -92.44" Parameter: C <- " -114.91" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -114.91" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.85" Parameter: D <- "4.85" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.04" Parameter: D <- " 18.89" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 7.89" Parameter: D <- " 26.78" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.87" Parameter: D <- " 29.65" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 29.65" 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= 10800 ENER= -85.26 GRMS= 0.14 ELEC= -22.47 VDW= -92.44 RDTITL> *EXTERNAL= -114.91 INTERNAL= 29.65 USER= 0.00 HARM= 15.42 RDTITL> *BOND= 4.85 ANGL= 14.04 DIHE= 7.89 IMPR= 2.87 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= -85.26 GRMS= 0.14 ELEC= -22.47 VDW= -92.44 RDTITL> *EXTERNAL= -114.91 INTERNAL= 29.65 USER= 0.00 HARM= 15.42 RDTITL> *BOND= 4.85 ANGL= 14.04 DIHE= 7.89 IMPR= 2.87 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= -85.26 GRMS= 0.14 ELEC= -22.47 VDW= -92.44 RDTITL> *EXTERNAL= -114.91 INTERNAL= 29.65 USER= 0.00 HARM= 15.42 RDTITL> *BOND= 4.85 ANGL= 14.04 DIHE= 7.89 IMPR= 2.87 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 10800 0.8069 0.6754 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "10800" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 8989 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8984 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 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 -74.22767 -11.03271 0.07433 0.02000 MINI INTERN> 4.84657 14.04441 0.00000 7.88605 2.86538 MINI EXTERN> -92.43564 -22.46715 0.00000 0.00000 0.00000 MINI CONSTR> 11.03271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -72.00139 -2.22629 4.46421 0.00360 MINI INTERN> 6.73179 15.01536 0.00000 7.85970 3.11951 MINI EXTERN> -93.88451 -22.09580 0.00000 0.00000 0.00000 MINI CONSTR> 11.25255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8970 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -74.35724 2.35585 0.34594 0.00065 MINI INTERN> 5.01732 14.32269 0.00000 7.93345 2.86823 MINI EXTERN> -93.69673 -22.05315 0.00000 0.00000 0.00000 MINI CONSTR> 11.25096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -74.37004 0.01280 0.45188 0.00028 MINI INTERN> 4.98801 14.23185 0.00000 7.93283 2.87171 MINI EXTERN> -93.51488 -22.13146 0.00000 0.00000 0.00000 MINI CONSTR> 11.25190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8970 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -74.39613 0.02609 0.09129 0.00012 MINI INTERN> 4.95506 14.20718 0.00000 7.91888 2.86961 MINI EXTERN> -93.43474 -22.16584 0.00000 0.00000 0.00000 MINI CONSTR> 11.25371 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -74.40025 0.00412 0.22063 0.00013 MINI INTERN> 4.94852 14.16889 0.00000 7.91098 2.86915 MINI EXTERN> -93.37654 -22.17735 0.00000 0.00000 0.00000 MINI CONSTR> 11.25610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8970 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -74.40814 0.00789 0.06282 0.00005 MINI INTERN> 4.94114 14.16203 0.00000 7.90803 2.87249 MINI EXTERN> -93.34513 -22.20488 0.00000 0.00000 0.00000 MINI CONSTR> 11.25817 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -74.41198 0.00384 0.04821 0.00006 MINI INTERN> 4.93486 14.15245 0.00000 7.90438 2.87270 MINI EXTERN> -93.32330 -22.21325 0.00000 0.00000 0.00000 MINI CONSTR> 11.26017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8970 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -74.41619 0.00421 0.04837 0.00006 MINI INTERN> 4.93034 14.14258 0.00000 7.90067 2.87317 MINI EXTERN> -93.30241 -22.22327 0.00000 0.00000 0.00000 MINI CONSTR> 11.26274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -74.42026 0.00407 0.08464 0.00006 MINI INTERN> 4.93091 14.13140 0.00000 7.89725 2.87375 MINI EXTERN> -93.28433 -22.23501 0.00000 0.00000 0.00000 MINI CONSTR> 11.26578 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8970 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -74.42428 0.00402 0.05693 0.00006 MINI INTERN> 4.92539 14.12564 0.00000 7.89450 2.87382 MINI EXTERN> -93.27339 -22.23869 0.00000 0.00000 0.00000 MINI CONSTR> 11.26845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -74.42834 0.00406 0.05566 0.00006 MINI INTERN> 4.92245 14.12018 0.00000 7.89186 2.87401 MINI EXTERN> -93.26355 -22.24489 0.00000 0.00000 0.00000 MINI CONSTR> 11.27158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8969 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -74.43238 0.00404 0.05899 0.00007 MINI INTERN> 4.92110 14.11398 0.00000 7.88939 2.87408 MINI EXTERN> -93.25621 -22.24959 0.00000 0.00000 0.00000 MINI CONSTR> 11.27487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -74.43613 0.00375 0.07409 0.00007 MINI INTERN> 4.92100 14.10882 0.00000 7.88754 2.87426 MINI EXTERN> -93.25105 -22.25487 0.00000 0.00000 0.00000 MINI CONSTR> 11.27816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8969 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -74.43909 0.00296 0.10668 0.00007 MINI INTERN> 4.92382 14.10273 0.00000 7.88600 2.87433 MINI EXTERN> -93.24781 -22.25933 0.00000 0.00000 0.00000 MINI CONSTR> 11.28116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -74.44283 0.00374 0.11048 0.00007 MINI INTERN> 4.92332 14.09847 0.00000 7.88414 2.87420 MINI EXTERN> -93.24555 -22.26191 0.00000 0.00000 0.00000 MINI CONSTR> 11.28451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8968 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -74.44634 0.00351 0.12293 0.00008 MINI INTERN> 4.92203 14.09636 0.00000 7.88311 2.87443 MINI EXTERN> -93.24444 -22.26569 0.00000 0.00000 0.00000 MINI CONSTR> 11.28787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -74.44971 0.00337 0.11776 0.00008 MINI INTERN> 4.92286 14.09178 0.00000 7.88138 2.87404 MINI EXTERN> -93.24437 -22.26623 0.00000 0.00000 0.00000 MINI CONSTR> 11.29084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8968 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -74.45309 0.00338 0.12630 0.00008 MINI INTERN> 4.92117 14.09083 0.00000 7.88040 2.87434 MINI EXTERN> -93.24485 -22.26910 0.00000 0.00000 0.00000 MINI CONSTR> 11.29411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -74.45648 0.00339 0.13068 0.00009 MINI INTERN> 4.92295 14.08532 0.00000 7.87870 2.87352 MINI EXTERN> -93.24600 -22.26828 0.00000 0.00000 0.00000 MINI CONSTR> 11.29729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8968 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -74.46077 0.00429 0.04190 0.00004 MINI INTERN> 4.91142 14.09079 0.00000 7.87696 2.87362 MINI EXTERN> -93.24873 -22.26492 0.00000 0.00000 0.00000 MINI CONSTR> 11.30010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -74.46267 0.00190 0.13925 0.00009 MINI INTERN> 4.92367 14.08136 0.00000 7.87699 2.87383 MINI EXTERN> -93.24931 -22.27257 0.00000 0.00000 0.00000 MINI CONSTR> 11.30337 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8968 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -74.46759 0.00492 0.04149 0.00004 MINI INTERN> 4.91147 14.08617 0.00000 7.87474 2.87344 MINI EXTERN> -93.25320 -22.26674 0.00000 0.00000 0.00000 MINI CONSTR> 11.30654 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -74.46923 0.00164 0.14975 0.00010 MINI INTERN> 4.92404 14.07696 0.00000 7.87505 2.87359 MINI EXTERN> -93.25407 -22.27465 0.00000 0.00000 0.00000 MINI CONSTR> 11.30985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8968 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -74.47254 0.00331 0.15586 0.00010 MINI INTERN> 4.92281 14.07651 0.00000 7.87409 2.87377 MINI EXTERN> -93.25689 -22.27599 0.00000 0.00000 0.00000 MINI CONSTR> 11.31317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -74.47780 0.00526 0.04761 0.00004 MINI INTERN> 4.91136 14.08041 0.00000 7.87148 2.87314 MINI EXTERN> -93.26256 -22.26797 0.00000 0.00000 0.00000 MINI CONSTR> 11.31634 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8968 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -74.48072 0.00291 0.04000 0.00005 MINI INTERN> 4.91215 14.07848 0.00000 7.87083 2.87312 MINI EXTERN> -93.26519 -22.26918 0.00000 0.00000 0.00000 MINI CONSTR> 11.31908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -74.48399 0.00328 0.04041 0.00005 MINI INTERN> 4.91247 14.07662 0.00000 7.86988 2.87300 MINI EXTERN> -93.26875 -22.26944 0.00000 0.00000 0.00000 MINI CONSTR> 11.32224 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8968 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -74.48717 0.00318 0.04194 0.00005 MINI INTERN> 4.91232 14.07533 0.00000 7.86892 2.87295 MINI EXTERN> -93.27242 -22.26959 0.00000 0.00000 0.00000 MINI CONSTR> 11.32532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -74.49044 0.00327 0.06755 0.00005 MINI INTERN> 4.91116 14.07475 0.00000 7.86750 2.87283 MINI EXTERN> -93.27727 -22.26812 0.00000 0.00000 0.00000 MINI CONSTR> 11.32872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8968 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -74.49328 0.00284 0.03916 0.00005 MINI INTERN> 4.91313 14.07222 0.00000 7.86729 2.87284 MINI EXTERN> -93.27952 -22.27044 0.00000 0.00000 0.00000 MINI CONSTR> 11.33120 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -74.49689 0.00361 0.07395 0.00006 MINI INTERN> 4.91208 14.07158 0.00000 7.86552 2.87271 MINI EXTERN> -93.28563 -22.26820 0.00000 0.00000 0.00000 MINI CONSTR> 11.33505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8967 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -74.50011 0.00322 0.05237 0.00006 MINI INTERN> 4.91308 14.06970 0.00000 7.86502 2.87272 MINI EXTERN> -93.28885 -22.26971 0.00000 0.00000 0.00000 MINI CONSTR> 11.33792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -74.50336 0.00326 0.05449 0.00006 MINI INTERN> 4.91382 14.06790 0.00000 7.86408 2.87259 MINI EXTERN> -93.29322 -22.26963 0.00000 0.00000 0.00000 MINI CONSTR> 11.34109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8967 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -74.50645 0.00309 0.06629 0.00006 MINI INTERN> 4.91344 14.06743 0.00000 7.86297 2.87269 MINI EXTERN> -93.29787 -22.26932 0.00000 0.00000 0.00000 MINI CONSTR> 11.34422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -74.50901 0.00256 0.09472 0.00006 MINI INTERN> 4.91350 14.06651 0.00000 7.86171 2.87254 MINI EXTERN> -93.30269 -22.26769 0.00000 0.00000 0.00000 MINI CONSTR> 11.34711 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8967 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -74.51224 0.00323 0.09354 0.00007 MINI INTERN> 4.91451 14.06481 0.00000 7.86077 2.87251 MINI EXTERN> -93.30722 -22.26785 0.00000 0.00000 0.00000 MINI CONSTR> 11.35022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -74.51565 0.00341 0.06691 0.00007 MINI INTERN> 4.91516 14.06321 0.00000 7.86034 2.87251 MINI EXTERN> -93.31065 -22.26938 0.00000 0.00000 0.00000 MINI CONSTR> 11.35315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8966 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -74.51802 0.00237 0.10343 0.00007 MINI INTERN> 4.91526 14.06265 0.00000 7.85895 2.87246 MINI EXTERN> -93.31583 -22.26750 0.00000 0.00000 0.00000 MINI CONSTR> 11.35599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -74.52115 0.00313 0.11266 0.00007 MINI INTERN> 4.91681 14.06077 0.00000 7.85778 2.87242 MINI EXTERN> -93.32104 -22.26708 0.00000 0.00000 0.00000 MINI CONSTR> 11.35919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8966 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -74.52403 0.00288 0.12513 0.00008 MINI INTERN> 4.91759 14.05986 0.00000 7.85663 2.87253 MINI EXTERN> -93.32609 -22.26679 0.00000 0.00000 0.00000 MINI CONSTR> 11.36224 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -74.52686 0.00283 0.11735 0.00008 MINI INTERN> 4.91771 14.05870 0.00000 7.85605 2.87242 MINI EXTERN> -93.32957 -22.26697 0.00000 0.00000 0.00000 MINI CONSTR> 11.36480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8966 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -74.52993 0.00307 0.12205 0.00008 MINI INTERN> 4.91919 14.05700 0.00000 7.85497 2.87242 MINI EXTERN> -93.33456 -22.26681 0.00000 0.00000 0.00000 MINI CONSTR> 11.36786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -74.53305 0.00312 0.12433 0.00009 MINI INTERN> 4.92065 14.05542 0.00000 7.85394 2.87246 MINI EXTERN> -93.33954 -22.26691 0.00000 0.00000 0.00000 MINI CONSTR> 11.37093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8966 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -74.53711 0.00406 0.03928 0.00004 MINI INTERN> 4.91704 14.05578 0.00000 7.85558 2.87234 MINI EXTERN> -93.33862 -22.27283 0.00000 0.00000 0.00000 MINI CONSTR> 11.37361 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -74.53856 0.00145 0.13617 0.00009 MINI INTERN> 4.92245 14.05309 0.00000 7.85199 2.87248 MINI EXTERN> -93.34862 -22.26645 0.00000 0.00000 0.00000 MINI CONSTR> 11.37650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8966 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -74.54151 0.00294 0.14045 0.00010 MINI INTERN> 4.92451 14.05062 0.00000 7.85100 2.87228 MINI EXTERN> -93.35334 -22.26600 0.00000 0.00000 0.00000 MINI CONSTR> 11.37942 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -74.54425 0.00274 0.15578 0.00010 MINI INTERN> 4.92382 14.05259 0.00000 7.85017 2.87310 MINI EXTERN> -93.35789 -22.26840 0.00000 0.00000 0.00000 MINI CONSTR> 11.38236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8966 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -74.54882 0.00457 0.04812 0.00004 MINI INTERN> 4.91726 14.05267 0.00000 7.85257 2.87226 MINI EXTERN> -93.35509 -22.27340 0.00000 0.00000 0.00000 MINI CONSTR> 11.38491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -74.54953 0.00071 0.15637 0.00011 MINI INTERN> 4.92679 14.04825 0.00000 7.84806 2.87258 MINI EXTERN> -93.36689 -22.26585 0.00000 0.00000 0.00000 MINI CONSTR> 11.38753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8965 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -74.55449 0.00497 0.05295 0.00005 MINI INTERN> 4.91728 14.05130 0.00000 7.85108 2.87223 MINI EXTERN> -93.36318 -22.27358 0.00000 0.00000 0.00000 MINI CONSTR> 11.39037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -74.55699 0.00249 0.03664 0.00005 MINI INTERN> 4.91904 14.04971 0.00000 7.84978 2.87228 MINI EXTERN> -93.36799 -22.27244 0.00000 0.00000 0.00000 MINI CONSTR> 11.39263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8964 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -74.56000 0.00301 0.03722 0.00005 MINI INTERN> 4.91928 14.04881 0.00000 7.84895 2.87224 MINI EXTERN> -93.37236 -22.27241 0.00000 0.00000 0.00000 MINI CONSTR> 11.39550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -74.56294 0.00294 0.07025 0.00005 MINI INTERN> 4.91632 14.05000 0.00000 7.84903 2.87220 MINI EXTERN> -93.37492 -22.27417 0.00000 0.00000 0.00000 MINI CONSTR> 11.39860 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8964 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -74.56578 0.00284 0.04770 0.00005 MINI INTERN> 4.91868 14.04773 0.00000 7.84764 2.87215 MINI EXTERN> -93.38014 -22.27289 0.00000 0.00000 0.00000 MINI CONSTR> 11.40106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -74.56852 0.00274 0.05665 0.00006 MINI INTERN> 4.91760 14.04815 0.00000 7.84702 2.87230 MINI EXTERN> -93.38382 -22.27351 0.00000 0.00000 0.00000 MINI CONSTR> 11.40373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8964 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -74.57088 0.00236 0.08385 0.00006 MINI INTERN> 4.91630 14.04803 0.00000 7.84698 2.87204 MINI EXTERN> -93.38621 -22.27431 0.00000 0.00000 0.00000 MINI CONSTR> 11.40628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -74.57384 0.00296 0.05654 0.00006 MINI INTERN> 4.91807 14.04679 0.00000 7.84541 2.87233 MINI EXTERN> -93.39177 -22.27340 0.00000 0.00000 0.00000 MINI CONSTR> 11.40875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -74.57606 0.00222 0.08916 0.00006 MINI INTERN> 4.91570 14.04769 0.00000 7.84552 2.87221 MINI EXTERN> -93.39373 -22.27469 0.00000 0.00000 0.00000 MINI CONSTR> 11.41125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -74.57869 0.00263 0.09867 0.00006 MINI INTERN> 4.91751 14.04511 0.00000 7.84472 2.87176 MINI EXTERN> -93.39785 -22.27376 0.00000 0.00000 0.00000 MINI CONSTR> 11.41382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -74.58115 0.00247 0.10225 0.00007 MINI INTERN> 4.91554 14.04642 0.00000 7.84429 2.87202 MINI EXTERN> -93.40083 -22.27484 0.00000 0.00000 0.00000 MINI CONSTR> 11.41624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -74.58378 0.00262 0.10734 0.00007 MINI INTERN> 4.91490 14.04657 0.00000 7.84355 2.87214 MINI EXTERN> -93.40463 -22.27509 0.00000 0.00000 0.00000 MINI CONSTR> 11.41878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -74.58633 0.00255 0.10173 0.00007 MINI INTERN> 4.91608 14.04494 0.00000 7.84273 2.87198 MINI EXTERN> -93.40849 -22.27463 0.00000 0.00000 0.00000 MINI CONSTR> 11.42106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -74.58893 0.00260 0.11101 0.00007 MINI INTERN> 4.91480 14.04604 0.00000 7.84185 2.87234 MINI EXTERN> -93.41253 -22.27508 0.00000 0.00000 0.00000 MINI CONSTR> 11.42364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -74.59127 0.00234 0.12274 0.00008 MINI INTERN> 4.91558 14.04400 0.00000 7.84152 2.87179 MINI EXTERN> -93.41548 -22.27473 0.00000 0.00000 0.00000 MINI CONSTR> 11.42604 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -74.59379 0.00252 0.11540 0.00008 MINI INTERN> 4.91512 14.04431 0.00000 7.84070 2.87206 MINI EXTERN> -93.41912 -22.27512 0.00000 0.00000 0.00000 MINI CONSTR> 11.42826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -74.59658 0.00279 0.11812 0.00008 MINI INTERN> 4.91620 14.04251 0.00000 7.83978 2.87179 MINI EXTERN> -93.42345 -22.27428 0.00000 0.00000 0.00000 MINI CONSTR> 11.43087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -74.60008 0.00350 0.03864 0.00004 MINI INTERN> 4.92608 14.03656 0.00000 7.83624 2.87233 MINI EXTERN> -93.43315 -22.27122 0.00000 0.00000 0.00000 MINI CONSTR> 11.43307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -74.60130 0.00122 0.12835 0.00009 MINI INTERN> 4.91430 14.04357 0.00000 7.83853 2.87211 MINI EXTERN> -93.43003 -22.27524 0.00000 0.00000 0.00000 MINI CONSTR> 11.43545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -74.60377 0.00247 0.14166 0.00009 MINI INTERN> 4.91862 14.03898 0.00000 7.83740 2.87139 MINI EXTERN> -93.43479 -22.27329 0.00000 0.00000 0.00000 MINI CONSTR> 11.43790 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -74.60773 0.00395 0.04386 0.00004 MINI INTERN> 4.92774 14.03422 0.00000 7.83369 2.87237 MINI EXTERN> -93.44481 -22.27108 0.00000 0.00000 0.00000 MINI CONSTR> 11.44013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -74.60849 0.00076 0.14331 0.00010 MINI INTERN> 4.91531 14.04081 0.00000 7.83648 2.87169 MINI EXTERN> -93.44049 -22.27465 0.00000 0.00000 0.00000 MINI CONSTR> 11.44236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -74.61273 0.00424 0.04943 0.00004 MINI INTERN> 4.92912 14.03248 0.00000 7.83198 2.87238 MINI EXTERN> -93.45252 -22.27093 0.00000 0.00000 0.00000 MINI CONSTR> 11.44475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -74.61497 0.00224 0.03479 0.00004 MINI INTERN> 4.92677 14.03334 0.00000 7.83185 2.87234 MINI EXTERN> -93.45440 -22.27154 0.00000 0.00000 0.00000 MINI CONSTR> 11.44668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -74.61756 0.00259 0.03697 0.00005 MINI INTERN> 4.92774 14.03224 0.00000 7.83092 2.87232 MINI EXTERN> -93.45846 -22.27137 0.00000 0.00000 0.00000 MINI CONSTR> 11.44904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -74.62009 0.00252 0.06259 0.00005 MINI INTERN> 4.93124 14.03017 0.00000 7.82935 2.87248 MINI EXTERN> -93.46403 -22.27085 0.00000 0.00000 0.00000 MINI CONSTR> 11.45155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -74.62233 0.00224 0.03587 0.00005 MINI INTERN> 4.92803 14.03114 0.00000 7.82950 2.87229 MINI EXTERN> -93.46519 -22.27145 0.00000 0.00000 0.00000 MINI CONSTR> 11.45335 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -74.62473 0.00240 0.07355 0.00005 MINI INTERN> 4.93345 14.02776 0.00000 7.82767 2.87234 MINI EXTERN> -93.47138 -22.27042 0.00000 0.00000 0.00000 MINI CONSTR> 11.45585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -74.62720 0.00248 0.05502 0.00005 MINI INTERN> 4.93073 14.02924 0.00000 7.82735 2.87252 MINI EXTERN> -93.47368 -22.27125 0.00000 0.00000 0.00000 MINI CONSTR> 11.45788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -74.62931 0.00210 0.07943 0.00005 MINI INTERN> 4.93468 14.02643 0.00000 7.82602 2.87242 MINI EXTERN> -93.47849 -22.27041 0.00000 0.00000 0.00000 MINI CONSTR> 11.46004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -74.63195 0.00264 0.05584 0.00006 MINI INTERN> 4.93090 14.02840 0.00000 7.82590 2.87256 MINI EXTERN> -93.48038 -22.27147 0.00000 0.00000 0.00000 MINI CONSTR> 11.46213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -74.63391 0.00196 0.08516 0.00006 MINI INTERN> 4.93473 14.02621 0.00000 7.82446 2.87268 MINI EXTERN> -93.48532 -22.27088 0.00000 0.00000 0.00000 MINI CONSTR> 11.46422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -74.63613 0.00223 0.09725 0.00006 MINI INTERN> 4.93717 14.02333 0.00000 7.82372 2.87217 MINI EXTERN> -93.48882 -22.27003 0.00000 0.00000 0.00000 MINI CONSTR> 11.46633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -74.63834 0.00221 0.09815 0.00006 MINI INTERN> 4.93808 14.02289 0.00000 7.82271 2.87238 MINI EXTERN> -93.49265 -22.27010 0.00000 0.00000 0.00000 MINI CONSTR> 11.46834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -74.64064 0.00230 0.09406 0.00007 MINI INTERN> 4.93657 14.02414 0.00000 7.82206 2.87273 MINI EXTERN> -93.49560 -22.27086 0.00000 0.00000 0.00000 MINI CONSTR> 11.47032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -74.64272 0.00209 0.11455 0.00007 MINI INTERN> 4.93985 14.02064 0.00000 7.82126 2.87212 MINI EXTERN> -93.49924 -22.26979 0.00000 0.00000 0.00000 MINI CONSTR> 11.47244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -74.64498 0.00226 0.10398 0.00007 MINI INTERN> 4.93959 14.02073 0.00000 7.82051 2.87229 MINI EXTERN> -93.50234 -22.27004 0.00000 0.00000 0.00000 MINI CONSTR> 11.47428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -74.64725 0.00226 0.10976 0.00007 MINI INTERN> 4.93570 14.02435 0.00000 7.82001 2.87303 MINI EXTERN> -93.50491 -22.27177 0.00000 0.00000 0.00000 MINI CONSTR> 11.47635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -74.65015 0.00290 0.03473 0.00003 MINI INTERN> 4.92845 14.02607 0.00000 7.82121 2.87226 MINI EXTERN> -93.50363 -22.27257 0.00000 0.00000 0.00000 MINI CONSTR> 11.47805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -74.65145 0.00131 0.11693 0.00008 MINI INTERN> 4.94212 14.01830 0.00000 7.81806 2.87230 MINI EXTERN> -93.51249 -22.26991 0.00000 0.00000 0.00000 MINI CONSTR> 11.48017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8963 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -74.65352 0.00207 0.13229 0.00008 MINI INTERN> 4.93655 14.02351 0.00000 7.81776 2.87325 MINI EXTERN> -93.51451 -22.27229 0.00000 0.00000 0.00000 MINI CONSTR> 11.48220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -74.65582 0.00230 0.12405 0.00008 MINI INTERN> 4.94324 14.01786 0.00000 7.81625 2.87266 MINI EXTERN> -93.51960 -22.27038 0.00000 0.00000 0.00000 MINI CONSTR> 11.48415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8962 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -74.65815 0.00232 0.12786 0.00009 MINI INTERN> 4.94382 14.01710 0.00000 7.81551 2.87262 MINI EXTERN> -93.52291 -22.27052 0.00000 0.00000 0.00000 MINI CONSTR> 11.48623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -74.66044 0.00229 0.13429 0.00009 MINI INTERN> 4.94346 14.01752 0.00000 7.81474 2.87284 MINI EXTERN> -93.52621 -22.27114 0.00000 0.00000 0.00000 MINI CONSTR> 11.48835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8962 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -74.66420 0.00376 0.04354 0.00004 MINI INTERN> 4.92876 14.02355 0.00000 7.81696 2.87219 MINI EXTERN> -93.52267 -22.27327 0.00000 0.00000 0.00000 MINI CONSTR> 11.49028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -74.66624 0.00204 0.03325 0.00004 MINI INTERN> 4.93047 14.02238 0.00000 7.81599 2.87228 MINI EXTERN> -93.52615 -22.27318 0.00000 0.00000 0.00000 MINI CONSTR> 11.49197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8962 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -74.66855 0.00231 0.03496 0.00004 MINI INTERN> 4.93041 14.02196 0.00000 7.81533 2.87222 MINI EXTERN> -93.52913 -22.27330 0.00000 0.00000 0.00000 MINI CONSTR> 11.49395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -74.67078 0.00223 0.03517 0.00004 MINI INTERN> 4.93048 14.02166 0.00000 7.81462 2.87226 MINI EXTERN> -93.53217 -22.27349 0.00000 0.00000 0.00000 MINI CONSTR> 11.49586 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8962 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -74.67305 0.00227 0.06045 0.00005 MINI INTERN> 4.92824 14.02242 0.00000 7.81441 2.87209 MINI EXTERN> -93.53425 -22.27392 0.00000 0.00000 0.00000 MINI CONSTR> 11.49797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -74.67509 0.00204 0.03408 0.00005 MINI INTERN> 4.93113 14.02068 0.00000 7.81319 2.87228 MINI EXTERN> -93.53815 -22.27373 0.00000 0.00000 0.00000 MINI CONSTR> 11.49951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8961 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -74.67727 0.00218 0.07033 0.00005 MINI INTERN> 4.92746 14.02263 0.00000 7.81314 2.87222 MINI EXTERN> -93.53980 -22.27457 0.00000 0.00000 0.00000 MINI CONSTR> 11.50165 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 -74.67727 0.00218 0.07033 0.00006 STPD INTERN> 4.92746 14.02263 0.00000 7.81314 2.87222 STPD EXTERN> -93.53980 -22.27457 0.00000 0.00000 0.00000 STPD CONSTR> 11.50165 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 8961 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8961 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 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 -74.67727 0.00218 0.07033 0.00000 MINI INTERN> 4.92746 14.02263 0.00000 7.81314 2.87222 MINI EXTERN> -93.53980 -22.27457 0.00000 0.00000 0.00000 MINI CONSTR> 11.50165 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -75.20799 0.53072 0.15372 0.15499 MINI INTERN> 5.21935 13.99968 0.00000 7.55512 2.90763 MINI EXTERN> -94.95842 -22.41822 0.00000 0.00000 0.00000 MINI CONSTR> 12.48686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -75.23256 0.02457 0.12878 0.01952 MINI INTERN> 5.02874 13.87644 0.00000 7.53420 2.87377 MINI EXTERN> -94.75711 -22.31005 0.00000 0.00000 0.00000 MINI CONSTR> 12.52146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -75.26284 0.03028 0.18443 0.02909 MINI INTERN> 4.98814 13.74611 0.00000 7.49833 2.86461 MINI EXTERN> -94.62205 -22.26058 0.00000 0.00000 0.00000 MINI CONSTR> 12.52261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -75.37832 0.11548 0.32326 0.11223 MINI INTERN> 4.92572 13.98365 0.00000 7.47023 2.86970 MINI EXTERN> -94.62314 -22.50218 0.00000 0.00000 0.00000 MINI CONSTR> 12.49771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -75.51746 0.13914 0.25437 0.08678 MINI INTERN> 4.94694 14.04472 0.00000 7.39309 2.80394 MINI EXTERN> -94.35824 -22.84169 0.00000 0.00000 0.00000 MINI CONSTR> 12.49377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -75.61044 0.09298 0.20849 0.07138 MINI INTERN> 5.02405 14.02892 0.00000 7.46865 2.87745 MINI EXTERN> -94.43644 -23.07774 0.00000 0.00000 0.00000 MINI CONSTR> 12.50466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -75.65183 0.04139 0.13396 0.02752 MINI INTERN> 5.00459 14.08143 0.00000 7.48326 2.88199 MINI EXTERN> -94.40896 -23.20229 0.00000 0.00000 0.00000 MINI CONSTR> 12.50815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -75.67982 0.02799 0.12015 0.02490 MINI INTERN> 4.99802 14.16156 0.00000 7.55883 2.87259 MINI EXTERN> -94.44403 -23.33393 0.00000 0.00000 0.00000 MINI CONSTR> 12.50713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -75.69831 0.01849 0.10534 0.01611 MINI INTERN> 5.01347 14.11407 0.00000 7.58556 2.84799 MINI EXTERN> -94.39298 -23.36996 0.00000 0.00000 0.00000 MINI CONSTR> 12.50355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -75.71197 0.01366 0.09009 0.01265 MINI INTERN> 5.01355 14.13264 0.00000 7.61681 2.84814 MINI EXTERN> -94.36244 -23.45702 0.00000 0.00000 0.00000 MINI CONSTR> 12.49635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -75.72226 0.01029 0.08525 0.01021 MINI INTERN> 5.03391 14.13525 0.00000 7.63003 2.86461 MINI EXTERN> -94.39320 -23.48032 0.00000 0.00000 0.00000 MINI CONSTR> 12.48747 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -75.73143 0.00917 0.07066 0.01125 MINI INTERN> 5.00406 14.13820 0.00000 7.65977 2.85958 MINI EXTERN> -94.34368 -23.52518 0.00000 0.00000 0.00000 MINI CONSTR> 12.47584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -75.73919 0.00776 0.07132 0.01195 MINI INTERN> 4.98785 14.08171 0.00000 7.69405 2.85348 MINI EXTERN> -94.30305 -23.51624 0.00000 0.00000 0.00000 MINI CONSTR> 12.46301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -75.74605 0.00685 0.06124 0.01000 MINI INTERN> 4.98505 14.07166 0.00000 7.71726 2.85939 MINI EXTERN> -94.33986 -23.48996 0.00000 0.00000 0.00000 MINI CONSTR> 12.45041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -75.75032 0.00427 0.04760 0.00717 MINI INTERN> 4.98685 14.09012 0.00000 7.75053 2.86892 MINI EXTERN> -94.35722 -23.53027 0.00000 0.00000 0.00000 MINI CONSTR> 12.44075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -75.75369 0.00337 0.04097 0.00579 MINI INTERN> 4.97992 14.08103 0.00000 7.76262 2.87291 MINI EXTERN> -94.35847 -23.52285 0.00000 0.00000 0.00000 MINI CONSTR> 12.43115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -75.75626 0.00258 0.03748 0.00492 MINI INTERN> 4.98012 14.08676 0.00000 7.77680 2.86266 MINI EXTERN> -94.33646 -23.54695 0.00000 0.00000 0.00000 MINI CONSTR> 12.42080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -75.75873 0.00247 0.03969 0.00656 MINI INTERN> 4.98981 14.10759 0.00000 7.78155 2.86849 MINI EXTERN> -94.30837 -23.60601 0.00000 0.00000 0.00000 MINI CONSTR> 12.40820 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -75.76090 0.00217 0.03624 0.00567 MINI INTERN> 4.98847 14.13575 0.00000 7.77085 2.86218 MINI EXTERN> -94.28694 -23.62773 0.00000 0.00000 0.00000 MINI CONSTR> 12.39653 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -75.76253 0.00163 0.03301 0.00494 MINI INTERN> 4.98959 14.12117 0.00000 7.76778 2.86761 MINI EXTERN> -94.26061 -23.63642 0.00000 0.00000 0.00000 MINI CONSTR> 12.38834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -75.76253 0.00163 0.03301 0.02000 CONJ INTERN> 4.98959 14.12117 0.00000 7.76778 2.86761 CONJ EXTERN> -94.26061 -23.63642 0.00000 0.00000 0.00000 CONJ CONSTR> 12.38834 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 ASP 1 HT1 ) 0.55768E-01 ( PROT ASP 1 HT2 ) 0.55768E-01 ( PROT ASP 1 N ) 0.69710E-01 ( PROT ASP 1 HT3 ) 0.55768E-01 ( PROT ASP 1 CA ) 0.69710E-01 ( PROT ASP 1 CB ) 0.55768E-01 ( PROT ASP 1 CG ) 0.55768E-01 ( PROT ASP 1 OD1 ) 0.55768E-01 ( PROT ASP 1 OD2 ) 0.55768E-01 ( PROT ASP 1 C ) 0.69710E-01 ( PROT ASP 1 O ) 0.69710E-01 ( PROT TYR 2 N ) 0.69710E-01 ( PROT TYR 2 H ) 0.55768E-01 ( PROT TYR 2 CA ) 0.69710E-01 ( PROT TYR 2 CB ) 0.55768E-01 ( PROT TYR 2 CG ) 0.55768E-01 ( PROT TYR 2 CD1 ) 0.55768E-01 ( PROT TYR 2 CE1 ) 0.55768E-01 ( PROT TYR 2 CD2 ) 0.55768E-01 ( PROT TYR 2 CE2 ) 0.55768E-01 ( PROT TYR 2 CZ ) 0.55768E-01 ( PROT TYR 2 OH ) 0.55768E-01 ( PROT TYR 2 HH ) 0.55768E-01 ( PROT TYR 2 C ) 0.69710E-01 ( PROT TYR 2 O ) 0.69710E-01 ( PROT ALA 3 N ) 0.69710E-01 ( PROT ALA 3 H ) 0.55768E-01 ( PROT ALA 3 CA ) 0.69710E-01 ( PROT ALA 3 CB ) 0.55768E-01 ( PROT ALA 3 C ) 0.69710E-01 ( PROT ALA 3 O ) 0.69710E-01 ( PROT PHE 4 N ) 0.69710E-01 ( PROT PHE 4 H ) 0.55768E-01 ( PROT PHE 4 CA ) 0.69710E-01 ( PROT PHE 4 CB ) 0.55768E-01 ( PROT PHE 4 CG ) 0.55768E-01 ( PROT PHE 4 CD1 ) 0.55768E-01 ( PROT PHE 4 CD2 ) 0.55768E-01 ( PROT PHE 4 CE1 ) 0.55768E-01 ( PROT PHE 4 CE2 ) 0.55768E-01 ( PROT PHE 4 CZ ) 0.55768E-01 ( PROT PHE 4 C ) 0.69710E-01 ( PROT PHE 4 O ) 0.69710E-01 ( PROT ILE 5 N ) 0.69710E-01 ( PROT ILE 5 H ) 0.55768E-01 ( PROT ILE 5 CA ) 0.69710E-01 ( PROT ILE 5 CB ) 0.55768E-01 ( PROT ILE 5 CG2 ) 0.55768E-01 ( PROT ILE 5 CG1 ) 0.55768E-01 ( PROT ILE 5 CD ) 0.55768E-01 ( PROT ILE 5 C ) 0.69710E-01 ( PROT ILE 5 O ) 0.69710E-01 ( PROT ALA 6 N ) 0.69710E-01 ( PROT ALA 6 H ) 0.55768E-01 ( PROT ALA 6 CA ) 0.69710E-01 ( PROT ALA 6 CB ) 0.55768E-01 ( PROT ALA 6 C ) 0.69710E-01 ( PROT ALA 6 O ) 0.69710E-01 ( PROT SER 7 N ) 0.69710E-01 ( PROT SER 7 H ) 0.55768E-01 ( PROT SER 7 CA ) 0.69710E-01 ( PROT SER 7 CB ) 0.55768E-01 ( PROT SER 7 OG ) 0.55768E-01 ( PROT SER 7 HG ) 0.55768E-01 ( PROT SER 7 C ) 0.69710E-01 ( PROT SER 7 O ) 0.69710E-01 ( PROT LEU 8 N ) 0.69710E-01 ( PROT LEU 8 H ) 0.55768E-01 ( PROT LEU 8 CA ) 0.69710E-01 ( PROT LEU 8 CB ) 0.55768E-01 ( PROT LEU 8 CG ) 0.55768E-01 ( PROT LEU 8 CD1 ) 0.55768E-01 ( PROT LEU 8 CD2 ) 0.55768E-01 ( PROT LEU 8 C ) 0.69710E-01 ( PROT LEU 8 O ) 0.69710E-01 ( PROT VAL 9 N ) 0.69710E-01 ( PROT VAL 9 H ) 0.55768E-01 ( PROT VAL 9 CA ) 0.69710E-01 ( PROT VAL 9 CB ) 0.55768E-01 ( PROT VAL 9 CG1 ) 0.55768E-01 ( PROT VAL 9 CG2 ) 0.55768E-01 ( PROT VAL 9 C ) 0.69710E-01 ( PROT VAL 9 O ) 0.69710E-01 ( PROT VAL 10 N ) 0.69710E-01 ( PROT VAL 10 H ) 0.55768E-01 ( PROT VAL 10 CA ) 0.69710E-01 ( PROT VAL 10 CB ) 0.55768E-01 ( PROT VAL 10 CG1 ) 0.55768E-01 ( PROT VAL 10 CG2 ) 0.55768E-01 ( PROT VAL 10 C ) 0.69710E-01 ( PROT VAL 10 O ) 0.69710E-01 ( PROT ILE 11 N ) 0.69710E-01 ( PROT ILE 11 H ) 0.55768E-01 ( PROT ILE 11 CA ) 0.69710E-01 ( PROT ILE 11 CB ) 0.55768E-01 ( PROT ILE 11 CG2 ) 0.55768E-01 ( PROT ILE 11 CG1 ) 0.55768E-01 ( PROT ILE 11 CD ) 0.55768E-01 ( PROT ILE 11 C ) 0.69710E-01 ( PROT ILE 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 ASP 13 N ) 0.69710E-01 ( PROT ASP 13 H ) 0.55768E-01 ( PROT ASP 13 CA ) 0.69710E-01 ( PROT ASP 13 CB ) 0.55768E-01 ( PROT ASP 13 CG ) 0.55768E-01 ( PROT ASP 13 OD1 ) 0.55768E-01 ( PROT ASP 13 OD2 ) 0.55768E-01 ( PROT ASP 13 C ) 0.69710E-01 ( PROT ASP 13 O ) 0.69710E-01 ( PROT ASP 14 N ) 0.69710E-01 ( PROT ASP 14 H ) 0.55768E-01 ( PROT ASP 14 CA ) 0.69710E-01 ( PROT ASP 14 CB ) 0.55768E-01 ( PROT ASP 14 CG ) 0.55768E-01 ( PROT ASP 14 OD1 ) 0.55768E-01 ( PROT ASP 14 OD2 ) 0.55768E-01 ( PROT ASP 14 C ) 0.69710E-01 ( PROT ASP 14 O ) 0.69710E-01 ( PROT VAL 15 N ) 0.69710E-01 ( PROT VAL 15 H ) 0.55768E-01 ( PROT VAL 15 CA ) 0.69710E-01 ( PROT VAL 15 CB ) 0.55768E-01 ( PROT VAL 15 CG1 ) 0.55768E-01 ( PROT VAL 15 CG2 ) 0.55768E-01 ( PROT VAL 15 C ) 0.69710E-01 ( PROT VAL 15 O ) 0.69710E-01 ( PROT ASN 16 N ) 0.69710E-01 ( PROT ASN 16 H ) 0.55768E-01 ( PROT ASN 16 CA ) 0.69710E-01 ( PROT ASN 16 CB ) 0.55768E-01 ( PROT ASN 16 CG ) 0.55768E-01 ( PROT ASN 16 OD1 ) 0.55768E-01 ( PROT ASN 16 ND2 ) 0.55768E-01 ( PROT ASN 16 HD21 ) 0.55768E-01 ( PROT ASN 16 HD22 ) 0.55768E-01 ( PROT ASN 16 C ) 0.69710E-01 ( PROT ASN 16 O ) 0.69710E-01 ( PROT ARG 17 N ) 0.69710E-01 ( PROT ARG 17 H ) 0.55768E-01 ( PROT ARG 17 CA ) 0.69710E-01 ( PROT ARG 17 CB ) 0.55768E-01 ( PROT ARG 17 CG ) 0.55768E-01 ( PROT ARG 17 CD ) 0.55768E-01 ( PROT ARG 17 NE ) 0.55768E-01 ( PROT ARG 17 HE ) 0.55768E-01 ( PROT ARG 17 CZ ) 0.55768E-01 ( PROT ARG 17 NH1 ) 0.55768E-01 ( PROT ARG 17 HH11 ) 0.55768E-01 ( PROT ARG 17 HH12 ) 0.55768E-01 ( PROT ARG 17 NH2 ) 0.55768E-01 ( PROT ARG 17 HH21 ) 0.55768E-01 ( PROT ARG 17 HH22 ) 0.55768E-01 ( PROT ARG 17 C ) 0.69710E-01 ( PROT ARG 17 OT1 ) 0.55768E-01 ( PROT ARG 17 OT2 ) 0.55768E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.95582 3.70633 -6.79660 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.00800 0.00500 -0.00540 ROTATION MATRIX 0.999998 -0.001010 -0.001918 0.001016 0.999995 0.003128 0.001915 -0.003130 0.999993 AXIS OF ROTATION IS 0.821961 0.503528 -0.266155 ANGLE IS 0.22 TOTAL SQUARE DIFF IS 132.9251 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.900288 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.9003" Parameter: A <- "0.9003" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.82401 3.80539 -6.99971 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.05184 -0.01368 0.02247 ROTATION MATRIX 0.998743 0.032424 0.038212 -0.030375 0.998131 -0.053024 -0.039860 0.051797 0.997862 AXIS OF ROTATION IS -0.722880 -0.538406 0.433085 ANGLE IS 4.16 CENTER OF ROTATION 7.713034 3.713083 -7.236699 SHIFT IS 0.054571 TOTAL SQUARE DIFF IS 8.7723 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.718344 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.9003" RDCMND substituted energy or value "?RMS" to " 0.7183" Parameter: A <- "0.9003 0.7183" 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 0.9003 0.7183 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 -88.15087 12.38834 0.10339 ENER INTERN> 4.98959 14.12117 0.00000 7.76778 2.86761 ENER EXTERN> -94.26061 -23.63642 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 " -88.15" Parameter: B <- "-88.15" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -23.64" Parameter: C <- "-23.64" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -94.26" Parameter: C <- " -117.90" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -117.90" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.99" Parameter: D <- "4.99" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.12" Parameter: D <- " 19.11" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 7.77" Parameter: D <- " 26.88" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.87" Parameter: D <- " 29.75" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 29.75" 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= -88.15 GRMS= 0.10 ELEC= -23.64 VDW= -94.26 RDTITL> *EXTERNAL= -117.90 INTERNAL= 29.75 USER= 0.00 HARM= 12.39 RDTITL> *BOND= 4.99 ANGL= 14.12 DIHE= 7.77 IMPR= 2.87 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 2/15/16 20:35:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 164 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 8961 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 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 -79.31211 -8.83876 0.05173 0.02000 MINI INTERN> 4.98959 14.12117 0.00000 7.76778 2.86761 MINI EXTERN> -94.26061 -23.63642 0.00000 0.00000 0.00000 MINI CONSTR> 8.83876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -77.51129 -1.80082 3.90357 0.00360 MINI INTERN> 6.52380 14.82020 0.00000 7.87337 2.91980 MINI EXTERN> -95.55577 -23.10071 0.00000 0.00000 0.00000 MINI CONSTR> 9.00801 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -79.39724 1.88595 0.26240 0.00065 MINI INTERN> 5.16156 14.37314 0.00000 7.83151 2.86539 MINI EXTERN> -95.40994 -23.22463 0.00000 0.00000 0.00000 MINI CONSTR> 9.00573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -79.41977 0.02253 0.15530 0.00028 MINI INTERN> 5.09799 14.31804 0.00000 7.81679 2.87917 MINI EXTERN> -95.24478 -23.29176 0.00000 0.00000 0.00000 MINI CONSTR> 9.00479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -79.42960 0.00983 0.09362 0.00012 MINI INTERN> 5.08600 14.27230 0.00000 7.80693 2.87439 MINI EXTERN> -95.15421 -23.31977 0.00000 0.00000 0.00000 MINI CONSTR> 9.00476 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -79.43454 0.00494 0.04904 0.00005 MINI INTERN> 5.07457 14.25347 0.00000 7.80061 2.87554 MINI EXTERN> -95.10427 -23.33954 0.00000 0.00000 0.00000 MINI CONSTR> 9.00507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -79.43798 0.00344 0.08823 0.00005 MINI INTERN> 5.06786 14.23498 0.00000 7.79544 2.87564 MINI EXTERN> -95.06122 -23.35633 0.00000 0.00000 0.00000 MINI CONSTR> 9.00566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -79.44099 0.00301 0.06116 0.00006 MINI INTERN> 5.06125 14.22576 0.00000 7.79154 2.87619 MINI EXTERN> -95.03211 -23.36993 0.00000 0.00000 0.00000 MINI CONSTR> 9.00632 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -79.44299 0.00201 0.09989 0.00006 MINI INTERN> 5.05756 14.21632 0.00000 7.78852 2.87643 MINI EXTERN> -95.00790 -23.38102 0.00000 0.00000 0.00000 MINI CONSTR> 9.00710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -79.44531 0.00232 0.11097 0.00006 MINI INTERN> 5.05370 14.20865 0.00000 7.78541 2.87685 MINI EXTERN> -94.98583 -23.39218 0.00000 0.00000 0.00000 MINI CONSTR> 9.00808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -79.44737 0.00206 0.10767 0.00006 MINI INTERN> 5.05081 14.20353 0.00000 7.78303 2.87716 MINI EXTERN> -94.96987 -23.40103 0.00000 0.00000 0.00000 MINI CONSTR> 9.00900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -79.44946 0.00209 0.10959 0.00006 MINI INTERN> 5.04828 14.19855 0.00000 7.78072 2.87748 MINI EXTERN> -94.95504 -23.40954 0.00000 0.00000 0.00000 MINI CONSTR> 9.01009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -79.45209 0.00263 0.03544 0.00003 MINI INTERN> 5.04532 14.19753 0.00000 7.77789 2.87805 MINI EXTERN> -94.94308 -23.41893 0.00000 0.00000 0.00000 MINI CONSTR> 9.01113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -79.45294 0.00085 0.12181 0.00007 MINI INTERN> 5.04525 14.19092 0.00000 7.77726 2.87783 MINI EXTERN> -94.93371 -23.42275 0.00000 0.00000 0.00000 MINI CONSTR> 9.01226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -79.45479 0.00185 0.12639 0.00007 MINI INTERN> 5.04381 14.18763 0.00000 7.77563 2.87804 MINI EXTERN> -94.92473 -23.42870 0.00000 0.00000 0.00000 MINI CONSTR> 9.01352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -79.45655 0.00176 0.13363 0.00007 MINI INTERN> 5.04264 14.18471 0.00000 7.77418 2.87822 MINI EXTERN> -94.91722 -23.43392 0.00000 0.00000 0.00000 MINI CONSTR> 9.01483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -79.45951 0.00295 0.04436 0.00003 MINI INTERN> 5.04127 14.18548 0.00000 7.77157 2.87855 MINI EXTERN> -94.91011 -23.44236 0.00000 0.00000 0.00000 MINI CONSTR> 9.01610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -79.46102 0.00151 0.03108 0.00003 MINI INTERN> 5.04057 14.18321 0.00000 7.77080 2.87858 MINI EXTERN> -94.90608 -23.44525 0.00000 0.00000 0.00000 MINI CONSTR> 9.01716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -79.46283 0.00181 0.03098 0.00003 MINI INTERN> 5.04013 14.18109 0.00000 7.76967 2.87861 MINI EXTERN> -94.90145 -23.44940 0.00000 0.00000 0.00000 MINI CONSTR> 9.01853 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -79.46464 0.00180 0.03156 0.00004 MINI INTERN> 5.03983 14.17919 0.00000 7.76862 2.87861 MINI EXTERN> -94.89759 -23.45324 0.00000 0.00000 0.00000 MINI CONSTR> 9.01994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -79.46635 0.00172 0.06207 0.00004 MINI INTERN> 5.04047 14.17790 0.00000 7.76730 2.87851 MINI EXTERN> -94.89376 -23.45828 0.00000 0.00000 0.00000 MINI CONSTR> 9.02149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -79.46808 0.00172 0.03927 0.00004 MINI INTERN> 5.03979 14.17611 0.00000 7.76675 2.87854 MINI EXTERN> -94.89186 -23.46015 0.00000 0.00000 0.00000 MINI CONSTR> 9.02275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -79.46983 0.00175 0.03928 0.00004 MINI INTERN> 5.03982 14.17461 0.00000 7.76596 2.87848 MINI EXTERN> -94.88982 -23.46307 0.00000 0.00000 0.00000 MINI CONSTR> 9.02420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -79.47159 0.00176 0.04164 0.00004 MINI INTERN> 5.04001 14.17323 0.00000 7.76521 2.87840 MINI EXTERN> -94.88818 -23.46594 0.00000 0.00000 0.00000 MINI CONSTR> 9.02569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -79.47329 0.00170 0.04887 0.00004 MINI INTERN> 5.04043 14.17202 0.00000 7.76448 2.87828 MINI EXTERN> -94.88689 -23.46879 0.00000 0.00000 0.00000 MINI CONSTR> 9.02717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -79.47462 0.00133 0.07579 0.00004 MINI INTERN> 5.04165 14.17116 0.00000 7.76376 2.87806 MINI EXTERN> -94.88576 -23.47203 0.00000 0.00000 0.00000 MINI CONSTR> 9.02854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -79.47630 0.00168 0.07725 0.00005 MINI INTERN> 5.04205 14.16998 0.00000 7.76321 2.87794 MINI EXTERN> -94.88521 -23.47429 0.00000 0.00000 0.00000 MINI CONSTR> 9.03002 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -79.47799 0.00169 0.08081 0.00005 MINI INTERN> 5.04261 14.16885 0.00000 7.76270 2.87780 MINI EXTERN> -94.88493 -23.47655 0.00000 0.00000 0.00000 MINI CONSTR> 9.03153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -79.47962 0.00163 0.08775 0.00005 MINI INTERN> 5.04332 14.16783 0.00000 7.76221 2.87765 MINI EXTERN> -94.88486 -23.47881 0.00000 0.00000 0.00000 MINI CONSTR> 9.03304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -79.48115 0.00153 0.09623 0.00005 MINI INTERN> 5.04404 14.16697 0.00000 7.76172 2.87751 MINI EXTERN> -94.88499 -23.48092 0.00000 0.00000 0.00000 MINI CONSTR> 9.03451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -79.48265 0.00150 0.09046 0.00005 MINI INTERN> 5.04381 14.16643 0.00000 7.76128 2.87754 MINI EXTERN> -94.88544 -23.48202 0.00000 0.00000 0.00000 MINI CONSTR> 9.03576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -79.48426 0.00161 0.09457 0.00006 MINI INTERN> 5.04440 14.16562 0.00000 7.76085 2.87744 MINI EXTERN> -94.88599 -23.48383 0.00000 0.00000 0.00000 MINI CONSTR> 9.03726 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -79.48592 0.00165 0.09725 0.00006 MINI INTERN> 5.04493 14.16486 0.00000 7.76042 2.87736 MINI EXTERN> -94.88675 -23.48552 0.00000 0.00000 0.00000 MINI CONSTR> 9.03878 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -79.48811 0.00219 0.02978 0.00002 MINI INTERN> 5.03987 14.16504 0.00000 7.75980 2.87835 MINI EXTERN> -94.88897 -23.48234 0.00000 0.00000 0.00000 MINI CONSTR> 9.04015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -79.48893 0.00082 0.10587 0.00006 MINI INTERN> 5.04600 14.16368 0.00000 7.75961 2.87722 MINI EXTERN> -94.88849 -23.48858 0.00000 0.00000 0.00000 MINI CONSTR> 9.04162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -79.49048 0.00156 0.10844 0.00006 MINI INTERN> 5.04647 14.16314 0.00000 7.75921 2.87718 MINI EXTERN> -94.88958 -23.48998 0.00000 0.00000 0.00000 MINI CONSTR> 9.04307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8953 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -79.49207 0.00158 0.11201 0.00007 MINI INTERN> 5.04707 14.16260 0.00000 7.75882 2.87713 MINI EXTERN> -94.89081 -23.49144 0.00000 0.00000 0.00000 MINI CONSTR> 9.04456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -79.49363 0.00157 0.11713 0.00007 MINI INTERN> 5.04781 14.16206 0.00000 7.75842 2.87709 MINI EXTERN> -94.89215 -23.49293 0.00000 0.00000 0.00000 MINI CONSTR> 9.04608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8952 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -79.49620 0.00256 0.03619 0.00003 MINI INTERN> 5.04037 14.16293 0.00000 7.75763 2.87840 MINI EXTERN> -94.89515 -23.48790 0.00000 0.00000 0.00000 MINI CONSTR> 9.04753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -79.49755 0.00135 0.02893 0.00003 MINI INTERN> 5.04135 14.16243 0.00000 7.75734 2.87826 MINI EXTERN> -94.89619 -23.48948 0.00000 0.00000 0.00000 MINI CONSTR> 9.04873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8952 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -79.49913 0.00158 0.02866 0.00003 MINI INTERN> 5.04164 14.16208 0.00000 7.75696 2.87826 MINI EXTERN> -94.89768 -23.49056 0.00000 0.00000 0.00000 MINI CONSTR> 9.05017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -79.50075 0.00162 0.02864 0.00003 MINI INTERN> 5.04189 14.16176 0.00000 7.75657 2.87826 MINI EXTERN> -94.89928 -23.49160 0.00000 0.00000 0.00000 MINI CONSTR> 9.05166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8952 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -79.50239 0.00163 0.02907 0.00003 MINI INTERN> 5.04206 14.16147 0.00000 7.75617 2.87828 MINI EXTERN> -94.90097 -23.49256 0.00000 0.00000 0.00000 MINI CONSTR> 9.05315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -79.50401 0.00162 0.05551 0.00004 MINI INTERN> 5.04024 14.16177 0.00000 7.75564 2.87859 MINI EXTERN> -94.90317 -23.49189 0.00000 0.00000 0.00000 MINI CONSTR> 9.05481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8952 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -79.50555 0.00154 0.03704 0.00004 MINI INTERN> 5.04173 14.16116 0.00000 7.75538 2.87841 MINI EXTERN> -94.90453 -23.49380 0.00000 0.00000 0.00000 MINI CONSTR> 9.05610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -79.50714 0.00159 0.03647 0.00004 MINI INTERN> 5.04203 14.16092 0.00000 7.75502 2.87840 MINI EXTERN> -94.90627 -23.49479 0.00000 0.00000 0.00000 MINI CONSTR> 9.05755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8952 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -79.50876 0.00162 0.03734 0.00004 MINI INTERN> 5.04223 14.16074 0.00000 7.75465 2.87840 MINI EXTERN> -94.90810 -23.49573 0.00000 0.00000 0.00000 MINI CONSTR> 9.05905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -79.51037 0.00161 0.04086 0.00004 MINI INTERN> 5.04226 14.16066 0.00000 7.75427 2.87842 MINI EXTERN> -94.90999 -23.49653 0.00000 0.00000 0.00000 MINI CONSTR> 9.06055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8952 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -79.51171 0.00134 0.07005 0.00004 MINI INTERN> 5.04079 14.16121 0.00000 7.75385 2.87855 MINI EXTERN> -94.91192 -23.49622 0.00000 0.00000 0.00000 MINI CONSTR> 9.06202 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -79.51328 0.00157 0.06887 0.00004 MINI INTERN> 5.04129 14.16108 0.00000 7.75352 2.87849 MINI EXTERN> -94.91371 -23.49741 0.00000 0.00000 0.00000 MINI CONSTR> 9.06346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8951 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -79.51499 0.00171 0.04697 0.00005 MINI INTERN> 5.04292 14.16035 0.00000 7.75324 2.87842 MINI EXTERN> -94.91555 -23.49919 0.00000 0.00000 0.00000 MINI CONSTR> 9.06483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -79.51622 0.00122 0.07439 0.00005 MINI INTERN> 5.04182 14.16092 0.00000 7.75287 2.87848 MINI EXTERN> -94.91736 -23.49917 0.00000 0.00000 0.00000 MINI CONSTR> 9.06621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8951 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -79.51780 0.00159 0.07925 0.00005 MINI INTERN> 5.04219 14.16106 0.00000 7.75252 2.87843 MINI EXTERN> -94.91935 -23.50037 0.00000 0.00000 0.00000 MINI CONSTR> 9.06773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -79.51932 0.00152 0.08677 0.00005 MINI INTERN> 5.04220 14.16128 0.00000 7.75215 2.87844 MINI EXTERN> -94.92140 -23.50121 0.00000 0.00000 0.00000 MINI CONSTR> 9.06921 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8950 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -79.52078 0.00146 0.08274 0.00005 MINI INTERN> 5.04264 14.16100 0.00000 7.75185 2.87848 MINI EXTERN> -94.92324 -23.50201 0.00000 0.00000 0.00000 MINI CONSTR> 9.07050 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -79.52231 0.00153 0.08749 0.00006 MINI INTERN> 5.04261 14.16120 0.00000 7.75148 2.87851 MINI EXTERN> -94.92532 -23.50276 0.00000 0.00000 0.00000 MINI CONSTR> 9.07196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8949 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -79.52374 0.00143 0.10171 0.00006 MINI INTERN> 5.04218 14.16174 0.00000 7.75110 2.87854 MINI EXTERN> -94.92746 -23.50331 0.00000 0.00000 0.00000 MINI CONSTR> 9.07348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -79.52519 0.00145 0.09403 0.00006 MINI INTERN> 5.04282 14.16127 0.00000 7.75083 2.87859 MINI EXTERN> -94.92926 -23.50412 0.00000 0.00000 0.00000 MINI CONSTR> 9.07469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -79.52683 0.00164 0.09402 0.00006 MINI INTERN> 5.04283 14.16139 0.00000 7.75046 2.87864 MINI EXTERN> -94.93148 -23.50486 0.00000 0.00000 0.00000 MINI CONSTR> 9.07619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -79.52892 0.00209 0.03024 0.00003 MINI INTERN> 5.04821 14.15748 0.00000 7.75030 2.87877 MINI EXTERN> -94.93382 -23.50733 0.00000 0.00000 0.00000 MINI CONSTR> 9.07748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -79.52959 0.00067 0.10373 0.00007 MINI INTERN> 5.04285 14.16163 0.00000 7.74983 2.87872 MINI EXTERN> -94.93540 -23.50606 0.00000 0.00000 0.00000 MINI CONSTR> 9.07885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -79.53112 0.00153 0.10733 0.00007 MINI INTERN> 5.04271 14.16187 0.00000 7.74947 2.87877 MINI EXTERN> -94.93757 -23.50668 0.00000 0.00000 0.00000 MINI CONSTR> 9.08031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -79.53263 0.00151 0.11262 0.00007 MINI INTERN> 5.04251 14.16218 0.00000 7.74911 2.87881 MINI EXTERN> -94.93977 -23.50725 0.00000 0.00000 0.00000 MINI CONSTR> 9.08177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -79.53512 0.00249 0.03594 0.00003 MINI INTERN> 5.05006 14.15657 0.00000 7.74902 2.87899 MINI EXTERN> -94.94239 -23.51052 0.00000 0.00000 0.00000 MINI CONSTR> 9.08314 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -79.53643 0.00131 0.02746 0.00003 MINI INTERN> 5.04921 14.15718 0.00000 7.74873 2.87902 MINI EXTERN> -94.94407 -23.51078 0.00000 0.00000 0.00000 MINI CONSTR> 9.08429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -79.53687 0.00045 0.12481 0.00008 MINI INTERN> 5.04237 14.16274 0.00000 7.74815 2.87895 MINI EXTERN> -94.94593 -23.50900 0.00000 0.00000 0.00000 MINI CONSTR> 9.08584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -79.53957 0.00270 0.04608 0.00003 MINI INTERN> 5.05185 14.15569 0.00000 7.74812 2.87917 MINI EXTERN> -94.94871 -23.51294 0.00000 0.00000 0.00000 MINI CONSTR> 9.08724 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -79.54088 0.00131 0.02731 0.00004 MINI INTERN> 5.05001 14.15692 0.00000 7.74782 2.87919 MINI EXTERN> -94.95026 -23.51287 0.00000 0.00000 0.00000 MINI CONSTR> 9.08831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -79.54257 0.00169 0.05092 0.00004 MINI INTERN> 5.05288 14.15523 0.00000 7.74753 2.87930 MINI EXTERN> -94.95297 -23.51451 0.00000 0.00000 0.00000 MINI CONSTR> 9.08998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -79.54405 0.00149 0.03661 0.00004 MINI INTERN> 5.05184 14.15595 0.00000 7.74721 2.87933 MINI EXTERN> -94.95484 -23.51478 0.00000 0.00000 0.00000 MINI CONSTR> 9.09122 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -79.54558 0.00153 0.03677 0.00004 MINI INTERN> 5.05214 14.15586 0.00000 7.74691 2.87940 MINI EXTERN> -94.95698 -23.51551 0.00000 0.00000 0.00000 MINI CONSTR> 9.09259 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -79.54711 0.00153 0.03942 0.00004 MINI INTERN> 5.05268 14.15563 0.00000 7.74662 2.87946 MINI EXTERN> -94.95916 -23.51632 0.00000 0.00000 0.00000 MINI CONSTR> 9.09398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -79.54837 0.00126 0.06714 0.00004 MINI INTERN> 5.05535 14.15414 0.00000 7.74640 2.87957 MINI EXTERN> -94.96141 -23.51776 0.00000 0.00000 0.00000 MINI CONSTR> 9.09534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -79.54988 0.00150 0.06608 0.00004 MINI INTERN> 5.05554 14.15413 0.00000 7.74611 2.87963 MINI EXTERN> -94.96350 -23.51845 0.00000 0.00000 0.00000 MINI CONSTR> 9.09667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -79.55150 0.00162 0.04528 0.00005 MINI INTERN> 5.05401 14.15512 0.00000 7.74578 2.87966 MINI EXTERN> -94.96541 -23.51860 0.00000 0.00000 0.00000 MINI CONSTR> 9.09794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -79.55263 0.00113 0.07220 0.00005 MINI INTERN> 5.05654 14.15374 0.00000 7.74558 2.87976 MINI EXTERN> -94.96750 -23.51995 0.00000 0.00000 0.00000 MINI CONSTR> 9.09919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -79.55412 0.00149 0.07767 0.00005 MINI INTERN> 5.05726 14.15344 0.00000 7.74531 2.87983 MINI EXTERN> -94.96971 -23.52084 0.00000 0.00000 0.00000 MINI CONSTR> 9.10059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -79.55552 0.00140 0.08600 0.00005 MINI INTERN> 5.05820 14.15302 0.00000 7.74505 2.87991 MINI EXTERN> -94.97187 -23.52177 0.00000 0.00000 0.00000 MINI CONSTR> 9.10193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -79.55688 0.00135 0.08146 0.00005 MINI INTERN> 5.05807 14.15318 0.00000 7.74479 2.87996 MINI EXTERN> -94.97367 -23.52228 0.00000 0.00000 0.00000 MINI CONSTR> 9.10308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -79.55832 0.00145 0.08546 0.00005 MINI INTERN> 5.05861 14.15299 0.00000 7.74453 2.88003 MINI EXTERN> -94.97579 -23.52310 0.00000 0.00000 0.00000 MINI CONSTR> 9.10441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -79.55981 0.00149 0.08837 0.00006 MINI INTERN> 5.05903 14.15287 0.00000 7.74427 2.88010 MINI EXTERN> -94.97793 -23.52391 0.00000 0.00000 0.00000 MINI CONSTR> 9.10576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -79.56133 0.00151 0.08918 0.00006 MINI INTERN> 5.05925 14.15285 0.00000 7.74401 2.88017 MINI EXTERN> -94.98005 -23.52466 0.00000 0.00000 0.00000 MINI CONSTR> 9.10711 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -79.56328 0.00195 0.02858 0.00003 MINI INTERN> 5.05263 14.15703 0.00000 7.74344 2.88010 MINI EXTERN> -94.98165 -23.52310 0.00000 0.00000 0.00000 MINI CONSTR> 9.10828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -79.56394 0.00066 0.09818 0.00006 MINI INTERN> 5.06042 14.15243 0.00000 7.74354 2.88030 MINI EXTERN> -94.98394 -23.52622 0.00000 0.00000 0.00000 MINI CONSTR> 9.10953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -79.56537 0.00144 0.10107 0.00007 MINI INTERN> 5.06079 14.15234 0.00000 7.74330 2.88037 MINI EXTERN> -94.98600 -23.52700 0.00000 0.00000 0.00000 MINI CONSTR> 9.11083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -79.56682 0.00144 0.10505 0.00007 MINI INTERN> 5.06118 14.15224 0.00000 7.74306 2.88044 MINI EXTERN> -94.98809 -23.52781 0.00000 0.00000 0.00000 MINI CONSTR> 9.11216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -79.56822 0.00140 0.11106 0.00007 MINI INTERN> 5.06171 14.15207 0.00000 7.74284 2.88051 MINI EXTERN> -94.99016 -23.52866 0.00000 0.00000 0.00000 MINI CONSTR> 9.11348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -79.57056 0.00235 0.03674 0.00003 MINI INTERN> 5.05324 14.15744 0.00000 7.74207 2.88042 MINI EXTERN> -94.99192 -23.52650 0.00000 0.00000 0.00000 MINI CONSTR> 9.11470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -79.57178 0.00122 0.02635 0.00003 MINI INTERN> 5.05447 14.15665 0.00000 7.74195 2.88049 MINI EXTERN> -94.99355 -23.52750 0.00000 0.00000 0.00000 MINI CONSTR> 9.11571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -79.57325 0.00147 0.02623 0.00003 MINI INTERN> 5.05476 14.15662 0.00000 7.74169 2.88056 MINI EXTERN> -94.99560 -23.52826 0.00000 0.00000 0.00000 MINI CONSTR> 9.11699 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -79.57475 0.00150 0.02640 0.00003 MINI INTERN> 5.05500 14.15662 0.00000 7.74143 2.88063 MINI EXTERN> -94.99769 -23.52903 0.00000 0.00000 0.00000 MINI CONSTR> 9.11829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -79.57624 0.00148 0.02726 0.00004 MINI INTERN> 5.05514 14.15671 0.00000 7.74117 2.88069 MINI EXTERN> -94.99976 -23.52976 0.00000 0.00000 0.00000 MINI CONSTR> 9.11957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -79.57762 0.00139 0.05484 0.00004 MINI INTERN> 5.05381 14.15809 0.00000 7.74071 2.88074 MINI EXTERN> -95.00203 -23.52988 0.00000 0.00000 0.00000 MINI CONSTR> 9.12094 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -79.57907 0.00145 0.03371 0.00004 MINI INTERN> 5.05515 14.15711 0.00000 7.74063 2.88082 MINI EXTERN> -95.00377 -23.53106 0.00000 0.00000 0.00000 MINI CONSTR> 9.12205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -79.58055 0.00147 0.03399 0.00004 MINI INTERN> 5.05546 14.15709 0.00000 7.74038 2.88089 MINI EXTERN> -95.00584 -23.53185 0.00000 0.00000 0.00000 MINI CONSTR> 9.12331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -79.58203 0.00148 0.03649 0.00004 MINI INTERN> 5.05567 14.15717 0.00000 7.74011 2.88097 MINI EXTERN> -95.00794 -23.53260 0.00000 0.00000 0.00000 MINI CONSTR> 9.12459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -79.58324 0.00121 0.06593 0.00004 MINI INTERN> 5.05494 14.15825 0.00000 7.73968 2.88103 MINI EXTERN> -95.01016 -23.53285 0.00000 0.00000 0.00000 MINI CONSTR> 9.12586 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -79.58464 0.00140 0.06580 0.00004 MINI INTERN> 5.05533 14.15818 0.00000 7.73946 2.88110 MINI EXTERN> -95.01213 -23.53364 0.00000 0.00000 0.00000 MINI CONSTR> 9.12705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8948 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -79.58608 0.00144 0.06699 0.00005 MINI INTERN> 5.05580 14.15810 0.00000 7.73921 2.88118 MINI EXTERN> -95.01421 -23.53445 0.00000 0.00000 0.00000 MINI CONSTR> 9.12829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -79.58753 0.00145 0.06967 0.00005 MINI INTERN> 5.05635 14.15800 0.00000 7.73894 2.88127 MINI EXTERN> -95.01640 -23.53525 0.00000 0.00000 0.00000 MINI CONSTR> 9.12955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8947 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -79.58895 0.00142 0.07511 0.00005 MINI INTERN> 5.05693 14.15794 0.00000 7.73866 2.88137 MINI EXTERN> -95.01864 -23.53602 0.00000 0.00000 0.00000 MINI CONSTR> 9.13081 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 -79.58895 0.00142 0.07511 0.00006 STPD INTERN> 5.05693 14.15794 0.00000 7.73866 2.88137 STPD EXTERN> -95.01864 -23.53602 0.00000 0.00000 0.00000 STPD CONSTR> 9.13081 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 8947 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8947 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 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 -79.58895 0.00142 0.07511 0.00000 MINI INTERN> 5.05693 14.15794 0.00000 7.73866 2.88137 MINI EXTERN> -95.01864 -23.53602 0.00000 0.00000 0.00000 MINI CONSTR> 9.13081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -79.98814 0.39919 0.24583 0.21439 MINI INTERN> 5.38818 14.32454 0.00000 7.69649 2.94298 MINI EXTERN> -96.07340 -24.08130 0.00000 0.00000 0.00000 MINI CONSTR> 9.81437 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -80.02355 0.03541 0.14263 0.01805 MINI INTERN> 5.23478 14.25527 0.00000 7.70480 2.93206 MINI EXTERN> -96.01658 -24.01443 0.00000 0.00000 0.00000 MINI CONSTR> 9.88055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -80.04230 0.01875 0.11023 0.01425 MINI INTERN> 5.15005 14.19305 0.00000 7.67932 2.93451 MINI EXTERN> -95.90307 -23.99508 0.00000 0.00000 0.00000 MINI CONSTR> 9.89892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -80.08875 0.04645 0.22760 0.04181 MINI INTERN> 5.17492 14.36412 0.00000 7.71773 2.92486 MINI EXTERN> -96.01345 -24.17061 0.00000 0.00000 0.00000 MINI CONSTR> 9.91368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -80.17418 0.08543 0.29113 0.07693 MINI INTERN> 5.23240 14.50214 0.00000 7.70437 2.86048 MINI EXTERN> -95.87808 -24.53152 0.00000 0.00000 0.00000 MINI CONSTR> 9.93603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -80.28400 0.10982 0.27182 0.09853 MINI INTERN> 5.19937 14.61069 0.00000 7.82950 2.99096 MINI EXTERN> -95.91307 -24.97299 0.00000 0.00000 0.00000 MINI CONSTR> 9.97152 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -80.35035 0.06634 0.17921 0.06364 MINI INTERN> 5.21119 14.64798 0.00000 7.88614 2.97742 MINI EXTERN> -95.88791 -25.17898 0.00000 0.00000 0.00000 MINI CONSTR> 9.99382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -80.39550 0.04515 0.17786 0.04068 MINI INTERN> 5.20186 14.63606 0.00000 7.93228 2.95520 MINI EXTERN> -95.68214 -25.44069 0.00000 0.00000 0.00000 MINI CONSTR> 10.00194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -80.42761 0.03211 0.14031 0.01716 MINI INTERN> 5.18142 14.62976 0.00000 7.96736 2.93258 MINI EXTERN> -95.63992 -25.50242 0.00000 0.00000 0.00000 MINI CONSTR> 10.00361 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -80.45530 0.02769 0.13775 0.03027 MINI INTERN> 5.18242 14.61457 0.00000 7.99866 2.96826 MINI EXTERN> -95.64132 -25.57562 0.00000 0.00000 0.00000 MINI CONSTR> 9.99773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -80.47534 0.02004 0.10473 0.01870 MINI INTERN> 5.23358 14.62671 0.00000 7.99401 2.95211 MINI EXTERN> -95.65846 -25.61099 0.00000 0.00000 0.00000 MINI CONSTR> 9.98770 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -80.49007 0.01473 0.10019 0.01431 MINI INTERN> 5.17703 14.62486 0.00000 8.00566 2.93316 MINI EXTERN> -95.65389 -25.55001 0.00000 0.00000 0.00000 MINI CONSTR> 9.97312 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -80.50338 0.01331 0.10222 0.01515 MINI INTERN> 5.16834 14.57457 0.00000 8.01327 2.92044 MINI EXTERN> -95.53119 -25.60110 0.00000 0.00000 0.00000 MINI CONSTR> 9.95230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -80.51834 0.01495 0.09497 0.01803 MINI INTERN> 5.12592 14.54189 0.00000 8.00330 2.94415 MINI EXTERN> -95.49532 -25.56273 0.00000 0.00000 0.00000 MINI CONSTR> 9.92445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -80.52796 0.00962 0.08052 0.01382 MINI INTERN> 5.15066 14.54945 0.00000 8.01691 2.95693 MINI EXTERN> -95.49523 -25.61124 0.00000 0.00000 0.00000 MINI CONSTR> 9.90456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -80.53902 0.01106 0.08398 0.01555 MINI INTERN> 5.17649 14.51160 0.00000 8.02557 2.93970 MINI EXTERN> -95.49223 -25.57990 0.00000 0.00000 0.00000 MINI CONSTR> 9.87974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -80.54775 0.00872 0.06433 0.01226 MINI INTERN> 5.11732 14.53044 0.00000 8.05254 2.91598 MINI EXTERN> -95.47401 -25.54872 0.00000 0.00000 0.00000 MINI CONSTR> 9.85872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -80.55345 0.00570 0.06026 0.00893 MINI INTERN> 5.14685 14.53372 0.00000 8.06553 2.93180 MINI EXTERN> -95.46037 -25.61505 0.00000 0.00000 0.00000 MINI CONSTR> 9.84407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -80.55893 0.00548 0.06583 0.00916 MINI INTERN> 5.15459 14.59299 0.00000 8.05535 2.92567 MINI EXTERN> -95.45151 -25.66571 0.00000 0.00000 0.00000 MINI CONSTR> 9.82969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -80.56474 0.00581 0.05847 0.01105 MINI INTERN> 5.14505 14.57846 0.00000 8.04958 2.90388 MINI EXTERN> -95.38516 -25.67216 0.00000 0.00000 0.00000 MINI CONSTR> 9.81562 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 -80.56474 0.00581 0.05847 0.02000 CONJ INTERN> 5.14505 14.57846 0.00000 8.04958 2.90388 CONJ EXTERN> -95.38516 -25.67216 0.00000 0.00000 0.00000 CONJ CONSTR> 9.81562 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 ASP 1 HT1 ) 0.36249E-01 ( PROT ASP 1 HT2 ) 0.36249E-01 ( PROT ASP 1 N ) 0.45311E-01 ( PROT ASP 1 HT3 ) 0.36249E-01 ( PROT ASP 1 CA ) 0.45311E-01 ( PROT ASP 1 CB ) 0.36249E-01 ( PROT ASP 1 CG ) 0.36249E-01 ( PROT ASP 1 OD1 ) 0.36249E-01 ( PROT ASP 1 OD2 ) 0.36249E-01 ( PROT ASP 1 C ) 0.45311E-01 ( PROT ASP 1 O ) 0.45311E-01 ( PROT TYR 2 N ) 0.45311E-01 ( PROT TYR 2 H ) 0.36249E-01 ( PROT TYR 2 CA ) 0.45311E-01 ( PROT TYR 2 CB ) 0.36249E-01 ( PROT TYR 2 CG ) 0.36249E-01 ( PROT TYR 2 CD1 ) 0.36249E-01 ( PROT TYR 2 CE1 ) 0.36249E-01 ( PROT TYR 2 CD2 ) 0.36249E-01 ( PROT TYR 2 CE2 ) 0.36249E-01 ( PROT TYR 2 CZ ) 0.36249E-01 ( PROT TYR 2 OH ) 0.36249E-01 ( PROT TYR 2 HH ) 0.36249E-01 ( PROT TYR 2 C ) 0.45311E-01 ( PROT TYR 2 O ) 0.45311E-01 ( PROT ALA 3 N ) 0.45311E-01 ( PROT ALA 3 H ) 0.36249E-01 ( PROT ALA 3 CA ) 0.45311E-01 ( PROT ALA 3 CB ) 0.36249E-01 ( PROT ALA 3 C ) 0.45311E-01 ( PROT ALA 3 O ) 0.45311E-01 ( PROT PHE 4 N ) 0.45311E-01 ( PROT PHE 4 H ) 0.36249E-01 ( PROT PHE 4 CA ) 0.45311E-01 ( PROT PHE 4 CB ) 0.36249E-01 ( PROT PHE 4 CG ) 0.36249E-01 ( PROT PHE 4 CD1 ) 0.36249E-01 ( PROT PHE 4 CD2 ) 0.36249E-01 ( PROT PHE 4 CE1 ) 0.36249E-01 ( PROT PHE 4 CE2 ) 0.36249E-01 ( PROT PHE 4 CZ ) 0.36249E-01 ( PROT PHE 4 C ) 0.45311E-01 ( PROT PHE 4 O ) 0.45311E-01 ( PROT ILE 5 N ) 0.45311E-01 ( PROT ILE 5 H ) 0.36249E-01 ( PROT ILE 5 CA ) 0.45311E-01 ( PROT ILE 5 CB ) 0.36249E-01 ( PROT ILE 5 CG2 ) 0.36249E-01 ( PROT ILE 5 CG1 ) 0.36249E-01 ( PROT ILE 5 CD ) 0.36249E-01 ( PROT ILE 5 C ) 0.45311E-01 ( PROT ILE 5 O ) 0.45311E-01 ( PROT ALA 6 N ) 0.45311E-01 ( PROT ALA 6 H ) 0.36249E-01 ( PROT ALA 6 CA ) 0.45311E-01 ( PROT ALA 6 CB ) 0.36249E-01 ( PROT ALA 6 C ) 0.45311E-01 ( PROT ALA 6 O ) 0.45311E-01 ( PROT SER 7 N ) 0.45311E-01 ( PROT SER 7 H ) 0.36249E-01 ( PROT SER 7 CA ) 0.45311E-01 ( PROT SER 7 CB ) 0.36249E-01 ( PROT SER 7 OG ) 0.36249E-01 ( PROT SER 7 HG ) 0.36249E-01 ( PROT SER 7 C ) 0.45311E-01 ( PROT SER 7 O ) 0.45311E-01 ( PROT LEU 8 N ) 0.45311E-01 ( PROT LEU 8 H ) 0.36249E-01 ( PROT LEU 8 CA ) 0.45311E-01 ( PROT LEU 8 CB ) 0.36249E-01 ( PROT LEU 8 CG ) 0.36249E-01 ( PROT LEU 8 CD1 ) 0.36249E-01 ( PROT LEU 8 CD2 ) 0.36249E-01 ( PROT LEU 8 C ) 0.45311E-01 ( PROT LEU 8 O ) 0.45311E-01 ( PROT VAL 9 N ) 0.45311E-01 ( PROT VAL 9 H ) 0.36249E-01 ( PROT VAL 9 CA ) 0.45311E-01 ( PROT VAL 9 CB ) 0.36249E-01 ( PROT VAL 9 CG1 ) 0.36249E-01 ( PROT VAL 9 CG2 ) 0.36249E-01 ( PROT VAL 9 C ) 0.45311E-01 ( PROT VAL 9 O ) 0.45311E-01 ( PROT VAL 10 N ) 0.45311E-01 ( PROT VAL 10 H ) 0.36249E-01 ( PROT VAL 10 CA ) 0.45311E-01 ( PROT VAL 10 CB ) 0.36249E-01 ( PROT VAL 10 CG1 ) 0.36249E-01 ( PROT VAL 10 CG2 ) 0.36249E-01 ( PROT VAL 10 C ) 0.45311E-01 ( PROT VAL 10 O ) 0.45311E-01 ( PROT ILE 11 N ) 0.45311E-01 ( PROT ILE 11 H ) 0.36249E-01 ( PROT ILE 11 CA ) 0.45311E-01 ( PROT ILE 11 CB ) 0.36249E-01 ( PROT ILE 11 CG2 ) 0.36249E-01 ( PROT ILE 11 CG1 ) 0.36249E-01 ( PROT ILE 11 CD ) 0.36249E-01 ( PROT ILE 11 C ) 0.45311E-01 ( PROT ILE 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 ASP 13 N ) 0.45311E-01 ( PROT ASP 13 H ) 0.36249E-01 ( PROT ASP 13 CA ) 0.45311E-01 ( PROT ASP 13 CB ) 0.36249E-01 ( PROT ASP 13 CG ) 0.36249E-01 ( PROT ASP 13 OD1 ) 0.36249E-01 ( PROT ASP 13 OD2 ) 0.36249E-01 ( PROT ASP 13 C ) 0.45311E-01 ( PROT ASP 13 O ) 0.45311E-01 ( PROT ASP 14 N ) 0.45311E-01 ( PROT ASP 14 H ) 0.36249E-01 ( PROT ASP 14 CA ) 0.45311E-01 ( PROT ASP 14 CB ) 0.36249E-01 ( PROT ASP 14 CG ) 0.36249E-01 ( PROT ASP 14 OD1 ) 0.36249E-01 ( PROT ASP 14 OD2 ) 0.36249E-01 ( PROT ASP 14 C ) 0.45311E-01 ( PROT ASP 14 O ) 0.45311E-01 ( PROT VAL 15 N ) 0.45311E-01 ( PROT VAL 15 H ) 0.36249E-01 ( PROT VAL 15 CA ) 0.45311E-01 ( PROT VAL 15 CB ) 0.36249E-01 ( PROT VAL 15 CG1 ) 0.36249E-01 ( PROT VAL 15 CG2 ) 0.36249E-01 ( PROT VAL 15 C ) 0.45311E-01 ( PROT VAL 15 O ) 0.45311E-01 ( PROT ASN 16 N ) 0.45311E-01 ( PROT ASN 16 H ) 0.36249E-01 ( PROT ASN 16 CA ) 0.45311E-01 ( PROT ASN 16 CB ) 0.36249E-01 ( PROT ASN 16 CG ) 0.36249E-01 ( PROT ASN 16 OD1 ) 0.36249E-01 ( PROT ASN 16 ND2 ) 0.36249E-01 ( PROT ASN 16 HD21 ) 0.36249E-01 ( PROT ASN 16 HD22 ) 0.36249E-01 ( PROT ASN 16 C ) 0.45311E-01 ( PROT ASN 16 O ) 0.45311E-01 ( PROT ARG 17 N ) 0.45311E-01 ( PROT ARG 17 H ) 0.36249E-01 ( PROT ARG 17 CA ) 0.45311E-01 ( PROT ARG 17 CB ) 0.36249E-01 ( PROT ARG 17 CG ) 0.36249E-01 ( PROT ARG 17 CD ) 0.36249E-01 ( PROT ARG 17 NE ) 0.36249E-01 ( PROT ARG 17 HE ) 0.36249E-01 ( PROT ARG 17 CZ ) 0.36249E-01 ( PROT ARG 17 NH1 ) 0.36249E-01 ( PROT ARG 17 HH11 ) 0.36249E-01 ( PROT ARG 17 HH12 ) 0.36249E-01 ( PROT ARG 17 NH2 ) 0.36249E-01 ( PROT ARG 17 HH21 ) 0.36249E-01 ( PROT ARG 17 HH22 ) 0.36249E-01 ( PROT ARG 17 C ) 0.45311E-01 ( PROT ARG 17 OT1 ) 0.36249E-01 ( PROT ARG 17 OT2 ) 0.36249E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.95232 3.70644 -6.79530 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.01150 0.00489 -0.00670 ROTATION MATRIX 0.999986 -0.002946 -0.004302 0.002974 0.999975 0.006441 0.004283 -0.006454 0.999970 AXIS OF ROTATION IS 0.777562 0.517686 -0.356930 ANGLE IS 0.48 TOTAL SQUARE DIFF IS 163.0875 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 0.997214 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.9972" Parameter: A <- "0.9972" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.83402 3.81042 -6.99604 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.06184 -0.01872 0.01881 ROTATION MATRIX 0.998549 0.034951 0.040965 -0.032555 0.997800 -0.057754 -0.042894 0.056337 0.997490 AXIS OF ROTATION IS -0.727326 -0.534601 0.430346 ANGLE IS 4.50 CENTER OF ROTATION 7.777654 3.636392 -7.234204 SHIFT IS 0.063077 TOTAL SQUARE DIFF IS 9.5435 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.749256 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.9972" RDCMND substituted energy or value "?RMS" to " 0.7493" Parameter: A <- "0.9972 0.7493" 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 0.9972 0.7493 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 " 9.82" Parameter: H <- "9.82" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -90.38036 9.81562 0.09203 ENER INTERN> 5.14505 14.57846 0.00000 8.04958 2.90388 ENER EXTERN> -95.38516 -25.67216 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 " -90.38" Parameter: B <- "-90.38" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -25.67" Parameter: C <- "-25.67" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -95.39" Parameter: C <- " -121.06" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -121.06" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.15" Parameter: D <- "5.15" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.58" Parameter: D <- " 19.73" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 8.05" Parameter: D <- " 27.78" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.90" Parameter: D <- " 30.68" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 30.68" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 12000 ENER= -90.38 GRMS= 0.09 ELEC= -25.67 VDW= -95.39 RDTITL> *EXTERNAL= -121.06 INTERNAL= 30.68 USER= 0.00 HARM= 9.82 RDTITL> *BOND= 5.15 ANGL= 14.58 DIHE= 8.05 IMPR= 2.90 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= -90.38 GRMS= 0.09 ELEC= -25.67 VDW= -95.39 RDTITL> *EXTERNAL= -121.06 INTERNAL= 30.68 USER= 0.00 HARM= 9.82 RDTITL> *BOND= 5.15 ANGL= 14.58 DIHE= 8.05 IMPR= 2.90 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= -90.38 GRMS= 0.09 ELEC= -25.67 VDW= -95.39 RDTITL> *EXTERNAL= -121.06 INTERNAL= 30.68 USER= 0.00 HARM= 9.82 RDTITL> *BOND= 5.15 ANGL= 14.58 DIHE= 8.05 IMPR= 2.90 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 12000 0.9972 0.7493 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 ASP 1 HT1 ) 0.0000 ( PROT ASP 1 HT2 ) 0.0000 ( PROT ASP 1 N ) 0.0000 ( PROT ASP 1 HT3 ) 0.0000 ( PROT ASP 1 CA ) 0.0000 ( PROT ASP 1 CB ) 0.0000 ( PROT ASP 1 CG ) 0.0000 ( PROT ASP 1 OD1 ) 0.0000 ( PROT ASP 1 OD2 ) 0.0000 ( PROT ASP 1 C ) 0.0000 ( PROT ASP 1 O ) 0.0000 ( PROT TYR 2 N ) 0.0000 ( PROT TYR 2 H ) 0.0000 ( PROT TYR 2 CA ) 0.0000 ( PROT TYR 2 CB ) 0.0000 ( PROT TYR 2 CG ) 0.0000 ( PROT TYR 2 CD1 ) 0.0000 ( PROT TYR 2 CE1 ) 0.0000 ( PROT TYR 2 CD2 ) 0.0000 ( PROT TYR 2 CE2 ) 0.0000 ( PROT TYR 2 CZ ) 0.0000 ( PROT TYR 2 OH ) 0.0000 ( PROT TYR 2 HH ) 0.0000 ( PROT TYR 2 C ) 0.0000 ( PROT TYR 2 O ) 0.0000 ( PROT ALA 3 N ) 0.0000 ( PROT ALA 3 H ) 0.0000 ( PROT ALA 3 CA ) 0.0000 ( PROT ALA 3 CB ) 0.0000 ( PROT ALA 3 C ) 0.0000 ( PROT ALA 3 O ) 0.0000 ( PROT PHE 4 N ) 0.0000 ( PROT PHE 4 H ) 0.0000 ( PROT PHE 4 CA ) 0.0000 ( PROT PHE 4 CB ) 0.0000 ( PROT PHE 4 CG ) 0.0000 ( PROT PHE 4 CD1 ) 0.0000 ( PROT PHE 4 CD2 ) 0.0000 ( PROT PHE 4 CE1 ) 0.0000 ( PROT PHE 4 CE2 ) 0.0000 ( PROT PHE 4 CZ ) 0.0000 ( PROT PHE 4 C ) 0.0000 ( PROT PHE 4 O ) 0.0000 ( PROT ILE 5 N ) 0.0000 ( PROT ILE 5 H ) 0.0000 ( PROT ILE 5 CA ) 0.0000 ( PROT ILE 5 CB ) 0.0000 ( PROT ILE 5 CG2 ) 0.0000 ( PROT ILE 5 CG1 ) 0.0000 ( PROT ILE 5 CD ) 0.0000 ( PROT ILE 5 C ) 0.0000 ( PROT ILE 5 O ) 0.0000 ( PROT ALA 6 N ) 0.0000 ( PROT ALA 6 H ) 0.0000 ( PROT ALA 6 CA ) 0.0000 ( PROT ALA 6 CB ) 0.0000 ( PROT ALA 6 C ) 0.0000 ( PROT ALA 6 O ) 0.0000 ( PROT SER 7 N ) 0.0000 ( PROT SER 7 H ) 0.0000 ( PROT SER 7 CA ) 0.0000 ( PROT SER 7 CB ) 0.0000 ( PROT SER 7 OG ) 0.0000 ( PROT SER 7 HG ) 0.0000 ( PROT SER 7 C ) 0.0000 ( PROT SER 7 O ) 0.0000 ( PROT LEU 8 N ) 0.0000 ( PROT LEU 8 H ) 0.0000 ( PROT LEU 8 CA ) 0.0000 ( PROT LEU 8 CB ) 0.0000 ( PROT LEU 8 CG ) 0.0000 ( PROT LEU 8 CD1 ) 0.0000 ( PROT LEU 8 CD2 ) 0.0000 ( PROT LEU 8 C ) 0.0000 ( PROT LEU 8 O ) 0.0000 ( PROT VAL 9 N ) 0.0000 ( PROT VAL 9 H ) 0.0000 ( PROT VAL 9 CA ) 0.0000 ( PROT VAL 9 CB ) 0.0000 ( PROT VAL 9 CG1 ) 0.0000 ( PROT VAL 9 CG2 ) 0.0000 ( PROT VAL 9 C ) 0.0000 ( PROT VAL 9 O ) 0.0000 ( PROT VAL 10 N ) 0.0000 ( PROT VAL 10 H ) 0.0000 ( PROT VAL 10 CA ) 0.0000 ( PROT VAL 10 CB ) 0.0000 ( PROT VAL 10 CG1 ) 0.0000 ( PROT VAL 10 CG2 ) 0.0000 ( PROT VAL 10 C ) 0.0000 ( PROT VAL 10 O ) 0.0000 ( PROT ILE 11 N ) 0.0000 ( PROT ILE 11 H ) 0.0000 ( PROT ILE 11 CA ) 0.0000 ( PROT ILE 11 CB ) 0.0000 ( PROT ILE 11 CG2 ) 0.0000 ( PROT ILE 11 CG1 ) 0.0000 ( PROT ILE 11 CD ) 0.0000 ( PROT ILE 11 C ) 0.0000 ( PROT ILE 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 ASP 13 N ) 0.0000 ( PROT ASP 13 H ) 0.0000 ( PROT ASP 13 CA ) 0.0000 ( PROT ASP 13 CB ) 0.0000 ( PROT ASP 13 CG ) 0.0000 ( PROT ASP 13 OD1 ) 0.0000 ( PROT ASP 13 OD2 ) 0.0000 ( PROT ASP 13 C ) 0.0000 ( PROT ASP 13 O ) 0.0000 ( PROT ASP 14 N ) 0.0000 ( PROT ASP 14 H ) 0.0000 ( PROT ASP 14 CA ) 0.0000 ( PROT ASP 14 CB ) 0.0000 ( PROT ASP 14 CG ) 0.0000 ( PROT ASP 14 OD1 ) 0.0000 ( PROT ASP 14 OD2 ) 0.0000 ( PROT ASP 14 C ) 0.0000 ( PROT ASP 14 O ) 0.0000 ( PROT VAL 15 N ) 0.0000 ( PROT VAL 15 H ) 0.0000 ( PROT VAL 15 CA ) 0.0000 ( PROT VAL 15 CB ) 0.0000 ( PROT VAL 15 CG1 ) 0.0000 ( PROT VAL 15 CG2 ) 0.0000 ( PROT VAL 15 C ) 0.0000 ( PROT VAL 15 O ) 0.0000 ( PROT ASN 16 N ) 0.0000 ( PROT ASN 16 H ) 0.0000 ( PROT ASN 16 CA ) 0.0000 ( PROT ASN 16 CB ) 0.0000 ( PROT ASN 16 CG ) 0.0000 ( PROT ASN 16 OD1 ) 0.0000 ( PROT ASN 16 ND2 ) 0.0000 ( PROT ASN 16 HD21 ) 0.0000 ( PROT ASN 16 HD22 ) 0.0000 ( PROT ASN 16 C ) 0.0000 ( PROT ASN 16 O ) 0.0000 ( PROT ARG 17 N ) 0.0000 ( PROT ARG 17 H ) 0.0000 ( PROT ARG 17 CA ) 0.0000 ( PROT ARG 17 CB ) 0.0000 ( PROT ARG 17 CG ) 0.0000 ( PROT ARG 17 CD ) 0.0000 ( PROT ARG 17 NE ) 0.0000 ( PROT ARG 17 HE ) 0.0000 ( PROT ARG 17 CZ ) 0.0000 ( PROT ARG 17 NH1 ) 0.0000 ( PROT ARG 17 HH11 ) 0.0000 ( PROT ARG 17 HH12 ) 0.0000 ( PROT ARG 17 NH2 ) 0.0000 ( PROT ARG 17 HH21 ) 0.0000 ( PROT ARG 17 HH22 ) 0.0000 ( PROT ARG 17 C ) 0.0000 ( PROT ARG 17 OT1 ) 0.0000 ( PROT ARG 17 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 8947 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8931 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 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 -90.38036 9.81562 0.09203 0.00000 MINI INTERN> 5.14505 14.57846 0.00000 8.04958 2.90388 MINI EXTERN> -95.38516 -25.67216 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -92.50601 2.12565 0.24998 0.09387 MINI INTERN> 5.78122 15.62818 0.00000 8.60438 3.05261 MINI EXTERN> -97.40217 -28.17024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8881 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -92.50601 2.12565 0.24998 0.00000 MINI INTERN> 5.78122 15.62818 0.00000 8.60438 3.05261 MINI EXTERN> -97.40217 -28.17024 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -93.55729 1.05128 0.15734 0.04027 MINI INTERN> 5.60036 15.51503 0.00000 8.96494 3.09695 MINI EXTERN> -96.83051 -29.90406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8947 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -93.55729 1.05128 0.15734 0.00000 MINI INTERN> 5.60036 15.51503 0.00000 8.96494 3.09695 MINI EXTERN> -96.83051 -29.90406 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -95.08572 1.52843 0.20882 0.05752 MINI INTERN> 6.05583 16.66825 0.00000 10.08322 3.28809 MINI EXTERN> -100.08265 -31.09845 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 8985 ATOM PAIRS WERE FOUND FOR ATOM LIST 251 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -95.08572 1.52843 0.20882 0.00000 MINI INTERN> 6.05583 16.66825 0.00000 10.08322 3.28809 MINI EXTERN> -100.08265 -31.09845 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -96.73251 1.64679 0.10532 0.01542 MINI INTERN> 5.78477 16.04657 0.00000 10.52526 3.19746 MINI EXTERN> -99.60409 -32.68248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9040 ATOM PAIRS WERE FOUND FOR ATOM LIST 254 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -96.73251 1.64679 0.10532 0.00000 MINI INTERN> 5.78477 16.04657 0.00000 10.52526 3.19746 MINI EXTERN> -99.60409 -32.68248 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -96.93232 0.19981 0.07364 0.01401 MINI INTERN> 5.81366 15.89760 0.00000 10.68004 3.21063 MINI EXTERN> -99.63813 -32.89611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9054 ATOM PAIRS WERE FOUND FOR ATOM LIST 251 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -96.93232 0.19981 0.07364 0.00000 MINI INTERN> 5.81366 15.89760 0.00000 10.68004 3.21063 MINI EXTERN> -99.63813 -32.89611 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -97.00808 0.07576 0.05283 0.00841 MINI INTERN> 5.79048 15.95471 0.00000 10.68228 3.20004 MINI EXTERN> -99.49041 -33.14519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9054 ATOM PAIRS WERE FOUND FOR ATOM LIST 250 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -97.00808 0.07576 0.05283 0.00000 MINI INTERN> 5.79048 15.95471 0.00000 10.68228 3.20004 MINI EXTERN> -99.49041 -33.14519 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -97.07492 0.06685 0.08140 0.01859 MINI INTERN> 5.81971 15.77801 0.00000 10.62236 3.19029 MINI EXTERN> -99.52202 -32.96327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9051 ATOM PAIRS WERE FOUND FOR ATOM LIST 249 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -97.07492 0.06685 0.08140 0.00000 MINI INTERN> 5.81971 15.77801 0.00000 10.62236 3.19029 MINI EXTERN> -99.52202 -32.96327 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -97.13998 0.06505 0.04074 0.00659 MINI INTERN> 5.79297 15.85715 0.00000 10.55018 3.18608 MINI EXTERN> -99.45693 -33.06942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9053 ATOM PAIRS WERE FOUND FOR ATOM LIST 251 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -97.13998 0.06505 0.04074 0.00000 MINI INTERN> 5.79297 15.85715 0.00000 10.55018 3.18608 MINI EXTERN> -99.45693 -33.06942 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -97.16754 0.02756 0.02578 0.00510 MINI INTERN> 5.80203 15.80766 0.00000 10.45654 3.17661 MINI EXTERN> -99.57148 -32.83889 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 251 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -97.16754 0.02756 0.02578 0.00000 MINI INTERN> 5.80203 15.80766 0.00000 10.45654 3.17661 MINI EXTERN> -99.57148 -32.83889 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -97.18877 0.02123 0.04322 0.01273 MINI INTERN> 5.78426 15.88404 0.00000 10.46442 3.17870 MINI EXTERN> -99.74792 -32.75226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9051 ATOM PAIRS WERE FOUND FOR ATOM LIST 251 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -97.18877 0.02123 0.04322 0.00000 MINI INTERN> 5.78426 15.88404 0.00000 10.46442 3.17870 MINI EXTERN> -99.74792 -32.75226 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -97.21280 0.02404 0.02960 0.00546 MINI INTERN> 5.79504 15.86305 0.00000 10.44129 3.17181 MINI EXTERN> -99.90725 -32.57675 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9052 ATOM PAIRS WERE FOUND FOR ATOM LIST 252 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -97.21280 0.02404 0.02960 0.00000 MINI INTERN> 5.79504 15.86305 0.00000 10.44129 3.17181 MINI EXTERN> -99.90725 -32.57675 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -97.23244 0.01963 0.03313 0.00794 MINI INTERN> 5.78143 15.92953 0.00000 10.45748 3.17875 MINI EXTERN> -99.99995 -32.57968 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9055 ATOM PAIRS WERE FOUND FOR ATOM LIST 252 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -97.23244 0.01963 0.03313 0.00000 MINI INTERN> 5.78143 15.92953 0.00000 10.45748 3.17875 MINI EXTERN> -99.99995 -32.57968 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -97.24483 0.01240 0.01633 0.00289 MINI INTERN> 5.78608 15.91322 0.00000 10.42506 3.17376 MINI EXTERN> -100.04874 -32.49422 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9056 ATOM PAIRS WERE FOUND FOR ATOM LIST 252 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -97.24483 0.01240 0.01633 0.00000 MINI INTERN> 5.78608 15.91322 0.00000 10.42506 3.17376 MINI EXTERN> -100.04874 -32.49422 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -97.25272 0.00789 0.02396 0.00573 MINI INTERN> 5.77643 15.95103 0.00000 10.43549 3.17818 MINI EXTERN> -100.07259 -32.52126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9056 ATOM PAIRS WERE FOUND FOR ATOM LIST 253 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -97.25272 0.00789 0.02396 0.00000 MINI INTERN> 5.77643 15.95103 0.00000 10.43549 3.17818 MINI EXTERN> -100.07259 -32.52126 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -97.25777 0.00505 0.01005 0.00184 MINI INTERN> 5.77812 15.94457 0.00000 10.40749 3.17366 MINI EXTERN> -100.08288 -32.47872 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9056 ATOM PAIRS WERE FOUND FOR ATOM LIST 253 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -97.25777 0.00505 0.01005 0.00000 MINI INTERN> 5.77812 15.94457 0.00000 10.40749 3.17366 MINI EXTERN> -100.08288 -32.47872 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -97.26107 0.00330 0.02302 0.00419 MINI INTERN> 5.77194 15.96592 0.00000 10.41226 3.17565 MINI EXTERN> -100.08185 -32.50499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9056 ATOM PAIRS WERE FOUND FOR ATOM LIST 253 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -97.26107 0.00330 0.02302 0.00000 MINI INTERN> 5.77194 15.96592 0.00000 10.41226 3.17565 MINI EXTERN> -100.08185 -32.50499 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -97.26323 0.00216 0.00728 0.00112 MINI INTERN> 5.77249 15.96204 0.00000 10.39169 3.17250 MINI EXTERN> -100.08183 -32.48012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 253 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -97.26323 0.00216 0.00728 0.00000 MINI INTERN> 5.77249 15.96204 0.00000 10.39169 3.17250 MINI EXTERN> -100.08183 -32.48012 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -97.26466 0.00143 0.01470 0.00257 MINI INTERN> 5.76811 15.97301 0.00000 10.39380 3.17335 MINI EXTERN> -100.07426 -32.49869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 253 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -97.26466 0.00143 0.01470 0.00000 MINI INTERN> 5.76811 15.97301 0.00000 10.39380 3.17335 MINI EXTERN> -100.07426 -32.49869 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -97.26562 0.00095 0.00432 0.00088 MINI INTERN> 5.76880 15.97091 0.00000 10.37850 3.17083 MINI EXTERN> -100.07227 -32.48239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 253 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -97.26562 0.00095 0.00432 0.00000 MINI INTERN> 5.76880 15.97091 0.00000 10.37850 3.17083 MINI EXTERN> -100.07227 -32.48239 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -97.26625 0.00063 0.00762 0.00153 MINI INTERN> 5.76608 15.97781 0.00000 10.37930 3.17115 MINI EXTERN> -100.06536 -32.49522 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 -97.26625 0.00063 0.00762 0.02000 CONJ INTERN> 5.76608 15.97781 0.00000 10.37930 3.17115 CONJ EXTERN> -100.06536 -32.49522 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 9057 atom pairs and 700 atom exclusions. There are 0 group pairs and 157 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 253 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 -97.26625 0.00063 0.00762 0.00000 MINI INTERN> 5.76608 15.97781 0.00000 10.37930 3.17115 MINI EXTERN> -100.06536 -32.49522 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -97.26667 0.00042 0.00314 0.00058 MINI INTERN> 5.76648 15.97575 0.00000 10.36853 3.16938 MINI EXTERN> -100.06269 -32.48411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 254 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -97.26667 0.00042 0.00314 0.00000 MINI INTERN> 5.76648 15.97575 0.00000 10.36853 3.16938 MINI EXTERN> -100.06269 -32.48411 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -97.26695 0.00028 0.00488 0.00100 MINI INTERN> 5.76468 15.97991 0.00000 10.36881 3.16949 MINI EXTERN> -100.05732 -32.49254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 254 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -97.26695 0.00028 0.00488 0.00000 MINI INTERN> 5.76468 15.97991 0.00000 10.36881 3.16949 MINI EXTERN> -100.05732 -32.49254 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -97.26714 0.00019 0.00264 0.00039 MINI INTERN> 5.76482 15.97871 0.00000 10.36124 3.16833 MINI EXTERN> -100.05519 -32.48506 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9057 ATOM PAIRS WERE FOUND FOR ATOM LIST 254 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -97.26714 0.00019 0.00264 0.00000 MINI INTERN> 5.76482 15.97871 0.00000 10.36124 3.16833 MINI EXTERN> -100.05519 -32.48506 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -97.26727 0.00013 0.00308 0.00064 MINI INTERN> 5.76362 15.98127 0.00000 10.36140 3.16839 MINI EXTERN> -100.05136 -32.49059 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9058 ATOM PAIRS WERE FOUND FOR ATOM LIST 254 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -97.26727 0.00013 0.00308 0.00000 MINI INTERN> 5.76362 15.98127 0.00000 10.36140 3.16839 MINI EXTERN> -100.05136 -32.49059 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -97.26736 0.00009 0.00184 0.00025 MINI INTERN> 5.76373 15.98052 0.00000 10.35618 3.16756 MINI EXTERN> -100.04972 -32.48564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13285 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9058 ATOM PAIRS WERE FOUND FOR ATOM LIST 254 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -97.26736 0.00009 0.00184 0.00000 MINI INTERN> 5.76373 15.98052 0.00000 10.35618 3.16756 MINI EXTERN> -100.04972 -32.48564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0010000) 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> 501 -97.26736 0.00000 0.00099 0.02000 CONJ INTERN> 5.76369 15.98052 0.00000 10.35618 3.16754 CONJ EXTERN> -100.04975 -32.48554 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> 164 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.89670 3.70830 -6.77264 CENTER OF REFERENCE COORDINATE SET 7.96382 3.71133 -6.80200 NET TRANSLATION OF ROTATED ATOMS 0.06713 0.00303 -0.02936 ROTATION MATRIX 0.998148 -0.037031 -0.048252 0.039837 0.997490 0.058535 0.045963 -0.060349 0.997119 AXIS OF ROTATION IS 0.699093 0.554029 -0.452019 ANGLE IS 4.88 CENTER OF ROTATION 7.755388 3.594556 -7.199043 SHIFT IS 0.061877 TOTAL SQUARE DIFF IS 412.2916 DENOMINATOR IS 164.0000 THUS RMS DIFF IS 1.585551 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.5856" Parameter: A <- "1.5856" CHARMM> set a @a ?RMS Parameter: A -> "1.5856" RDCMND substituted energy or value "?RMS" to " 1.5856" Parameter: A <- "1.5856 1.5856" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 17 atoms have been selected out of 164 CENTER OF ATOMS BEFORE TRANSLATION 7.89528 3.78950 -7.13552 CENTER OF REFERENCE COORDINATE SET 7.77218 3.79171 -6.97724 NET TRANSLATION OF ROTATED ATOMS -0.12311 0.00220 0.15828 ROTATION MATRIX 0.991891 0.082011 0.097094 -0.070337 0.990509 -0.118091 -0.105857 0.110304 0.988244 AXIS OF ROTATION IS -0.668969 -0.594443 0.446226 ANGLE IS 9.83 CENTER OF ROTATION 7.280889 4.086890 -7.490481 SHIFT IS 0.151675 TOTAL SQUARE DIFF IS 14.3856 DENOMINATOR IS 17.0000 THUS RMS DIFF IS 0.919898 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.5856 1.5856" RDCMND substituted energy or value "?RMS" to " 0.9199" Parameter: A <- "1.5856 1.5856 0.9199" 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 1.5856 1.5856 0.9199 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" $$$$$$ New timer profile $$$$$ List time 0.00 Other: 0.00 Electrostatic & VDW 5.31 Other: 0.00 Nonbond force 5.33 Other: 0.02 Bond energy 0.06 Other: 0.00 Angle energy 0.46 Other: 0.00 Dihedral energy 0.28 Other: 0.00 Restraints energy 0.00 Other: 0.00 INTRNL energy 0.83 Other: 0.03 Energy time 6.22 Other: 0.06 Total time 6.90 Other: 0.68 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47522 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL 2 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 24056 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 6.90 SECONDS CPU TIME: 0.00 SECONDS