1 Chemistry at HARvard Macromolecular Mechanics (CHARMM) - Developmental Version 33b1 August 15, 2006 Copyright(c) 1984-2001 President and Fellows of Harvard College All Rights Reserved Current operating system: Linux-2.6.32-431.17.1.el6.x86_64(x86_64)@kon Created on 6/18/14 at 10:52:34 by user: annesc Maximum number of ATOMS: 360720, and RESidues: 120240 Current HEAP size: 10240000, and STACK size: 10000000 RDTITL> * GENERATE PSF AND CHARMM COORDINATE SET FOR RDTITL> * HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * CHARMM> CHARMM> set name "helix_allh" Parameter: NAME <- ""helix_allh"" CHARMM> set output mini_@name ! this is the output : replace by any other complexe name ! Parameter: NAME -> ""helix_allh"" Parameter: OUTPUT <- "MINI_"helix_allh"" CHARMM> CHARMM> CHARMM> ! Read in Topology and Parameter files CHARMM> !_____________________________________ CHARMM> CHARMM> open unit 1 card read name "../lib/toph19_eef1.1.inp" VOPEN> Attempting to open::../lib/toph19_eef1.1.inp:: OPNLGU> Unit 1 opened for READONLY access to ../lib/toph19_eef1.1.inp CHARMM> read RTF card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 TITLE> * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL TITLE> * THIS DIFFERS FROM TOPH19_EEF1.INP IN: TITLE> * SCALED DOWN PARTIAL CHARGE DISTRIBUTIONS OF PSEUDO-IONIC AND TITLE> * POLAR SIDECHAINS, CTER, NTER TITLE> * INCLUDES (DE-)PROTONATED IONIC SIDECHAINS, PSEUDO-IONIC HIS AND AIB TITLE> * IN TYR CZ IS NOW TYPE CR TITLE> * THIS IS WORK IN PROGRESS. NO EXTENSIVE TESTS HAVE BEEN MADE. TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 card read name "../lib/param19_eef1.1.inp" VOPEN> Attempting to open::../lib/param19_eef1.1.inp:: OPNLGU> Unit 1 opened for READONLY access to ../lib/param19_eef1.1.inp CHARMM> read PARA card unit 1 PARAMETER FILE BEING READ FROM UNIT 1 TITLE> * - PARAMETER FILE PARAM19 * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 TITLE> * PARRDR> NOTE: atom type "CR " is removed from previous group PARRDR> NOTE: atom type "OC " is removed from previous group PARRDR> NOTE: atom type "OT " is removed from previous group PARRDR> NOTE: atom type "OH2 " is removed from previous group PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> CHARMM> CHARMM> ! Read in structure and psf file of the Bovine alpha lactalbumine 1f6r CHARMM> !_____________________________________________________________________ CHARMM> CHARMM> open read unit 9 card name ../lib/@name.psf Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../lib/helix_allh.psf:: OPNLGU> Unit 9 opened for READONLY access to ../lib/helix_allh.psf CHARMM> read psf card unit 9 MAINIO> Protein structure file being read from unit 9. TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 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 = 19 Number of atoms = 168 Number of groups = 64 Number of bonds = 169 Number of angles = 242 Number of dihedrals = 93 Number of impropers = 78 Number of cross-terms = 0 Number of HB acceptors = 28 Number of HB donors = 29 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: 6/18/14 10:51:41 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 417 exclusions and 293 interactions(1-4) found 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9992 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 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 9992 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9992 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 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 4024.34987 0.00000 524.19108 ENER INTERN> 180.18413 108.87896 0.00000 2.30389 1.70593 ENER EXTERN> 3804.61139 -73.33443 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> 168 atoms have been selected out of 168 CHARMM> define water sele ( segid solv) end SELRPN> 0 atoms have been selected out of 168 CHARMM> define nonh sele ( .not. hydrogen ) end SELRPN> 139 atoms have been selected out of 168 CHARMM> define trace sele ( type ca ) end SELRPN> 19 atoms have been selected out of 168 CHARMM> define back sele ( type n .or. type ca .or. type c ) end SELRPN> 57 atoms have been selected out of 168 CHARMM> define main sele ( type n .or. type ca .or. type c .or. type o) end SELRPN> 75 atoms have been selected out of 168 CHARMM> define side sele ( (.not. main) ) end SELRPN> 93 atoms have been selected out of 168 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: 168 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 168 atoms are restrained. CHARMM> CHARMM> ! { very tight on backbone of pcna } CHARMM> SCALar CONSTraint SET 250. SELEct ( prot .AND. main ) END SELRPN> 75 atoms have been selected out of 168 CHARMM> CHARMM> ! { quite tight on sidechains of pcna } CHARMM> SCALar CONSTraint SET 200. SELEct ( prot .AND. side ) END SELRPN> 93 atoms have been selected out of 168 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 ALA 1 HT1 ) 200.00 ( PROT ALA 1 HT2 ) 200.00 ( PROT ALA 1 N ) 250.00 ( PROT ALA 1 HT3 ) 200.00 ( PROT ALA 1 CA ) 250.00 ( PROT ALA 1 CB ) 200.00 ( PROT ALA 1 C ) 250.00 ( PROT ALA 1 O ) 250.00 ( PROT LEU 2 N ) 250.00 ( PROT LEU 2 H ) 200.00 ( PROT LEU 2 CA ) 250.00 ( PROT LEU 2 CB ) 200.00 ( PROT LEU 2 CG ) 200.00 ( PROT LEU 2 CD1 ) 200.00 ( PROT LEU 2 CD2 ) 200.00 ( PROT LEU 2 C ) 250.00 ( PROT LEU 2 O ) 250.00 ( PROT GLN 3 N ) 250.00 ( PROT GLN 3 H ) 200.00 ( PROT GLN 3 CA ) 250.00 ( PROT GLN 3 CB ) 200.00 ( PROT GLN 3 CG ) 200.00 ( PROT GLN 3 CD ) 200.00 ( PROT GLN 3 OE1 ) 200.00 ( PROT GLN 3 NE2 ) 200.00 ( PROT GLN 3 HE21 ) 200.00 ( PROT GLN 3 HE22 ) 200.00 ( PROT GLN 3 C ) 250.00 ( PROT GLN 3 O ) 250.00 ( PROT ALA 4 N ) 250.00 ( PROT ALA 4 H ) 200.00 ( PROT ALA 4 CA ) 250.00 ( PROT ALA 4 CB ) 200.00 ( PROT ALA 4 C ) 250.00 ( PROT ALA 4 O ) 250.00 ( PROT PHE 5 N ) 250.00 ( PROT PHE 5 H ) 200.00 ( PROT PHE 5 CA ) 250.00 ( PROT PHE 5 CB ) 200.00 ( PROT PHE 5 CG ) 200.00 ( PROT PHE 5 CD1 ) 200.00 ( PROT PHE 5 CD2 ) 200.00 ( PROT PHE 5 CE1 ) 200.00 ( PROT PHE 5 CE2 ) 200.00 ( PROT PHE 5 CZ ) 200.00 ( PROT PHE 5 C ) 250.00 ( PROT PHE 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 ILE 7 N ) 250.00 ( PROT ILE 7 H ) 200.00 ( PROT ILE 7 CA ) 250.00 ( PROT ILE 7 CB ) 200.00 ( PROT ILE 7 CG2 ) 200.00 ( PROT ILE 7 CG1 ) 200.00 ( PROT ILE 7 CD ) 200.00 ( PROT ILE 7 C ) 250.00 ( PROT ILE 7 O ) 250.00 ( PROT ALA 8 N ) 250.00 ( PROT ALA 8 H ) 200.00 ( PROT ALA 8 CA ) 250.00 ( PROT ALA 8 CB ) 200.00 ( PROT ALA 8 C ) 250.00 ( PROT ALA 8 O ) 250.00 ( PROT LEU 9 N ) 250.00 ( PROT LEU 9 H ) 200.00 ( PROT LEU 9 CA ) 250.00 ( PROT LEU 9 CB ) 200.00 ( PROT LEU 9 CG ) 200.00 ( PROT LEU 9 CD1 ) 200.00 ( PROT LEU 9 CD2 ) 200.00 ( PROT LEU 9 C ) 250.00 ( PROT LEU 9 O ) 250.00 ( PROT SER 10 N ) 250.00 ( PROT SER 10 H ) 200.00 ( PROT SER 10 CA ) 250.00 ( PROT SER 10 CB ) 200.00 ( PROT SER 10 OG ) 200.00 ( PROT SER 10 HG ) 200.00 ( PROT SER 10 C ) 250.00 ( PROT SER 10 O ) 250.00 ( PROT SER 11 N ) 250.00 ( PROT SER 11 H ) 200.00 ( PROT SER 11 CA ) 250.00 ( PROT SER 11 CB ) 200.00 ( PROT SER 11 OG ) 200.00 ( PROT SER 11 HG ) 200.00 ( PROT SER 11 C ) 250.00 ( PROT SER 11 O ) 250.00 ( PROT PHE 12 N ) 250.00 ( PROT PHE 12 H ) 200.00 ( PROT PHE 12 CA ) 250.00 ( PROT PHE 12 CB ) 200.00 ( PROT PHE 12 CG ) 200.00 ( PROT PHE 12 CD1 ) 200.00 ( PROT PHE 12 CD2 ) 200.00 ( PROT PHE 12 CE1 ) 200.00 ( PROT PHE 12 CE2 ) 200.00 ( PROT PHE 12 CZ ) 200.00 ( PROT PHE 12 C ) 250.00 ( PROT PHE 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 SER 14 N ) 250.00 ( PROT SER 14 H ) 200.00 ( PROT SER 14 CA ) 250.00 ( PROT SER 14 CB ) 200.00 ( PROT SER 14 OG ) 200.00 ( PROT SER 14 HG ) 200.00 ( PROT SER 14 C ) 250.00 ( PROT SER 14 O ) 250.00 ( PROT LYS 15 N ) 250.00 ( PROT LYS 15 H ) 200.00 ( PROT LYS 15 CA ) 250.00 ( PROT LYS 15 CB ) 200.00 ( PROT LYS 15 CG ) 200.00 ( PROT LYS 15 CD ) 200.00 ( PROT LYS 15 CE ) 200.00 ( PROT LYS 15 NZ ) 200.00 ( PROT LYS 15 HZ1 ) 200.00 ( PROT LYS 15 HZ2 ) 200.00 ( PROT LYS 15 HZ3 ) 200.00 ( PROT LYS 15 C ) 250.00 ( PROT LYS 15 O ) 250.00 ( PROT LEU 16 N ) 250.00 ( PROT LEU 16 H ) 200.00 ( PROT LEU 16 CA ) 250.00 ( PROT LEU 16 CB ) 200.00 ( PROT LEU 16 CG ) 200.00 ( PROT LEU 16 CD1 ) 200.00 ( PROT LEU 16 CD2 ) 200.00 ( PROT LEU 16 C ) 250.00 ( PROT LEU 16 O ) 250.00 ( PROT ALA 17 N ) 250.00 ( PROT ALA 17 H ) 200.00 ( PROT ALA 17 CA ) 250.00 ( PROT ALA 17 CB ) 200.00 ( PROT ALA 17 C ) 250.00 ( PROT ALA 17 O ) 250.00 ( PROT CYS 18 N ) 250.00 ( PROT CYS 18 H ) 200.00 ( PROT CYS 18 CA ) 250.00 ( PROT CYS 18 CB ) 200.00 ( PROT CYS 18 SG ) 200.00 ( PROT CYS 18 C ) 250.00 ( PROT CYS 18 O ) 250.00 ( PROT GLU 19 N ) 250.00 ( PROT GLU 19 H ) 200.00 ( PROT GLU 19 CA ) 250.00 ( PROT GLU 19 CB ) 200.00 ( PROT GLU 19 CG ) 200.00 ( PROT GLU 19 CD ) 200.00 ( PROT GLU 19 OE1 ) 200.00 ( PROT GLU 19 OE2 ) 200.00 ( PROT GLU 19 C ) 250.00 ( PROT GLU 19 OT1 ) 200.00 ( PROT GLU 19 OT2 ) 200.00 CHARMM> CHARMM> !stop ! OK CHARMM> CHARMM> !do @2 steps of steepest descent with constraints CHARMM> label mini CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 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 9992 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9992 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> 0 4024.34987 0.00000 524.19108 0.02000 MINI INTERN> 180.18413 108.87896 0.00000 2.30389 1.70593 MINI EXTERN> 3804.61139 -73.33443 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 950.60149 3073.74837 46.93858 0.02074 MINI INTERN> 235.04879 46.61710 0.00000 4.43812 9.92333 MINI EXTERN> 297.72617 -2.46959 0.00000 0.00000 0.00000 MINI CONSTR> 359.31757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9970 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 799.74651 150.85498 1.78777 0.00373 MINI INTERN> 42.09961 53.48030 0.00000 3.94638 8.43162 MINI EXTERN> 389.85776 -16.02475 0.00000 0.00000 0.00000 MINI CONSTR> 317.95560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 799.70660 0.03991 1.83474 0.00161 MINI INTERN> 40.96171 54.25943 0.00000 3.87351 8.58453 MINI EXTERN> 383.98611 -16.06393 0.00000 0.00000 0.00000 MINI CONSTR> 324.10525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9969 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 799.68745 0.01915 1.76301 0.00070 MINI INTERN> 42.59332 52.91596 0.00000 3.96397 8.44317 MINI EXTERN> 388.50062 -16.19072 0.00000 0.00000 0.00000 MINI CONSTR> 319.46114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 799.45932 0.22814 0.32360 0.00013 MINI INTERN> 41.69778 53.45504 0.00000 3.92592 8.50188 MINI EXTERN> 386.76958 -16.14914 0.00000 0.00000 0.00000 MINI CONSTR> 321.25827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9969 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 799.45137 0.00795 0.04841 0.00005 MINI INTERN> 41.51344 53.56930 0.00000 3.91771 8.52470 MINI EXTERN> 386.35797 -16.14753 0.00000 0.00000 0.00000 MINI CONSTR> 321.71578 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> 34 799.45119 0.00018 0.00623 0.00002 STPD INTERN> 41.53412 53.55484 0.00000 3.91871 8.52227 STPD EXTERN> 386.40633 -16.14789 0.00000 0.00000 0.00000 STPD CONSTR> 321.66281 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 9969 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9969 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> 0 799.45119 0.00018 0.00623 0.00000 MINI INTERN> 41.53412 53.55484 0.00000 3.91871 8.52227 MINI EXTERN> 386.40633 -16.14789 0.00000 0.00000 0.00000 MINI CONSTR> 321.66281 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> 1 799.45119 0.00000 0.00033 0.02000 CONJ INTERN> 41.53692 53.55350 0.00000 3.91881 8.52178 CONJ EXTERN> 386.41219 -16.14779 0.00000 0.00000 0.00000 CONJ CONSTR> 321.65578 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 ALA 1 HT1 ) 130.00 ( PROT ALA 1 HT2 ) 130.00 ( PROT ALA 1 N ) 162.50 ( PROT ALA 1 HT3 ) 130.00 ( PROT ALA 1 CA ) 162.50 ( PROT ALA 1 CB ) 130.00 ( PROT ALA 1 C ) 162.50 ( PROT ALA 1 O ) 162.50 ( PROT LEU 2 N ) 162.50 ( PROT LEU 2 H ) 130.00 ( PROT LEU 2 CA ) 162.50 ( PROT LEU 2 CB ) 130.00 ( PROT LEU 2 CG ) 130.00 ( PROT LEU 2 CD1 ) 130.00 ( PROT LEU 2 CD2 ) 130.00 ( PROT LEU 2 C ) 162.50 ( PROT LEU 2 O ) 162.50 ( PROT GLN 3 N ) 162.50 ( PROT GLN 3 H ) 130.00 ( PROT GLN 3 CA ) 162.50 ( PROT GLN 3 CB ) 130.00 ( PROT GLN 3 CG ) 130.00 ( PROT GLN 3 CD ) 130.00 ( PROT GLN 3 OE1 ) 130.00 ( PROT GLN 3 NE2 ) 130.00 ( PROT GLN 3 HE21 ) 130.00 ( PROT GLN 3 HE22 ) 130.00 ( PROT GLN 3 C ) 162.50 ( PROT GLN 3 O ) 162.50 ( PROT ALA 4 N ) 162.50 ( PROT ALA 4 H ) 130.00 ( PROT ALA 4 CA ) 162.50 ( PROT ALA 4 CB ) 130.00 ( PROT ALA 4 C ) 162.50 ( PROT ALA 4 O ) 162.50 ( PROT PHE 5 N ) 162.50 ( PROT PHE 5 H ) 130.00 ( PROT PHE 5 CA ) 162.50 ( PROT PHE 5 CB ) 130.00 ( PROT PHE 5 CG ) 130.00 ( PROT PHE 5 CD1 ) 130.00 ( PROT PHE 5 CD2 ) 130.00 ( PROT PHE 5 CE1 ) 130.00 ( PROT PHE 5 CE2 ) 130.00 ( PROT PHE 5 CZ ) 130.00 ( PROT PHE 5 C ) 162.50 ( PROT PHE 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 ILE 7 N ) 162.50 ( PROT ILE 7 H ) 130.00 ( PROT ILE 7 CA ) 162.50 ( PROT ILE 7 CB ) 130.00 ( PROT ILE 7 CG2 ) 130.00 ( PROT ILE 7 CG1 ) 130.00 ( PROT ILE 7 CD ) 130.00 ( PROT ILE 7 C ) 162.50 ( PROT ILE 7 O ) 162.50 ( PROT ALA 8 N ) 162.50 ( PROT ALA 8 H ) 130.00 ( PROT ALA 8 CA ) 162.50 ( PROT ALA 8 CB ) 130.00 ( PROT ALA 8 C ) 162.50 ( PROT ALA 8 O ) 162.50 ( PROT LEU 9 N ) 162.50 ( PROT LEU 9 H ) 130.00 ( PROT LEU 9 CA ) 162.50 ( PROT LEU 9 CB ) 130.00 ( PROT LEU 9 CG ) 130.00 ( PROT LEU 9 CD1 ) 130.00 ( PROT LEU 9 CD2 ) 130.00 ( PROT LEU 9 C ) 162.50 ( PROT LEU 9 O ) 162.50 ( PROT SER 10 N ) 162.50 ( PROT SER 10 H ) 130.00 ( PROT SER 10 CA ) 162.50 ( PROT SER 10 CB ) 130.00 ( PROT SER 10 OG ) 130.00 ( PROT SER 10 HG ) 130.00 ( PROT SER 10 C ) 162.50 ( PROT SER 10 O ) 162.50 ( PROT SER 11 N ) 162.50 ( PROT SER 11 H ) 130.00 ( PROT SER 11 CA ) 162.50 ( PROT SER 11 CB ) 130.00 ( PROT SER 11 OG ) 130.00 ( PROT SER 11 HG ) 130.00 ( PROT SER 11 C ) 162.50 ( PROT SER 11 O ) 162.50 ( PROT PHE 12 N ) 162.50 ( PROT PHE 12 H ) 130.00 ( PROT PHE 12 CA ) 162.50 ( PROT PHE 12 CB ) 130.00 ( PROT PHE 12 CG ) 130.00 ( PROT PHE 12 CD1 ) 130.00 ( PROT PHE 12 CD2 ) 130.00 ( PROT PHE 12 CE1 ) 130.00 ( PROT PHE 12 CE2 ) 130.00 ( PROT PHE 12 CZ ) 130.00 ( PROT PHE 12 C ) 162.50 ( PROT PHE 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 SER 14 N ) 162.50 ( PROT SER 14 H ) 130.00 ( PROT SER 14 CA ) 162.50 ( PROT SER 14 CB ) 130.00 ( PROT SER 14 OG ) 130.00 ( PROT SER 14 HG ) 130.00 ( PROT SER 14 C ) 162.50 ( PROT SER 14 O ) 162.50 ( PROT LYS 15 N ) 162.50 ( PROT LYS 15 H ) 130.00 ( PROT LYS 15 CA ) 162.50 ( PROT LYS 15 CB ) 130.00 ( PROT LYS 15 CG ) 130.00 ( PROT LYS 15 CD ) 130.00 ( PROT LYS 15 CE ) 130.00 ( PROT LYS 15 NZ ) 130.00 ( PROT LYS 15 HZ1 ) 130.00 ( PROT LYS 15 HZ2 ) 130.00 ( PROT LYS 15 HZ3 ) 130.00 ( PROT LYS 15 C ) 162.50 ( PROT LYS 15 O ) 162.50 ( PROT LEU 16 N ) 162.50 ( PROT LEU 16 H ) 130.00 ( PROT LEU 16 CA ) 162.50 ( PROT LEU 16 CB ) 130.00 ( PROT LEU 16 CG ) 130.00 ( PROT LEU 16 CD1 ) 130.00 ( PROT LEU 16 CD2 ) 130.00 ( PROT LEU 16 C ) 162.50 ( PROT LEU 16 O ) 162.50 ( PROT ALA 17 N ) 162.50 ( PROT ALA 17 H ) 130.00 ( PROT ALA 17 CA ) 162.50 ( PROT ALA 17 CB ) 130.00 ( PROT ALA 17 C ) 162.50 ( PROT ALA 17 O ) 162.50 ( PROT CYS 18 N ) 162.50 ( PROT CYS 18 H ) 130.00 ( PROT CYS 18 CA ) 162.50 ( PROT CYS 18 CB ) 130.00 ( PROT CYS 18 SG ) 130.00 ( PROT CYS 18 C ) 162.50 ( PROT CYS 18 O ) 162.50 ( PROT GLU 19 N ) 162.50 ( PROT GLU 19 H ) 130.00 ( PROT GLU 19 CA ) 162.50 ( PROT GLU 19 CB ) 130.00 ( PROT GLU 19 CG ) 130.00 ( PROT GLU 19 CD ) 130.00 ( PROT GLU 19 OE1 ) 130.00 ( PROT GLU 19 OE2 ) 130.00 ( PROT GLU 19 C ) 162.50 ( PROT GLU 19 OT1 ) 130.00 ( PROT GLU 19 OT2 ) 130.00 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43642 4.57696 -7.53398 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS -0.00172 -0.00174 0.00136 ROTATION MATRIX 1.000000 -0.000066 -0.000051 0.000066 1.000000 0.000040 0.000051 -0.000040 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 1.3914 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.091007 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.0910" Parameter: A <- "0.0910" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.92270 4.27069 -7.72410 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00951 0.00957 -0.00816 ROTATION MATRIX 0.999966 0.006206 0.005388 -0.006165 0.999953 -0.007505 -0.005434 0.007472 0.999957 AXIS OF ROTATION IS -0.673527 -0.486682 0.556328 ANGLE IS 0.64 TOTAL SQUARE DIFF IS 0.0269 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.037616 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.0910" RDCMND substituted energy or value "?RMS" to " 0.0376" Parameter: A <- "0.0910 0.0376" 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 0.0910 0.0376 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 " 321.66" Parameter: H <- "321.66" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 477.79541 321.65578 24.41493 ENER INTERN> 41.53692 53.55350 0.00000 3.91881 8.52178 ENER EXTERN> 386.41219 -16.14779 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 " 477.80" Parameter: B <- "477.80" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -16.15" Parameter: C <- "-16.15" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 386.41" Parameter: C <- " 370.26" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 370.26" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 41.54" Parameter: D <- "41.54" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 53.55" Parameter: D <- " 95.09" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 3.92" Parameter: D <- " 99.01" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.52" Parameter: D <- " 107.53" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 107.53" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 600 ENER= 477.80 GRMS= 24.41 ELEC= -16.15 VDW= 386.41 RDTITL> *EXTERNAL= 370.26 INTERNAL= 107.53 USER= 0.00 HARM= 321.66 RDTITL> *BOND= 41.54 ANGL= 53.55 DIHE= 3.92 IMPR= 8.52 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9969 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9969 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> 0 727.36476 -249.56935 10.85553 0.02000 MINI INTERN> 41.53692 53.55350 0.00000 3.91881 8.52178 MINI EXTERN> 386.41219 -16.14779 0.00000 0.00000 0.00000 MINI CONSTR> 249.56935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 675.20139 52.16337 2.74885 0.00360 MINI INTERN> 39.48602 58.72888 0.00000 4.81710 9.43974 MINI EXTERN> 297.15044 -14.09041 0.00000 0.00000 0.00000 MINI CONSTR> 279.66962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9964 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 672.30379 2.89760 3.02915 0.00156 MINI INTERN> 43.23767 56.00603 0.00000 4.65537 8.69371 MINI EXTERN> 301.59310 -14.54578 0.00000 0.00000 0.00000 MINI CONSTR> 272.66369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 671.47746 0.82633 0.21270 0.00028 MINI INTERN> 38.64797 56.59202 0.00000 4.75822 8.77860 MINI EXTERN> 304.67858 -15.11037 0.00000 0.00000 0.00000 MINI CONSTR> 273.13243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9963 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 671.46591 0.01155 0.17194 0.00012 MINI INTERN> 38.53159 56.71791 0.00000 4.77293 8.81048 MINI EXTERN> 303.77068 -15.07485 0.00000 0.00000 0.00000 MINI CONSTR> 273.93717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 671.46247 0.00344 0.01993 0.00002 MINI INTERN> 38.39824 56.63351 0.00000 4.76922 8.79137 MINI EXTERN> 304.45883 -15.12453 0.00000 0.00000 0.00000 MINI CONSTR> 273.53583 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> 29 671.46240 0.00006 0.00639 0.00001 STPD INTERN> 38.42139 56.62162 0.00000 4.76882 8.78943 STPD EXTERN> 304.45924 -15.12326 0.00000 0.00000 0.00000 STPD CONSTR> 273.52516 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 9963 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9963 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 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> 0 671.46240 0.00006 0.00639 0.00000 MINI INTERN> 38.42139 56.62162 0.00000 4.76882 8.78943 MINI EXTERN> 304.45924 -15.12326 0.00000 0.00000 0.00000 MINI CONSTR> 273.52516 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> 1 671.46240 0.00001 0.00368 0.02000 CONJ INTERN> 38.43135 56.61567 0.00000 4.76858 8.78843 CONJ EXTERN> 304.46933 -15.12333 0.00000 0.00000 0.00000 CONJ CONSTR> 273.51238 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 ALA 1 HT1 ) 84.500 ( PROT ALA 1 HT2 ) 84.500 ( PROT ALA 1 N ) 105.63 ( PROT ALA 1 HT3 ) 84.500 ( PROT ALA 1 CA ) 105.63 ( PROT ALA 1 CB ) 84.500 ( PROT ALA 1 C ) 105.63 ( PROT ALA 1 O ) 105.63 ( PROT LEU 2 N ) 105.63 ( PROT LEU 2 H ) 84.500 ( PROT LEU 2 CA ) 105.63 ( PROT LEU 2 CB ) 84.500 ( PROT LEU 2 CG ) 84.500 ( PROT LEU 2 CD1 ) 84.500 ( PROT LEU 2 CD2 ) 84.500 ( PROT LEU 2 C ) 105.63 ( PROT LEU 2 O ) 105.63 ( PROT GLN 3 N ) 105.63 ( PROT GLN 3 H ) 84.500 ( PROT GLN 3 CA ) 105.63 ( PROT GLN 3 CB ) 84.500 ( PROT GLN 3 CG ) 84.500 ( PROT GLN 3 CD ) 84.500 ( PROT GLN 3 OE1 ) 84.500 ( PROT GLN 3 NE2 ) 84.500 ( PROT GLN 3 HE21 ) 84.500 ( PROT GLN 3 HE22 ) 84.500 ( PROT GLN 3 C ) 105.63 ( PROT GLN 3 O ) 105.63 ( PROT ALA 4 N ) 105.63 ( PROT ALA 4 H ) 84.500 ( PROT ALA 4 CA ) 105.63 ( PROT ALA 4 CB ) 84.500 ( PROT ALA 4 C ) 105.63 ( PROT ALA 4 O ) 105.63 ( PROT PHE 5 N ) 105.63 ( PROT PHE 5 H ) 84.500 ( PROT PHE 5 CA ) 105.63 ( PROT PHE 5 CB ) 84.500 ( PROT PHE 5 CG ) 84.500 ( PROT PHE 5 CD1 ) 84.500 ( PROT PHE 5 CD2 ) 84.500 ( PROT PHE 5 CE1 ) 84.500 ( PROT PHE 5 CE2 ) 84.500 ( PROT PHE 5 CZ ) 84.500 ( PROT PHE 5 C ) 105.63 ( PROT PHE 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 ILE 7 N ) 105.63 ( PROT ILE 7 H ) 84.500 ( PROT ILE 7 CA ) 105.63 ( PROT ILE 7 CB ) 84.500 ( PROT ILE 7 CG2 ) 84.500 ( PROT ILE 7 CG1 ) 84.500 ( PROT ILE 7 CD ) 84.500 ( PROT ILE 7 C ) 105.63 ( PROT ILE 7 O ) 105.63 ( PROT ALA 8 N ) 105.63 ( PROT ALA 8 H ) 84.500 ( PROT ALA 8 CA ) 105.63 ( PROT ALA 8 CB ) 84.500 ( PROT ALA 8 C ) 105.63 ( PROT ALA 8 O ) 105.63 ( PROT LEU 9 N ) 105.63 ( PROT LEU 9 H ) 84.500 ( PROT LEU 9 CA ) 105.63 ( PROT LEU 9 CB ) 84.500 ( PROT LEU 9 CG ) 84.500 ( PROT LEU 9 CD1 ) 84.500 ( PROT LEU 9 CD2 ) 84.500 ( PROT LEU 9 C ) 105.63 ( PROT LEU 9 O ) 105.63 ( PROT SER 10 N ) 105.63 ( PROT SER 10 H ) 84.500 ( PROT SER 10 CA ) 105.63 ( PROT SER 10 CB ) 84.500 ( PROT SER 10 OG ) 84.500 ( PROT SER 10 HG ) 84.500 ( PROT SER 10 C ) 105.63 ( PROT SER 10 O ) 105.63 ( PROT SER 11 N ) 105.63 ( PROT SER 11 H ) 84.500 ( PROT SER 11 CA ) 105.63 ( PROT SER 11 CB ) 84.500 ( PROT SER 11 OG ) 84.500 ( PROT SER 11 HG ) 84.500 ( PROT SER 11 C ) 105.63 ( PROT SER 11 O ) 105.63 ( PROT PHE 12 N ) 105.63 ( PROT PHE 12 H ) 84.500 ( PROT PHE 12 CA ) 105.63 ( PROT PHE 12 CB ) 84.500 ( PROT PHE 12 CG ) 84.500 ( PROT PHE 12 CD1 ) 84.500 ( PROT PHE 12 CD2 ) 84.500 ( PROT PHE 12 CE1 ) 84.500 ( PROT PHE 12 CE2 ) 84.500 ( PROT PHE 12 CZ ) 84.500 ( PROT PHE 12 C ) 105.63 ( PROT PHE 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 SER 14 N ) 105.63 ( PROT SER 14 H ) 84.500 ( PROT SER 14 CA ) 105.63 ( PROT SER 14 CB ) 84.500 ( PROT SER 14 OG ) 84.500 ( PROT SER 14 HG ) 84.500 ( PROT SER 14 C ) 105.63 ( PROT SER 14 O ) 105.63 ( PROT LYS 15 N ) 105.63 ( PROT LYS 15 H ) 84.500 ( PROT LYS 15 CA ) 105.63 ( PROT LYS 15 CB ) 84.500 ( PROT LYS 15 CG ) 84.500 ( PROT LYS 15 CD ) 84.500 ( PROT LYS 15 CE ) 84.500 ( PROT LYS 15 NZ ) 84.500 ( PROT LYS 15 HZ1 ) 84.500 ( PROT LYS 15 HZ2 ) 84.500 ( PROT LYS 15 HZ3 ) 84.500 ( PROT LYS 15 C ) 105.63 ( PROT LYS 15 O ) 105.63 ( PROT LEU 16 N ) 105.63 ( PROT LEU 16 H ) 84.500 ( PROT LEU 16 CA ) 105.63 ( PROT LEU 16 CB ) 84.500 ( PROT LEU 16 CG ) 84.500 ( PROT LEU 16 CD1 ) 84.500 ( PROT LEU 16 CD2 ) 84.500 ( PROT LEU 16 C ) 105.63 ( PROT LEU 16 O ) 105.63 ( PROT ALA 17 N ) 105.63 ( PROT ALA 17 H ) 84.500 ( PROT ALA 17 CA ) 105.63 ( PROT ALA 17 CB ) 84.500 ( PROT ALA 17 C ) 105.63 ( PROT ALA 17 O ) 105.63 ( PROT CYS 18 N ) 105.63 ( PROT CYS 18 H ) 84.500 ( PROT CYS 18 CA ) 105.63 ( PROT CYS 18 CB ) 84.500 ( PROT CYS 18 SG ) 84.500 ( PROT CYS 18 C ) 105.63 ( PROT CYS 18 O ) 105.63 ( PROT GLU 19 N ) 105.63 ( PROT GLU 19 H ) 84.500 ( PROT GLU 19 CA ) 105.63 ( PROT GLU 19 CB ) 84.500 ( PROT GLU 19 CG ) 84.500 ( PROT GLU 19 CD ) 84.500 ( PROT GLU 19 OE1 ) 84.500 ( PROT GLU 19 OE2 ) 84.500 ( PROT GLU 19 C ) 105.63 ( PROT GLU 19 OT1 ) 84.500 ( PROT GLU 19 OT2 ) 84.500 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43640 4.57709 -7.53393 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS -0.00170 -0.00186 0.00131 ROTATION MATRIX 1.000000 -0.000071 -0.000058 0.000071 1.000000 0.000049 0.000058 -0.000049 1.000000 AXIS OF ROTATION IS 0.474933 0.557871 -0.680602 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 1.8179 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.104022 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1040" Parameter: A <- "0.1040" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.92247 4.26982 -7.72369 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00974 0.01045 -0.00858 ROTATION MATRIX 0.999951 0.007526 0.006456 -0.007468 0.999931 -0.009099 -0.006524 0.009050 0.999938 AXIS OF ROTATION IS -0.675121 -0.482840 0.557742 ANGLE IS 0.77 TOTAL SQUARE DIFF IS 0.0448 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.048555 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1040" RDCMND substituted energy or value "?RMS" to " 0.0486" Parameter: A <- "0.1040 0.0486" 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 0.1040 0.0486 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 " 273.51" Parameter: H <- "273.51" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 397.95002 273.51238 18.16393 ENER INTERN> 38.43135 56.61567 0.00000 4.76858 8.78843 ENER EXTERN> 304.46933 -15.12333 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 " 397.95" Parameter: B <- "397.95" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -15.12" Parameter: C <- "-15.12" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 304.47" Parameter: C <- " 289.35" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 289.35" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 38.43" Parameter: D <- "38.43" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 56.62" Parameter: D <- " 95.05" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 4.77" Parameter: D <- " 99.82" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.79" Parameter: D <- " 108.61" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 108.61" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 1200 ENER= 397.95 GRMS= 18.16 ELEC= -15.12 VDW= 304.47 RDTITL> *EXTERNAL= 289.35 INTERNAL= 108.61 USER= 0.00 HARM= 273.51 RDTITL> *BOND= 38.43 ANGL= 56.62 DIHE= 4.77 IMPR= 8.79 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 397.95 GRMS= 18.16 ELEC= -15.12 VDW= 304.47 RDTITL> *EXTERNAL= 289.35 INTERNAL= 108.61 USER= 0.00 HARM= 273.51 RDTITL> *BOND= 38.43 ANGL= 56.62 DIHE= 4.77 IMPR= 8.79 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 397.95 GRMS= 18.16 ELEC= -15.12 VDW= 304.47 RDTITL> *EXTERNAL= 289.35 INTERNAL= 108.61 USER= 0.00 HARM= 273.51 RDTITL> *BOND= 38.43 ANGL= 56.62 DIHE= 4.77 IMPR= 8.79 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 1200 0.1040 0.0486 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "1200" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9963 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9963 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> 0 613.55522 -215.60520 8.20610 0.02000 MINI INTERN> 38.43135 56.61567 0.00000 4.76858 8.78843 MINI EXTERN> 304.46933 -15.12333 0.00000 0.00000 0.00000 MINI CONSTR> 215.60520 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 569.60207 43.95314 2.91658 0.00360 MINI INTERN> 38.88627 62.69774 0.00000 5.96430 9.34177 MINI EXTERN> 229.98543 -13.62364 0.00000 0.00000 0.00000 MINI CONSTR> 236.35020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9953 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 564.06402 5.53805 1.36338 0.00156 MINI INTERN> 35.69511 59.80202 0.00000 5.83905 8.46891 MINI EXTERN> 240.17320 -15.23231 0.00000 0.00000 0.00000 MINI CONSTR> 229.31804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 562.97670 1.08732 0.59812 0.00067 MINI INTERN> 35.42154 60.30070 0.00000 5.94664 8.57617 MINI EXTERN> 235.42830 -15.14437 0.00000 0.00000 0.00000 MINI CONSTR> 232.44772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9953 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 562.81040 0.16630 0.24374 0.00029 MINI INTERN> 35.48730 59.64909 0.00000 5.91610 8.47091 MINI EXTERN> 236.67724 -15.28059 0.00000 0.00000 0.00000 MINI CONSTR> 231.89034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 562.78089 0.02951 0.14050 0.00013 MINI INTERN> 35.58916 59.65535 0.00000 5.92935 8.47310 MINI EXTERN> 235.93156 -15.23369 0.00000 0.00000 0.00000 MINI CONSTR> 232.43606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9953 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 562.77527 0.00562 0.04492 0.00005 MINI INTERN> 35.35793 59.64732 0.00000 5.92651 8.46561 MINI EXTERN> 236.28304 -15.29179 0.00000 0.00000 0.00000 MINI CONSTR> 232.38664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 562.77394 0.00133 0.02194 0.00002 MINI INTERN> 35.40375 59.61819 0.00000 5.92785 8.46209 MINI EXTERN> 236.17360 -15.28136 0.00000 0.00000 0.00000 MINI CONSTR> 232.46981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9953 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 562.77377 0.00017 0.02919 0.00002 MINI INTERN> 35.40650 59.60557 0.00000 5.92824 8.46033 MINI EXTERN> 236.15732 -15.28066 0.00000 0.00000 0.00000 MINI CONSTR> 232.49647 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> 41 562.77368 0.00009 0.00812 0.00001 STPD INTERN> 35.37549 59.60989 0.00000 5.92800 8.46100 STPD EXTERN> 236.20427 -15.28794 0.00000 0.00000 0.00000 STPD CONSTR> 232.48298 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 9953 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9953 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> 0 562.77368 0.00009 0.00812 0.00000 MINI INTERN> 35.37549 59.60989 0.00000 5.92800 8.46100 MINI EXTERN> 236.20427 -15.28794 0.00000 0.00000 0.00000 MINI CONSTR> 232.48298 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> 1 562.77367 0.00001 0.00608 0.02000 CONJ INTERN> 35.38719 59.60434 0.00000 5.92799 8.46082 CONJ EXTERN> 236.19653 -15.28614 0.00000 0.00000 0.00000 CONJ CONSTR> 232.48294 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 ALA 1 HT1 ) 54.925 ( PROT ALA 1 HT2 ) 54.925 ( PROT ALA 1 N ) 68.656 ( PROT ALA 1 HT3 ) 54.925 ( PROT ALA 1 CA ) 68.656 ( PROT ALA 1 CB ) 54.925 ( PROT ALA 1 C ) 68.656 ( PROT ALA 1 O ) 68.656 ( PROT LEU 2 N ) 68.656 ( PROT LEU 2 H ) 54.925 ( PROT LEU 2 CA ) 68.656 ( PROT LEU 2 CB ) 54.925 ( PROT LEU 2 CG ) 54.925 ( PROT LEU 2 CD1 ) 54.925 ( PROT LEU 2 CD2 ) 54.925 ( PROT LEU 2 C ) 68.656 ( PROT LEU 2 O ) 68.656 ( PROT GLN 3 N ) 68.656 ( PROT GLN 3 H ) 54.925 ( PROT GLN 3 CA ) 68.656 ( PROT GLN 3 CB ) 54.925 ( PROT GLN 3 CG ) 54.925 ( PROT GLN 3 CD ) 54.925 ( PROT GLN 3 OE1 ) 54.925 ( PROT GLN 3 NE2 ) 54.925 ( PROT GLN 3 HE21 ) 54.925 ( PROT GLN 3 HE22 ) 54.925 ( PROT GLN 3 C ) 68.656 ( PROT GLN 3 O ) 68.656 ( PROT ALA 4 N ) 68.656 ( PROT ALA 4 H ) 54.925 ( PROT ALA 4 CA ) 68.656 ( PROT ALA 4 CB ) 54.925 ( PROT ALA 4 C ) 68.656 ( PROT ALA 4 O ) 68.656 ( PROT PHE 5 N ) 68.656 ( PROT PHE 5 H ) 54.925 ( PROT PHE 5 CA ) 68.656 ( PROT PHE 5 CB ) 54.925 ( PROT PHE 5 CG ) 54.925 ( PROT PHE 5 CD1 ) 54.925 ( PROT PHE 5 CD2 ) 54.925 ( PROT PHE 5 CE1 ) 54.925 ( PROT PHE 5 CE2 ) 54.925 ( PROT PHE 5 CZ ) 54.925 ( PROT PHE 5 C ) 68.656 ( PROT PHE 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 ILE 7 N ) 68.656 ( PROT ILE 7 H ) 54.925 ( PROT ILE 7 CA ) 68.656 ( PROT ILE 7 CB ) 54.925 ( PROT ILE 7 CG2 ) 54.925 ( PROT ILE 7 CG1 ) 54.925 ( PROT ILE 7 CD ) 54.925 ( PROT ILE 7 C ) 68.656 ( PROT ILE 7 O ) 68.656 ( PROT ALA 8 N ) 68.656 ( PROT ALA 8 H ) 54.925 ( PROT ALA 8 CA ) 68.656 ( PROT ALA 8 CB ) 54.925 ( PROT ALA 8 C ) 68.656 ( PROT ALA 8 O ) 68.656 ( PROT LEU 9 N ) 68.656 ( PROT LEU 9 H ) 54.925 ( PROT LEU 9 CA ) 68.656 ( PROT LEU 9 CB ) 54.925 ( PROT LEU 9 CG ) 54.925 ( PROT LEU 9 CD1 ) 54.925 ( PROT LEU 9 CD2 ) 54.925 ( PROT LEU 9 C ) 68.656 ( PROT LEU 9 O ) 68.656 ( PROT SER 10 N ) 68.656 ( PROT SER 10 H ) 54.925 ( PROT SER 10 CA ) 68.656 ( PROT SER 10 CB ) 54.925 ( PROT SER 10 OG ) 54.925 ( PROT SER 10 HG ) 54.925 ( PROT SER 10 C ) 68.656 ( PROT SER 10 O ) 68.656 ( PROT SER 11 N ) 68.656 ( PROT SER 11 H ) 54.925 ( PROT SER 11 CA ) 68.656 ( PROT SER 11 CB ) 54.925 ( PROT SER 11 OG ) 54.925 ( PROT SER 11 HG ) 54.925 ( PROT SER 11 C ) 68.656 ( PROT SER 11 O ) 68.656 ( PROT PHE 12 N ) 68.656 ( PROT PHE 12 H ) 54.925 ( PROT PHE 12 CA ) 68.656 ( PROT PHE 12 CB ) 54.925 ( PROT PHE 12 CG ) 54.925 ( PROT PHE 12 CD1 ) 54.925 ( PROT PHE 12 CD2 ) 54.925 ( PROT PHE 12 CE1 ) 54.925 ( PROT PHE 12 CE2 ) 54.925 ( PROT PHE 12 CZ ) 54.925 ( PROT PHE 12 C ) 68.656 ( PROT PHE 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 SER 14 N ) 68.656 ( PROT SER 14 H ) 54.925 ( PROT SER 14 CA ) 68.656 ( PROT SER 14 CB ) 54.925 ( PROT SER 14 OG ) 54.925 ( PROT SER 14 HG ) 54.925 ( PROT SER 14 C ) 68.656 ( PROT SER 14 O ) 68.656 ( PROT LYS 15 N ) 68.656 ( PROT LYS 15 H ) 54.925 ( PROT LYS 15 CA ) 68.656 ( PROT LYS 15 CB ) 54.925 ( PROT LYS 15 CG ) 54.925 ( PROT LYS 15 CD ) 54.925 ( PROT LYS 15 CE ) 54.925 ( PROT LYS 15 NZ ) 54.925 ( PROT LYS 15 HZ1 ) 54.925 ( PROT LYS 15 HZ2 ) 54.925 ( PROT LYS 15 HZ3 ) 54.925 ( PROT LYS 15 C ) 68.656 ( PROT LYS 15 O ) 68.656 ( PROT LEU 16 N ) 68.656 ( PROT LEU 16 H ) 54.925 ( PROT LEU 16 CA ) 68.656 ( PROT LEU 16 CB ) 54.925 ( PROT LEU 16 CG ) 54.925 ( PROT LEU 16 CD1 ) 54.925 ( PROT LEU 16 CD2 ) 54.925 ( PROT LEU 16 C ) 68.656 ( PROT LEU 16 O ) 68.656 ( PROT ALA 17 N ) 68.656 ( PROT ALA 17 H ) 54.925 ( PROT ALA 17 CA ) 68.656 ( PROT ALA 17 CB ) 54.925 ( PROT ALA 17 C ) 68.656 ( PROT ALA 17 O ) 68.656 ( PROT CYS 18 N ) 68.656 ( PROT CYS 18 H ) 54.925 ( PROT CYS 18 CA ) 68.656 ( PROT CYS 18 CB ) 54.925 ( PROT CYS 18 SG ) 54.925 ( PROT CYS 18 C ) 68.656 ( PROT CYS 18 O ) 68.656 ( PROT GLU 19 N ) 68.656 ( PROT GLU 19 H ) 54.925 ( PROT GLU 19 CA ) 68.656 ( PROT GLU 19 CB ) 54.925 ( PROT GLU 19 CG ) 54.925 ( PROT GLU 19 CD ) 54.925 ( PROT GLU 19 OE1 ) 54.925 ( PROT GLU 19 OE2 ) 54.925 ( PROT GLU 19 C ) 68.656 ( PROT GLU 19 OT1 ) 54.925 ( PROT GLU 19 OT2 ) 54.925 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43626 4.57717 -7.53377 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS -0.00156 -0.00194 0.00115 ROTATION MATRIX 1.000000 -0.000080 -0.000071 0.000080 1.000000 0.000069 0.000071 -0.000069 1.000000 AXIS OF ROTATION IS 0.540373 0.558042 -0.629751 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 2.3785 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.118986 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1190" Parameter: A <- "0.1190" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.92242 4.26898 -7.72326 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00979 0.01128 -0.00900 ROTATION MATRIX 0.999933 0.008859 0.007503 -0.008779 0.999904 -0.010723 -0.007597 0.010656 0.999914 AXIS OF ROTATION IS -0.677360 -0.478429 0.558829 ANGLE IS 0.90 TOTAL SQUARE DIFF IS 0.0707 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.060986 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1190" RDCMND substituted energy or value "?RMS" to " 0.0610" Parameter: A <- "0.1190 0.0610" 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 0.1190 0.0610 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 " 232.48" Parameter: H <- "232.48" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 330.29073 232.48294 13.49916 ENER INTERN> 35.38719 59.60434 0.00000 5.92799 8.46082 ENER EXTERN> 236.19653 -15.28614 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 " 330.29" Parameter: B <- "330.29" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -15.29" Parameter: C <- "-15.29" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 236.20" Parameter: C <- " 220.91" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 220.91" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 35.39" Parameter: D <- "35.39" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 59.60" Parameter: D <- " 94.99" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 5.93" Parameter: D <- " 100.92" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.46" Parameter: D <- " 109.38" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 109.38" 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= 330.29 GRMS= 13.50 ELEC= -15.29 VDW= 236.20 RDTITL> *EXTERNAL= 220.91 INTERNAL= 109.38 USER= 0.00 HARM= 232.48 RDTITL> *BOND= 35.39 ANGL= 59.60 DIHE= 5.93 IMPR= 8.46 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9953 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9953 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> 0 515.00514 -184.71442 6.14367 0.02000 MINI INTERN> 35.38719 59.60434 0.00000 5.92799 8.46082 MINI EXTERN> 236.19653 -15.28614 0.00000 0.00000 0.00000 MINI CONSTR> 184.71442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 479.99661 35.00853 3.02582 0.00360 MINI INTERN> 36.65234 65.27331 0.00000 7.44234 8.71367 MINI EXTERN> 175.43245 -14.33029 0.00000 0.00000 0.00000 MINI CONSTR> 200.81279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9942 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 473.31677 6.67984 1.48001 0.00156 MINI INTERN> 31.72776 62.80506 0.00000 7.29566 7.95351 MINI EXTERN> 182.64104 -16.11721 0.00000 0.00000 0.00000 MINI CONSTR> 197.01096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 471.57213 1.74464 2.83913 0.00161 MINI INTERN> 30.34087 63.46970 0.00000 7.27963 7.89751 MINI EXTERN> 180.22859 -16.53050 0.00000 0.00000 0.00000 MINI CONSTR> 198.88633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9938 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 470.28678 1.28535 0.82276 0.00070 MINI INTERN> 31.49920 60.99984 0.00000 7.49432 7.78822 MINI EXTERN> 180.08012 -16.42719 0.00000 0.00000 0.00000 MINI CONSTR> 198.85227 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 469.97873 0.30805 0.30730 0.00030 MINI INTERN> 31.63021 60.84258 0.00000 7.45456 7.74798 MINI EXTERN> 179.13042 -16.46680 0.00000 0.00000 0.00000 MINI CONSTR> 199.63978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9938 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 469.86593 0.11280 0.19833 0.00031 MINI INTERN> 31.52553 60.63211 0.00000 7.46470 7.72527 MINI EXTERN> 178.96559 -16.51756 0.00000 0.00000 0.00000 MINI CONSTR> 200.07028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 469.81924 0.04669 0.13146 0.00013 MINI INTERN> 31.36417 60.46230 0.00000 7.48307 7.71420 MINI EXTERN> 179.00940 -16.56088 0.00000 0.00000 0.00000 MINI CONSTR> 200.34699 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9938 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 469.80810 0.01114 0.24132 0.00014 MINI INTERN> 31.24715 60.36147 0.00000 7.49703 7.71071 MINI EXTERN> 179.06621 -16.58623 0.00000 0.00000 0.00000 MINI CONSTR> 200.51177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 469.79923 0.00887 0.06177 0.00006 MINI INTERN> 31.36248 60.34122 0.00000 7.48063 7.69833 MINI EXTERN> 178.82495 -16.57911 0.00000 0.00000 0.00000 MINI CONSTR> 200.67072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9938 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 469.79733 0.00190 0.02397 0.00003 MINI INTERN> 31.31857 60.31669 0.00000 7.48541 7.69954 MINI EXTERN> 178.83430 -16.58554 0.00000 0.00000 0.00000 MINI CONSTR> 200.72837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 469.79669 0.00065 0.03826 0.00003 MINI INTERN> 31.29951 60.30055 0.00000 7.48711 7.69994 MINI EXTERN> 178.81529 -16.58838 0.00000 0.00000 0.00000 MINI CONSTR> 200.78268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9938 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 469.79651 0.00018 0.04328 0.00003 MINI INTERN> 31.29025 60.29038 0.00000 7.48777 7.69962 MINI EXTERN> 178.80565 -16.58974 0.00000 0.00000 0.00000 MINI CONSTR> 200.81258 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 63 469.79629 0.00022 0.00678 0.00001 STPD INTERN> 31.29859 60.27638 0.00000 7.48756 7.69659 STPD EXTERN> 178.81243 -16.58941 0.00000 0.00000 0.00000 STPD CONSTR> 200.81416 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 9938 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9938 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> 0 469.79629 0.00022 0.00678 0.00000 MINI INTERN> 31.29859 60.27638 0.00000 7.48756 7.69659 MINI EXTERN> 178.81243 -16.58941 0.00000 0.00000 0.00000 MINI CONSTR> 200.81416 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> 1 469.79628 0.00001 0.00678 0.02000 CONJ INTERN> 31.29624 60.27723 0.00000 7.48770 7.69689 CONJ EXTERN> 178.81012 -16.58962 0.00000 0.00000 0.00000 CONJ CONSTR> 200.81772 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 ALA 1 HT1 ) 35.701 ( PROT ALA 1 HT2 ) 35.701 ( PROT ALA 1 N ) 44.627 ( PROT ALA 1 HT3 ) 35.701 ( PROT ALA 1 CA ) 44.627 ( PROT ALA 1 CB ) 35.701 ( PROT ALA 1 C ) 44.627 ( PROT ALA 1 O ) 44.627 ( PROT LEU 2 N ) 44.627 ( PROT LEU 2 H ) 35.701 ( PROT LEU 2 CA ) 44.627 ( PROT LEU 2 CB ) 35.701 ( PROT LEU 2 CG ) 35.701 ( PROT LEU 2 CD1 ) 35.701 ( PROT LEU 2 CD2 ) 35.701 ( PROT LEU 2 C ) 44.627 ( PROT LEU 2 O ) 44.627 ( PROT GLN 3 N ) 44.627 ( PROT GLN 3 H ) 35.701 ( PROT GLN 3 CA ) 44.627 ( PROT GLN 3 CB ) 35.701 ( PROT GLN 3 CG ) 35.701 ( PROT GLN 3 CD ) 35.701 ( PROT GLN 3 OE1 ) 35.701 ( PROT GLN 3 NE2 ) 35.701 ( PROT GLN 3 HE21 ) 35.701 ( PROT GLN 3 HE22 ) 35.701 ( PROT GLN 3 C ) 44.627 ( PROT GLN 3 O ) 44.627 ( PROT ALA 4 N ) 44.627 ( PROT ALA 4 H ) 35.701 ( PROT ALA 4 CA ) 44.627 ( PROT ALA 4 CB ) 35.701 ( PROT ALA 4 C ) 44.627 ( PROT ALA 4 O ) 44.627 ( PROT PHE 5 N ) 44.627 ( PROT PHE 5 H ) 35.701 ( PROT PHE 5 CA ) 44.627 ( PROT PHE 5 CB ) 35.701 ( PROT PHE 5 CG ) 35.701 ( PROT PHE 5 CD1 ) 35.701 ( PROT PHE 5 CD2 ) 35.701 ( PROT PHE 5 CE1 ) 35.701 ( PROT PHE 5 CE2 ) 35.701 ( PROT PHE 5 CZ ) 35.701 ( PROT PHE 5 C ) 44.627 ( PROT PHE 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 ILE 7 N ) 44.627 ( PROT ILE 7 H ) 35.701 ( PROT ILE 7 CA ) 44.627 ( PROT ILE 7 CB ) 35.701 ( PROT ILE 7 CG2 ) 35.701 ( PROT ILE 7 CG1 ) 35.701 ( PROT ILE 7 CD ) 35.701 ( PROT ILE 7 C ) 44.627 ( PROT ILE 7 O ) 44.627 ( PROT ALA 8 N ) 44.627 ( PROT ALA 8 H ) 35.701 ( PROT ALA 8 CA ) 44.627 ( PROT ALA 8 CB ) 35.701 ( PROT ALA 8 C ) 44.627 ( PROT ALA 8 O ) 44.627 ( PROT LEU 9 N ) 44.627 ( PROT LEU 9 H ) 35.701 ( PROT LEU 9 CA ) 44.627 ( PROT LEU 9 CB ) 35.701 ( PROT LEU 9 CG ) 35.701 ( PROT LEU 9 CD1 ) 35.701 ( PROT LEU 9 CD2 ) 35.701 ( PROT LEU 9 C ) 44.627 ( PROT LEU 9 O ) 44.627 ( PROT SER 10 N ) 44.627 ( PROT SER 10 H ) 35.701 ( PROT SER 10 CA ) 44.627 ( PROT SER 10 CB ) 35.701 ( PROT SER 10 OG ) 35.701 ( PROT SER 10 HG ) 35.701 ( PROT SER 10 C ) 44.627 ( PROT SER 10 O ) 44.627 ( PROT SER 11 N ) 44.627 ( PROT SER 11 H ) 35.701 ( PROT SER 11 CA ) 44.627 ( PROT SER 11 CB ) 35.701 ( PROT SER 11 OG ) 35.701 ( PROT SER 11 HG ) 35.701 ( PROT SER 11 C ) 44.627 ( PROT SER 11 O ) 44.627 ( PROT PHE 12 N ) 44.627 ( PROT PHE 12 H ) 35.701 ( PROT PHE 12 CA ) 44.627 ( PROT PHE 12 CB ) 35.701 ( PROT PHE 12 CG ) 35.701 ( PROT PHE 12 CD1 ) 35.701 ( PROT PHE 12 CD2 ) 35.701 ( PROT PHE 12 CE1 ) 35.701 ( PROT PHE 12 CE2 ) 35.701 ( PROT PHE 12 CZ ) 35.701 ( PROT PHE 12 C ) 44.627 ( PROT PHE 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 SER 14 N ) 44.627 ( PROT SER 14 H ) 35.701 ( PROT SER 14 CA ) 44.627 ( PROT SER 14 CB ) 35.701 ( PROT SER 14 OG ) 35.701 ( PROT SER 14 HG ) 35.701 ( PROT SER 14 C ) 44.627 ( PROT SER 14 O ) 44.627 ( PROT LYS 15 N ) 44.627 ( PROT LYS 15 H ) 35.701 ( PROT LYS 15 CA ) 44.627 ( PROT LYS 15 CB ) 35.701 ( PROT LYS 15 CG ) 35.701 ( PROT LYS 15 CD ) 35.701 ( PROT LYS 15 CE ) 35.701 ( PROT LYS 15 NZ ) 35.701 ( PROT LYS 15 HZ1 ) 35.701 ( PROT LYS 15 HZ2 ) 35.701 ( PROT LYS 15 HZ3 ) 35.701 ( PROT LYS 15 C ) 44.627 ( PROT LYS 15 O ) 44.627 ( PROT LEU 16 N ) 44.627 ( PROT LEU 16 H ) 35.701 ( PROT LEU 16 CA ) 44.627 ( PROT LEU 16 CB ) 35.701 ( PROT LEU 16 CG ) 35.701 ( PROT LEU 16 CD1 ) 35.701 ( PROT LEU 16 CD2 ) 35.701 ( PROT LEU 16 C ) 44.627 ( PROT LEU 16 O ) 44.627 ( PROT ALA 17 N ) 44.627 ( PROT ALA 17 H ) 35.701 ( PROT ALA 17 CA ) 44.627 ( PROT ALA 17 CB ) 35.701 ( PROT ALA 17 C ) 44.627 ( PROT ALA 17 O ) 44.627 ( PROT CYS 18 N ) 44.627 ( PROT CYS 18 H ) 35.701 ( PROT CYS 18 CA ) 44.627 ( PROT CYS 18 CB ) 35.701 ( PROT CYS 18 SG ) 35.701 ( PROT CYS 18 C ) 44.627 ( PROT CYS 18 O ) 44.627 ( PROT GLU 19 N ) 44.627 ( PROT GLU 19 H ) 35.701 ( PROT GLU 19 CA ) 44.627 ( PROT GLU 19 CB ) 35.701 ( PROT GLU 19 CG ) 35.701 ( PROT GLU 19 CD ) 35.701 ( PROT GLU 19 OE1 ) 35.701 ( PROT GLU 19 OE2 ) 35.701 ( PROT GLU 19 C ) 44.627 ( PROT GLU 19 OT1 ) 35.701 ( PROT GLU 19 OT2 ) 35.701 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43598 4.57720 -7.53347 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS -0.00128 -0.00197 0.00085 ROTATION MATRIX 1.000000 -0.000098 -0.000096 0.000098 1.000000 0.000104 0.000096 -0.000104 1.000000 AXIS OF ROTATION IS 0.602550 0.556607 -0.571946 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 3.1696 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.137356 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1374" Parameter: A <- "0.1374" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.92244 4.26816 -7.72263 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00977 0.01211 -0.00963 ROTATION MATRIX 0.999911 0.010254 0.008560 -0.010148 0.999871 -0.012440 -0.008686 0.012352 0.999886 AXIS OF ROTATION IS -0.680226 -0.473203 0.559796 ANGLE IS 1.04 CENTER OF ROTATION 8.805586 4.214841 -7.925559 SHIFT IS -0.017771 TOTAL SQUARE DIFF IS 0.1051 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.074365 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1374" RDCMND substituted energy or value "?RMS" to " 0.0744" Parameter: A <- "0.1374 0.0744" 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 0.1374 0.0744 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 " 200.82" Parameter: H <- "200.82" 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> 0 268.97856 200.81772 10.10317 ENER INTERN> 31.29624 60.27723 0.00000 7.48770 7.69689 ENER EXTERN> 178.81012 -16.58962 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 " 268.98" Parameter: B <- "268.98" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -16.59" Parameter: C <- "-16.59" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 178.81" Parameter: C <- " 162.22" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 162.22" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 31.30" Parameter: D <- "31.30" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 60.28" Parameter: D <- " 91.58" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 7.49" Parameter: D <- " 99.07" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.70" Parameter: D <- " 106.77" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 106.77" 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= 268.98 GRMS= 10.10 ELEC= -16.59 VDW= 178.81 RDTITL> *EXTERNAL= 162.22 INTERNAL= 106.77 USER= 0.00 HARM= 200.82 RDTITL> *BOND= 31.30 ANGL= 60.28 DIHE= 7.49 IMPR= 7.70 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "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= 268.98 GRMS= 10.10 ELEC= -16.59 VDW= 178.81 RDTITL> *EXTERNAL= 162.22 INTERNAL= 106.77 USER= 0.00 HARM= 200.82 RDTITL> *BOND= 31.30 ANGL= 60.28 DIHE= 7.49 IMPR= 7.70 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= 268.98 GRMS= 10.10 ELEC= -16.59 VDW= 178.81 RDTITL> *EXTERNAL= 162.22 INTERNAL= 106.77 USER= 0.00 HARM= 200.82 RDTITL> *BOND= 31.30 ANGL= 60.28 DIHE= 7.49 IMPR= 7.70 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 2400 0.1374 0.0744 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "2400" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9938 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9938 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> 0 428.55441 -159.57585 4.59553 0.02000 MINI INTERN> 31.29624 60.27723 0.00000 7.48770 7.69689 MINI EXTERN> 178.81012 -16.58962 0.00000 0.00000 0.00000 MINI CONSTR> 159.57585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 401.50053 27.05388 2.90096 0.00360 MINI INTERN> 31.71966 64.87237 0.00000 9.31662 7.77038 MINI EXTERN> 130.17605 -16.12042 0.00000 0.00000 0.00000 MINI CONSTR> 173.76587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9923 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 394.62587 6.87466 1.47685 0.00156 MINI INTERN> 27.95268 61.28310 0.00000 9.17176 7.17206 MINI EXTERN> 134.40187 -17.66562 0.00000 0.00000 0.00000 MINI CONSTR> 172.31002 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 391.27326 3.35260 1.45289 0.00161 MINI INTERN> 27.35770 60.14132 0.00000 9.27803 7.14230 MINI EXTERN> 131.33851 -18.05872 0.00000 0.00000 0.00000 MINI CONSTR> 174.07413 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9922 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 389.85321 1.42006 0.71745 0.00070 MINI INTERN> 26.51404 59.05115 0.00000 9.43638 7.04637 MINI EXTERN> 131.15819 -18.24746 0.00000 0.00000 0.00000 MINI CONSTR> 174.89454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 389.14924 0.70397 0.51143 0.00072 MINI INTERN> 26.28042 58.49198 0.00000 9.46520 7.03364 MINI EXTERN> 130.46392 -18.38886 0.00000 0.00000 0.00000 MINI CONSTR> 175.80294 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9921 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 388.82094 0.32829 1.14626 0.00075 MINI INTERN> 25.65733 57.95633 0.00000 9.56146 6.97820 MINI EXTERN> 130.75297 -18.55266 0.00000 0.00000 0.00000 MINI CONSTR> 176.46731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 388.54621 0.27473 0.33573 0.00032 MINI INTERN> 26.14755 57.81123 0.00000 9.47699 7.04065 MINI EXTERN> 129.34006 -18.55274 0.00000 0.00000 0.00000 MINI CONSTR> 177.28247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9921 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 388.45322 0.09299 0.31526 0.00034 MINI INTERN> 26.05666 57.63633 0.00000 9.48515 7.03870 MINI EXTERN> 129.14339 -18.60367 0.00000 0.00000 0.00000 MINI CONSTR> 177.69665 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 388.42850 0.02472 0.53770 0.00035 MINI INTERN> 26.15144 57.54884 0.00000 9.47145 7.04818 MINI EXTERN> 128.81873 -18.62348 0.00000 0.00000 0.00000 MINI CONSTR> 178.01334 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9920 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 388.38358 0.04491 0.22578 0.00015 MINI INTERN> 25.78925 57.38005 0.00000 9.52569 6.99936 MINI EXTERN> 129.29576 -18.67015 0.00000 0.00000 0.00000 MINI CONSTR> 178.06361 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 388.37374 0.00984 0.27363 0.00016 MINI INTERN> 25.78607 57.30010 0.00000 9.53051 6.99137 MINI EXTERN> 129.24604 -18.68216 0.00000 0.00000 0.00000 MINI CONSTR> 178.20182 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9920 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 388.36277 0.01097 0.04714 0.00007 MINI INTERN> 25.82430 57.31904 0.00000 9.51641 7.01341 MINI EXTERN> 129.04905 -18.69014 0.00000 0.00000 0.00000 MINI CONSTR> 178.33070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 388.35969 0.00308 0.10455 0.00007 MINI INTERN> 25.81786 57.30223 0.00000 9.51456 7.01990 MINI EXTERN> 128.97434 -18.70098 0.00000 0.00000 0.00000 MINI CONSTR> 178.43179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9920 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 388.35713 0.00256 0.02703 0.00003 MINI INTERN> 25.80980 57.26033 0.00000 9.51876 7.00727 MINI EXTERN> 129.00367 -18.70543 0.00000 0.00000 0.00000 MINI CONSTR> 178.46273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 388.35633 0.00081 0.04410 0.00003 MINI INTERN> 25.81990 57.23713 0.00000 9.51873 7.00338 MINI EXTERN> 128.98611 -18.70847 0.00000 0.00000 0.00000 MINI CONSTR> 178.49955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9920 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 388.35594 0.00038 0.05488 0.00003 MINI INTERN> 25.79804 57.23726 0.00000 9.51828 7.00196 MINI EXTERN> 128.98973 -18.71612 0.00000 0.00000 0.00000 MINI CONSTR> 178.52678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 388.35548 0.00047 0.00976 0.00001 MINI INTERN> 25.79248 57.23802 0.00000 9.51979 7.00699 MINI EXTERN> 128.97027 -18.71662 0.00000 0.00000 0.00000 MINI CONSTR> 178.54454 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> 85 388.35548 0.00047 0.00976 0.00002 STPD INTERN> 25.79248 57.23802 0.00000 9.51979 7.00699 STPD EXTERN> 128.97027 -18.71662 0.00000 0.00000 0.00000 STPD CONSTR> 178.54454 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 9920 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9920 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> 0 388.35548 0.00047 0.00976 0.00000 MINI INTERN> 25.79248 57.23802 0.00000 9.51979 7.00699 MINI EXTERN> 128.97027 -18.71662 0.00000 0.00000 0.00000 MINI CONSTR> 178.54454 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> 3 388.35507 0.00041 0.00377 0.02000 CONJ INTERN> 25.79063 57.21609 0.00000 9.52010 7.00422 CONJ EXTERN> 128.94129 -18.72481 0.00000 0.00000 0.00000 CONJ CONSTR> 178.60756 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 ALA 1 HT1 ) 23.206 ( PROT ALA 1 HT2 ) 23.206 ( PROT ALA 1 N ) 29.007 ( PROT ALA 1 HT3 ) 23.206 ( PROT ALA 1 CA ) 29.007 ( PROT ALA 1 CB ) 23.206 ( PROT ALA 1 C ) 29.007 ( PROT ALA 1 O ) 29.007 ( PROT LEU 2 N ) 29.007 ( PROT LEU 2 H ) 23.206 ( PROT LEU 2 CA ) 29.007 ( PROT LEU 2 CB ) 23.206 ( PROT LEU 2 CG ) 23.206 ( PROT LEU 2 CD1 ) 23.206 ( PROT LEU 2 CD2 ) 23.206 ( PROT LEU 2 C ) 29.007 ( PROT LEU 2 O ) 29.007 ( PROT GLN 3 N ) 29.007 ( PROT GLN 3 H ) 23.206 ( PROT GLN 3 CA ) 29.007 ( PROT GLN 3 CB ) 23.206 ( PROT GLN 3 CG ) 23.206 ( PROT GLN 3 CD ) 23.206 ( PROT GLN 3 OE1 ) 23.206 ( PROT GLN 3 NE2 ) 23.206 ( PROT GLN 3 HE21 ) 23.206 ( PROT GLN 3 HE22 ) 23.206 ( PROT GLN 3 C ) 29.007 ( PROT GLN 3 O ) 29.007 ( PROT ALA 4 N ) 29.007 ( PROT ALA 4 H ) 23.206 ( PROT ALA 4 CA ) 29.007 ( PROT ALA 4 CB ) 23.206 ( PROT ALA 4 C ) 29.007 ( PROT ALA 4 O ) 29.007 ( PROT PHE 5 N ) 29.007 ( PROT PHE 5 H ) 23.206 ( PROT PHE 5 CA ) 29.007 ( PROT PHE 5 CB ) 23.206 ( PROT PHE 5 CG ) 23.206 ( PROT PHE 5 CD1 ) 23.206 ( PROT PHE 5 CD2 ) 23.206 ( PROT PHE 5 CE1 ) 23.206 ( PROT PHE 5 CE2 ) 23.206 ( PROT PHE 5 CZ ) 23.206 ( PROT PHE 5 C ) 29.007 ( PROT PHE 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 ILE 7 N ) 29.007 ( PROT ILE 7 H ) 23.206 ( PROT ILE 7 CA ) 29.007 ( PROT ILE 7 CB ) 23.206 ( PROT ILE 7 CG2 ) 23.206 ( PROT ILE 7 CG1 ) 23.206 ( PROT ILE 7 CD ) 23.206 ( PROT ILE 7 C ) 29.007 ( PROT ILE 7 O ) 29.007 ( PROT ALA 8 N ) 29.007 ( PROT ALA 8 H ) 23.206 ( PROT ALA 8 CA ) 29.007 ( PROT ALA 8 CB ) 23.206 ( PROT ALA 8 C ) 29.007 ( PROT ALA 8 O ) 29.007 ( PROT LEU 9 N ) 29.007 ( PROT LEU 9 H ) 23.206 ( PROT LEU 9 CA ) 29.007 ( PROT LEU 9 CB ) 23.206 ( PROT LEU 9 CG ) 23.206 ( PROT LEU 9 CD1 ) 23.206 ( PROT LEU 9 CD2 ) 23.206 ( PROT LEU 9 C ) 29.007 ( PROT LEU 9 O ) 29.007 ( PROT SER 10 N ) 29.007 ( PROT SER 10 H ) 23.206 ( PROT SER 10 CA ) 29.007 ( PROT SER 10 CB ) 23.206 ( PROT SER 10 OG ) 23.206 ( PROT SER 10 HG ) 23.206 ( PROT SER 10 C ) 29.007 ( PROT SER 10 O ) 29.007 ( PROT SER 11 N ) 29.007 ( PROT SER 11 H ) 23.206 ( PROT SER 11 CA ) 29.007 ( PROT SER 11 CB ) 23.206 ( PROT SER 11 OG ) 23.206 ( PROT SER 11 HG ) 23.206 ( PROT SER 11 C ) 29.007 ( PROT SER 11 O ) 29.007 ( PROT PHE 12 N ) 29.007 ( PROT PHE 12 H ) 23.206 ( PROT PHE 12 CA ) 29.007 ( PROT PHE 12 CB ) 23.206 ( PROT PHE 12 CG ) 23.206 ( PROT PHE 12 CD1 ) 23.206 ( PROT PHE 12 CD2 ) 23.206 ( PROT PHE 12 CE1 ) 23.206 ( PROT PHE 12 CE2 ) 23.206 ( PROT PHE 12 CZ ) 23.206 ( PROT PHE 12 C ) 29.007 ( PROT PHE 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 SER 14 N ) 29.007 ( PROT SER 14 H ) 23.206 ( PROT SER 14 CA ) 29.007 ( PROT SER 14 CB ) 23.206 ( PROT SER 14 OG ) 23.206 ( PROT SER 14 HG ) 23.206 ( PROT SER 14 C ) 29.007 ( PROT SER 14 O ) 29.007 ( PROT LYS 15 N ) 29.007 ( PROT LYS 15 H ) 23.206 ( PROT LYS 15 CA ) 29.007 ( PROT LYS 15 CB ) 23.206 ( PROT LYS 15 CG ) 23.206 ( PROT LYS 15 CD ) 23.206 ( PROT LYS 15 CE ) 23.206 ( PROT LYS 15 NZ ) 23.206 ( PROT LYS 15 HZ1 ) 23.206 ( PROT LYS 15 HZ2 ) 23.206 ( PROT LYS 15 HZ3 ) 23.206 ( PROT LYS 15 C ) 29.007 ( PROT LYS 15 O ) 29.007 ( PROT LEU 16 N ) 29.007 ( PROT LEU 16 H ) 23.206 ( PROT LEU 16 CA ) 29.007 ( PROT LEU 16 CB ) 23.206 ( PROT LEU 16 CG ) 23.206 ( PROT LEU 16 CD1 ) 23.206 ( PROT LEU 16 CD2 ) 23.206 ( PROT LEU 16 C ) 29.007 ( PROT LEU 16 O ) 29.007 ( PROT ALA 17 N ) 29.007 ( PROT ALA 17 H ) 23.206 ( PROT ALA 17 CA ) 29.007 ( PROT ALA 17 CB ) 23.206 ( PROT ALA 17 C ) 29.007 ( PROT ALA 17 O ) 29.007 ( PROT CYS 18 N ) 29.007 ( PROT CYS 18 H ) 23.206 ( PROT CYS 18 CA ) 29.007 ( PROT CYS 18 CB ) 23.206 ( PROT CYS 18 SG ) 23.206 ( PROT CYS 18 C ) 29.007 ( PROT CYS 18 O ) 29.007 ( PROT GLU 19 N ) 29.007 ( PROT GLU 19 H ) 23.206 ( PROT GLU 19 CA ) 29.007 ( PROT GLU 19 CB ) 23.206 ( PROT GLU 19 CG ) 23.206 ( PROT GLU 19 CD ) 23.206 ( PROT GLU 19 OE1 ) 23.206 ( PROT GLU 19 OE2 ) 23.206 ( PROT GLU 19 C ) 29.007 ( PROT GLU 19 OT1 ) 23.206 ( PROT GLU 19 OT2 ) 23.206 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43553 4.57717 -7.53301 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS -0.00083 -0.00194 0.00039 ROTATION MATRIX 1.000000 -0.000111 -0.000122 0.000111 1.000000 0.000137 0.000122 -0.000137 1.000000 AXIS OF ROTATION IS 0.639502 0.566931 -0.519256 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 4.3527 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.160963 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1610" Parameter: A <- "0.1610" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.92247 4.26746 -7.72153 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00974 0.01280 -0.01074 ROTATION MATRIX 0.999886 0.011685 0.009593 -0.011548 0.999832 -0.014222 -0.009758 0.014109 0.999853 AXIS OF ROTATION IS -0.683746 -0.467004 0.560712 ANGLE IS 1.19 CENTER OF ROTATION 8.822859 4.183268 -7.929755 SHIFT IS -0.018659 TOTAL SQUARE DIFF IS 0.1483 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.088356 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1610" RDCMND substituted energy or value "?RMS" to " 0.0884" Parameter: A <- "0.1610 0.0884" 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 0.1610 0.0884 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 " 178.61" Parameter: H <- "178.61" 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> 0 209.74750 178.60756 7.66898 ENER INTERN> 25.79063 57.21609 0.00000 9.52010 7.00422 ENER EXTERN> 128.94129 -18.72481 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 " 209.75" Parameter: B <- "209.75" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -18.72" Parameter: C <- "-18.72" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 128.94" Parameter: C <- " 110.22" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 110.22" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 25.79" Parameter: D <- "25.79" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 57.22" Parameter: D <- " 83.01" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 9.52" Parameter: D <- " 92.53" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.00" Parameter: D <- " 99.53" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 99.53" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 3000 ENER= 209.75 GRMS= 7.67 ELEC= -18.72 VDW= 128.94 RDTITL> *EXTERNAL= 110.22 INTERNAL= 99.53 USER= 0.00 HARM= 178.61 RDTITL> *BOND= 25.79 ANGL= 57.22 DIHE= 9.52 IMPR= 7.00 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9920 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9920 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 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> 0 350.31394 -140.56644 3.44989 0.02000 MINI INTERN> 25.79063 57.21609 0.00000 9.52010 7.00422 MINI EXTERN> 128.94129 -18.72481 0.00000 0.00000 0.00000 MINI CONSTR> 140.56644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 329.85312 20.46082 2.52439 0.00360 MINI INTERN> 25.20110 60.35480 0.00000 11.59503 7.13616 MINI EXTERN> 90.06218 -18.45230 0.00000 0.00000 0.00000 MINI CONSTR> 153.95613 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9909 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 323.61931 6.23381 1.43511 0.00156 MINI INTERN> 22.15281 55.93998 0.00000 11.49890 6.80013 MINI EXTERN> 92.76726 -19.72412 0.00000 0.00000 0.00000 MINI CONSTR> 154.18436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 320.38566 3.23364 2.04564 0.00161 MINI INTERN> 24.10026 53.34930 0.00000 11.66968 6.88000 MINI EXTERN> 88.12226 -19.70498 0.00000 0.00000 0.00000 MINI CONSTR> 155.96915 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 319.03395 1.35171 2.74312 0.00167 MINI INTERN> 25.42160 51.88195 0.00000 11.73249 6.93064 MINI EXTERN> 85.67646 -19.65444 0.00000 0.00000 0.00000 MINI CONSTR> 157.04525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 317.44648 1.58748 0.81146 0.00072 MINI INTERN> 19.76966 53.63192 0.00000 11.88436 6.96229 MINI EXTERN> 87.80950 -20.41719 0.00000 0.00000 0.00000 MINI CONSTR> 157.80593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 316.75349 0.69298 0.60125 0.00075 MINI INTERN> 19.92212 53.04666 0.00000 11.90107 6.98340 MINI EXTERN> 86.94325 -20.48424 0.00000 0.00000 0.00000 MINI CONSTR> 158.44123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 316.28460 0.46889 1.29627 0.00078 MINI INTERN> 18.47718 53.24419 0.00000 11.97569 6.98421 MINI EXTERN> 87.27706 -20.73956 0.00000 0.00000 0.00000 MINI CONSTR> 159.06582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9908 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 315.98713 0.29747 1.46251 0.00080 MINI INTERN> 18.29447 52.98810 0.00000 12.00740 6.97719 MINI EXTERN> 87.01711 -20.81230 0.00000 0.00000 0.00000 MINI CONSTR> 159.51515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 315.77104 0.21609 1.38017 0.00083 MINI INTERN> 18.31661 52.80795 0.00000 11.99438 6.98643 MINI EXTERN> 86.66560 -20.86041 0.00000 0.00000 0.00000 MINI CONSTR> 159.86047 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 315.47617 0.29487 0.49274 0.00036 MINI INTERN> 20.35349 51.77740 0.00000 11.88475 7.02820 MINI EXTERN> 84.88127 -20.71712 0.00000 0.00000 0.00000 MINI CONSTR> 160.26819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 315.36632 0.10986 0.39954 0.00037 MINI INTERN> 20.18549 51.72914 0.00000 11.88687 7.02308 MINI EXTERN> 84.80294 -20.77130 0.00000 0.00000 0.00000 MINI CONSTR> 160.51009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 315.31488 0.05144 0.57734 0.00039 MINI INTERN> 20.35499 51.61688 0.00000 11.86396 7.02921 MINI EXTERN> 84.51806 -20.79393 0.00000 0.00000 0.00000 MINI CONSTR> 160.72570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 315.24123 0.07365 0.17388 0.00017 MINI INTERN> 19.78059 51.67381 0.00000 11.92072 6.98651 MINI EXTERN> 84.93975 -20.86187 0.00000 0.00000 0.00000 MINI CONSTR> 160.80172 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 315.21004 0.03118 0.12239 0.00017 MINI INTERN> 19.83164 51.61901 0.00000 11.90963 6.98423 MINI EXTERN> 84.81682 -20.88046 0.00000 0.00000 0.00000 MINI CONSTR> 160.92917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 315.18820 0.02185 0.27887 0.00018 MINI INTERN> 19.66720 51.61343 0.00000 11.92329 6.96407 MINI EXTERN> 84.90630 -20.91950 0.00000 0.00000 0.00000 MINI CONSTR> 161.03342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 315.17361 0.01459 0.32624 0.00019 MINI INTERN> 19.63261 51.59374 0.00000 11.92225 6.95385 MINI EXTERN> 84.88679 -20.94244 0.00000 0.00000 0.00000 MINI CONSTR> 161.12680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 315.16210 0.01151 0.29888 0.00019 MINI INTERN> 19.65757 51.56782 0.00000 11.91504 6.94956 MINI EXTERN> 84.82940 -20.95494 0.00000 0.00000 0.00000 MINI CONSTR> 161.19765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 315.14616 0.01594 0.11003 0.00008 MINI INTERN> 19.96281 51.48019 0.00000 11.87359 6.96529 MINI EXTERN> 84.49308 -20.94616 0.00000 0.00000 0.00000 MINI CONSTR> 161.31736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 315.13927 0.00689 0.08273 0.00009 MINI INTERN> 19.94639 51.47091 0.00000 11.87160 6.95801 MINI EXTERN> 84.48056 -20.95965 0.00000 0.00000 0.00000 MINI CONSTR> 161.37144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 315.13503 0.00423 0.13412 0.00009 MINI INTERN> 20.00078 51.44795 0.00000 11.86141 6.95598 MINI EXTERN> 84.40418 -20.96709 0.00000 0.00000 0.00000 MINI CONSTR> 161.43183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 315.13086 0.00417 0.14248 0.00009 MINI INTERN> 20.01419 51.43512 0.00000 11.85613 6.95104 MINI EXTERN> 84.36946 -20.97684 0.00000 0.00000 0.00000 MINI CONSTR> 161.48177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 315.12574 0.00512 0.04044 0.00004 MINI INTERN> 19.90439 51.45455 0.00000 11.86628 6.93760 MINI EXTERN> 84.45051 -20.99278 0.00000 0.00000 0.00000 MINI CONSTR> 161.50520 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 315.12461 0.00113 0.15228 0.00010 MINI INTERN> 20.03267 51.41644 0.00000 11.84756 6.94187 MINI EXTERN> 84.31478 -20.99301 0.00000 0.00000 0.00000 MINI CONSTR> 161.56429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 315.12010 0.00451 0.05262 0.00004 MINI INTERN> 19.89862 51.44534 0.00000 11.86124 6.92678 MINI EXTERN> 84.41769 -21.00845 0.00000 0.00000 0.00000 MINI CONSTR> 161.57887 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 315.11787 0.00223 0.04055 0.00004 MINI INTERN> 19.91469 51.43697 0.00000 11.85690 6.92365 MINI EXTERN> 84.38807 -21.01337 0.00000 0.00000 0.00000 MINI CONSTR> 161.61097 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 315.11598 0.00188 0.03155 0.00005 MINI INTERN> 19.92955 51.42941 0.00000 11.85296 6.92086 MINI EXTERN> 84.36139 -21.01759 0.00000 0.00000 0.00000 MINI CONSTR> 161.63940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 315.11424 0.00174 0.07407 0.00005 MINI INTERN> 19.89703 51.43530 0.00000 11.85467 6.91359 MINI EXTERN> 84.37281 -21.02511 0.00000 0.00000 0.00000 MINI CONSTR> 161.66596 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 315.11255 0.00169 0.07678 0.00005 MINI INTERN> 19.90048 51.43183 0.00000 11.85223 6.90986 MINI EXTERN> 84.35487 -21.02940 0.00000 0.00000 0.00000 MINI CONSTR> 161.69269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 315.11104 0.00151 0.08417 0.00005 MINI INTERN> 19.90054 51.42975 0.00000 11.85032 6.90605 MINI EXTERN> 84.34016 -21.03347 0.00000 0.00000 0.00000 MINI CONSTR> 161.71769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 315.10967 0.00136 0.08033 0.00005 MINI INTERN> 19.90686 51.42541 0.00000 11.84795 6.90326 MINI EXTERN> 84.32371 -21.03643 0.00000 0.00000 0.00000 MINI CONSTR> 161.73891 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 315.10829 0.00139 0.08233 0.00006 MINI INTERN> 19.91042 51.42277 0.00000 11.84580 6.90009 MINI EXTERN> 84.30672 -21.03954 0.00000 0.00000 0.00000 MINI CONSTR> 161.76202 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 315.10654 0.00175 0.02594 0.00002 MINI INTERN> 19.96913 51.40171 0.00000 11.83655 6.90167 MINI EXTERN> 84.24719 -21.03987 0.00000 0.00000 0.00000 MINI CONSTR> 161.79015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 315.10601 0.00052 0.09032 0.00006 MINI INTERN> 19.91294 51.41849 0.00000 11.84261 6.89414 MINI EXTERN> 84.28161 -21.04469 0.00000 0.00000 0.00000 MINI CONSTR> 161.80091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 315.10488 0.00113 0.09466 0.00006 MINI INTERN> 19.91483 51.41693 0.00000 11.84094 6.89128 MINI EXTERN> 84.26677 -21.04691 0.00000 0.00000 0.00000 MINI CONSTR> 161.82104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 315.10308 0.00181 0.03117 0.00003 MINI INTERN> 19.98364 51.39134 0.00000 11.83028 6.89393 MINI EXTERN> 84.20117 -21.04667 0.00000 0.00000 0.00000 MINI CONSTR> 161.84939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 315.10218 0.00089 0.02180 0.00003 MINI INTERN> 19.97591 51.39311 0.00000 11.83023 6.89126 MINI EXTERN> 84.19762 -21.04849 0.00000 0.00000 0.00000 MINI CONSTR> 161.86254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 315.10114 0.00104 0.02167 0.00003 MINI INTERN> 19.97880 51.39054 0.00000 11.82854 6.88880 MINI EXTERN> 84.18425 -21.05022 0.00000 0.00000 0.00000 MINI CONSTR> 161.88042 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 315.10018 0.00096 0.04362 0.00003 MINI INTERN> 19.99851 51.38114 0.00000 11.82454 6.88732 MINI EXTERN> 84.15851 -21.05143 0.00000 0.00000 0.00000 MINI CONSTR> 161.90159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 315.09924 0.00094 0.02711 0.00003 MINI INTERN> 19.98896 51.38374 0.00000 11.82475 6.88453 MINI EXTERN> 84.15562 -21.05295 0.00000 0.00000 0.00000 MINI CONSTR> 161.91458 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 315.09834 0.00090 0.02952 0.00003 MINI INTERN> 19.99263 51.38077 0.00000 11.82311 6.88238 MINI EXTERN> 84.14271 -21.05404 0.00000 0.00000 0.00000 MINI CONSTR> 161.93078 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 315.09766 0.00069 0.05010 0.00003 MINI INTERN> 20.00690 51.37374 0.00000 11.82013 6.88117 MINI EXTERN> 84.12348 -21.05490 0.00000 0.00000 0.00000 MINI CONSTR> 161.94714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 315.09685 0.00080 0.05211 0.00003 MINI INTERN> 20.00911 51.37097 0.00000 11.81879 6.87910 MINI EXTERN> 84.11251 -21.05534 0.00000 0.00000 0.00000 MINI CONSTR> 161.96172 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 315.09612 0.00074 0.05787 0.00004 MINI INTERN> 20.01397 51.36852 0.00000 11.81724 6.87713 MINI EXTERN> 84.10109 -21.05770 0.00000 0.00000 0.00000 MINI CONSTR> 161.97586 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 315.09543 0.00069 0.05520 0.00004 MINI INTERN> 20.01169 51.36744 0.00000 11.81650 6.87565 MINI EXTERN> 84.09242 -21.05620 0.00000 0.00000 0.00000 MINI CONSTR> 161.98793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 315.09474 0.00068 0.05898 0.00004 MINI INTERN> 20.01363 51.36774 0.00000 11.81549 6.87367 MINI EXTERN> 84.08404 -21.06012 0.00000 0.00000 0.00000 MINI CONSTR> 162.00030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 315.09389 0.00086 0.01865 0.00002 MINI INTERN> 19.98346 51.37910 0.00000 11.81855 6.87071 MINI EXTERN> 84.09283 -21.05862 0.00000 0.00000 0.00000 MINI CONSTR> 162.00786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 315.09354 0.00035 0.06271 0.00004 MINI INTERN> 20.01824 51.36330 0.00000 11.81298 6.87126 MINI EXTERN> 84.06269 -21.05920 0.00000 0.00000 0.00000 MINI CONSTR> 162.02427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 315.09291 0.00063 0.06639 0.00004 MINI INTERN> 20.01495 51.36115 0.00000 11.81241 6.86951 MINI EXTERN> 84.05491 -21.05622 0.00000 0.00000 0.00000 MINI CONSTR> 162.03620 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 315.09198 0.00094 0.02096 0.00002 MINI INTERN> 19.98291 51.37673 0.00000 11.81606 6.86583 MINI EXTERN> 84.06724 -21.05959 0.00000 0.00000 0.00000 MINI CONSTR> 162.04279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 315.09179 0.00019 0.06905 0.00005 MINI INTERN> 20.02203 51.35850 0.00000 11.80991 6.86709 MINI EXTERN> 84.03516 -21.05934 0.00000 0.00000 0.00000 MINI CONSTR> 162.05845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 315.09077 0.00102 0.02136 0.00002 MINI INTERN> 19.98342 51.37479 0.00000 11.81434 6.86287 MINI EXTERN> 84.04993 -21.05985 0.00000 0.00000 0.00000 MINI CONSTR> 162.06527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 315.09026 0.00051 0.01655 0.00002 MINI INTERN> 19.98867 51.37144 0.00000 11.81299 6.86185 MINI EXTERN> 84.04021 -21.05987 0.00000 0.00000 0.00000 MINI CONSTR> 162.07498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 315.08968 0.00058 0.01690 0.00002 MINI INTERN> 19.98823 51.37064 0.00000 11.81223 6.86039 MINI EXTERN> 84.03196 -21.05971 0.00000 0.00000 0.00000 MINI CONSTR> 162.08594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 315.08914 0.00054 0.03189 0.00002 MINI INTERN> 19.97797 51.37502 0.00000 11.81273 6.85840 MINI EXTERN> 84.02860 -21.05997 0.00000 0.00000 0.00000 MINI CONSTR> 162.09639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 315.08859 0.00055 0.02014 0.00002 MINI INTERN> 19.98562 51.37044 0.00000 11.81102 6.85755 MINI EXTERN> 84.01720 -21.05985 0.00000 0.00000 0.00000 MINI CONSTR> 162.10660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 315.08810 0.00048 0.01630 0.00002 MINI INTERN> 19.98927 51.36763 0.00000 11.80988 6.85654 MINI EXTERN> 84.00827 -21.05948 0.00000 0.00000 0.00000 MINI CONSTR> 162.11599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 315.08762 0.00048 0.03756 0.00002 MINI INTERN> 19.97574 51.37347 0.00000 11.81083 6.85444 MINI EXTERN> 84.00655 -21.05933 0.00000 0.00000 0.00000 MINI CONSTR> 162.12591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 315.08713 0.00050 0.03822 0.00003 MINI INTERN> 19.97724 51.37297 0.00000 11.80995 6.85327 MINI EXTERN> 83.99844 -21.06044 0.00000 0.00000 0.00000 MINI CONSTR> 162.13570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 315.08669 0.00044 0.04360 0.00003 MINI INTERN> 19.97420 51.37167 0.00000 11.80955 6.85206 MINI EXTERN> 83.99176 -21.05755 0.00000 0.00000 0.00000 MINI CONSTR> 162.14501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 315.08626 0.00043 0.04437 0.00003 MINI INTERN> 19.97362 51.37170 0.00000 11.80914 6.85062 MINI EXTERN> 83.98635 -21.05840 0.00000 0.00000 0.00000 MINI CONSTR> 162.15322 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 315.08582 0.00044 0.04221 0.00003 MINI INTERN> 19.97582 51.37030 0.00000 11.80831 6.84954 MINI EXTERN> 83.97917 -21.05893 0.00000 0.00000 0.00000 MINI CONSTR> 162.16161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 315.08538 0.00044 0.04579 0.00003 MINI INTERN> 19.97374 51.36939 0.00000 11.80777 6.84849 MINI EXTERN> 83.97187 -21.05692 0.00000 0.00000 0.00000 MINI CONSTR> 162.17105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 315.08495 0.00043 0.04806 0.00003 MINI INTERN> 19.98031 51.36826 0.00000 11.80644 6.84753 MINI EXTERN> 83.96301 -21.06056 0.00000 0.00000 0.00000 MINI CONSTR> 162.17996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 315.08441 0.00054 0.01502 0.00001 MINI INTERN> 19.99605 51.35753 0.00000 11.80357 6.84779 MINI EXTERN> 83.94736 -21.05739 0.00000 0.00000 0.00000 MINI CONSTR> 162.18950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 315.08419 0.00023 0.05006 0.00003 MINI INTERN> 19.97285 51.36746 0.00000 11.80623 6.84498 MINI EXTERN> 83.95375 -21.05648 0.00000 0.00000 0.00000 MINI CONSTR> 162.19540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 315.08378 0.00041 0.05288 0.00003 MINI INTERN> 19.97582 51.36731 0.00000 11.80526 6.84403 MINI EXTERN> 83.94586 -21.05878 0.00000 0.00000 0.00000 MINI CONSTR> 162.20428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 315.08319 0.00059 0.01557 0.00001 MINI INTERN> 19.99638 51.35496 0.00000 11.80160 6.84490 MINI EXTERN> 83.92679 -21.05624 0.00000 0.00000 0.00000 MINI CONSTR> 162.21481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 315.08304 0.00015 0.05510 0.00004 MINI INTERN> 19.97140 51.36575 0.00000 11.80467 6.84174 MINI EXTERN> 83.93526 -21.05553 0.00000 0.00000 0.00000 MINI CONSTR> 162.21974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 315.08265 0.00039 0.05919 0.00004 MINI INTERN> 19.97112 51.36639 0.00000 11.80407 6.84069 MINI EXTERN> 83.92833 -21.05664 0.00000 0.00000 0.00000 MINI CONSTR> 162.22869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 315.08199 0.00066 0.02023 0.00002 MINI INTERN> 19.99906 51.35106 0.00000 11.79927 6.84219 MINI EXTERN> 83.90461 -21.05490 0.00000 0.00000 0.00000 MINI CONSTR> 162.24070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 315.08166 0.00033 0.01344 0.00002 MINI INTERN> 19.99365 51.35302 0.00000 11.79950 6.84109 MINI EXTERN> 83.90205 -21.05447 0.00000 0.00000 0.00000 MINI CONSTR> 162.24681 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 315.08126 0.00040 0.01397 0.00002 MINI INTERN> 19.99425 51.35196 0.00000 11.79876 6.84017 MINI EXTERN> 83.89478 -21.05413 0.00000 0.00000 0.00000 MINI CONSTR> 162.25546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 315.08090 0.00036 0.02676 0.00002 MINI INTERN> 20.00160 51.34740 0.00000 11.79703 6.83975 MINI EXTERN> 83.88341 -21.05356 0.00000 0.00000 0.00000 MINI CONSTR> 162.26526 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 315.08053 0.00038 0.01715 0.00002 MINI INTERN> 19.99582 51.34917 0.00000 11.79726 6.83857 MINI EXTERN> 83.88041 -21.05272 0.00000 0.00000 0.00000 MINI CONSTR> 162.27202 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 315.08017 0.00035 0.02085 0.00002 MINI INTERN> 19.99790 51.34784 0.00000 11.79637 6.83781 MINI EXTERN> 83.87286 -21.05294 0.00000 0.00000 0.00000 MINI CONSTR> 162.28032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 315.07988 0.00029 0.03082 0.00002 MINI INTERN> 20.00213 51.34467 0.00000 11.79511 6.83745 MINI EXTERN> 83.86386 -21.05194 0.00000 0.00000 0.00000 MINI CONSTR> 162.28860 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 315.07949 0.00039 0.01847 0.00002 MINI INTERN> 19.99601 51.34685 0.00000 11.79542 6.83616 MINI EXTERN> 83.86125 -21.05151 0.00000 0.00000 0.00000 MINI CONSTR> 162.29531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 315.07920 0.00029 0.03302 0.00002 MINI INTERN> 20.00240 51.34275 0.00000 11.79385 6.83586 MINI EXTERN> 83.85088 -21.05079 0.00000 0.00000 0.00000 MINI CONSTR> 162.30426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 315.07886 0.00034 0.03477 0.00002 MINI INTERN> 20.00336 51.34161 0.00000 11.79314 6.83500 MINI EXTERN> 83.84409 -21.05066 0.00000 0.00000 0.00000 MINI CONSTR> 162.31232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 315.07855 0.00031 0.03925 0.00002 MINI INTERN> 20.00289 51.33976 0.00000 11.79251 6.83428 MINI EXTERN> 83.83731 -21.04851 0.00000 0.00000 0.00000 MINI CONSTR> 162.32032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 315.07825 0.00031 0.03647 0.00002 MINI INTERN> 20.00281 51.34019 0.00000 11.79200 6.83364 MINI EXTERN> 83.83196 -21.04937 0.00000 0.00000 0.00000 MINI CONSTR> 162.32702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 315.07793 0.00032 0.03882 0.00003 MINI INTERN> 20.00316 51.33855 0.00000 11.79133 6.83286 MINI EXTERN> 83.82523 -21.04815 0.00000 0.00000 0.00000 MINI CONSTR> 162.33495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 315.07765 0.00028 0.04586 0.00003 MINI INTERN> 20.00620 51.33751 0.00000 11.79040 6.83215 MINI EXTERN> 83.81799 -21.04942 0.00000 0.00000 0.00000 MINI CONSTR> 162.34282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 315.07735 0.00030 0.04185 0.00003 MINI INTERN> 20.00355 51.33799 0.00000 11.79015 6.83160 MINI EXTERN> 83.81340 -21.04851 0.00000 0.00000 0.00000 MINI CONSTR> 162.34917 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 315.07693 0.00042 0.01333 0.00001 MINI INTERN> 19.98408 51.34625 0.00000 11.79237 6.82948 MINI EXTERN> 83.81826 -21.04715 0.00000 0.00000 0.00000 MINI CONSTR> 162.35365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 315.07680 0.00013 0.04569 0.00003 MINI INTERN> 20.00029 51.33625 0.00000 11.78929 6.83039 MINI EXTERN> 83.80215 -21.04487 0.00000 0.00000 0.00000 MINI CONSTR> 162.36332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 315.07636 0.00044 0.01429 0.00001 MINI INTERN> 19.98245 51.34537 0.00000 11.79149 6.82804 MINI EXTERN> 83.80750 -21.04598 0.00000 0.00000 0.00000 MINI CONSTR> 162.36749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 315.07626 0.00010 0.04752 0.00003 MINI INTERN> 20.00215 51.33474 0.00000 11.78790 6.82933 MINI EXTERN> 83.78970 -21.04495 0.00000 0.00000 0.00000 MINI CONSTR> 162.37739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 315.07578 0.00048 0.01513 0.00001 MINI INTERN> 19.98091 51.34449 0.00000 11.79054 6.82662 MINI EXTERN> 83.79629 -21.04485 0.00000 0.00000 0.00000 MINI CONSTR> 162.38178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 315.07553 0.00025 0.01176 0.00001 MINI INTERN> 19.98304 51.34254 0.00000 11.78973 6.82624 MINI EXTERN> 83.78999 -21.04417 0.00000 0.00000 0.00000 MINI CONSTR> 162.38816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 315.07525 0.00028 0.01233 0.00001 MINI INTERN> 19.98198 51.34230 0.00000 11.78932 6.82551 MINI EXTERN> 83.78467 -21.04370 0.00000 0.00000 0.00000 MINI CONSTR> 162.39517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 315.07497 0.00028 0.02087 0.00002 MINI INTERN> 19.97652 51.34401 0.00000 11.78949 6.82440 MINI EXTERN> 83.78124 -21.04290 0.00000 0.00000 0.00000 MINI CONSTR> 162.40222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 315.07473 0.00024 0.01151 0.00002 MINI INTERN> 19.98179 51.34080 0.00000 11.78826 6.82435 MINI EXTERN> 83.77361 -21.04259 0.00000 0.00000 0.00000 MINI CONSTR> 162.40851 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 315.07445 0.00028 0.02424 0.00002 MINI INTERN> 19.97414 51.34357 0.00000 11.78871 6.82299 MINI EXTERN> 83.77100 -21.04181 0.00000 0.00000 0.00000 MINI CONSTR> 162.41584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 315.07416 0.00028 0.01471 0.00002 MINI INTERN> 19.97799 51.34077 0.00000 11.78758 6.82281 MINI EXTERN> 83.76316 -21.04114 0.00000 0.00000 0.00000 MINI CONSTR> 162.42299 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 315.07389 0.00028 0.01664 0.00002 MINI INTERN> 19.97683 51.34079 0.00000 11.78715 6.82209 MINI EXTERN> 83.75768 -21.04092 0.00000 0.00000 0.00000 MINI CONSTR> 162.43027 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 315.07367 0.00022 0.02742 0.00002 MINI INTERN> 19.97092 51.34251 0.00000 11.78744 6.82104 MINI EXTERN> 83.75506 -21.03981 0.00000 0.00000 0.00000 MINI CONSTR> 162.43650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 315.07341 0.00026 0.02774 0.00002 MINI INTERN> 19.97067 51.34226 0.00000 11.78689 6.82046 MINI EXTERN> 83.74932 -21.03979 0.00000 0.00000 0.00000 MINI CONSTR> 162.44359 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 315.07317 0.00024 0.03245 0.00002 MINI INTERN> 19.96829 51.34120 0.00000 11.78653 6.81990 MINI EXTERN> 83.74384 -21.03726 0.00000 0.00000 0.00000 MINI CONSTR> 162.45066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 315.07294 0.00024 0.02997 0.00002 MINI INTERN> 19.96845 51.34142 0.00000 11.78613 6.81921 MINI EXTERN> 83.73946 -21.03829 0.00000 0.00000 0.00000 MINI CONSTR> 162.45655 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> 500 315.07294 0.00024 0.02997 0.00002 STPD INTERN> 19.96845 51.34142 0.00000 11.78613 6.81921 STPD EXTERN> 83.73946 -21.03829 0.00000 0.00000 0.00000 STPD CONSTR> 162.45655 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 9907 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9907 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 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> 0 315.07294 0.00024 0.02997 0.00000 MINI INTERN> 19.96845 51.34142 0.00000 11.78613 6.81921 MINI EXTERN> 83.73946 -21.03829 0.00000 0.00000 0.00000 MINI CONSTR> 162.45655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 315.05823 0.01470 0.07184 0.01115 MINI INTERN> 19.76568 51.23879 0.00000 11.73838 6.80374 MINI EXTERN> 82.98261 -20.90484 0.00000 0.00000 0.00000 MINI CONSTR> 163.43388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 315.05607 0.00216 0.04239 0.00342 MINI INTERN> 19.79038 51.21822 0.00000 11.73379 6.80363 MINI EXTERN> 82.88632 -20.89006 0.00000 0.00000 0.00000 MINI CONSTR> 163.51381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 315.05516 0.00091 0.02545 0.00142 MINI INTERN> 19.80065 51.24203 0.00000 11.71834 6.79406 MINI EXTERN> 82.95569 -20.89097 0.00000 0.00000 0.00000 MINI CONSTR> 163.43536 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 315.05489 0.00027 0.01577 0.00065 MINI INTERN> 19.81373 51.24415 0.00000 11.71483 6.79305 MINI EXTERN> 82.95144 -20.88889 0.00000 0.00000 0.00000 MINI CONSTR> 163.42659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 315.05475 0.00014 0.01130 0.00041 MINI INTERN> 19.81542 51.23951 0.00000 11.71167 6.79363 MINI EXTERN> 82.93090 -20.89190 0.00000 0.00000 0.00000 MINI CONSTR> 163.45553 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> 26 315.05473 0.00002 0.00890 0.02000 CONJ INTERN> 19.81365 51.23585 0.00000 11.71115 6.79289 CONJ EXTERN> 82.93399 -20.89375 0.00000 0.00000 0.00000 CONJ CONSTR> 163.46096 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 ALA 1 HT1 ) 15.084 ( PROT ALA 1 HT2 ) 15.084 ( PROT ALA 1 N ) 18.855 ( PROT ALA 1 HT3 ) 15.084 ( PROT ALA 1 CA ) 18.855 ( PROT ALA 1 CB ) 15.084 ( PROT ALA 1 C ) 18.855 ( PROT ALA 1 O ) 18.855 ( PROT LEU 2 N ) 18.855 ( PROT LEU 2 H ) 15.084 ( PROT LEU 2 CA ) 18.855 ( PROT LEU 2 CB ) 15.084 ( PROT LEU 2 CG ) 15.084 ( PROT LEU 2 CD1 ) 15.084 ( PROT LEU 2 CD2 ) 15.084 ( PROT LEU 2 C ) 18.855 ( PROT LEU 2 O ) 18.855 ( PROT GLN 3 N ) 18.855 ( PROT GLN 3 H ) 15.084 ( PROT GLN 3 CA ) 18.855 ( PROT GLN 3 CB ) 15.084 ( PROT GLN 3 CG ) 15.084 ( PROT GLN 3 CD ) 15.084 ( PROT GLN 3 OE1 ) 15.084 ( PROT GLN 3 NE2 ) 15.084 ( PROT GLN 3 HE21 ) 15.084 ( PROT GLN 3 HE22 ) 15.084 ( PROT GLN 3 C ) 18.855 ( PROT GLN 3 O ) 18.855 ( PROT ALA 4 N ) 18.855 ( PROT ALA 4 H ) 15.084 ( PROT ALA 4 CA ) 18.855 ( PROT ALA 4 CB ) 15.084 ( PROT ALA 4 C ) 18.855 ( PROT ALA 4 O ) 18.855 ( PROT PHE 5 N ) 18.855 ( PROT PHE 5 H ) 15.084 ( PROT PHE 5 CA ) 18.855 ( PROT PHE 5 CB ) 15.084 ( PROT PHE 5 CG ) 15.084 ( PROT PHE 5 CD1 ) 15.084 ( PROT PHE 5 CD2 ) 15.084 ( PROT PHE 5 CE1 ) 15.084 ( PROT PHE 5 CE2 ) 15.084 ( PROT PHE 5 CZ ) 15.084 ( PROT PHE 5 C ) 18.855 ( PROT PHE 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 ILE 7 N ) 18.855 ( PROT ILE 7 H ) 15.084 ( PROT ILE 7 CA ) 18.855 ( PROT ILE 7 CB ) 15.084 ( PROT ILE 7 CG2 ) 15.084 ( PROT ILE 7 CG1 ) 15.084 ( PROT ILE 7 CD ) 15.084 ( PROT ILE 7 C ) 18.855 ( PROT ILE 7 O ) 18.855 ( PROT ALA 8 N ) 18.855 ( PROT ALA 8 H ) 15.084 ( PROT ALA 8 CA ) 18.855 ( PROT ALA 8 CB ) 15.084 ( PROT ALA 8 C ) 18.855 ( PROT ALA 8 O ) 18.855 ( PROT LEU 9 N ) 18.855 ( PROT LEU 9 H ) 15.084 ( PROT LEU 9 CA ) 18.855 ( PROT LEU 9 CB ) 15.084 ( PROT LEU 9 CG ) 15.084 ( PROT LEU 9 CD1 ) 15.084 ( PROT LEU 9 CD2 ) 15.084 ( PROT LEU 9 C ) 18.855 ( PROT LEU 9 O ) 18.855 ( PROT SER 10 N ) 18.855 ( PROT SER 10 H ) 15.084 ( PROT SER 10 CA ) 18.855 ( PROT SER 10 CB ) 15.084 ( PROT SER 10 OG ) 15.084 ( PROT SER 10 HG ) 15.084 ( PROT SER 10 C ) 18.855 ( PROT SER 10 O ) 18.855 ( PROT SER 11 N ) 18.855 ( PROT SER 11 H ) 15.084 ( PROT SER 11 CA ) 18.855 ( PROT SER 11 CB ) 15.084 ( PROT SER 11 OG ) 15.084 ( PROT SER 11 HG ) 15.084 ( PROT SER 11 C ) 18.855 ( PROT SER 11 O ) 18.855 ( PROT PHE 12 N ) 18.855 ( PROT PHE 12 H ) 15.084 ( PROT PHE 12 CA ) 18.855 ( PROT PHE 12 CB ) 15.084 ( PROT PHE 12 CG ) 15.084 ( PROT PHE 12 CD1 ) 15.084 ( PROT PHE 12 CD2 ) 15.084 ( PROT PHE 12 CE1 ) 15.084 ( PROT PHE 12 CE2 ) 15.084 ( PROT PHE 12 CZ ) 15.084 ( PROT PHE 12 C ) 18.855 ( PROT PHE 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 SER 14 N ) 18.855 ( PROT SER 14 H ) 15.084 ( PROT SER 14 CA ) 18.855 ( PROT SER 14 CB ) 15.084 ( PROT SER 14 OG ) 15.084 ( PROT SER 14 HG ) 15.084 ( PROT SER 14 C ) 18.855 ( PROT SER 14 O ) 18.855 ( PROT LYS 15 N ) 18.855 ( PROT LYS 15 H ) 15.084 ( PROT LYS 15 CA ) 18.855 ( PROT LYS 15 CB ) 15.084 ( PROT LYS 15 CG ) 15.084 ( PROT LYS 15 CD ) 15.084 ( PROT LYS 15 CE ) 15.084 ( PROT LYS 15 NZ ) 15.084 ( PROT LYS 15 HZ1 ) 15.084 ( PROT LYS 15 HZ2 ) 15.084 ( PROT LYS 15 HZ3 ) 15.084 ( PROT LYS 15 C ) 18.855 ( PROT LYS 15 O ) 18.855 ( PROT LEU 16 N ) 18.855 ( PROT LEU 16 H ) 15.084 ( PROT LEU 16 CA ) 18.855 ( PROT LEU 16 CB ) 15.084 ( PROT LEU 16 CG ) 15.084 ( PROT LEU 16 CD1 ) 15.084 ( PROT LEU 16 CD2 ) 15.084 ( PROT LEU 16 C ) 18.855 ( PROT LEU 16 O ) 18.855 ( PROT ALA 17 N ) 18.855 ( PROT ALA 17 H ) 15.084 ( PROT ALA 17 CA ) 18.855 ( PROT ALA 17 CB ) 15.084 ( PROT ALA 17 C ) 18.855 ( PROT ALA 17 O ) 18.855 ( PROT CYS 18 N ) 18.855 ( PROT CYS 18 H ) 15.084 ( PROT CYS 18 CA ) 18.855 ( PROT CYS 18 CB ) 15.084 ( PROT CYS 18 SG ) 15.084 ( PROT CYS 18 C ) 18.855 ( PROT CYS 18 O ) 18.855 ( PROT GLU 19 N ) 18.855 ( PROT GLU 19 H ) 15.084 ( PROT GLU 19 CA ) 18.855 ( PROT GLU 19 CB ) 15.084 ( PROT GLU 19 CG ) 15.084 ( PROT GLU 19 CD ) 15.084 ( PROT GLU 19 OE1 ) 15.084 ( PROT GLU 19 OE2 ) 15.084 ( PROT GLU 19 C ) 18.855 ( PROT GLU 19 OT1 ) 15.084 ( PROT GLU 19 OT2 ) 15.084 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43472 4.57721 -7.53263 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS -0.00002 -0.00198 0.00000 ROTATION MATRIX 1.000000 -0.000138 -0.000168 0.000138 1.000000 0.000206 0.000168 -0.000206 1.000000 AXIS OF ROTATION IS 0.688175 0.561143 -0.459928 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 6.1164 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.190806 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1908" Parameter: A <- "0.1908" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.92358 4.26751 -7.71895 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00863 0.01276 -0.01332 ROTATION MATRIX 0.999868 0.012621 0.010260 -0.012462 0.999803 -0.015468 -0.010453 0.015338 0.999828 AXIS OF ROTATION IS -0.687623 -0.462314 0.559857 ANGLE IS 1.28 CENTER OF ROTATION 8.883865 4.080941 -7.939010 SHIFT IS -0.019289 TOTAL SQUARE DIFF IS 0.2036 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.103519 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1908" RDCMND substituted energy or value "?RMS" to " 0.1035" Parameter: A <- "0.1908 0.1035" 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 0.1908 0.1035 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 " 163.46" Parameter: H <- "163.46" 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> 0 151.59377 163.46096 5.92117 ENER INTERN> 19.81365 51.23585 0.00000 11.71115 6.79289 ENER EXTERN> 82.93399 -20.89375 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 " 151.59" Parameter: B <- "151.59" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -20.89" Parameter: C <- "-20.89" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 82.93" Parameter: C <- " 62.04" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 62.04" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 19.81" Parameter: D <- "19.81" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 51.24" Parameter: D <- " 71.05" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.71" Parameter: D <- " 82.76" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.79" Parameter: D <- " 89.55" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 89.55" 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= 151.59 GRMS= 5.92 ELEC= -20.89 VDW= 82.93 RDTITL> *EXTERNAL= 62.04 INTERNAL= 89.55 USER= 0.00 HARM= 163.46 RDTITL> *BOND= 19.81 ANGL= 51.24 DIHE= 11.71 IMPR= 6.79 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 151.59 GRMS= 5.92 ELEC= -20.89 VDW= 82.93 RDTITL> *EXTERNAL= 62.04 INTERNAL= 89.55 USER= 0.00 HARM= 163.46 RDTITL> *BOND= 19.81 ANGL= 51.24 DIHE= 11.71 IMPR= 6.79 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 151.59 GRMS= 5.92 ELEC= -20.89 VDW= 82.93 RDTITL> *EXTERNAL= 62.04 INTERNAL= 89.55 USER= 0.00 HARM= 163.46 RDTITL> *BOND= 19.81 ANGL= 51.24 DIHE= 11.71 IMPR= 6.79 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 3600 0.1908 0.1035 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "3600" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9907 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9908 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> 0 276.68998 -125.09621 2.57709 0.02000 MINI INTERN> 19.81365 51.23585 0.00000 11.71115 6.79289 MINI EXTERN> 82.93399 -20.89375 0.00000 0.00000 0.00000 MINI CONSTR> 125.09621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 261.98978 14.70020 2.04870 0.00360 MINI INTERN> 18.90345 52.25323 0.00000 13.79588 7.15850 MINI EXTERN> 52.09952 -20.22655 0.00000 0.00000 0.00000 MINI CONSTR> 138.00575 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9896 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 258.79094 3.19884 4.47008 0.00373 MINI INTERN> 15.86140 51.47215 0.00000 13.86336 7.61778 MINI EXTERN> 50.41612 -20.98565 0.00000 0.00000 0.00000 MINI CONSTR> 140.54578 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 254.65615 4.13479 1.99123 0.00161 MINI INTERN> 14.26538 48.68884 0.00000 13.95917 7.21435 MINI EXTERN> 50.52353 -21.37628 0.00000 0.00000 0.00000 MINI CONSTR> 141.38117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9894 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 253.37829 1.27786 2.64147 0.00167 MINI INTERN> 13.78229 48.51823 0.00000 13.96600 7.38962 MINI EXTERN> 48.84231 -21.50323 0.00000 0.00000 0.00000 MINI CONSTR> 142.38307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 251.77793 1.60036 0.76709 0.00072 MINI INTERN> 14.88893 46.40622 0.00000 14.16317 7.16597 MINI EXTERN> 47.54350 -21.15637 0.00000 0.00000 0.00000 MINI CONSTR> 142.76652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9892 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 250.94066 0.83728 0.62283 0.00075 MINI INTERN> 14.64522 46.10042 0.00000 14.16982 7.19021 MINI EXTERN> 46.79009 -21.21834 0.00000 0.00000 0.00000 MINI CONSTR> 143.26324 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 250.22471 0.71595 0.55927 0.00078 MINI INTERN> 14.57745 45.72053 0.00000 14.17439 7.18238 MINI EXTERN> 46.11576 -21.24191 0.00000 0.00000 0.00000 MINI CONSTR> 143.69611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9893 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 249.74353 0.48118 1.20717 0.00080 MINI INTERN> 14.41242 45.34365 0.00000 14.21767 7.08015 MINI EXTERN> 45.93664 -21.26068 0.00000 0.00000 0.00000 MINI CONSTR> 144.01369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 249.37635 0.36718 1.32770 0.00083 MINI INTERN> 14.25943 45.20000 0.00000 14.19635 7.05356 MINI EXTERN> 45.67357 -21.30427 0.00000 0.00000 0.00000 MINI CONSTR> 144.29771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9892 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 249.09735 0.27900 1.27040 0.00087 MINI INTERN> 14.24631 45.04876 0.00000 14.18205 7.04154 MINI EXTERN> 45.36768 -21.29804 0.00000 0.00000 0.00000 MINI CONSTR> 144.50906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 248.87140 0.22595 1.30831 0.00090 MINI INTERN> 14.50525 44.75338 0.00000 14.14153 7.01612 MINI EXTERN> 44.99754 -21.26738 0.00000 0.00000 0.00000 MINI CONSTR> 144.72497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9888 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 248.55020 0.32121 0.46421 0.00039 MINI INTERN> 14.19367 45.06956 0.00000 14.06376 7.15788 MINI EXTERN> 44.36417 -21.32654 0.00000 0.00000 0.00000 MINI CONSTR> 145.02769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 248.41018 0.14002 0.35567 0.00040 MINI INTERN> 14.16824 44.96479 0.00000 14.04394 7.12756 MINI EXTERN> 44.24327 -21.31892 0.00000 0.00000 0.00000 MINI CONSTR> 145.18130 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9888 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 248.32218 0.08800 0.57330 0.00042 MINI INTERN> 14.03854 45.01691 0.00000 14.02577 7.12899 MINI EXTERN> 44.09435 -21.32947 0.00000 0.00000 0.00000 MINI CONSTR> 145.34709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 248.25346 0.06872 0.74881 0.00043 MINI INTERN> 13.87693 45.02360 0.00000 14.00968 7.11223 MINI EXTERN> 44.02901 -21.29506 0.00000 0.00000 0.00000 MINI CONSTR> 145.49708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9888 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 248.19040 0.06307 0.67552 0.00045 MINI INTERN> 13.88510 44.96818 0.00000 13.98810 7.09647 MINI EXTERN> 43.94154 -21.29134 0.00000 0.00000 0.00000 MINI CONSTR> 145.60235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 248.10623 0.08416 0.22246 0.00019 MINI INTERN> 14.39411 44.52185 0.00000 13.94476 7.02999 MINI EXTERN> 43.78606 -21.24914 0.00000 0.00000 0.00000 MINI CONSTR> 145.67861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9888 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 248.06700 0.03924 0.14388 0.00020 MINI INTERN> 14.32147 44.54665 0.00000 13.93232 7.02633 MINI EXTERN> 43.71451 -21.24792 0.00000 0.00000 0.00000 MINI CONSTR> 145.77364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 248.03600 0.03099 0.31808 0.00021 MINI INTERN> 14.47197 44.40586 0.00000 13.90596 6.99958 MINI EXTERN> 43.60620 -21.22839 0.00000 0.00000 0.00000 MINI CONSTR> 145.87483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9888 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 248.01012 0.02589 0.33773 0.00022 MINI INTERN> 14.50977 44.34437 0.00000 13.88883 6.98500 MINI EXTERN> 43.52889 -21.20711 0.00000 0.00000 0.00000 MINI CONSTR> 145.96037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 247.98735 0.02277 0.33967 0.00022 MINI INTERN> 14.41438 44.35460 0.00000 13.87599 6.97915 MINI EXTERN> 43.49363 -21.17452 0.00000 0.00000 0.00000 MINI CONSTR> 146.04412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9888 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 247.95984 0.02751 0.09839 0.00010 MINI INTERN> 14.23846 44.48189 0.00000 13.87195 6.98802 MINI EXTERN> 43.45578 -21.19888 0.00000 0.00000 0.00000 MINI CONSTR> 146.12263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 247.95060 0.00924 0.34878 0.00024 MINI INTERN> 14.47010 44.26598 0.00000 13.84511 6.95372 MINI EXTERN> 43.36737 -21.14697 0.00000 0.00000 0.00000 MINI CONSTR> 146.19529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 247.92575 0.02485 0.12180 0.00010 MINI INTERN> 14.19545 44.46402 0.00000 13.84596 6.97170 MINI EXTERN> 43.34481 -21.17211 0.00000 0.00000 0.00000 MINI CONSTR> 146.27592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 247.91359 0.01216 0.08654 0.00011 MINI INTERN> 14.22549 44.42281 0.00000 13.83356 6.96106 MINI EXTERN> 43.30001 -21.15956 0.00000 0.00000 0.00000 MINI CONSTR> 146.33022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 247.90113 0.01247 0.15003 0.00011 MINI INTERN> 14.16423 44.44537 0.00000 13.82341 6.95683 MINI EXTERN> 43.25194 -21.14633 0.00000 0.00000 0.00000 MINI CONSTR> 146.40568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 247.89051 0.01062 0.12774 0.00012 MINI INTERN> 14.17542 44.42209 0.00000 13.81220 6.94823 MINI EXTERN> 43.20896 -21.13705 0.00000 0.00000 0.00000 MINI CONSTR> 146.46065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 247.88165 0.00887 0.16886 0.00012 MINI INTERN> 14.14299 44.42861 0.00000 13.80330 6.94330 MINI EXTERN> 43.16714 -21.12445 0.00000 0.00000 0.00000 MINI CONSTR> 146.52076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 247.87375 0.00790 0.21301 0.00012 MINI INTERN> 14.15643 44.41305 0.00000 13.79178 6.93433 MINI EXTERN> 43.12889 -21.12568 0.00000 0.00000 0.00000 MINI CONSTR> 146.57495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 247.86598 0.00778 0.19186 0.00013 MINI INTERN> 14.14506 44.40445 0.00000 13.78390 6.92858 MINI EXTERN> 43.09583 -21.11267 0.00000 0.00000 0.00000 MINI CONSTR> 146.62082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 247.85660 0.00938 0.06056 0.00006 MINI INTERN> 14.25485 44.29335 0.00000 13.77062 6.91167 MINI EXTERN> 43.04863 -21.07973 0.00000 0.00000 0.00000 MINI CONSTR> 146.65722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 247.85384 0.00276 0.23674 0.00014 MINI INTERN> 14.18550 44.35412 0.00000 13.76576 6.91288 MINI EXTERN> 43.02241 -21.09416 0.00000 0.00000 0.00000 MINI CONSTR> 146.70732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 247.84795 0.00590 0.23661 0.00014 MINI INTERN> 14.15537 44.36394 0.00000 13.75973 6.90948 MINI EXTERN> 42.99303 -21.08472 0.00000 0.00000 0.00000 MINI CONSTR> 146.75110 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 247.84185 0.00610 0.21267 0.00015 MINI INTERN> 14.09827 44.38188 0.00000 13.75561 6.90802 MINI EXTERN> 42.96584 -21.06278 0.00000 0.00000 0.00000 MINI CONSTR> 146.79500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 247.83230 0.00955 0.07271 0.00006 MINI INTERN> 14.26840 44.23127 0.00000 13.73887 6.88519 MINI EXTERN> 42.91737 -21.03607 0.00000 0.00000 0.00000 MINI CONSTR> 146.82726 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 247.82768 0.00462 0.05376 0.00007 MINI INTERN> 14.24595 44.23794 0.00000 13.73434 6.88229 MINI EXTERN> 42.89480 -21.02842 0.00000 0.00000 0.00000 MINI CONSTR> 146.86077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 247.82295 0.00473 0.09233 0.00007 MINI INTERN> 14.28251 44.19857 0.00000 13.72530 6.87286 MINI EXTERN> 42.86076 -21.01588 0.00000 0.00000 0.00000 MINI CONSTR> 146.89883 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 247.81836 0.00459 0.08011 0.00007 MINI INTERN> 14.25890 44.20336 0.00000 13.72082 6.86965 MINI EXTERN> 42.83726 -21.00497 0.00000 0.00000 0.00000 MINI CONSTR> 146.93335 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 247.81476 0.00360 0.10692 0.00007 MINI INTERN> 14.28102 44.17613 0.00000 13.71412 6.86259 MINI EXTERN> 42.81062 -20.99386 0.00000 0.00000 0.00000 MINI CONSTR> 146.96414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 247.81100 0.00376 0.11360 0.00008 MINI INTERN> 14.29234 44.16393 0.00000 13.70803 6.85703 MINI EXTERN> 42.78643 -20.99122 0.00000 0.00000 0.00000 MINI CONSTR> 146.99447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 247.80746 0.00354 0.12293 0.00008 MINI INTERN> 14.28656 44.15289 0.00000 13.70340 6.85238 MINI EXTERN> 42.76345 -20.97593 0.00000 0.00000 0.00000 MINI CONSTR> 147.02472 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 247.80400 0.00346 0.12120 0.00008 MINI INTERN> 14.29586 44.14013 0.00000 13.69803 6.84713 MINI EXTERN> 42.74120 -20.97088 0.00000 0.00000 0.00000 MINI CONSTR> 147.05253 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 247.80073 0.00327 0.14126 0.00009 MINI INTERN> 14.29936 44.13567 0.00000 13.69258 6.84240 MINI EXTERN> 42.71841 -20.97014 0.00000 0.00000 0.00000 MINI CONSTR> 147.08244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 247.79737 0.00336 0.12363 0.00009 MINI INTERN> 14.29536 44.12448 0.00000 13.68871 6.83816 MINI EXTERN> 42.69875 -20.95614 0.00000 0.00000 0.00000 MINI CONSTR> 147.10803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 247.79288 0.00449 0.04080 0.00004 MINI INTERN> 14.20335 44.19163 0.00000 13.68910 6.84235 MINI EXTERN> 42.68815 -20.96063 0.00000 0.00000 0.00000 MINI CONSTR> 147.13893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 247.79167 0.00121 0.15585 0.00010 MINI INTERN> 14.26784 44.12383 0.00000 13.68155 6.83144 MINI EXTERN> 42.66018 -20.93586 0.00000 0.00000 0.00000 MINI CONSTR> 147.16269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 247.78883 0.00284 0.14782 0.00010 MINI INTERN> 14.30371 44.10169 0.00000 13.67531 6.82481 MINI EXTERN> 42.63929 -20.94127 0.00000 0.00000 0.00000 MINI CONSTR> 147.18530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 247.78444 0.00439 0.04829 0.00004 MINI INTERN> 14.18843 44.18248 0.00000 13.67785 6.83127 MINI EXTERN> 42.63366 -20.94243 0.00000 0.00000 0.00000 MINI CONSTR> 147.21317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 247.78379 0.00066 0.15063 0.00011 MINI INTERN> 14.30842 44.08320 0.00000 13.66769 6.81648 MINI EXTERN> 42.60383 -20.92666 0.00000 0.00000 0.00000 MINI CONSTR> 147.23082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 247.77940 0.00439 0.05980 0.00005 MINI INTERN> 14.17986 44.17823 0.00000 13.67086 6.82421 MINI EXTERN> 42.59988 -20.93320 0.00000 0.00000 0.00000 MINI CONSTR> 147.25956 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 247.77712 0.00228 0.04949 0.00005 MINI INTERN> 14.18327 44.16872 0.00000 13.66753 6.82033 MINI EXTERN> 42.58436 -20.92632 0.00000 0.00000 0.00000 MINI CONSTR> 147.27922 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 247.77478 0.00234 0.05217 0.00005 MINI INTERN> 14.18301 44.16069 0.00000 13.66417 6.81640 MINI EXTERN> 42.56776 -20.91818 0.00000 0.00000 0.00000 MINI CONSTR> 147.30093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 247.77283 0.00195 0.07109 0.00005 MINI INTERN> 14.16314 44.17259 0.00000 13.66200 6.81471 MINI EXTERN> 42.55469 -20.91650 0.00000 0.00000 0.00000 MINI CONSTR> 147.32222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 247.77060 0.00223 0.06155 0.00005 MINI INTERN> 14.17972 44.15694 0.00000 13.65793 6.80982 MINI EXTERN> 42.53857 -20.91341 0.00000 0.00000 0.00000 MINI CONSTR> 147.34102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 247.76899 0.00161 0.08390 0.00006 MINI INTERN> 14.16890 44.16245 0.00000 13.65565 6.80764 MINI EXTERN> 42.52638 -20.91167 0.00000 0.00000 0.00000 MINI CONSTR> 147.35964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 247.76708 0.00190 0.08062 0.00006 MINI INTERN> 14.15370 44.16432 0.00000 13.65373 6.80536 MINI EXTERN> 42.51362 -20.90248 0.00000 0.00000 0.00000 MINI CONSTR> 147.37884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 247.76545 0.00164 0.10024 0.00006 MINI INTERN> 14.16252 44.15920 0.00000 13.65028 6.80160 MINI EXTERN> 42.49947 -20.90448 0.00000 0.00000 0.00000 MINI CONSTR> 147.39686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 247.76362 0.00183 0.08728 0.00006 MINI INTERN> 14.15323 44.15951 0.00000 13.64826 6.79920 MINI EXTERN> 42.48778 -20.89832 0.00000 0.00000 0.00000 MINI CONSTR> 147.41395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 247.76144 0.00217 0.03084 0.00003 MINI INTERN> 14.20988 44.10638 0.00000 13.64291 6.79093 MINI EXTERN> 42.46997 -20.88542 0.00000 0.00000 0.00000 MINI CONSTR> 147.42679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 247.76053 0.00091 0.10263 0.00007 MINI INTERN> 14.14790 44.14773 0.00000 13.64359 6.79302 MINI EXTERN> 42.46311 -20.88247 0.00000 0.00000 0.00000 MINI CONSTR> 147.44765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 247.75918 0.00134 0.11764 0.00007 MINI INTERN> 14.17133 44.13743 0.00000 13.63967 6.78868 MINI EXTERN> 42.45012 -20.89032 0.00000 0.00000 0.00000 MINI CONSTR> 147.46227 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 247.75771 0.00147 0.11770 0.00007 MINI INTERN> 14.15954 44.14230 0.00000 13.63790 6.78671 MINI EXTERN> 42.43967 -20.88710 0.00000 0.00000 0.00000 MINI CONSTR> 147.47869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 247.75611 0.00160 0.10468 0.00007 MINI INTERN> 14.13126 44.15434 0.00000 13.63713 6.78584 MINI EXTERN> 42.43031 -20.87882 0.00000 0.00000 0.00000 MINI CONSTR> 147.49605 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 247.75359 0.00252 0.03217 0.00003 MINI INTERN> 14.21012 44.08484 0.00000 13.63043 6.77542 MINI EXTERN> 42.40965 -20.86584 0.00000 0.00000 0.00000 MINI CONSTR> 147.50898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 247.75224 0.00135 0.02594 0.00003 MINI INTERN> 14.20117 44.08830 0.00000 13.62875 6.77348 MINI EXTERN> 42.40009 -20.86331 0.00000 0.00000 0.00000 MINI CONSTR> 147.52375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 247.75081 0.00142 0.02793 0.00003 MINI INTERN> 14.20475 44.08153 0.00000 13.62618 6.77011 MINI EXTERN> 42.38824 -20.85944 0.00000 0.00000 0.00000 MINI CONSTR> 147.53944 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 247.74942 0.00139 0.04472 0.00004 MINI INTERN> 14.21919 44.06639 0.00000 13.62283 6.76552 MINI EXTERN> 42.37489 -20.85511 0.00000 0.00000 0.00000 MINI CONSTR> 147.55572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 247.74820 0.00123 0.04061 0.00004 MINI INTERN> 14.21449 44.06533 0.00000 13.62110 6.76324 MINI EXTERN> 42.36520 -20.85079 0.00000 0.00000 0.00000 MINI CONSTR> 147.56963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 247.74703 0.00117 0.04356 0.00004 MINI INTERN> 14.21840 44.05986 0.00000 13.61881 6.76025 MINI EXTERN> 42.35503 -20.84859 0.00000 0.00000 0.00000 MINI CONSTR> 147.58327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 247.74581 0.00122 0.04367 0.00004 MINI INTERN> 14.21355 44.05869 0.00000 13.61698 6.75781 MINI EXTERN> 42.34519 -20.84418 0.00000 0.00000 0.00000 MINI CONSTR> 147.59777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 247.74483 0.00098 0.05628 0.00004 MINI INTERN> 14.22707 44.04581 0.00000 13.61427 6.75405 MINI EXTERN> 42.33449 -20.84131 0.00000 0.00000 0.00000 MINI CONSTR> 147.61044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 247.74348 0.00135 0.03623 0.00004 MINI INTERN> 14.21106 44.05609 0.00000 13.61295 6.75270 MINI EXTERN> 42.32640 -20.84107 0.00000 0.00000 0.00000 MINI CONSTR> 147.62535 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 247.74259 0.00089 0.06081 0.00004 MINI INTERN> 14.22713 44.03810 0.00000 13.61012 6.74842 MINI EXTERN> 42.31473 -20.83441 0.00000 0.00000 0.00000 MINI CONSTR> 147.63850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 247.74173 0.00086 0.07989 0.00005 MINI INTERN> 14.22838 44.03979 0.00000 13.60799 6.74605 MINI EXTERN> 42.30599 -20.83796 0.00000 0.00000 0.00000 MINI CONSTR> 147.65149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 247.74079 0.00094 0.07597 0.00005 MINI INTERN> 14.22558 44.03925 0.00000 13.60647 6.74405 MINI EXTERN> 42.29840 -20.83587 0.00000 0.00000 0.00000 MINI CONSTR> 147.66292 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 247.73987 0.00092 0.07642 0.00005 MINI INTERN> 14.22190 44.03134 0.00000 13.60505 6.74149 MINI EXTERN> 42.28951 -20.82476 0.00000 0.00000 0.00000 MINI CONSTR> 147.67534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 247.73909 0.00078 0.08705 0.00005 MINI INTERN> 14.22169 44.03849 0.00000 13.60310 6.73973 MINI EXTERN> 42.28261 -20.83339 0.00000 0.00000 0.00000 MINI CONSTR> 147.68686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 247.73821 0.00087 0.08577 0.00005 MINI INTERN> 14.23017 44.02801 0.00000 13.60093 6.73655 MINI EXTERN> 42.27354 -20.82925 0.00000 0.00000 0.00000 MINI CONSTR> 147.69827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 247.73733 0.00088 0.08166 0.00005 MINI INTERN> 14.23356 44.01495 0.00000 13.59919 6.73344 MINI EXTERN> 42.26426 -20.81808 0.00000 0.00000 0.00000 MINI CONSTR> 147.71002 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 247.73597 0.00136 0.02656 0.00002 MINI INTERN> 14.17805 44.06071 0.00000 13.60033 6.73636 MINI EXTERN> 42.26289 -20.82590 0.00000 0.00000 0.00000 MINI CONSTR> 147.72354 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 247.73573 0.00025 0.08277 0.00006 MINI INTERN> 14.23951 44.00633 0.00000 13.59548 6.72839 MINI EXTERN> 42.24830 -20.81476 0.00000 0.00000 0.00000 MINI CONSTR> 147.73249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 247.73433 0.00139 0.03205 0.00003 MINI INTERN> 14.17311 44.05900 0.00000 13.59711 6.73202 MINI EXTERN> 42.24749 -20.82162 0.00000 0.00000 0.00000 MINI CONSTR> 147.74722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 247.73359 0.00075 0.02735 0.00003 MINI INTERN> 14.17657 44.05482 0.00000 13.59537 6.72965 MINI EXTERN> 42.24027 -20.82049 0.00000 0.00000 0.00000 MINI CONSTR> 147.75739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 247.73287 0.00072 0.02092 0.00003 MINI INTERN> 14.18313 44.04671 0.00000 13.59356 6.72699 MINI EXTERN> 42.23287 -20.81743 0.00000 0.00000 0.00000 MINI CONSTR> 147.76704 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 247.73217 0.00071 0.04006 0.00003 MINI INTERN> 14.16706 44.05684 0.00000 13.59260 6.72596 MINI EXTERN> 42.22649 -20.81663 0.00000 0.00000 0.00000 MINI CONSTR> 147.77985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 247.73144 0.00073 0.03123 0.00003 MINI INTERN> 14.17241 44.05127 0.00000 13.59080 6.72348 MINI EXTERN> 42.21939 -20.81550 0.00000 0.00000 0.00000 MINI CONSTR> 147.78959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 247.73070 0.00074 0.03165 0.00003 MINI INTERN> 14.17435 44.04836 0.00000 13.58900 6.72107 MINI EXTERN> 42.21188 -20.81467 0.00000 0.00000 0.00000 MINI CONSTR> 147.80071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 247.73011 0.00059 0.04396 0.00003 MINI INTERN> 14.16314 44.05398 0.00000 13.58804 6.71984 MINI EXTERN> 42.20601 -20.81266 0.00000 0.00000 0.00000 MINI CONSTR> 147.81176 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 247.72953 0.00059 0.05596 0.00003 MINI INTERN> 14.16959 44.05046 0.00000 13.58604 6.71733 MINI EXTERN> 42.19893 -20.81470 0.00000 0.00000 0.00000 MINI CONSTR> 147.82188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 247.72890 0.00063 0.05021 0.00003 MINI INTERN> 14.16639 44.05026 0.00000 13.58481 6.71563 MINI EXTERN> 42.19305 -20.81269 0.00000 0.00000 0.00000 MINI CONSTR> 147.83144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 247.72830 0.00060 0.05172 0.00004 MINI INTERN> 14.16215 44.04749 0.00000 13.58366 6.71374 MINI EXTERN> 42.18665 -20.80693 0.00000 0.00000 0.00000 MINI CONSTR> 147.84153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 247.72770 0.00060 0.05095 0.00004 MINI INTERN> 14.16271 44.04899 0.00000 13.58206 6.71190 MINI EXTERN> 42.18073 -20.80988 0.00000 0.00000 0.00000 MINI CONSTR> 147.85119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 247.72696 0.00074 0.01782 0.00002 MINI INTERN> 14.19410 44.01951 0.00000 13.57918 6.70719 MINI EXTERN> 42.17166 -20.80310 0.00000 0.00000 0.00000 MINI CONSTR> 147.85844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 247.72666 0.00031 0.06205 0.00004 MINI INTERN> 14.16637 44.04417 0.00000 13.57896 6.70777 MINI EXTERN> 42.16841 -20.80899 0.00000 0.00000 0.00000 MINI CONSTR> 147.86996 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 247.72615 0.00051 0.06699 0.00004 MINI INTERN> 14.16151 44.03917 0.00000 13.57797 6.70587 MINI EXTERN> 42.16219 -20.80022 0.00000 0.00000 0.00000 MINI CONSTR> 147.87966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 247.72557 0.00058 0.05984 0.00004 MINI INTERN> 14.15379 44.04844 0.00000 13.57680 6.70485 MINI EXTERN> 42.15749 -20.80526 0.00000 0.00000 0.00000 MINI CONSTR> 147.88946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 247.72509 0.00048 0.07261 0.00004 MINI INTERN> 14.15945 44.03697 0.00000 13.57511 6.70201 MINI EXTERN> 42.14999 -20.79777 0.00000 0.00000 0.00000 MINI CONSTR> 147.89933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 247.72453 0.00056 0.06469 0.00005 MINI INTERN> 14.14969 44.04730 0.00000 13.57407 6.70117 MINI EXTERN> 42.14557 -20.80235 0.00000 0.00000 0.00000 MINI CONSTR> 147.90907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 247.72362 0.00091 0.02130 0.00002 MINI INTERN> 14.19999 44.00413 0.00000 13.57000 6.69465 MINI EXTERN> 42.13427 -20.79588 0.00000 0.00000 0.00000 MINI CONSTR> 147.91645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 247.72316 0.00046 0.01697 0.00002 MINI INTERN> 14.19521 44.00623 0.00000 13.56902 6.69339 MINI EXTERN> 42.12971 -20.79514 0.00000 0.00000 0.00000 MINI CONSTR> 147.92475 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> 500 247.72316 0.00046 0.01697 0.00002 STPD INTERN> 14.19521 44.00623 0.00000 13.56902 6.69339 STPD EXTERN> 42.12971 -20.79514 0.00000 0.00000 0.00000 STPD CONSTR> 147.92475 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 9889 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9889 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> 0 247.72316 0.00046 0.01697 0.00000 MINI INTERN> 14.19521 44.00623 0.00000 13.56902 6.69339 MINI EXTERN> 42.12971 -20.79514 0.00000 0.00000 0.00000 MINI CONSTR> 147.92475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 247.70035 0.02280 0.04853 0.00353 MINI INTERN> 14.11934 43.75589 0.00000 13.45608 6.54025 MINI EXTERN> 41.53191 -20.63699 0.00000 0.00000 0.00000 MINI CONSTR> 148.93388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 247.69467 0.00568 0.07983 0.00996 MINI INTERN> 14.23910 43.90329 0.00000 13.38346 6.44937 MINI EXTERN> 41.59496 -20.67419 0.00000 0.00000 0.00000 MINI CONSTR> 148.79868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 247.65199 0.04268 0.35734 0.12049 MINI INTERN> 14.23905 43.85300 0.00000 13.07420 6.11937 MINI EXTERN> 40.32555 -20.32001 0.00000 0.00000 0.00000 MINI CONSTR> 150.36082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 247.63277 0.01922 0.37129 0.02363 MINI INTERN> 13.74749 43.36491 0.00000 12.92916 6.06517 MINI EXTERN> 39.26983 -19.82953 0.00000 0.00000 0.00000 MINI CONSTR> 152.08573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 247.62225 0.01052 0.34225 0.01420 MINI INTERN> 13.40547 42.88563 0.00000 12.86912 6.07388 MINI EXTERN> 38.72459 -19.56944 0.00000 0.00000 0.00000 MINI CONSTR> 153.23300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 247.61464 0.00761 0.28876 0.01050 MINI INTERN> 13.22372 42.59524 0.00000 12.85300 6.11191 MINI EXTERN> 38.08765 -19.37053 0.00000 0.00000 0.00000 MINI CONSTR> 154.11365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 247.60945 0.00519 0.26804 0.00762 MINI INTERN> 13.16185 42.51567 0.00000 12.84759 6.14494 MINI EXTERN> 37.53772 -19.25127 0.00000 0.00000 0.00000 MINI CONSTR> 154.65296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 247.60430 0.00514 0.27532 0.00790 MINI INTERN> 13.14618 42.47366 0.00000 12.82617 6.15428 MINI EXTERN> 37.19283 -19.19279 0.00000 0.00000 0.00000 MINI CONSTR> 155.00396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 247.59854 0.00576 0.29135 0.00908 MINI INTERN> 13.09969 42.43182 0.00000 12.77065 6.14728 MINI EXTERN> 37.13772 -19.15278 0.00000 0.00000 0.00000 MINI CONSTR> 155.16416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 247.59288 0.00566 0.27840 0.00848 MINI INTERN> 12.96789 42.49364 0.00000 12.68720 6.15245 MINI EXTERN> 37.24465 -19.11791 0.00000 0.00000 0.00000 MINI CONSTR> 155.16496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 247.58756 0.00532 0.28594 0.00831 MINI INTERN> 12.89567 42.62250 0.00000 12.60239 6.16909 MINI EXTERN> 37.30249 -19.06816 0.00000 0.00000 0.00000 MINI CONSTR> 155.06358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 247.58246 0.00510 0.27321 0.00765 MINI INTERN> 12.95995 42.73921 0.00000 12.53809 6.18320 MINI EXTERN> 37.23207 -18.97863 0.00000 0.00000 0.00000 MINI CONSTR> 154.90855 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 247.57770 0.00476 0.26945 0.00742 MINI INTERN> 13.04601 42.85913 0.00000 12.49160 6.18502 MINI EXTERN> 37.19727 -18.90921 0.00000 0.00000 0.00000 MINI CONSTR> 154.70788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 247.57340 0.00430 0.26341 0.00659 MINI INTERN> 13.09783 42.90985 0.00000 12.44671 6.17701 MINI EXTERN> 37.37620 -18.89803 0.00000 0.00000 0.00000 MINI CONSTR> 154.46383 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 247.56894 0.00446 0.26671 0.00707 MINI INTERN> 13.16299 42.82966 0.00000 12.39101 6.17141 MINI EXTERN> 37.74328 -18.90153 0.00000 0.00000 0.00000 MINI CONSTR> 154.17212 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 247.56446 0.00448 0.27690 0.00717 MINI INTERN> 13.19189 42.76995 0.00000 12.33296 6.17922 MINI EXTERN> 38.05825 -18.90004 0.00000 0.00000 0.00000 MINI CONSTR> 153.93223 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 247.55967 0.00479 0.28060 0.00762 MINI INTERN> 13.19794 42.84325 0.00000 12.28389 6.18771 MINI EXTERN> 38.12634 -18.89270 0.00000 0.00000 0.00000 MINI CONSTR> 153.81323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 247.55485 0.00482 0.28750 0.00771 MINI INTERN> 13.28606 42.95344 0.00000 12.25803 6.17609 MINI EXTERN> 37.89531 -18.85956 0.00000 0.00000 0.00000 MINI CONSTR> 153.84548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 247.54948 0.00537 0.30954 0.00887 MINI INTERN> 13.38586 43.04227 0.00000 12.25062 6.14608 MINI EXTERN> 37.57016 -18.84642 0.00000 0.00000 0.00000 MINI CONSTR> 154.00091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 247.54347 0.00601 0.32541 0.00980 MINI INTERN> 13.33646 43.08523 0.00000 12.25981 6.10971 MINI EXTERN> 37.44324 -18.93019 0.00000 0.00000 0.00000 MINI CONSTR> 154.23920 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> 100 247.54347 0.00601 0.32541 0.02000 CONJ INTERN> 13.33646 43.08523 0.00000 12.25981 6.10971 CONJ EXTERN> 37.44324 -18.93019 0.00000 0.00000 0.00000 CONJ CONSTR> 154.23920 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 ALA 1 HT1 ) 9.8045 ( PROT ALA 1 HT2 ) 9.8045 ( PROT ALA 1 N ) 12.256 ( PROT ALA 1 HT3 ) 9.8045 ( PROT ALA 1 CA ) 12.256 ( PROT ALA 1 CB ) 9.8045 ( PROT ALA 1 C ) 12.256 ( PROT ALA 1 O ) 12.256 ( PROT LEU 2 N ) 12.256 ( PROT LEU 2 H ) 9.8045 ( PROT LEU 2 CA ) 12.256 ( PROT LEU 2 CB ) 9.8045 ( PROT LEU 2 CG ) 9.8045 ( PROT LEU 2 CD1 ) 9.8045 ( PROT LEU 2 CD2 ) 9.8045 ( PROT LEU 2 C ) 12.256 ( PROT LEU 2 O ) 12.256 ( PROT GLN 3 N ) 12.256 ( PROT GLN 3 H ) 9.8045 ( PROT GLN 3 CA ) 12.256 ( PROT GLN 3 CB ) 9.8045 ( PROT GLN 3 CG ) 9.8045 ( PROT GLN 3 CD ) 9.8045 ( PROT GLN 3 OE1 ) 9.8045 ( PROT GLN 3 NE2 ) 9.8045 ( PROT GLN 3 HE21 ) 9.8045 ( PROT GLN 3 HE22 ) 9.8045 ( PROT GLN 3 C ) 12.256 ( PROT GLN 3 O ) 12.256 ( PROT ALA 4 N ) 12.256 ( PROT ALA 4 H ) 9.8045 ( PROT ALA 4 CA ) 12.256 ( PROT ALA 4 CB ) 9.8045 ( PROT ALA 4 C ) 12.256 ( PROT ALA 4 O ) 12.256 ( PROT PHE 5 N ) 12.256 ( PROT PHE 5 H ) 9.8045 ( PROT PHE 5 CA ) 12.256 ( PROT PHE 5 CB ) 9.8045 ( PROT PHE 5 CG ) 9.8045 ( PROT PHE 5 CD1 ) 9.8045 ( PROT PHE 5 CD2 ) 9.8045 ( PROT PHE 5 CE1 ) 9.8045 ( PROT PHE 5 CE2 ) 9.8045 ( PROT PHE 5 CZ ) 9.8045 ( PROT PHE 5 C ) 12.256 ( PROT PHE 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 ILE 7 N ) 12.256 ( PROT ILE 7 H ) 9.8045 ( PROT ILE 7 CA ) 12.256 ( PROT ILE 7 CB ) 9.8045 ( PROT ILE 7 CG2 ) 9.8045 ( PROT ILE 7 CG1 ) 9.8045 ( PROT ILE 7 CD ) 9.8045 ( PROT ILE 7 C ) 12.256 ( PROT ILE 7 O ) 12.256 ( PROT ALA 8 N ) 12.256 ( PROT ALA 8 H ) 9.8045 ( PROT ALA 8 CA ) 12.256 ( PROT ALA 8 CB ) 9.8045 ( PROT ALA 8 C ) 12.256 ( PROT ALA 8 O ) 12.256 ( PROT LEU 9 N ) 12.256 ( PROT LEU 9 H ) 9.8045 ( PROT LEU 9 CA ) 12.256 ( PROT LEU 9 CB ) 9.8045 ( PROT LEU 9 CG ) 9.8045 ( PROT LEU 9 CD1 ) 9.8045 ( PROT LEU 9 CD2 ) 9.8045 ( PROT LEU 9 C ) 12.256 ( PROT LEU 9 O ) 12.256 ( PROT SER 10 N ) 12.256 ( PROT SER 10 H ) 9.8045 ( PROT SER 10 CA ) 12.256 ( PROT SER 10 CB ) 9.8045 ( PROT SER 10 OG ) 9.8045 ( PROT SER 10 HG ) 9.8045 ( PROT SER 10 C ) 12.256 ( PROT SER 10 O ) 12.256 ( PROT SER 11 N ) 12.256 ( PROT SER 11 H ) 9.8045 ( PROT SER 11 CA ) 12.256 ( PROT SER 11 CB ) 9.8045 ( PROT SER 11 OG ) 9.8045 ( PROT SER 11 HG ) 9.8045 ( PROT SER 11 C ) 12.256 ( PROT SER 11 O ) 12.256 ( PROT PHE 12 N ) 12.256 ( PROT PHE 12 H ) 9.8045 ( PROT PHE 12 CA ) 12.256 ( PROT PHE 12 CB ) 9.8045 ( PROT PHE 12 CG ) 9.8045 ( PROT PHE 12 CD1 ) 9.8045 ( PROT PHE 12 CD2 ) 9.8045 ( PROT PHE 12 CE1 ) 9.8045 ( PROT PHE 12 CE2 ) 9.8045 ( PROT PHE 12 CZ ) 9.8045 ( PROT PHE 12 C ) 12.256 ( PROT PHE 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 SER 14 N ) 12.256 ( PROT SER 14 H ) 9.8045 ( PROT SER 14 CA ) 12.256 ( PROT SER 14 CB ) 9.8045 ( PROT SER 14 OG ) 9.8045 ( PROT SER 14 HG ) 9.8045 ( PROT SER 14 C ) 12.256 ( PROT SER 14 O ) 12.256 ( PROT LYS 15 N ) 12.256 ( PROT LYS 15 H ) 9.8045 ( PROT LYS 15 CA ) 12.256 ( PROT LYS 15 CB ) 9.8045 ( PROT LYS 15 CG ) 9.8045 ( PROT LYS 15 CD ) 9.8045 ( PROT LYS 15 CE ) 9.8045 ( PROT LYS 15 NZ ) 9.8045 ( PROT LYS 15 HZ1 ) 9.8045 ( PROT LYS 15 HZ2 ) 9.8045 ( PROT LYS 15 HZ3 ) 9.8045 ( PROT LYS 15 C ) 12.256 ( PROT LYS 15 O ) 12.256 ( PROT LEU 16 N ) 12.256 ( PROT LEU 16 H ) 9.8045 ( PROT LEU 16 CA ) 12.256 ( PROT LEU 16 CB ) 9.8045 ( PROT LEU 16 CG ) 9.8045 ( PROT LEU 16 CD1 ) 9.8045 ( PROT LEU 16 CD2 ) 9.8045 ( PROT LEU 16 C ) 12.256 ( PROT LEU 16 O ) 12.256 ( PROT ALA 17 N ) 12.256 ( PROT ALA 17 H ) 9.8045 ( PROT ALA 17 CA ) 12.256 ( PROT ALA 17 CB ) 9.8045 ( PROT ALA 17 C ) 12.256 ( PROT ALA 17 O ) 12.256 ( PROT CYS 18 N ) 12.256 ( PROT CYS 18 H ) 9.8045 ( PROT CYS 18 CA ) 12.256 ( PROT CYS 18 CB ) 9.8045 ( PROT CYS 18 SG ) 9.8045 ( PROT CYS 18 C ) 12.256 ( PROT CYS 18 O ) 12.256 ( PROT GLU 19 N ) 12.256 ( PROT GLU 19 H ) 9.8045 ( PROT GLU 19 CA ) 12.256 ( PROT GLU 19 CB ) 9.8045 ( PROT GLU 19 CG ) 9.8045 ( PROT GLU 19 CD ) 9.8045 ( PROT GLU 19 OE1 ) 9.8045 ( PROT GLU 19 OE2 ) 9.8045 ( PROT GLU 19 C ) 12.256 ( PROT GLU 19 OT1 ) 9.8045 ( PROT GLU 19 OT2 ) 9.8045 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43421 4.57712 -7.53148 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00049 -0.00189 -0.00114 ROTATION MATRIX 1.000000 -0.000136 -0.000179 0.000136 1.000000 0.000299 0.000179 -0.000299 1.000000 AXIS OF ROTATION IS 0.799413 0.478663 -0.363072 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 8.8203 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.229133 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2291" Parameter: A <- "0.2291" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.92399 4.26527 -7.72150 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00822 0.01499 -0.01076 ROTATION MATRIX 0.999886 0.011738 0.009515 -0.011591 0.999814 -0.015395 -0.009694 0.015283 0.999836 AXIS OF ROTATION IS -0.712402 -0.446082 0.541751 ANGLE IS 1.23 CENTER OF ROTATION 8.773811 4.123602 -8.052591 SHIFT IS -0.018378 TOTAL SQUARE DIFF IS 0.2743 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.120164 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2291" RDCMND substituted energy or value "?RMS" to " 0.1202" Parameter: A <- "0.2291 0.1202" 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 0.2291 0.1202 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 " 154.24" Parameter: H <- "154.24" 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 93.30428 154.23920 4.64320 ENER INTERN> 13.33646 43.08523 0.00000 12.25981 6.10971 ENER EXTERN> 37.44324 -18.93019 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 " 93.30" Parameter: B <- "93.30" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -18.93" Parameter: C <- "-18.93" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 37.44" Parameter: C <- " 18.51" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 18.51" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 13.34" Parameter: D <- "13.34" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 43.09" Parameter: D <- " 56.43" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 12.26" Parameter: D <- " 68.69" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.11" Parameter: D <- " 74.80" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 74.80" 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= 4200 ENER= 93.30 GRMS= 4.64 ELEC= -18.93 VDW= 37.44 RDTITL> *EXTERNAL= 18.51 INTERNAL= 74.80 USER= 0.00 HARM= 154.24 RDTITL> *BOND= 13.34 ANGL= 43.09 DIHE= 12.26 IMPR= 6.11 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9889 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9904 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 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> 0 205.26081 -111.95653 1.90792 0.02000 MINI INTERN> 13.33646 43.08523 0.00000 12.25981 6.10971 MINI EXTERN> 37.44324 -18.93019 0.00000 0.00000 0.00000 MINI CONSTR> 111.95653 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 195.68895 9.57186 1.95525 0.00360 MINI INTERN> 11.77861 41.05955 0.00000 13.80059 6.18425 MINI EXTERN> 16.36271 -17.39780 0.00000 0.00000 0.00000 MINI CONSTR> 123.90105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9886 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 193.19084 2.49810 1.47468 0.00156 MINI INTERN> 10.41029 39.93328 0.00000 14.02666 5.91172 MINI EXTERN> 14.19203 -17.29337 0.00000 0.00000 0.00000 MINI CONSTR> 126.01024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 191.65064 1.54021 1.76705 0.00161 MINI INTERN> 11.04421 38.51329 0.00000 14.14348 5.89136 MINI EXTERN> 11.78813 -17.06141 0.00000 0.00000 0.00000 MINI CONSTR> 127.33157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9879 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 190.73475 0.91589 2.17018 0.00167 MINI INTERN> 10.99028 38.03190 0.00000 14.17598 5.87163 MINI EXTERN> 10.69498 -17.15126 0.00000 0.00000 0.00000 MINI CONSTR> 128.12125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 189.54989 1.18486 0.68884 0.00072 MINI INTERN> 9.72472 38.32454 0.00000 14.25089 5.85355 MINI EXTERN> 9.97351 -17.22125 0.00000 0.00000 0.00000 MINI CONSTR> 128.64393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9877 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 188.85347 0.69642 0.62544 0.00075 MINI INTERN> 9.56361 38.03217 0.00000 14.26826 5.81907 MINI EXTERN> 9.36838 -17.23523 0.00000 0.00000 0.00000 MINI CONSTR> 129.03723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 188.28736 0.56612 0.97629 0.00078 MINI INTERN> 9.41355 37.91954 0.00000 14.27963 5.78730 MINI EXTERN> 8.83717 -17.31272 0.00000 0.00000 0.00000 MINI CONSTR> 129.36290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9877 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 187.87148 0.41588 1.21719 0.00080 MINI INTERN> 9.28133 37.74788 0.00000 14.28422 5.76378 MINI EXTERN> 8.47311 -17.25875 0.00000 0.00000 0.00000 MINI CONSTR> 129.57990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 187.55771 0.31376 1.47605 0.00083 MINI INTERN> 9.18824 37.63964 0.00000 14.28026 5.74545 MINI EXTERN> 8.21742 -17.25398 0.00000 0.00000 0.00000 MINI CONSTR> 129.74069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9877 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 187.27342 0.28429 1.48387 0.00087 MINI INTERN> 9.20187 37.45746 0.00000 14.26551 5.72210 MINI EXTERN> 8.02250 -17.25008 0.00000 0.00000 0.00000 MINI CONSTR> 129.85407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 187.02915 0.24427 1.53943 0.00090 MINI INTERN> 9.09688 37.41702 0.00000 14.25692 5.70631 MINI EXTERN> 7.85501 -17.26764 0.00000 0.00000 0.00000 MINI CONSTR> 129.96464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9877 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 186.64281 0.38634 0.42107 0.00039 MINI INTERN> 9.58606 36.84577 0.00000 14.19622 5.64871 MINI EXTERN> 7.64278 -17.31066 0.00000 0.00000 0.00000 MINI CONSTR> 130.03393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 186.47081 0.17201 0.32119 0.00040 MINI INTERN> 9.49920 36.84038 0.00000 14.18431 5.63745 MINI EXTERN> 7.53338 -17.33345 0.00000 0.00000 0.00000 MINI CONSTR> 130.10954 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9876 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 186.31112 0.15969 0.57434 0.00042 MINI INTERN> 9.69685 36.58639 0.00000 14.15235 5.60442 MINI EXTERN> 7.37901 -17.29924 0.00000 0.00000 0.00000 MINI CONSTR> 130.19134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 186.19106 0.12007 0.64503 0.00043 MINI INTERN> 9.77622 36.50022 0.00000 14.12852 5.58595 MINI EXTERN> 7.27959 -17.33406 0.00000 0.00000 0.00000 MINI CONSTR> 130.25462 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9875 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 186.08766 0.10339 0.65155 0.00045 MINI INTERN> 9.83512 36.38843 0.00000 14.10677 5.56928 MINI EXTERN> 7.18505 -17.31173 0.00000 0.00000 0.00000 MINI CONSTR> 130.31475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 185.99345 0.09421 0.64577 0.00046 MINI INTERN> 9.76473 36.37068 0.00000 14.09530 5.55835 MINI EXTERN> 7.12746 -17.29602 0.00000 0.00000 0.00000 MINI CONSTR> 130.37293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9875 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 185.88871 0.10473 0.20895 0.00020 MINI INTERN> 9.26454 36.72750 0.00000 14.10764 5.58306 MINI EXTERN> 7.14383 -17.36932 0.00000 0.00000 0.00000 MINI CONSTR> 130.43146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 185.86333 0.02538 0.71147 0.00050 MINI INTERN> 9.84986 36.26841 0.00000 14.05745 5.53389 MINI EXTERN> 7.01058 -17.32635 0.00000 0.00000 0.00000 MINI CONSTR> 130.46949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9875 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 185.76835 0.09498 0.27655 0.00022 MINI INTERN> 9.20528 36.71399 0.00000 14.07866 5.56896 MINI EXTERN> 7.05334 -17.38233 0.00000 0.00000 0.00000 MINI CONSTR> 130.53044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 185.72325 0.04510 0.23611 0.00022 MINI INTERN> 9.21891 36.67095 0.00000 14.06470 5.55961 MINI EXTERN> 7.01500 -17.37548 0.00000 0.00000 0.00000 MINI CONSTR> 130.56956 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9875 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 185.68833 0.03492 0.33642 0.00023 MINI INTERN> 9.13426 36.70158 0.00000 14.05623 5.55807 MINI EXTERN> 6.98911 -17.36441 0.00000 0.00000 0.00000 MINI CONSTR> 130.61349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 185.65619 0.03214 0.34813 0.00024 MINI INTERN> 9.10178 36.71671 0.00000 14.04517 5.55398 MINI EXTERN> 6.96550 -17.37831 0.00000 0.00000 0.00000 MINI CONSTR> 130.65134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9875 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 185.62822 0.02797 0.40420 0.00025 MINI INTERN> 9.09245 36.69097 0.00000 14.03194 5.54854 MINI EXTERN> 6.93032 -17.35778 0.00000 0.00000 0.00000 MINI CONSTR> 130.69177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 185.60273 0.02549 0.35929 0.00026 MINI INTERN> 9.09880 36.68403 0.00000 14.02017 5.54310 MINI EXTERN> 6.90857 -17.37402 0.00000 0.00000 0.00000 MINI CONSTR> 130.72208 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9874 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 185.57124 0.03149 0.12178 0.00011 MINI INTERN> 9.36920 36.43212 0.00000 13.99476 5.51449 MINI EXTERN> 6.84833 -17.33161 0.00000 0.00000 0.00000 MINI CONSTR> 130.74395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 185.55520 0.01604 0.09670 0.00012 MINI INTERN> 9.34384 36.43887 0.00000 13.98716 5.51250 MINI EXTERN> 6.83282 -17.32977 0.00000 0.00000 0.00000 MINI CONSTR> 130.76978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9874 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 185.53879 0.01641 0.15205 0.00012 MINI INTERN> 9.40348 36.37268 0.00000 13.97312 5.50225 MINI EXTERN> 6.80337 -17.31524 0.00000 0.00000 0.00000 MINI CONSTR> 130.79913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 185.52358 0.01521 0.10559 0.00012 MINI INTERN> 9.36362 36.39422 0.00000 13.96573 5.50148 MINI EXTERN> 6.78953 -17.31779 0.00000 0.00000 0.00000 MINI CONSTR> 130.82679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9874 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 185.51191 0.01167 0.14556 0.00013 MINI INTERN> 9.40418 36.34817 0.00000 13.95448 5.49390 MINI EXTERN> 6.76646 -17.30691 0.00000 0.00000 0.00000 MINI CONSTR> 130.85162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 185.50285 0.00905 0.19381 0.00013 MINI INTERN> 9.40622 36.32713 0.00000 13.94565 5.48922 MINI EXTERN> 6.75241 -17.29302 0.00000 0.00000 0.00000 MINI CONSTR> 130.87524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9874 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 185.49451 0.00834 0.21189 0.00014 MINI INTERN> 9.41058 36.33148 0.00000 13.93748 5.48702 MINI EXTERN> 6.73896 -17.30641 0.00000 0.00000 0.00000 MINI CONSTR> 130.89540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 185.48409 0.01043 0.06405 0.00006 MINI INTERN> 9.29287 36.40998 0.00000 13.93686 5.49431 MINI EXTERN> 6.73904 -17.30592 0.00000 0.00000 0.00000 MINI CONSTR> 130.91695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9874 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 185.48145 0.00264 0.25113 0.00015 MINI INTERN> 9.37626 36.32001 0.00000 13.92609 5.48333 MINI EXTERN> 6.71536 -17.27416 0.00000 0.00000 0.00000 MINI CONSTR> 130.93455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 185.47059 0.01086 0.06696 0.00006 MINI INTERN> 9.28121 36.40204 0.00000 13.92349 5.48997 MINI EXTERN> 6.71599 -17.29654 0.00000 0.00000 0.00000 MINI CONSTR> 130.95444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9873 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 185.46553 0.00506 0.05509 0.00007 MINI INTERN> 9.29154 36.38736 0.00000 13.91740 5.48699 MINI EXTERN> 6.70542 -17.29182 0.00000 0.00000 0.00000 MINI CONSTR> 130.96865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 185.46027 0.00526 0.09111 0.00007 MINI INTERN> 9.26213 36.40754 0.00000 13.91183 5.48741 MINI EXTERN> 6.69749 -17.29363 0.00000 0.00000 0.00000 MINI CONSTR> 130.98750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9873 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 185.45576 0.00451 0.07574 0.00007 MINI INTERN> 9.26691 36.39583 0.00000 13.90623 5.48496 MINI EXTERN> 6.68771 -17.28717 0.00000 0.00000 0.00000 MINI CONSTR> 131.00130 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 185.45154 0.00422 0.08445 0.00007 MINI INTERN> 9.26266 36.39024 0.00000 13.90076 5.48324 MINI EXTERN> 6.67827 -17.27985 0.00000 0.00000 0.00000 MINI CONSTR> 131.01622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9873 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 185.44829 0.00325 0.10455 0.00008 MINI INTERN> 9.24185 36.40490 0.00000 13.89659 5.48360 MINI EXTERN> 6.67250 -17.28092 0.00000 0.00000 0.00000 MINI CONSTR> 131.02976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 185.44489 0.00341 0.12931 0.00008 MINI INTERN> 9.24942 36.39894 0.00000 13.89034 5.48159 MINI EXTERN> 6.66338 -17.28221 0.00000 0.00000 0.00000 MINI CONSTR> 131.04344 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9873 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 185.44175 0.00314 0.11582 0.00008 MINI INTERN> 9.23482 36.39866 0.00000 13.88684 5.48106 MINI EXTERN> 6.65664 -17.27144 0.00000 0.00000 0.00000 MINI CONSTR> 131.05517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 185.43807 0.00368 0.04017 0.00004 MINI INTERN> 9.31673 36.32635 0.00000 13.87880 5.47234 MINI EXTERN> 6.64148 -17.25978 0.00000 0.00000 0.00000 MINI CONSTR> 131.06215 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 185.43712 0.00095 0.14976 0.00009 MINI INTERN> 9.26872 36.37323 0.00000 13.87653 5.47620 MINI EXTERN> 6.64094 -17.27259 0.00000 0.00000 0.00000 MINI CONSTR> 131.07409 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 185.43467 0.00244 0.14208 0.00009 MINI INTERN> 9.23865 36.39192 0.00000 13.87396 5.47765 MINI EXTERN> 6.63712 -17.26973 0.00000 0.00000 0.00000 MINI CONSTR> 131.08511 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 185.43091 0.00376 0.04350 0.00004 MINI INTERN> 9.32128 36.31021 0.00000 13.86646 5.46848 MINI EXTERN> 6.62171 -17.24844 0.00000 0.00000 0.00000 MINI CONSTR> 131.09122 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 185.42905 0.00186 0.03390 0.00004 MINI INTERN> 9.31249 36.31505 0.00000 13.86365 5.46846 MINI EXTERN> 6.61767 -17.24735 0.00000 0.00000 0.00000 MINI CONSTR> 131.09908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 185.42703 0.00202 0.03133 0.00004 MINI INTERN> 9.30962 36.31416 0.00000 13.86009 5.46779 MINI EXTERN> 6.61221 -17.24467 0.00000 0.00000 0.00000 MINI CONSTR> 131.10783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 185.42515 0.00188 0.06078 0.00004 MINI INTERN> 9.33399 36.28850 0.00000 13.85493 5.46448 MINI EXTERN> 6.60314 -17.23639 0.00000 0.00000 0.00000 MINI CONSTR> 131.11651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 185.42346 0.00169 0.05188 0.00005 MINI INTERN> 9.32891 36.29184 0.00000 13.85201 5.46432 MINI EXTERN> 6.59913 -17.23650 0.00000 0.00000 0.00000 MINI CONSTR> 131.12373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 185.42211 0.00135 0.07110 0.00005 MINI INTERN> 9.33239 36.28253 0.00000 13.84891 5.46309 MINI EXTERN> 6.59355 -17.22914 0.00000 0.00000 0.00000 MINI CONSTR> 131.13076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 185.42074 0.00137 0.07374 0.00005 MINI INTERN> 9.34066 36.27380 0.00000 13.84560 5.46176 MINI EXTERN> 6.58835 -17.22645 0.00000 0.00000 0.00000 MINI CONSTR> 131.13703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 185.41945 0.00130 0.07704 0.00005 MINI INTERN> 9.34490 36.27125 0.00000 13.84250 5.46099 MINI EXTERN> 6.58410 -17.22734 0.00000 0.00000 0.00000 MINI CONSTR> 131.14304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 185.41829 0.00116 0.08597 0.00005 MINI INTERN> 9.32463 36.27974 0.00000 13.84116 5.46194 MINI EXTERN> 6.58147 -17.22026 0.00000 0.00000 0.00000 MINI CONSTR> 131.14962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 185.41668 0.00161 0.02563 0.00002 MINI INTERN> 9.29023 36.31120 0.00000 13.84036 5.46488 MINI EXTERN> 6.58211 -17.22773 0.00000 0.00000 0.00000 MINI CONSTR> 131.15563 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 185.41604 0.00064 0.08102 0.00006 MINI INTERN> 9.34734 36.26228 0.00000 13.83496 5.45930 MINI EXTERN> 6.57242 -17.21980 0.00000 0.00000 0.00000 MINI CONSTR> 131.15954 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 185.41446 0.00158 0.02729 0.00002 MINI INTERN> 9.28653 36.31019 0.00000 13.83563 5.46431 MINI EXTERN> 6.57499 -17.22377 0.00000 0.00000 0.00000 MINI CONSTR> 131.16658 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 185.41354 0.00092 0.02321 0.00003 MINI INTERN> 9.29022 36.30477 0.00000 13.83345 5.46358 MINI EXTERN> 6.57146 -17.22083 0.00000 0.00000 0.00000 MINI CONSTR> 131.17090 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 185.41263 0.00091 0.02291 0.00003 MINI INTERN> 9.28942 36.30370 0.00000 13.83141 5.46329 MINI EXTERN> 6.56838 -17.21901 0.00000 0.00000 0.00000 MINI CONSTR> 131.17545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 185.41174 0.00089 0.02293 0.00003 MINI INTERN> 9.28893 36.30262 0.00000 13.82935 5.46301 MINI EXTERN> 6.56531 -17.21743 0.00000 0.00000 0.00000 MINI CONSTR> 131.17995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 185.41089 0.00085 0.03815 0.00003 MINI INTERN> 9.27557 36.31102 0.00000 13.82782 5.46383 MINI EXTERN> 6.56318 -17.21573 0.00000 0.00000 0.00000 MINI CONSTR> 131.18521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 185.41011 0.00078 0.03112 0.00003 MINI INTERN> 9.27932 36.30677 0.00000 13.82585 5.46324 MINI EXTERN> 6.56019 -17.21411 0.00000 0.00000 0.00000 MINI CONSTR> 131.18885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 185.40938 0.00073 0.03586 0.00003 MINI INTERN> 9.27721 36.30815 0.00000 13.82406 5.46324 MINI EXTERN> 6.55775 -17.21386 0.00000 0.00000 0.00000 MINI CONSTR> 131.19284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 185.40877 0.00061 0.04769 0.00003 MINI INTERN> 9.27060 36.30979 0.00000 13.82274 5.46346 MINI EXTERN> 6.55550 -17.21014 0.00000 0.00000 0.00000 MINI CONSTR> 131.19682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 185.40815 0.00063 0.04960 0.00003 MINI INTERN> 9.26613 36.31272 0.00000 13.82130 5.46367 MINI EXTERN> 6.55355 -17.20966 0.00000 0.00000 0.00000 MINI CONSTR> 131.20043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 185.40754 0.00061 0.04963 0.00003 MINI INTERN> 9.26486 36.31428 0.00000 13.81972 5.46369 MINI EXTERN> 6.55156 -17.21031 0.00000 0.00000 0.00000 MINI CONSTR> 131.20374 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 185.40699 0.00055 0.05898 0.00004 MINI INTERN> 9.26420 36.31054 0.00000 13.81824 5.46340 MINI EXTERN> 6.54884 -17.20547 0.00000 0.00000 0.00000 MINI CONSTR> 131.20725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 185.40640 0.00058 0.05065 0.00004 MINI INTERN> 9.26254 36.31273 0.00000 13.81686 5.46349 MINI EXTERN> 6.54719 -17.20655 0.00000 0.00000 0.00000 MINI CONSTR> 131.21014 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 185.40566 0.00075 0.01745 0.00002 MINI INTERN> 9.29912 36.28022 0.00000 13.81370 5.46000 MINI EXTERN> 6.54147 -17.20067 0.00000 0.00000 0.00000 MINI CONSTR> 131.21180 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 185.40543 0.00023 0.05979 0.00004 MINI INTERN> 9.26707 36.30948 0.00000 13.81370 5.46299 MINI EXTERN> 6.54286 -17.20647 0.00000 0.00000 0.00000 MINI CONSTR> 131.21580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 185.40470 0.00073 0.01886 0.00002 MINI INTERN> 9.30098 36.27640 0.00000 13.81097 5.45957 MINI EXTERN> 6.53743 -17.19786 0.00000 0.00000 0.00000 MINI CONSTR> 131.21720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 185.40455 0.00016 0.05842 0.00004 MINI INTERN> 9.25706 36.31402 0.00000 13.81173 5.46355 MINI EXTERN> 6.53998 -17.20315 0.00000 0.00000 0.00000 MINI CONSTR> 131.22136 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 185.40379 0.00076 0.02101 0.00002 MINI INTERN> 9.30271 36.27254 0.00000 13.80827 5.45917 MINI EXTERN> 6.53343 -17.19488 0.00000 0.00000 0.00000 MINI CONSTR> 131.22255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 185.40342 0.00037 0.01500 0.00002 MINI INTERN> 9.29671 36.27723 0.00000 13.80752 5.45966 MINI EXTERN> 6.53260 -17.19512 0.00000 0.00000 0.00000 MINI CONSTR> 131.22481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 185.40305 0.00036 0.02686 0.00002 MINI INTERN> 9.30704 36.26757 0.00000 13.80581 5.45864 MINI EXTERN> 6.52987 -17.19281 0.00000 0.00000 0.00000 MINI CONSTR> 131.22694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 185.40270 0.00036 0.02240 0.00002 MINI INTERN> 9.30322 36.26918 0.00000 13.80501 5.45887 MINI EXTERN> 6.52872 -17.19144 0.00000 0.00000 0.00000 MINI CONSTR> 131.22913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 185.40238 0.00032 0.02523 0.00002 MINI INTERN> 9.30583 36.26678 0.00000 13.80384 5.45861 MINI EXTERN> 6.52710 -17.19088 0.00000 0.00000 0.00000 MINI CONSTR> 131.23110 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 185.40210 0.00028 0.03385 0.00002 MINI INTERN> 9.30501 36.26484 0.00000 13.80295 5.45852 MINI EXTERN> 6.52559 -17.18798 0.00000 0.00000 0.00000 MINI CONSTR> 131.23317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 185.40183 0.00027 0.03734 0.00002 MINI INTERN> 9.30689 36.26233 0.00000 13.80195 5.45829 MINI EXTERN> 6.52411 -17.18670 0.00000 0.00000 0.00000 MINI CONSTR> 131.23495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 185.40155 0.00029 0.03220 0.00002 MINI INTERN> 9.31063 36.26024 0.00000 13.80085 5.45801 MINI EXTERN> 6.52278 -17.18746 0.00000 0.00000 0.00000 MINI CONSTR> 131.23649 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 185.40132 0.00022 0.04428 0.00002 MINI INTERN> 9.30589 36.26108 0.00000 13.80022 5.45826 MINI EXTERN> 6.52163 -17.18436 0.00000 0.00000 0.00000 MINI CONSTR> 131.23862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 185.40109 0.00023 0.04343 0.00003 MINI INTERN> 9.29976 36.26549 0.00000 13.79980 5.45878 MINI EXTERN> 6.52121 -17.18419 0.00000 0.00000 0.00000 MINI CONSTR> 131.24025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 185.40087 0.00023 0.04368 0.00003 MINI INTERN> 9.30327 36.26197 0.00000 13.79884 5.45844 MINI EXTERN> 6.51982 -17.18316 0.00000 0.00000 0.00000 MINI CONSTR> 131.24169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 185.40063 0.00024 0.03843 0.00003 MINI INTERN> 9.31369 36.25426 0.00000 13.79750 5.45757 MINI EXTERN> 6.51799 -17.18321 0.00000 0.00000 0.00000 MINI CONSTR> 131.24283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 185.40028 0.00035 0.01271 0.00001 MINI INTERN> 9.28542 36.27868 0.00000 13.79801 5.46018 MINI EXTERN> 6.51973 -17.18704 0.00000 0.00000 0.00000 MINI CONSTR> 131.24530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 185.40010 0.00018 0.01035 0.00001 MINI INTERN> 9.28744 36.27632 0.00000 13.79731 5.45997 MINI EXTERN> 6.51871 -17.18609 0.00000 0.00000 0.00000 MINI CONSTR> 131.24644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 185.39991 0.00019 0.01063 0.00001 MINI INTERN> 9.28652 36.27653 0.00000 13.79667 5.46004 MINI EXTERN> 6.51788 -17.18553 0.00000 0.00000 0.00000 MINI CONSTR> 131.24782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 185.39973 0.00018 0.00995 0.00001 MINI INTERN> 9.28706 36.27536 0.00000 13.79597 5.45997 MINI EXTERN> 6.51693 -17.18468 0.00000 0.00000 0.00000 MINI CONSTR> 131.24912 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> 440 185.39973 0.00018 0.00995 0.00002 STPD INTERN> 9.28706 36.27536 0.00000 13.79597 5.45997 STPD EXTERN> 6.51693 -17.18468 0.00000 0.00000 0.00000 STPD CONSTR> 131.24912 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 9872 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9872 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> 0 185.39973 0.00018 0.00995 0.00000 MINI INTERN> 9.28706 36.27536 0.00000 13.79597 5.45997 MINI EXTERN> 6.51693 -17.18468 0.00000 0.00000 0.00000 MINI CONSTR> 131.24912 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> 3 185.39675 0.00298 0.00443 0.02000 CONJ INTERN> 9.28323 36.25786 0.00000 13.77422 5.46113 CONJ EXTERN> 6.48029 -17.16140 0.00000 0.00000 0.00000 CONJ CONSTR> 131.30141 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 ALA 1 HT1 ) 6.3729 ( PROT ALA 1 HT2 ) 6.3729 ( PROT ALA 1 N ) 7.9661 ( PROT ALA 1 HT3 ) 6.3729 ( PROT ALA 1 CA ) 7.9661 ( PROT ALA 1 CB ) 6.3729 ( PROT ALA 1 C ) 7.9661 ( PROT ALA 1 O ) 7.9661 ( PROT LEU 2 N ) 7.9661 ( PROT LEU 2 H ) 6.3729 ( PROT LEU 2 CA ) 7.9661 ( PROT LEU 2 CB ) 6.3729 ( PROT LEU 2 CG ) 6.3729 ( PROT LEU 2 CD1 ) 6.3729 ( PROT LEU 2 CD2 ) 6.3729 ( PROT LEU 2 C ) 7.9661 ( PROT LEU 2 O ) 7.9661 ( PROT GLN 3 N ) 7.9661 ( PROT GLN 3 H ) 6.3729 ( PROT GLN 3 CA ) 7.9661 ( PROT GLN 3 CB ) 6.3729 ( PROT GLN 3 CG ) 6.3729 ( PROT GLN 3 CD ) 6.3729 ( PROT GLN 3 OE1 ) 6.3729 ( PROT GLN 3 NE2 ) 6.3729 ( PROT GLN 3 HE21 ) 6.3729 ( PROT GLN 3 HE22 ) 6.3729 ( PROT GLN 3 C ) 7.9661 ( PROT GLN 3 O ) 7.9661 ( PROT ALA 4 N ) 7.9661 ( PROT ALA 4 H ) 6.3729 ( PROT ALA 4 CA ) 7.9661 ( PROT ALA 4 CB ) 6.3729 ( PROT ALA 4 C ) 7.9661 ( PROT ALA 4 O ) 7.9661 ( PROT PHE 5 N ) 7.9661 ( PROT PHE 5 H ) 6.3729 ( PROT PHE 5 CA ) 7.9661 ( PROT PHE 5 CB ) 6.3729 ( PROT PHE 5 CG ) 6.3729 ( PROT PHE 5 CD1 ) 6.3729 ( PROT PHE 5 CD2 ) 6.3729 ( PROT PHE 5 CE1 ) 6.3729 ( PROT PHE 5 CE2 ) 6.3729 ( PROT PHE 5 CZ ) 6.3729 ( PROT PHE 5 C ) 7.9661 ( PROT PHE 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 ILE 7 N ) 7.9661 ( PROT ILE 7 H ) 6.3729 ( PROT ILE 7 CA ) 7.9661 ( PROT ILE 7 CB ) 6.3729 ( PROT ILE 7 CG2 ) 6.3729 ( PROT ILE 7 CG1 ) 6.3729 ( PROT ILE 7 CD ) 6.3729 ( PROT ILE 7 C ) 7.9661 ( PROT ILE 7 O ) 7.9661 ( PROT ALA 8 N ) 7.9661 ( PROT ALA 8 H ) 6.3729 ( PROT ALA 8 CA ) 7.9661 ( PROT ALA 8 CB ) 6.3729 ( PROT ALA 8 C ) 7.9661 ( PROT ALA 8 O ) 7.9661 ( PROT LEU 9 N ) 7.9661 ( PROT LEU 9 H ) 6.3729 ( PROT LEU 9 CA ) 7.9661 ( PROT LEU 9 CB ) 6.3729 ( PROT LEU 9 CG ) 6.3729 ( PROT LEU 9 CD1 ) 6.3729 ( PROT LEU 9 CD2 ) 6.3729 ( PROT LEU 9 C ) 7.9661 ( PROT LEU 9 O ) 7.9661 ( PROT SER 10 N ) 7.9661 ( PROT SER 10 H ) 6.3729 ( PROT SER 10 CA ) 7.9661 ( PROT SER 10 CB ) 6.3729 ( PROT SER 10 OG ) 6.3729 ( PROT SER 10 HG ) 6.3729 ( PROT SER 10 C ) 7.9661 ( PROT SER 10 O ) 7.9661 ( PROT SER 11 N ) 7.9661 ( PROT SER 11 H ) 6.3729 ( PROT SER 11 CA ) 7.9661 ( PROT SER 11 CB ) 6.3729 ( PROT SER 11 OG ) 6.3729 ( PROT SER 11 HG ) 6.3729 ( PROT SER 11 C ) 7.9661 ( PROT SER 11 O ) 7.9661 ( PROT PHE 12 N ) 7.9661 ( PROT PHE 12 H ) 6.3729 ( PROT PHE 12 CA ) 7.9661 ( PROT PHE 12 CB ) 6.3729 ( PROT PHE 12 CG ) 6.3729 ( PROT PHE 12 CD1 ) 6.3729 ( PROT PHE 12 CD2 ) 6.3729 ( PROT PHE 12 CE1 ) 6.3729 ( PROT PHE 12 CE2 ) 6.3729 ( PROT PHE 12 CZ ) 6.3729 ( PROT PHE 12 C ) 7.9661 ( PROT PHE 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 SER 14 N ) 7.9661 ( PROT SER 14 H ) 6.3729 ( PROT SER 14 CA ) 7.9661 ( PROT SER 14 CB ) 6.3729 ( PROT SER 14 OG ) 6.3729 ( PROT SER 14 HG ) 6.3729 ( PROT SER 14 C ) 7.9661 ( PROT SER 14 O ) 7.9661 ( PROT LYS 15 N ) 7.9661 ( PROT LYS 15 H ) 6.3729 ( PROT LYS 15 CA ) 7.9661 ( PROT LYS 15 CB ) 6.3729 ( PROT LYS 15 CG ) 6.3729 ( PROT LYS 15 CD ) 6.3729 ( PROT LYS 15 CE ) 6.3729 ( PROT LYS 15 NZ ) 6.3729 ( PROT LYS 15 HZ1 ) 6.3729 ( PROT LYS 15 HZ2 ) 6.3729 ( PROT LYS 15 HZ3 ) 6.3729 ( PROT LYS 15 C ) 7.9661 ( PROT LYS 15 O ) 7.9661 ( PROT LEU 16 N ) 7.9661 ( PROT LEU 16 H ) 6.3729 ( PROT LEU 16 CA ) 7.9661 ( PROT LEU 16 CB ) 6.3729 ( PROT LEU 16 CG ) 6.3729 ( PROT LEU 16 CD1 ) 6.3729 ( PROT LEU 16 CD2 ) 6.3729 ( PROT LEU 16 C ) 7.9661 ( PROT LEU 16 O ) 7.9661 ( PROT ALA 17 N ) 7.9661 ( PROT ALA 17 H ) 6.3729 ( PROT ALA 17 CA ) 7.9661 ( PROT ALA 17 CB ) 6.3729 ( PROT ALA 17 C ) 7.9661 ( PROT ALA 17 O ) 7.9661 ( PROT CYS 18 N ) 7.9661 ( PROT CYS 18 H ) 6.3729 ( PROT CYS 18 CA ) 7.9661 ( PROT CYS 18 CB ) 6.3729 ( PROT CYS 18 SG ) 6.3729 ( PROT CYS 18 C ) 7.9661 ( PROT CYS 18 O ) 7.9661 ( PROT GLU 19 N ) 7.9661 ( PROT GLU 19 H ) 6.3729 ( PROT GLU 19 CA ) 7.9661 ( PROT GLU 19 CB ) 6.3729 ( PROT GLU 19 CG ) 6.3729 ( PROT GLU 19 CD ) 6.3729 ( PROT GLU 19 OE1 ) 6.3729 ( PROT GLU 19 OE2 ) 6.3729 ( PROT GLU 19 C ) 7.9661 ( PROT GLU 19 OT1 ) 6.3729 ( PROT GLU 19 OT2 ) 6.3729 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43309 4.57712 -7.53118 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00161 -0.00190 -0.00145 ROTATION MATRIX 1.000000 -0.000160 -0.000192 0.000160 1.000000 0.000332 0.000192 -0.000332 1.000000 AXIS OF ROTATION IS 0.798772 0.461975 -0.385412 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 11.5508 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.262211 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2622" Parameter: A <- "0.2622" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.92800 4.26544 -7.71972 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00421 0.01482 -0.01254 ROTATION MATRIX 0.999864 0.012803 0.010385 -0.012626 0.999777 -0.016947 -0.010599 0.016814 0.999802 AXIS OF ROTATION IS -0.715454 -0.444681 0.538873 ANGLE IS 1.35 CENTER OF ROTATION 8.827959 3.988731 -8.096073 SHIFT IS -0.016358 TOTAL SQUARE DIFF IS 0.3852 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.142390 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2622" RDCMND substituted energy or value "?RMS" to " 0.1424" Parameter: A <- "0.2622 0.1424" 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 0.2622 0.1424 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 " 131.30" Parameter: H <- "131.30" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 54.09534 131.30141 3.45929 ENER INTERN> 9.28323 36.25786 0.00000 13.77422 5.46113 ENER EXTERN> 6.48029 -17.16140 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 " 54.10" Parameter: B <- "54.10" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -17.16" Parameter: C <- "-17.16" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 6.48" Parameter: C <- " -10.68" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -10.68" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 9.28" Parameter: D <- "9.28" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 36.26" Parameter: D <- " 45.54" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 13.77" Parameter: D <- " 59.31" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.46" Parameter: D <- " 64.77" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 64.77" 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= 54.10 GRMS= 3.46 ELEC= -17.16 VDW= 6.48 RDTITL> *EXTERNAL= -10.68 INTERNAL= 64.77 USER= 0.00 HARM= 131.30 RDTITL> *BOND= 9.28 ANGL= 36.26 DIHE= 13.77 IMPR= 5.46 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 54.10 GRMS= 3.46 ELEC= -17.16 VDW= 6.48 RDTITL> *EXTERNAL= -10.68 INTERNAL= 64.77 USER= 0.00 HARM= 131.30 RDTITL> *BOND= 9.28 ANGL= 36.26 DIHE= 13.77 IMPR= 5.46 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 54.10 GRMS= 3.46 ELEC= -17.16 VDW= 6.48 RDTITL> *EXTERNAL= -10.68 INTERNAL= 64.77 USER= 0.00 HARM= 131.30 RDTITL> *BOND= 9.28 ANGL= 36.26 DIHE= 13.77 IMPR= 5.46 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 4800 0.2622 0.1424 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "4800" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9872 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9873 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 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> 0 148.59597 -94.50063 1.39534 0.02000 MINI INTERN> 9.28323 36.25786 0.00000 13.77422 5.46113 MINI EXTERN> 6.48029 -17.16140 0.00000 0.00000 0.00000 MINI CONSTR> 94.50063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 142.37958 6.21639 1.78833 0.00360 MINI INTERN> 8.11071 34.15495 0.00000 15.00123 5.58750 MINI EXTERN> -8.04940 -15.45731 0.00000 0.00000 0.00000 MINI CONSTR> 103.03191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9860 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 140.96198 1.41760 1.81849 0.00156 MINI INTERN> 7.57497 34.04350 0.00000 15.33816 5.21853 MINI EXTERN> -10.47143 -15.03184 0.00000 0.00000 0.00000 MINI CONSTR> 104.29008 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 140.10334 0.85864 2.14894 0.00161 MINI INTERN> 8.59047 32.86385 0.00000 15.40329 5.20473 MINI EXTERN> -12.09594 -14.80749 0.00000 0.00000 0.00000 MINI CONSTR> 104.94443 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9857 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 138.99038 1.11296 0.63385 0.00070 MINI INTERN> 7.38633 33.57510 0.00000 15.35848 5.35972 MINI EXTERN> -13.11161 -15.03557 0.00000 0.00000 0.00000 MINI CONSTR> 105.45793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 138.35759 0.63279 0.54343 0.00072 MINI INTERN> 7.37319 33.23828 0.00000 15.38296 5.31838 MINI EXTERN> -13.69557 -15.04305 0.00000 0.00000 0.00000 MINI CONSTR> 105.78340 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9855 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 137.77267 0.58492 0.93596 0.00075 MINI INTERN> 6.95286 33.37403 0.00000 15.39396 5.31750 MINI EXTERN> -14.21206 -15.16157 0.00000 0.00000 0.00000 MINI CONSTR> 106.10796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 137.29931 0.47336 0.83916 0.00078 MINI INTERN> 7.12751 32.99885 0.00000 15.39881 5.28270 MINI EXTERN> -14.66209 -15.13342 0.00000 0.00000 0.00000 MINI CONSTR> 106.28695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9853 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 136.95469 0.34463 1.12240 0.00080 MINI INTERN> 6.92301 33.06745 0.00000 15.38754 5.28489 MINI EXTERN> -14.93557 -15.22207 0.00000 0.00000 0.00000 MINI CONSTR> 106.44944 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 136.63647 0.31822 1.24310 0.00083 MINI INTERN> 6.77297 33.05145 0.00000 15.38448 5.27979 MINI EXTERN> -15.18699 -15.24657 0.00000 0.00000 0.00000 MINI CONSTR> 106.58135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9853 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 136.35899 0.27748 1.37840 0.00087 MINI INTERN> 6.95733 32.79987 0.00000 15.35366 5.24942 MINI EXTERN> -15.38183 -15.29378 0.00000 0.00000 0.00000 MINI CONSTR> 106.67432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 136.10037 0.25862 1.37807 0.00090 MINI INTERN> 6.74896 32.81141 0.00000 15.35472 5.24821 MINI EXTERN> -15.57213 -15.26427 0.00000 0.00000 0.00000 MINI CONSTR> 106.77347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9849 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 135.72612 0.37424 0.41622 0.00039 MINI INTERN> 7.30477 32.06336 0.00000 15.31100 5.16257 MINI EXTERN> -15.73239 -15.20483 0.00000 0.00000 0.00000 MINI CONSTR> 106.82165 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 135.53653 0.18960 0.33553 0.00040 MINI INTERN> 7.22586 32.05071 0.00000 15.29743 5.15716 MINI EXTERN> -15.85467 -15.22726 0.00000 0.00000 0.00000 MINI CONSTR> 106.88729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9848 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 135.34220 0.19432 0.31348 0.00042 MINI INTERN> 7.19716 31.99041 0.00000 15.27861 5.14714 MINI EXTERN> -15.98480 -15.24313 0.00000 0.00000 0.00000 MINI CONSTR> 106.95682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 135.17881 0.16339 0.58053 0.00043 MINI INTERN> 7.42003 31.71751 0.00000 15.24925 5.11315 MINI EXTERN> -16.11740 -15.22363 0.00000 0.00000 0.00000 MINI CONSTR> 107.01990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9848 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 135.01268 0.16613 0.41781 0.00045 MINI INTERN> 7.27590 31.78034 0.00000 15.23199 5.11864 MINI EXTERN> -16.21572 -15.26137 0.00000 0.00000 0.00000 MINI CONSTR> 107.08291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 134.91069 0.10199 0.66538 0.00046 MINI INTERN> 7.44505 31.59035 0.00000 15.20647 5.09601 MINI EXTERN> -16.31190 -15.24699 0.00000 0.00000 0.00000 MINI CONSTR> 107.13170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9847 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 134.80648 0.10421 0.72669 0.00048 MINI INTERN> 7.37459 31.59078 0.00000 15.19723 5.09112 MINI EXTERN> -16.38126 -15.24890 0.00000 0.00000 0.00000 MINI CONSTR> 107.18292 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 134.70710 0.09938 0.68988 0.00050 MINI INTERN> 7.43251 31.49323 0.00000 15.17676 5.07815 MINI EXTERN> -16.44985 -15.25136 0.00000 0.00000 0.00000 MINI CONSTR> 107.22766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9847 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 134.58747 0.11963 0.21286 0.00022 MINI INTERN> 7.01431 31.81019 0.00000 15.17592 5.11085 MINI EXTERN> -16.47862 -15.32410 0.00000 0.00000 0.00000 MINI CONSTR> 107.27893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 134.51109 0.07638 0.20089 0.00022 MINI INTERN> 7.00894 31.77494 0.00000 15.16097 5.10514 MINI EXTERN> -16.53165 -15.32784 0.00000 0.00000 0.00000 MINI CONSTR> 107.32059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 134.43939 0.07170 0.19371 0.00023 MINI INTERN> 7.00737 31.74013 0.00000 15.14514 5.09954 MINI EXTERN> -16.58211 -15.33337 0.00000 0.00000 0.00000 MINI CONSTR> 107.36270 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 134.37632 0.06307 0.30465 0.00024 MINI INTERN> 6.89978 31.80535 0.00000 15.13400 5.10465 MINI EXTERN> -16.62452 -15.35280 0.00000 0.00000 0.00000 MINI CONSTR> 107.40986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 134.32135 0.05497 0.16348 0.00025 MINI INTERN> 7.01235 31.66877 0.00000 15.11678 5.08856 MINI EXTERN> -16.66872 -15.33615 0.00000 0.00000 0.00000 MINI CONSTR> 107.43977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 134.27264 0.04871 0.36719 0.00026 MINI INTERN> 6.86480 31.77980 0.00000 15.10854 5.09796 MINI EXTERN> -16.70178 -15.36485 0.00000 0.00000 0.00000 MINI CONSTR> 107.48818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 134.23204 0.04061 0.39497 0.00027 MINI INTERN> 6.83825 31.77619 0.00000 15.09555 5.09726 MINI EXTERN> -16.73295 -15.36626 0.00000 0.00000 0.00000 MINI CONSTR> 107.52399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 134.19541 0.03662 0.41269 0.00028 MINI INTERN> 6.82530 31.76948 0.00000 15.08571 5.09454 MINI EXTERN> -16.76348 -15.37361 0.00000 0.00000 0.00000 MINI CONSTR> 107.55748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 134.16410 0.03131 0.45662 0.00029 MINI INTERN> 6.88591 31.68702 0.00000 15.06924 5.08616 MINI EXTERN> -16.79371 -15.35766 0.00000 0.00000 0.00000 MINI CONSTR> 107.58715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 134.13474 0.02936 0.45752 0.00030 MINI INTERN> 6.84751 31.71205 0.00000 15.06348 5.08614 MINI EXTERN> -16.81949 -15.37338 0.00000 0.00000 0.00000 MINI CONSTR> 107.61843 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 134.09251 0.04223 0.13786 0.00013 MINI INTERN> 7.07915 31.46277 0.00000 15.04071 5.05994 MINI EXTERN> -16.85916 -15.33045 0.00000 0.00000 0.00000 MINI CONSTR> 107.63955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 134.07058 0.02193 0.11349 0.00013 MINI INTERN> 7.05716 31.46712 0.00000 15.03307 5.05962 MINI EXTERN> -16.87712 -15.33422 0.00000 0.00000 0.00000 MINI CONSTR> 107.66496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 134.04793 0.02264 0.10227 0.00014 MINI INTERN> 7.04581 31.46060 0.00000 15.02386 5.05813 MINI EXTERN> -16.89757 -15.33613 0.00000 0.00000 0.00000 MINI CONSTR> 107.69323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 134.02751 0.02042 0.19409 0.00014 MINI INTERN> 7.12412 31.37269 0.00000 15.00912 5.04830 MINI EXTERN> -16.92613 -15.32311 0.00000 0.00000 0.00000 MINI CONSTR> 107.72253 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 134.01031 0.01721 0.16620 0.00015 MINI INTERN> 7.10496 31.37729 0.00000 15.00231 5.04793 MINI EXTERN> -16.94159 -15.32721 0.00000 0.00000 0.00000 MINI CONSTR> 107.74662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 133.99720 0.01310 0.22550 0.00015 MINI INTERN> 7.12729 31.34320 0.00000 14.99240 5.04423 MINI EXTERN> -16.95863 -15.32119 0.00000 0.00000 0.00000 MINI CONSTR> 107.76989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 133.98462 0.01258 0.23559 0.00016 MINI INTERN> 7.15477 31.30818 0.00000 14.98385 5.03991 MINI EXTERN> -16.97580 -15.31780 0.00000 0.00000 0.00000 MINI CONSTR> 107.79150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 133.97288 0.01174 0.24353 0.00017 MINI INTERN> 7.13188 31.32102 0.00000 14.97878 5.04028 MINI EXTERN> -16.98812 -15.32391 0.00000 0.00000 0.00000 MINI CONSTR> 107.81294 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 133.95846 0.01442 0.07264 0.00007 MINI INTERN> 6.99598 31.42835 0.00000 14.97817 5.05162 MINI EXTERN> -16.98869 -15.34152 0.00000 0.00000 0.00000 MINI CONSTR> 107.83456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 133.95516 0.00331 0.29736 0.00018 MINI INTERN> 7.10549 31.32908 0.00000 14.96754 5.04019 MINI EXTERN> -17.01069 -15.32885 0.00000 0.00000 0.00000 MINI CONSTR> 107.85240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 133.94016 0.01500 0.07964 0.00008 MINI INTERN> 6.98029 31.42391 0.00000 14.96603 5.05046 MINI EXTERN> -17.01097 -15.34321 0.00000 0.00000 0.00000 MINI CONSTR> 107.87366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 133.93329 0.00687 0.06442 0.00008 MINI INTERN> 6.99150 31.40597 0.00000 14.96026 5.04839 MINI EXTERN> -17.02087 -15.34078 0.00000 0.00000 0.00000 MINI CONSTR> 107.88880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 133.92599 0.00729 0.10457 0.00008 MINI INTERN> 6.95718 31.42801 0.00000 14.95521 5.05052 MINI EXTERN> -17.02930 -15.34507 0.00000 0.00000 0.00000 MINI CONSTR> 107.90944 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 133.92002 0.00597 0.09549 0.00009 MINI INTERN> 6.96131 31.41779 0.00000 14.95015 5.04914 MINI EXTERN> -17.03846 -15.34457 0.00000 0.00000 0.00000 MINI CONSTR> 107.92467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 133.91532 0.00470 0.13344 0.00009 MINI INTERN> 6.94943 31.42070 0.00000 14.94516 5.04954 MINI EXTERN> -17.04554 -15.34442 0.00000 0.00000 0.00000 MINI CONSTR> 107.94045 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 133.91088 0.00444 0.14123 0.00009 MINI INTERN> 6.93657 31.42658 0.00000 14.94117 5.05001 MINI EXTERN> -17.05233 -15.34605 0.00000 0.00000 0.00000 MINI CONSTR> 107.95493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 133.90682 0.00406 0.14616 0.00010 MINI INTERN> 6.94969 31.41164 0.00000 14.93708 5.04792 MINI EXTERN> -17.06096 -15.34599 0.00000 0.00000 0.00000 MINI CONSTR> 107.96744 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 133.90280 0.00402 0.13101 0.00010 MINI INTERN> 6.93371 31.41924 0.00000 14.93324 5.04881 MINI EXTERN> -17.06622 -15.34682 0.00000 0.00000 0.00000 MINI CONSTR> 107.98084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 133.89809 0.00471 0.04469 0.00004 MINI INTERN> 7.02115 31.33321 0.00000 14.92497 5.03989 MINI EXTERN> -17.07901 -15.33226 0.00000 0.00000 0.00000 MINI CONSTR> 107.99015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 133.89671 0.00139 0.14525 0.00011 MINI INTERN> 6.92100 31.42045 0.00000 14.92571 5.04899 MINI EXTERN> -17.07773 -15.34710 0.00000 0.00000 0.00000 MINI CONSTR> 108.00539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 133.89164 0.00507 0.04449 0.00005 MINI INTERN> 7.02232 31.32154 0.00000 14.91656 5.03857 MINI EXTERN> -17.09196 -15.33105 0.00000 0.00000 0.00000 MINI CONSTR> 108.01565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 133.88922 0.00241 0.04853 0.00005 MINI INTERN> 7.02644 31.31350 0.00000 14.91270 5.03789 MINI EXTERN> -17.09796 -15.32960 0.00000 0.00000 0.00000 MINI CONSTR> 108.02626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 133.88711 0.00212 0.05296 0.00005 MINI INTERN> 7.03180 31.30465 0.00000 14.90923 5.03692 MINI EXTERN> -17.10315 -15.32849 0.00000 0.00000 0.00000 MINI CONSTR> 108.03615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 133.88498 0.00213 0.04735 0.00005 MINI INTERN> 7.02748 31.30444 0.00000 14.90600 5.03700 MINI EXTERN> -17.10794 -15.32851 0.00000 0.00000 0.00000 MINI CONSTR> 108.04650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 133.88347 0.00150 0.07505 0.00005 MINI INTERN> 7.04289 31.28703 0.00000 14.90239 5.03505 MINI EXTERN> -17.11347 -15.32608 0.00000 0.00000 0.00000 MINI CONSTR> 108.05566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 133.88205 0.00142 0.08343 0.00006 MINI INTERN> 7.04972 31.27758 0.00000 14.89879 5.03444 MINI EXTERN> -17.11853 -15.32411 0.00000 0.00000 0.00000 MINI CONSTR> 108.06415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 133.88074 0.00131 0.08755 0.00006 MINI INTERN> 7.03936 31.28393 0.00000 14.89736 5.03478 MINI EXTERN> -17.12103 -15.32581 0.00000 0.00000 0.00000 MINI CONSTR> 108.07215 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 133.87900 0.00174 0.02468 0.00002 MINI INTERN> 6.99747 31.31873 0.00000 14.89667 5.03875 MINI EXTERN> -17.12139 -15.33142 0.00000 0.00000 0.00000 MINI CONSTR> 108.08019 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 133.87844 0.00056 0.08944 0.00006 MINI INTERN> 7.05019 31.26809 0.00000 14.89113 5.03385 MINI EXTERN> -17.12983 -15.32216 0.00000 0.00000 0.00000 MINI CONSTR> 108.08716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 133.87681 0.00163 0.03017 0.00003 MINI INTERN> 6.98946 31.32031 0.00000 14.89209 5.03918 MINI EXTERN> -17.12791 -15.33170 0.00000 0.00000 0.00000 MINI CONSTR> 108.09536 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 133.87597 0.00084 0.02242 0.00003 MINI INTERN> 6.99617 31.31207 0.00000 14.88989 5.03838 MINI EXTERN> -17.13110 -15.33047 0.00000 0.00000 0.00000 MINI CONSTR> 108.10102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 133.87512 0.00084 0.03758 0.00003 MINI INTERN> 6.98358 31.32075 0.00000 14.88805 5.03951 MINI EXTERN> -17.13364 -15.33167 0.00000 0.00000 0.00000 MINI CONSTR> 108.10855 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 133.87438 0.00074 0.03174 0.00003 MINI INTERN> 6.98628 31.31631 0.00000 14.88611 5.03910 MINI EXTERN> -17.13640 -15.33124 0.00000 0.00000 0.00000 MINI CONSTR> 108.11422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 133.87370 0.00068 0.03565 0.00003 MINI INTERN> 6.98505 31.31492 0.00000 14.88407 5.03921 MINI EXTERN> -17.13926 -15.33056 0.00000 0.00000 0.00000 MINI CONSTR> 108.12028 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 133.87317 0.00053 0.04318 0.00003 MINI INTERN> 6.97791 31.31991 0.00000 14.88277 5.03975 MINI EXTERN> -17.14107 -15.33194 0.00000 0.00000 0.00000 MINI CONSTR> 108.12584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 133.87270 0.00047 0.05810 0.00003 MINI INTERN> 6.98040 31.31438 0.00000 14.88054 5.03960 MINI EXTERN> -17.14410 -15.32950 0.00000 0.00000 0.00000 MINI CONSTR> 108.13138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 133.87224 0.00046 0.05669 0.00003 MINI INTERN> 6.98524 31.30835 0.00000 14.87884 5.03913 MINI EXTERN> -17.14652 -15.32840 0.00000 0.00000 0.00000 MINI CONSTR> 108.13560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 133.87177 0.00048 0.05107 0.00004 MINI INTERN> 6.97549 31.31626 0.00000 14.87785 5.04000 MINI EXTERN> -17.14792 -15.33051 0.00000 0.00000 0.00000 MINI CONSTR> 108.14060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 133.87116 0.00060 0.01678 0.00002 MINI INTERN> 7.00795 31.28550 0.00000 14.87499 5.03684 MINI EXTERN> -17.15224 -15.32586 0.00000 0.00000 0.00000 MINI CONSTR> 108.14399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 133.87082 0.00035 0.01406 0.00002 MINI INTERN> 7.00526 31.28659 0.00000 14.87385 5.03708 MINI EXTERN> -17.15382 -15.32610 0.00000 0.00000 0.00000 MINI CONSTR> 108.14795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 133.87049 0.00033 0.01382 0.00002 MINI INTERN> 7.00563 31.28478 0.00000 14.87249 5.03707 MINI EXTERN> -17.15572 -15.32574 0.00000 0.00000 0.00000 MINI CONSTR> 108.15197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 133.87017 0.00032 0.01320 0.00002 MINI INTERN> 7.00511 31.28378 0.00000 14.87116 5.03715 MINI EXTERN> -17.15758 -15.32548 0.00000 0.00000 0.00000 MINI CONSTR> 108.15601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 133.86988 0.00028 0.02367 0.00002 MINI INTERN> 7.01421 31.27410 0.00000 14.86933 5.03633 MINI EXTERN> -17.16024 -15.32389 0.00000 0.00000 0.00000 MINI CONSTR> 108.16005 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 133.86959 0.00030 0.01595 0.00002 MINI INTERN> 7.00755 31.27862 0.00000 14.86838 5.03701 MINI EXTERN> -17.16148 -15.32442 0.00000 0.00000 0.00000 MINI CONSTR> 108.16394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 133.86938 0.00021 0.02607 0.00002 MINI INTERN> 7.01564 31.27035 0.00000 14.86684 5.03629 MINI EXTERN> -17.16379 -15.32331 0.00000 0.00000 0.00000 MINI CONSTR> 108.16737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 133.86919 0.00019 0.03391 0.00002 MINI INTERN> 7.01339 31.27026 0.00000 14.86569 5.03658 MINI EXTERN> -17.16519 -15.32237 0.00000 0.00000 0.00000 MINI CONSTR> 108.17083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 133.86901 0.00019 0.03193 0.00002 MINI INTERN> 7.01283 31.26985 0.00000 14.86479 5.03669 MINI EXTERN> -17.16648 -15.32234 0.00000 0.00000 0.00000 MINI CONSTR> 108.17367 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 133.86882 0.00019 0.02889 0.00002 MINI INTERN> 7.01597 31.26633 0.00000 14.86369 5.03646 MINI EXTERN> -17.16812 -15.32207 0.00000 0.00000 0.00000 MINI CONSTR> 108.17655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 133.86860 0.00022 0.00939 0.00001 MINI INTERN> 6.99821 31.28180 0.00000 14.86379 5.03817 MINI EXTERN> -17.16799 -15.32491 0.00000 0.00000 0.00000 MINI CONSTR> 108.17954 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> 390 133.86860 0.00022 0.00939 0.00001 STPD INTERN> 6.99821 31.28180 0.00000 14.86379 5.03817 STPD EXTERN> -17.16799 -15.32491 0.00000 0.00000 0.00000 STPD CONSTR> 108.17954 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 9846 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 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> 0 133.86860 0.00022 0.00939 0.00000 MINI INTERN> 6.99821 31.28180 0.00000 14.86379 5.03817 MINI EXTERN> -17.16799 -15.32491 0.00000 0.00000 0.00000 MINI CONSTR> 108.17954 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> 3 133.86670 0.00190 0.00350 0.02000 CONJ INTERN> 6.99899 31.25698 0.00000 14.84179 5.03997 CONJ EXTERN> -17.20091 -15.31883 0.00000 0.00000 0.00000 CONJ CONSTR> 108.24871 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 ALA 1 HT1 ) 4.1424 ( PROT ALA 1 HT2 ) 4.1424 ( PROT ALA 1 N ) 5.1780 ( PROT ALA 1 HT3 ) 4.1424 ( PROT ALA 1 CA ) 5.1780 ( PROT ALA 1 CB ) 4.1424 ( PROT ALA 1 C ) 5.1780 ( PROT ALA 1 O ) 5.1780 ( PROT LEU 2 N ) 5.1780 ( PROT LEU 2 H ) 4.1424 ( PROT LEU 2 CA ) 5.1780 ( PROT LEU 2 CB ) 4.1424 ( PROT LEU 2 CG ) 4.1424 ( PROT LEU 2 CD1 ) 4.1424 ( PROT LEU 2 CD2 ) 4.1424 ( PROT LEU 2 C ) 5.1780 ( PROT LEU 2 O ) 5.1780 ( PROT GLN 3 N ) 5.1780 ( PROT GLN 3 H ) 4.1424 ( PROT GLN 3 CA ) 5.1780 ( PROT GLN 3 CB ) 4.1424 ( PROT GLN 3 CG ) 4.1424 ( PROT GLN 3 CD ) 4.1424 ( PROT GLN 3 OE1 ) 4.1424 ( PROT GLN 3 NE2 ) 4.1424 ( PROT GLN 3 HE21 ) 4.1424 ( PROT GLN 3 HE22 ) 4.1424 ( PROT GLN 3 C ) 5.1780 ( PROT GLN 3 O ) 5.1780 ( PROT ALA 4 N ) 5.1780 ( PROT ALA 4 H ) 4.1424 ( PROT ALA 4 CA ) 5.1780 ( PROT ALA 4 CB ) 4.1424 ( PROT ALA 4 C ) 5.1780 ( PROT ALA 4 O ) 5.1780 ( PROT PHE 5 N ) 5.1780 ( PROT PHE 5 H ) 4.1424 ( PROT PHE 5 CA ) 5.1780 ( PROT PHE 5 CB ) 4.1424 ( PROT PHE 5 CG ) 4.1424 ( PROT PHE 5 CD1 ) 4.1424 ( PROT PHE 5 CD2 ) 4.1424 ( PROT PHE 5 CE1 ) 4.1424 ( PROT PHE 5 CE2 ) 4.1424 ( PROT PHE 5 CZ ) 4.1424 ( PROT PHE 5 C ) 5.1780 ( PROT PHE 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 ILE 7 N ) 5.1780 ( PROT ILE 7 H ) 4.1424 ( PROT ILE 7 CA ) 5.1780 ( PROT ILE 7 CB ) 4.1424 ( PROT ILE 7 CG2 ) 4.1424 ( PROT ILE 7 CG1 ) 4.1424 ( PROT ILE 7 CD ) 4.1424 ( PROT ILE 7 C ) 5.1780 ( PROT ILE 7 O ) 5.1780 ( PROT ALA 8 N ) 5.1780 ( PROT ALA 8 H ) 4.1424 ( PROT ALA 8 CA ) 5.1780 ( PROT ALA 8 CB ) 4.1424 ( PROT ALA 8 C ) 5.1780 ( PROT ALA 8 O ) 5.1780 ( PROT LEU 9 N ) 5.1780 ( PROT LEU 9 H ) 4.1424 ( PROT LEU 9 CA ) 5.1780 ( PROT LEU 9 CB ) 4.1424 ( PROT LEU 9 CG ) 4.1424 ( PROT LEU 9 CD1 ) 4.1424 ( PROT LEU 9 CD2 ) 4.1424 ( PROT LEU 9 C ) 5.1780 ( PROT LEU 9 O ) 5.1780 ( PROT SER 10 N ) 5.1780 ( PROT SER 10 H ) 4.1424 ( PROT SER 10 CA ) 5.1780 ( PROT SER 10 CB ) 4.1424 ( PROT SER 10 OG ) 4.1424 ( PROT SER 10 HG ) 4.1424 ( PROT SER 10 C ) 5.1780 ( PROT SER 10 O ) 5.1780 ( PROT SER 11 N ) 5.1780 ( PROT SER 11 H ) 4.1424 ( PROT SER 11 CA ) 5.1780 ( PROT SER 11 CB ) 4.1424 ( PROT SER 11 OG ) 4.1424 ( PROT SER 11 HG ) 4.1424 ( PROT SER 11 C ) 5.1780 ( PROT SER 11 O ) 5.1780 ( PROT PHE 12 N ) 5.1780 ( PROT PHE 12 H ) 4.1424 ( PROT PHE 12 CA ) 5.1780 ( PROT PHE 12 CB ) 4.1424 ( PROT PHE 12 CG ) 4.1424 ( PROT PHE 12 CD1 ) 4.1424 ( PROT PHE 12 CD2 ) 4.1424 ( PROT PHE 12 CE1 ) 4.1424 ( PROT PHE 12 CE2 ) 4.1424 ( PROT PHE 12 CZ ) 4.1424 ( PROT PHE 12 C ) 5.1780 ( PROT PHE 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 SER 14 N ) 5.1780 ( PROT SER 14 H ) 4.1424 ( PROT SER 14 CA ) 5.1780 ( PROT SER 14 CB ) 4.1424 ( PROT SER 14 OG ) 4.1424 ( PROT SER 14 HG ) 4.1424 ( PROT SER 14 C ) 5.1780 ( PROT SER 14 O ) 5.1780 ( PROT LYS 15 N ) 5.1780 ( PROT LYS 15 H ) 4.1424 ( PROT LYS 15 CA ) 5.1780 ( PROT LYS 15 CB ) 4.1424 ( PROT LYS 15 CG ) 4.1424 ( PROT LYS 15 CD ) 4.1424 ( PROT LYS 15 CE ) 4.1424 ( PROT LYS 15 NZ ) 4.1424 ( PROT LYS 15 HZ1 ) 4.1424 ( PROT LYS 15 HZ2 ) 4.1424 ( PROT LYS 15 HZ3 ) 4.1424 ( PROT LYS 15 C ) 5.1780 ( PROT LYS 15 O ) 5.1780 ( PROT LEU 16 N ) 5.1780 ( PROT LEU 16 H ) 4.1424 ( PROT LEU 16 CA ) 5.1780 ( PROT LEU 16 CB ) 4.1424 ( PROT LEU 16 CG ) 4.1424 ( PROT LEU 16 CD1 ) 4.1424 ( PROT LEU 16 CD2 ) 4.1424 ( PROT LEU 16 C ) 5.1780 ( PROT LEU 16 O ) 5.1780 ( PROT ALA 17 N ) 5.1780 ( PROT ALA 17 H ) 4.1424 ( PROT ALA 17 CA ) 5.1780 ( PROT ALA 17 CB ) 4.1424 ( PROT ALA 17 C ) 5.1780 ( PROT ALA 17 O ) 5.1780 ( PROT CYS 18 N ) 5.1780 ( PROT CYS 18 H ) 4.1424 ( PROT CYS 18 CA ) 5.1780 ( PROT CYS 18 CB ) 4.1424 ( PROT CYS 18 SG ) 4.1424 ( PROT CYS 18 C ) 5.1780 ( PROT CYS 18 O ) 5.1780 ( PROT GLU 19 N ) 5.1780 ( PROT GLU 19 H ) 4.1424 ( PROT GLU 19 CA ) 5.1780 ( PROT GLU 19 CB ) 4.1424 ( PROT GLU 19 CG ) 4.1424 ( PROT GLU 19 CD ) 4.1424 ( PROT GLU 19 OE1 ) 4.1424 ( PROT GLU 19 OE2 ) 4.1424 ( PROT GLU 19 C ) 5.1780 ( PROT GLU 19 OT1 ) 4.1424 ( PROT GLU 19 OT2 ) 4.1424 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43242 4.57689 -7.53049 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00228 -0.00167 -0.00213 ROTATION MATRIX 1.000000 -0.000146 -0.000201 0.000146 1.000000 0.000351 0.000201 -0.000351 1.000000 AXIS OF ROTATION IS 0.816173 0.467097 -0.340120 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 14.7178 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.295983 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2960" Parameter: A <- "0.2960" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.93035 4.26612 -7.72127 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS 0.00186 0.01414 -0.01099 ROTATION MATRIX 0.999840 0.013870 0.011338 -0.013655 0.999730 -0.018797 -0.011596 0.018639 0.999759 AXIS OF ROTATION IS -0.722459 -0.442590 0.531193 ANGLE IS 1.48 CENTER OF ROTATION 8.829077 4.004970 -8.089251 SHIFT IS -0.013445 TOTAL SQUARE DIFF IS 0.5545 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.170835 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2960" RDCMND substituted energy or value "?RMS" to " 0.1708" Parameter: A <- "0.2960 0.1708" 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 0.2960 0.1708 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 108.25" Parameter: H <- "108.25" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 25.61800 108.24871 2.52730 ENER INTERN> 6.99899 31.25698 0.00000 14.84179 5.03997 ENER EXTERN> -17.20091 -15.31883 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 " 25.62" Parameter: B <- "25.62" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -15.32" Parameter: C <- "-15.32" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -17.20" Parameter: C <- " -32.52" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -32.52" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.00" Parameter: D <- "7.00" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 31.26" Parameter: D <- " 38.26" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 14.84" Parameter: D <- " 53.10" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.04" Parameter: D <- " 58.14" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 58.14" 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= 25.62 GRMS= 2.53 ELEC= -15.32 VDW= -17.20 RDTITL> *EXTERNAL= -32.52 INTERNAL= 58.14 USER= 0.00 HARM= 108.25 RDTITL> *BOND= 7.00 ANGL= 31.26 DIHE= 14.84 IMPR= 5.04 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9846 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9846 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> 0 103.11063 -77.49264 1.01298 0.02000 MINI INTERN> 6.99899 31.25698 0.00000 14.84179 5.03997 MINI EXTERN> -17.20091 -15.31883 0.00000 0.00000 0.00000 MINI CONSTR> 77.49264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 98.98449 4.12614 1.23905 0.00360 MINI INTERN> 6.49020 28.85245 0.00000 15.87996 5.00347 MINI EXTERN> -26.95367 -13.71405 0.00000 0.00000 0.00000 MINI CONSTR> 83.42615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9831 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 97.94252 1.04197 1.80748 0.00156 MINI INTERN> 6.49287 29.92758 0.00000 16.09107 4.96547 MINI EXTERN> -30.59167 -13.40036 0.00000 0.00000 0.00000 MINI CONSTR> 84.45757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 97.16970 0.77282 0.82780 0.00067 MINI INTERN> 6.24162 29.56829 0.00000 16.11338 4.98720 MINI EXTERN> -31.08515 -13.38419 0.00000 0.00000 0.00000 MINI CONSTR> 84.72856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9829 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 96.83527 0.33443 1.21235 0.00070 MINI INTERN> 6.19808 29.44910 0.00000 16.12300 4.96169 MINI EXTERN> -31.43006 -13.42508 0.00000 0.00000 0.00000 MINI CONSTR> 84.95854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 96.47594 0.35933 1.31856 0.00072 MINI INTERN> 6.13729 29.33874 0.00000 16.13141 4.94294 MINI EXTERN> -31.76517 -13.47715 0.00000 0.00000 0.00000 MINI CONSTR> 85.16788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9828 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 96.15457 0.32136 1.28175 0.00075 MINI INTERN> 6.05013 29.24590 0.00000 16.14470 4.92030 MINI EXTERN> -32.01259 -13.52233 0.00000 0.00000 0.00000 MINI CONSTR> 85.32845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 95.84801 0.30657 1.31600 0.00078 MINI INTERN> 5.98445 29.16407 0.00000 16.14568 4.90368 MINI EXTERN> -32.26099 -13.57356 0.00000 0.00000 0.00000 MINI CONSTR> 85.48469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9827 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 95.46715 0.38086 0.41985 0.00034 MINI INTERN> 6.04194 28.92536 0.00000 16.17303 4.85945 MINI EXTERN> -32.49855 -13.62532 0.00000 0.00000 0.00000 MINI CONSTR> 85.59124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 95.36076 0.10638 1.46804 0.00083 MINI INTERN> 5.88100 29.02931 0.00000 16.14486 4.87239 MINI EXTERN> -32.64353 -13.65126 0.00000 0.00000 0.00000 MINI CONSTR> 85.72799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9825 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 94.95820 0.40256 0.42565 0.00036 MINI INTERN> 6.03905 28.72562 0.00000 16.15537 4.83267 MINI EXTERN> -32.91759 -13.69868 0.00000 0.00000 0.00000 MINI CONSTR> 85.82177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 94.75702 0.20118 0.35011 0.00037 MINI INTERN> 5.99824 28.67741 0.00000 16.14074 4.82673 MINI EXTERN> -33.06418 -13.73177 0.00000 0.00000 0.00000 MINI CONSTR> 85.90985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9824 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 94.54297 0.21406 0.34418 0.00039 MINI INTERN> 5.99295 28.59676 0.00000 16.12782 4.81547 MINI EXTERN> -33.22799 -13.76391 0.00000 0.00000 0.00000 MINI CONSTR> 86.00187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 94.35022 0.19274 0.67531 0.00040 MINI INTERN> 6.15612 28.41102 0.00000 16.12011 4.79368 MINI EXTERN> -33.44011 -13.77908 0.00000 0.00000 0.00000 MINI CONSTR> 86.08848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9824 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 94.16031 0.18992 0.42216 0.00042 MINI INTERN> 6.04360 28.40954 0.00000 16.10086 4.79153 MINI EXTERN> -33.53530 -13.81400 0.00000 0.00000 0.00000 MINI CONSTR> 86.16409 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 93.98720 0.17311 0.48846 0.00043 MINI INTERN> 6.08523 28.31031 0.00000 16.08623 4.77971 MINI EXTERN> -33.67996 -13.83235 0.00000 0.00000 0.00000 MINI CONSTR> 86.23803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9822 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 93.86207 0.12513 0.75247 0.00045 MINI INTERN> 6.22764 28.16663 0.00000 16.07438 4.76546 MINI EXTERN> -33.83340 -13.83649 0.00000 0.00000 0.00000 MINI CONSTR> 86.29786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 93.71624 0.14583 0.81465 0.00046 MINI INTERN> 6.28308 28.06205 0.00000 16.06007 4.75416 MINI EXTERN> -33.96470 -13.84088 0.00000 0.00000 0.00000 MINI CONSTR> 86.36245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9822 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 93.58929 0.12695 0.89855 0.00048 MINI INTERN> 6.34094 27.96712 0.00000 16.04526 4.74408 MINI EXTERN> -34.08328 -13.84640 0.00000 0.00000 0.00000 MINI CONSTR> 86.42156 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 93.47052 0.11877 0.84278 0.00050 MINI INTERN> 6.30670 27.94481 0.00000 16.02847 4.74032 MINI EXTERN> -34.15182 -13.87034 0.00000 0.00000 0.00000 MINI CONSTR> 86.47239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9821 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 93.30348 0.16704 0.24918 0.00022 MINI INTERN> 5.83040 28.22093 0.00000 15.99815 4.75627 MINI EXTERN> -34.06621 -13.97723 0.00000 0.00000 0.00000 MINI CONSTR> 86.54117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 93.25027 0.05322 0.90919 0.00054 MINI INTERN> 6.35321 27.81258 0.00000 15.99771 4.72541 MINI EXTERN> -34.33136 -13.88453 0.00000 0.00000 0.00000 MINI CONSTR> 86.57726 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9821 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 93.15177 0.09849 0.95325 0.00056 MINI INTERN> 6.37821 27.75096 0.00000 15.98228 4.71827 MINI EXTERN> -34.41311 -13.89204 0.00000 0.00000 0.00000 MINI CONSTR> 86.62718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 92.99274 0.15903 0.31804 0.00024 MINI INTERN> 5.73692 28.16442 0.00000 15.94642 4.74294 MINI EXTERN> -34.24623 -14.04728 0.00000 0.00000 0.00000 MINI CONSTR> 86.69556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9821 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 92.91543 0.07731 0.21253 0.00025 MINI INTERN> 5.81482 28.06649 0.00000 15.93730 4.73399 MINI EXTERN> -34.32921 -14.03725 0.00000 0.00000 0.00000 MINI CONSTR> 86.72929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 92.82698 0.08845 0.21127 0.00026 MINI INTERN> 5.80021 28.03902 0.00000 15.92080 4.72939 MINI EXTERN> -34.38491 -14.05396 0.00000 0.00000 0.00000 MINI CONSTR> 86.77643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9821 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 92.75213 0.07484 0.44979 0.00027 MINI INTERN> 5.64150 28.13638 0.00000 15.89800 4.73283 MINI EXTERN> -34.37784 -14.10978 0.00000 0.00000 0.00000 MINI CONSTR> 86.83104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 92.67395 0.07819 0.26254 0.00028 MINI INTERN> 5.73695 28.02090 0.00000 15.88818 4.72316 MINI EXTERN> -34.46699 -14.09349 0.00000 0.00000 0.00000 MINI CONSTR> 86.86523 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9820 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 92.61680 0.05715 0.48964 0.00029 MINI INTERN> 5.61039 28.10029 0.00000 15.86827 4.72586 MINI EXTERN> -34.46127 -14.13934 0.00000 0.00000 0.00000 MINI CONSTR> 86.91261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 92.55635 0.06045 0.52429 0.00030 MINI INTERN> 5.58892 28.08995 0.00000 15.85343 4.72299 MINI EXTERN> -34.49631 -14.15511 0.00000 0.00000 0.00000 MINI CONSTR> 86.95249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9819 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 92.50194 0.05441 0.50541 0.00031 MINI INTERN> 5.59132 28.06089 0.00000 15.84172 4.71910 MINI EXTERN> -34.53508 -14.16197 0.00000 0.00000 0.00000 MINI CONSTR> 86.98597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 92.44921 0.05273 0.52675 0.00032 MINI INTERN> 5.57719 28.04728 0.00000 15.82795 4.71631 MINI EXTERN> -34.56778 -14.17457 0.00000 0.00000 0.00000 MINI CONSTR> 87.02283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9819 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 92.38218 0.06703 0.16456 0.00014 MINI INTERN> 5.84125 27.79694 0.00000 15.82611 4.69878 MINI EXTERN> -34.71466 -14.11036 0.00000 0.00000 0.00000 MINI CONSTR> 87.04412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 92.36036 0.02183 0.57943 0.00034 MINI INTERN> 5.54416 28.03036 0.00000 15.80294 4.71166 MINI EXTERN> -34.62024 -14.19868 0.00000 0.00000 0.00000 MINI CONSTR> 87.09016 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9819 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 92.31817 0.04219 0.60518 0.00036 MINI INTERN> 5.52980 28.02110 0.00000 15.79008 4.70940 MINI EXTERN> -34.64629 -14.21026 0.00000 0.00000 0.00000 MINI CONSTR> 87.12433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 92.25136 0.06680 0.19797 0.00015 MINI INTERN> 5.87333 27.70501 0.00000 15.79113 4.68820 MINI EXTERN> -34.82391 -14.12399 0.00000 0.00000 0.00000 MINI CONSTR> 87.14158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9819 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 92.21878 0.03259 0.13795 0.00016 MINI INTERN> 5.81926 27.73092 0.00000 15.77990 4.68878 MINI EXTERN> -34.82607 -14.14276 0.00000 0.00000 0.00000 MINI CONSTR> 87.16874 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 92.18172 0.03706 0.13666 0.00017 MINI INTERN> 5.82162 27.70918 0.00000 15.76860 4.68601 MINI EXTERN> -34.85501 -14.14856 0.00000 0.00000 0.00000 MINI CONSTR> 87.19989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9819 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 92.14966 0.03206 0.28595 0.00017 MINI INTERN> 5.92610 27.60950 0.00000 15.76028 4.67827 MINI EXTERN> -34.92365 -14.12974 0.00000 0.00000 0.00000 MINI CONSTR> 87.22889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 92.11692 0.03274 0.16942 0.00018 MINI INTERN> 5.85270 27.64892 0.00000 15.74822 4.67971 MINI EXTERN> -34.91771 -14.15265 0.00000 0.00000 0.00000 MINI CONSTR> 87.25773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9818 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 92.09233 0.02460 0.31576 0.00019 MINI INTERN> 5.93902 27.56756 0.00000 15.74062 4.67340 MINI EXTERN> -34.97437 -14.13771 0.00000 0.00000 0.00000 MINI CONSTR> 87.28382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 92.06661 0.02572 0.33321 0.00019 MINI INTERN> 5.94621 27.54727 0.00000 15.73124 4.67108 MINI EXTERN> -34.99822 -14.14125 0.00000 0.00000 0.00000 MINI CONSTR> 87.31029 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9818 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 92.04362 0.02299 0.36262 0.00020 MINI INTERN> 5.96052 27.52292 0.00000 15.72238 4.66860 MINI EXTERN> -35.02343 -14.14296 0.00000 0.00000 0.00000 MINI CONSTR> 87.33560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 92.02239 0.02123 0.34197 0.00021 MINI INTERN> 5.95198 27.51736 0.00000 15.71387 4.66760 MINI EXTERN> -35.03698 -14.14919 0.00000 0.00000 0.00000 MINI CONSTR> 87.35774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9816 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 92.00032 0.02206 0.34715 0.00021 MINI INTERN> 5.94998 27.50562 0.00000 15.70490 4.66594 MINI EXTERN> -35.05474 -14.15446 0.00000 0.00000 0.00000 MINI CONSTR> 87.38308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 91.97285 0.02747 0.10920 0.00009 MINI INTERN> 5.76154 27.63632 0.00000 15.69053 4.67321 MINI EXTERN> -34.99675 -14.20386 0.00000 0.00000 0.00000 MINI CONSTR> 87.41185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9816 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 91.96550 0.00736 0.38049 0.00023 MINI INTERN> 5.96765 27.47085 0.00000 15.68939 4.66240 MINI EXTERN> -35.09274 -14.15878 0.00000 0.00000 0.00000 MINI CONSTR> 87.42672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 91.94856 0.01693 0.40278 0.00024 MINI INTERN> 5.97194 27.45693 0.00000 15.68143 4.66075 MINI EXTERN> -35.11017 -14.16233 0.00000 0.00000 0.00000 MINI CONSTR> 87.45001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 91.92083 0.02773 0.13846 0.00010 MINI INTERN> 5.73779 27.62142 0.00000 15.66581 4.66998 MINI EXTERN> -35.03216 -14.22180 0.00000 0.00000 0.00000 MINI CONSTR> 87.47980 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 91.90767 0.01317 0.08714 0.00011 MINI INTERN> 5.76985 27.58701 0.00000 15.66129 4.66733 MINI EXTERN> -35.05659 -14.21649 0.00000 0.00000 0.00000 MINI CONSTR> 87.49527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 91.89204 0.01563 0.16652 0.00011 MINI INTERN> 5.72816 27.60932 0.00000 15.65060 4.66789 MINI EXTERN> -35.05430 -14.23151 0.00000 0.00000 0.00000 MINI CONSTR> 87.52187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 91.87854 0.01350 0.11517 0.00011 MINI INTERN> 5.75024 27.58223 0.00000 15.64518 4.66569 MINI EXTERN> -35.07522 -14.22891 0.00000 0.00000 0.00000 MINI CONSTR> 87.53934 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 91.86610 0.01243 0.13176 0.00012 MINI INTERN> 5.74493 27.57744 0.00000 15.63791 4.66480 MINI EXTERN> -35.08479 -14.23366 0.00000 0.00000 0.00000 MINI CONSTR> 87.55949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 91.85693 0.00917 0.19768 0.00012 MINI INTERN> 5.72114 27.58911 0.00000 15.63067 4.66491 MINI EXTERN> -35.08446 -14.24276 0.00000 0.00000 0.00000 MINI CONSTR> 87.57831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 91.84616 0.01077 0.21261 0.00013 MINI INTERN> 5.72854 27.57526 0.00000 15.62393 4.66354 MINI EXTERN> -35.09811 -14.24421 0.00000 0.00000 0.00000 MINI CONSTR> 87.59720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 91.83678 0.00939 0.23533 0.00013 MINI INTERN> 5.73215 27.56521 0.00000 15.61748 4.66243 MINI EXTERN> -35.10923 -14.24647 0.00000 0.00000 0.00000 MINI CONSTR> 87.61521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 91.82802 0.00875 0.22138 0.00014 MINI INTERN> 5.73121 27.55859 0.00000 15.61264 4.66158 MINI EXTERN> -35.11719 -14.24894 0.00000 0.00000 0.00000 MINI CONSTR> 87.63013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 91.81582 0.01220 0.06589 0.00006 MINI INTERN> 5.77377 27.51620 0.00000 15.61016 4.65881 MINI EXTERN> -35.14620 -14.24092 0.00000 0.00000 0.00000 MINI CONSTR> 87.64400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 91.81170 0.00413 0.23868 0.00015 MINI INTERN> 5.75124 27.53002 0.00000 15.60141 4.65903 MINI EXTERN> -35.14275 -14.24969 0.00000 0.00000 0.00000 MINI CONSTR> 87.66244 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 91.80432 0.00738 0.24813 0.00015 MINI INTERN> 5.76124 27.51653 0.00000 15.59590 4.65787 MINI EXTERN> -35.15519 -14.25017 0.00000 0.00000 0.00000 MINI CONSTR> 87.67813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 91.79258 0.01174 0.08009 0.00007 MINI INTERN> 5.77097 27.49839 0.00000 15.59425 4.65661 MINI EXTERN> -35.17010 -14.24951 0.00000 0.00000 0.00000 MINI CONSTR> 87.69196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 91.78677 0.00581 0.05676 0.00007 MINI INTERN> 5.77026 27.49432 0.00000 15.58956 4.65613 MINI EXTERN> -35.17604 -14.25179 0.00000 0.00000 0.00000 MINI CONSTR> 87.70432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 91.78020 0.00657 0.05587 0.00007 MINI INTERN> 5.76953 27.48886 0.00000 15.58452 4.65548 MINI EXTERN> -35.18317 -14.25443 0.00000 0.00000 0.00000 MINI CONSTR> 87.71941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 91.77436 0.00584 0.11397 0.00007 MINI INTERN> 5.76686 27.48379 0.00000 15.58024 4.65477 MINI EXTERN> -35.18923 -14.25739 0.00000 0.00000 0.00000 MINI CONSTR> 87.73534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 91.76860 0.00576 0.06937 0.00008 MINI INTERN> 5.76739 27.47883 0.00000 15.57532 4.65427 MINI EXTERN> -35.19579 -14.25944 0.00000 0.00000 0.00000 MINI CONSTR> 87.74804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 91.76340 0.00520 0.08207 0.00008 MINI INTERN> 5.76618 27.47397 0.00000 15.57095 4.65367 MINI EXTERN> -35.20151 -14.26183 0.00000 0.00000 0.00000 MINI CONSTR> 87.76196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 91.75972 0.00368 0.12596 0.00008 MINI INTERN> 5.76462 27.47008 0.00000 15.56761 4.65317 MINI EXTERN> -35.20579 -14.26397 0.00000 0.00000 0.00000 MINI CONSTR> 87.77400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 91.75534 0.00438 0.13812 0.00009 MINI INTERN> 5.76343 27.46524 0.00000 15.56360 4.65251 MINI EXTERN> -35.21045 -14.26604 0.00000 0.00000 0.00000 MINI CONSTR> 87.78705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 91.75145 0.00390 0.13418 0.00009 MINI INTERN> 5.76338 27.46121 0.00000 15.55984 4.65210 MINI EXTERN> -35.21538 -14.26789 0.00000 0.00000 0.00000 MINI CONSTR> 87.79818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 91.74766 0.00379 0.13693 0.00009 MINI INTERN> 5.76269 27.45709 0.00000 15.55609 4.65158 MINI EXTERN> -35.21985 -14.26980 0.00000 0.00000 0.00000 MINI CONSTR> 87.80987 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 91.74295 0.00470 0.04412 0.00004 MINI INTERN> 5.76907 27.45364 0.00000 15.55001 4.65189 MINI EXTERN> -35.23022 -14.27185 0.00000 0.00000 0.00000 MINI CONSTR> 87.82041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 91.74158 0.00137 0.15243 0.00010 MINI INTERN> 5.76216 27.44985 0.00000 15.54944 4.65082 MINI EXTERN> -35.22807 -14.27325 0.00000 0.00000 0.00000 MINI CONSTR> 87.83064 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 91.73856 0.00301 0.16040 0.00010 MINI INTERN> 5.76084 27.44627 0.00000 15.54610 4.65023 MINI EXTERN> -35.23143 -14.27504 0.00000 0.00000 0.00000 MINI CONSTR> 87.84160 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 91.73372 0.00485 0.05469 0.00004 MINI INTERN> 5.77026 27.44323 0.00000 15.53903 4.65113 MINI EXTERN> -35.24478 -14.27737 0.00000 0.00000 0.00000 MINI CONSTR> 87.85221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 91.73140 0.00232 0.03530 0.00005 MINI INTERN> 5.76772 27.44078 0.00000 15.53708 4.65066 MINI EXTERN> -35.24621 -14.27866 0.00000 0.00000 0.00000 MINI CONSTR> 87.86003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 91.72862 0.00278 0.06533 0.00005 MINI INTERN> 5.77193 27.43661 0.00000 15.53218 4.65081 MINI EXTERN> -35.25398 -14.28075 0.00000 0.00000 0.00000 MINI CONSTR> 87.87182 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 91.72629 0.00234 0.04679 0.00005 MINI INTERN> 5.76993 27.43403 0.00000 15.52984 4.65040 MINI EXTERN> -35.25605 -14.28217 0.00000 0.00000 0.00000 MINI CONSTR> 87.88030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 91.72412 0.00216 0.05289 0.00005 MINI INTERN> 5.77089 27.43096 0.00000 15.52660 4.65029 MINI EXTERN> -35.26036 -14.28375 0.00000 0.00000 0.00000 MINI CONSTR> 87.88950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 91.72254 0.00159 0.07987 0.00005 MINI INTERN> 5.77375 27.42814 0.00000 15.52324 4.65041 MINI EXTERN> -35.26557 -14.28523 0.00000 0.00000 0.00000 MINI CONSTR> 87.89779 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 91.72066 0.00187 0.08608 0.00005 MINI INTERN> 5.77559 27.42474 0.00000 15.52007 4.65039 MINI EXTERN> -35.27004 -14.28669 0.00000 0.00000 0.00000 MINI CONSTR> 87.90659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 91.71905 0.00161 0.09631 0.00006 MINI INTERN> 5.77766 27.42157 0.00000 15.51701 4.65041 MINI EXTERN> -35.27443 -14.28807 0.00000 0.00000 0.00000 MINI CONSTR> 87.91490 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 91.71755 0.00150 0.09036 0.00006 MINI INTERN> 5.77612 27.42003 0.00000 15.51506 4.65015 MINI EXTERN> -35.27611 -14.28929 0.00000 0.00000 0.00000 MINI CONSTR> 87.92158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 91.71544 0.00212 0.02663 0.00003 MINI INTERN> 5.76438 27.42035 0.00000 15.51509 4.64883 MINI EXTERN> -35.27110 -14.29052 0.00000 0.00000 0.00000 MINI CONSTR> 87.92840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 91.71477 0.00067 0.09786 0.00006 MINI INTERN> 5.77885 27.41445 0.00000 15.50981 4.65012 MINI EXTERN> -35.28316 -14.29174 0.00000 0.00000 0.00000 MINI CONSTR> 87.93644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 91.71353 0.00124 0.10269 0.00007 MINI INTERN> 5.78063 27.41160 0.00000 15.50720 4.65015 MINI EXTERN> -35.28677 -14.29290 0.00000 0.00000 0.00000 MINI CONSTR> 87.94362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 91.71151 0.00201 0.03424 0.00003 MINI INTERN> 5.76099 27.41522 0.00000 15.50873 4.64819 MINI EXTERN> -35.27688 -14.29431 0.00000 0.00000 0.00000 MINI CONSTR> 87.94957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 91.71053 0.00098 0.02285 0.00003 MINI INTERN> 5.76425 27.41258 0.00000 15.50636 4.64843 MINI EXTERN> -35.28091 -14.29516 0.00000 0.00000 0.00000 MINI CONSTR> 87.95499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 91.70941 0.00112 0.02273 0.00003 MINI INTERN> 5.76370 27.41084 0.00000 15.50426 4.64830 MINI EXTERN> -35.28301 -14.29636 0.00000 0.00000 0.00000 MINI CONSTR> 87.96169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 91.70846 0.00095 0.04821 0.00003 MINI INTERN> 5.75666 27.41139 0.00000 15.50328 4.64757 MINI EXTERN> -35.28109 -14.29780 0.00000 0.00000 0.00000 MINI CONSTR> 87.96844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 91.70746 0.00099 0.02825 0.00003 MINI INTERN> 5.76082 27.40833 0.00000 15.50068 4.64791 MINI EXTERN> -35.28573 -14.29866 0.00000 0.00000 0.00000 MINI CONSTR> 87.97411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 91.70673 0.00073 0.05258 0.00003 MINI INTERN> 5.75417 27.40916 0.00000 15.49989 4.64727 MINI EXTERN> -35.28380 -14.30000 0.00000 0.00000 0.00000 MINI CONSTR> 87.98004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 91.70596 0.00077 0.05603 0.00004 MINI INTERN> 5.75244 27.40831 0.00000 15.49834 4.64708 MINI EXTERN> -35.28477 -14.30110 0.00000 0.00000 0.00000 MINI CONSTR> 87.98564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 91.70527 0.00069 0.06108 0.00004 MINI INTERN> 5.75055 27.40760 0.00000 15.49692 4.64689 MINI EXTERN> -35.28551 -14.30216 0.00000 0.00000 0.00000 MINI CONSTR> 87.99097 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 91.70463 0.00064 0.05742 0.00004 MINI INTERN> 5.75197 27.40574 0.00000 15.49520 4.64699 MINI EXTERN> -35.28791 -14.30287 0.00000 0.00000 0.00000 MINI CONSTR> 87.99550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 91.70396 0.00067 0.05798 0.00004 MINI INTERN> 5.75036 27.40503 0.00000 15.49375 4.64685 MINI EXTERN> -35.28884 -14.30393 0.00000 0.00000 0.00000 MINI CONSTR> 88.00073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 91.70313 0.00083 0.01832 0.00002 MINI INTERN> 5.76818 27.39669 0.00000 15.48913 4.64837 MINI EXTERN> -35.30104 -14.30388 0.00000 0.00000 0.00000 MINI CONSTR> 88.00568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 91.70292 0.00021 0.06362 0.00004 MINI INTERN> 5.74848 27.40332 0.00000 15.49114 4.64668 MINI EXTERN> -35.29079 -14.30564 0.00000 0.00000 0.00000 MINI CONSTR> 88.00973 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 91.70204 0.00088 0.01869 0.00002 MINI INTERN> 5.76929 27.39366 0.00000 15.48592 4.64845 MINI EXTERN> -35.30480 -14.30545 0.00000 0.00000 0.00000 MINI CONSTR> 88.01499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 91.70161 0.00043 0.01512 0.00002 MINI INTERN> 5.76700 27.39355 0.00000 15.48508 4.64826 MINI EXTERN> -35.30474 -14.30625 0.00000 0.00000 0.00000 MINI CONSTR> 88.01872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 91.70114 0.00047 0.01498 0.00002 MINI INTERN> 5.76740 27.39220 0.00000 15.48360 4.64830 MINI EXTERN> -35.30642 -14.30700 0.00000 0.00000 0.00000 MINI CONSTR> 88.02306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 91.70073 0.00041 0.03016 0.00002 MINI INTERN> 5.77555 27.38761 0.00000 15.48070 4.64897 MINI EXTERN> -35.31263 -14.30733 0.00000 0.00000 0.00000 MINI CONSTR> 88.02785 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 91.70073 0.00041 0.03016 0.00002 STPD INTERN> 5.77555 27.38761 0.00000 15.48070 4.64897 STPD EXTERN> -35.31263 -14.30733 0.00000 0.00000 0.00000 STPD CONSTR> 88.02785 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 9814 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 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 91.70073 0.00041 0.03016 0.00000 MINI INTERN> 5.77555 27.38761 0.00000 15.48070 4.64897 MINI EXTERN> -35.31263 -14.30733 0.00000 0.00000 0.00000 MINI CONSTR> 88.02785 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 91.69481 0.00592 0.00340 0.02000 CONJ INTERN> 5.76443 27.36077 0.00000 15.44536 4.64870 CONJ EXTERN> -35.34610 -14.32756 0.00000 0.00000 0.00000 CONJ CONSTR> 88.14923 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 ALA 1 HT1 ) 2.6925 ( PROT ALA 1 HT2 ) 2.6925 ( PROT ALA 1 N ) 3.3657 ( PROT ALA 1 HT3 ) 2.6925 ( PROT ALA 1 CA ) 3.3657 ( PROT ALA 1 CB ) 2.6925 ( PROT ALA 1 C ) 3.3657 ( PROT ALA 1 O ) 3.3657 ( PROT LEU 2 N ) 3.3657 ( PROT LEU 2 H ) 2.6925 ( PROT LEU 2 CA ) 3.3657 ( PROT LEU 2 CB ) 2.6925 ( PROT LEU 2 CG ) 2.6925 ( PROT LEU 2 CD1 ) 2.6925 ( PROT LEU 2 CD2 ) 2.6925 ( PROT LEU 2 C ) 3.3657 ( PROT LEU 2 O ) 3.3657 ( PROT GLN 3 N ) 3.3657 ( PROT GLN 3 H ) 2.6925 ( PROT GLN 3 CA ) 3.3657 ( PROT GLN 3 CB ) 2.6925 ( PROT GLN 3 CG ) 2.6925 ( PROT GLN 3 CD ) 2.6925 ( PROT GLN 3 OE1 ) 2.6925 ( PROT GLN 3 NE2 ) 2.6925 ( PROT GLN 3 HE21 ) 2.6925 ( PROT GLN 3 HE22 ) 2.6925 ( PROT GLN 3 C ) 3.3657 ( PROT GLN 3 O ) 3.3657 ( PROT ALA 4 N ) 3.3657 ( PROT ALA 4 H ) 2.6925 ( PROT ALA 4 CA ) 3.3657 ( PROT ALA 4 CB ) 2.6925 ( PROT ALA 4 C ) 3.3657 ( PROT ALA 4 O ) 3.3657 ( PROT PHE 5 N ) 3.3657 ( PROT PHE 5 H ) 2.6925 ( PROT PHE 5 CA ) 3.3657 ( PROT PHE 5 CB ) 2.6925 ( PROT PHE 5 CG ) 2.6925 ( PROT PHE 5 CD1 ) 2.6925 ( PROT PHE 5 CD2 ) 2.6925 ( PROT PHE 5 CE1 ) 2.6925 ( PROT PHE 5 CE2 ) 2.6925 ( PROT PHE 5 CZ ) 2.6925 ( PROT PHE 5 C ) 3.3657 ( PROT PHE 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 ILE 7 N ) 3.3657 ( PROT ILE 7 H ) 2.6925 ( PROT ILE 7 CA ) 3.3657 ( PROT ILE 7 CB ) 2.6925 ( PROT ILE 7 CG2 ) 2.6925 ( PROT ILE 7 CG1 ) 2.6925 ( PROT ILE 7 CD ) 2.6925 ( PROT ILE 7 C ) 3.3657 ( PROT ILE 7 O ) 3.3657 ( PROT ALA 8 N ) 3.3657 ( PROT ALA 8 H ) 2.6925 ( PROT ALA 8 CA ) 3.3657 ( PROT ALA 8 CB ) 2.6925 ( PROT ALA 8 C ) 3.3657 ( PROT ALA 8 O ) 3.3657 ( PROT LEU 9 N ) 3.3657 ( PROT LEU 9 H ) 2.6925 ( PROT LEU 9 CA ) 3.3657 ( PROT LEU 9 CB ) 2.6925 ( PROT LEU 9 CG ) 2.6925 ( PROT LEU 9 CD1 ) 2.6925 ( PROT LEU 9 CD2 ) 2.6925 ( PROT LEU 9 C ) 3.3657 ( PROT LEU 9 O ) 3.3657 ( PROT SER 10 N ) 3.3657 ( PROT SER 10 H ) 2.6925 ( PROT SER 10 CA ) 3.3657 ( PROT SER 10 CB ) 2.6925 ( PROT SER 10 OG ) 2.6925 ( PROT SER 10 HG ) 2.6925 ( PROT SER 10 C ) 3.3657 ( PROT SER 10 O ) 3.3657 ( PROT SER 11 N ) 3.3657 ( PROT SER 11 H ) 2.6925 ( PROT SER 11 CA ) 3.3657 ( PROT SER 11 CB ) 2.6925 ( PROT SER 11 OG ) 2.6925 ( PROT SER 11 HG ) 2.6925 ( PROT SER 11 C ) 3.3657 ( PROT SER 11 O ) 3.3657 ( PROT PHE 12 N ) 3.3657 ( PROT PHE 12 H ) 2.6925 ( PROT PHE 12 CA ) 3.3657 ( PROT PHE 12 CB ) 2.6925 ( PROT PHE 12 CG ) 2.6925 ( PROT PHE 12 CD1 ) 2.6925 ( PROT PHE 12 CD2 ) 2.6925 ( PROT PHE 12 CE1 ) 2.6925 ( PROT PHE 12 CE2 ) 2.6925 ( PROT PHE 12 CZ ) 2.6925 ( PROT PHE 12 C ) 3.3657 ( PROT PHE 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 SER 14 N ) 3.3657 ( PROT SER 14 H ) 2.6925 ( PROT SER 14 CA ) 3.3657 ( PROT SER 14 CB ) 2.6925 ( PROT SER 14 OG ) 2.6925 ( PROT SER 14 HG ) 2.6925 ( PROT SER 14 C ) 3.3657 ( PROT SER 14 O ) 3.3657 ( PROT LYS 15 N ) 3.3657 ( PROT LYS 15 H ) 2.6925 ( PROT LYS 15 CA ) 3.3657 ( PROT LYS 15 CB ) 2.6925 ( PROT LYS 15 CG ) 2.6925 ( PROT LYS 15 CD ) 2.6925 ( PROT LYS 15 CE ) 2.6925 ( PROT LYS 15 NZ ) 2.6925 ( PROT LYS 15 HZ1 ) 2.6925 ( PROT LYS 15 HZ2 ) 2.6925 ( PROT LYS 15 HZ3 ) 2.6925 ( PROT LYS 15 C ) 3.3657 ( PROT LYS 15 O ) 3.3657 ( PROT LEU 16 N ) 3.3657 ( PROT LEU 16 H ) 2.6925 ( PROT LEU 16 CA ) 3.3657 ( PROT LEU 16 CB ) 2.6925 ( PROT LEU 16 CG ) 2.6925 ( PROT LEU 16 CD1 ) 2.6925 ( PROT LEU 16 CD2 ) 2.6925 ( PROT LEU 16 C ) 3.3657 ( PROT LEU 16 O ) 3.3657 ( PROT ALA 17 N ) 3.3657 ( PROT ALA 17 H ) 2.6925 ( PROT ALA 17 CA ) 3.3657 ( PROT ALA 17 CB ) 2.6925 ( PROT ALA 17 C ) 3.3657 ( PROT ALA 17 O ) 3.3657 ( PROT CYS 18 N ) 3.3657 ( PROT CYS 18 H ) 2.6925 ( PROT CYS 18 CA ) 3.3657 ( PROT CYS 18 CB ) 2.6925 ( PROT CYS 18 SG ) 2.6925 ( PROT CYS 18 C ) 3.3657 ( PROT CYS 18 O ) 3.3657 ( PROT GLU 19 N ) 3.3657 ( PROT GLU 19 H ) 2.6925 ( PROT GLU 19 CA ) 3.3657 ( PROT GLU 19 CB ) 2.6925 ( PROT GLU 19 CG ) 2.6925 ( PROT GLU 19 CD ) 2.6925 ( PROT GLU 19 OE1 ) 2.6925 ( PROT GLU 19 OE2 ) 2.6925 ( PROT GLU 19 C ) 3.3657 ( PROT GLU 19 OT1 ) 2.6925 ( PROT GLU 19 OT2 ) 2.6925 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43182 4.57662 -7.52983 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00288 -0.00140 -0.00279 ROTATION MATRIX 1.000000 -0.000184 -0.000252 0.000184 1.000000 0.000427 0.000252 -0.000427 1.000000 AXIS OF ROTATION IS 0.807607 0.476206 -0.347849 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 18.5481 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.332273 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3323" Parameter: A <- "0.3323" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.93304 4.26739 -7.72367 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.00083 0.01287 -0.00859 ROTATION MATRIX 0.999807 0.015162 0.012516 -0.014897 0.999669 -0.020976 -0.012830 0.020786 0.999702 AXIS OF ROTATION IS -0.728094 -0.441874 0.524049 ANGLE IS 1.64 CENTER OF ROTATION 8.829894 4.040602 -8.067351 SHIFT IS -0.009586 TOTAL SQUARE DIFF IS 0.8149 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.207092 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3323" RDCMND substituted energy or value "?RMS" to " 0.2071" Parameter: A <- "0.3323 0.2071" 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 0.3323 0.2071 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 " 88.15" Parameter: H <- "88.15" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 3.54559 88.14923 1.83356 ENER INTERN> 5.76443 27.36077 0.00000 15.44536 4.64870 ENER EXTERN> -35.34610 -14.32756 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 3.55" Parameter: B <- "3.55" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -14.33" Parameter: C <- "-14.33" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -35.35" Parameter: C <- " -49.68" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -49.68" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.76" Parameter: D <- "5.76" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 27.36" Parameter: D <- " 33.12" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 15.45" Parameter: D <- " 48.57" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.65" Parameter: D <- " 53.22" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 53.22" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 6000 ENER= 3.55 GRMS= 1.83 ELEC= -14.33 VDW= -35.35 RDTITL> *EXTERNAL= -49.68 INTERNAL= 53.22 USER= 0.00 HARM= 88.15 RDTITL> *BOND= 5.76 ANGL= 27.36 DIHE= 15.45 IMPR= 4.65 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "6000" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../pdb/mini_helix_allh_6000.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../pdb/mini_helix_allh_6000.pdb CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 6000 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 6000 ENER= 3.55 GRMS= 1.83 ELEC= -14.33 VDW= -35.35 RDTITL> *EXTERNAL= -49.68 INTERNAL= 53.22 USER= 0.00 HARM= 88.15 RDTITL> *BOND= 5.76 ANGL= 27.36 DIHE= 15.45 IMPR= 4.65 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "6000" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../crd/mini_helix_allh_6000.crd:: OPNLGU> Unit 1 opened for WRITE access to ../crd/mini_helix_allh_6000.crd CHARMM> CHARMM> FORMAT (F8.2) CHARMM> write coor pdb unit 1 RDTITL> * MINIMIZATION OF HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * JOBNAME: MINI_"helix_allh" : MINIMIZATION STEP= 6000 RDTITL> *=========================================================== RDTITL> * ENERGIES: RDTITL> *STEP= 6000 ENER= 3.55 GRMS= 1.83 ELEC= -14.33 VDW= -35.35 RDTITL> *EXTERNAL= -49.68 INTERNAL= 53.22 USER= 0.00 HARM= 88.15 RDTITL> *BOND= 5.76 ANGL= 27.36 DIHE= 15.45 IMPR= 4.65 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 6000 0.3323 0.2071 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "6000" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9814 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9814 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 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 66.47665 -62.93106 0.73275 0.02000 MINI INTERN> 5.76443 27.36077 0.00000 15.44536 4.64870 MINI EXTERN> -35.34610 -14.32756 0.00000 0.00000 0.00000 MINI CONSTR> 62.93106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 84.36323 -17.88658 15.82960 0.00864 MINI INTERN> 28.37447 23.20765 0.00000 17.09513 3.92156 MINI EXTERN> -44.17294 -11.03756 0.00000 0.00000 0.00000 MINI CONSTR> 66.97493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9808 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 66.70872 17.65451 6.60126 0.00373 MINI INTERN> 6.44872 29.24007 0.00000 16.19121 4.95135 MINI EXTERN> -44.35897 -13.37481 0.00000 0.00000 0.00000 MINI CONSTR> 67.61115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 62.82091 3.88781 0.40279 0.00067 MINI INTERN> 5.45694 26.40661 0.00000 16.46702 4.61790 MINI EXTERN> -45.10278 -12.68294 0.00000 0.00000 0.00000 MINI CONSTR> 67.65816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9805 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 62.49619 0.32472 1.00915 0.00070 MINI INTERN> 5.67425 26.29788 0.00000 16.40804 4.65001 MINI EXTERN> -45.62988 -12.81928 0.00000 0.00000 0.00000 MINI CONSTR> 67.91517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 62.19710 0.29909 1.08787 0.00072 MINI INTERN> 5.62229 26.23185 0.00000 16.40797 4.64059 MINI EXTERN> -45.91238 -12.90206 0.00000 0.00000 0.00000 MINI CONSTR> 68.10883 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9805 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 61.92707 0.27002 1.05912 0.00075 MINI INTERN> 5.61168 26.13537 0.00000 16.40839 4.62190 MINI EXTERN> -46.13642 -12.97976 0.00000 0.00000 0.00000 MINI CONSTR> 68.26591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 61.60162 0.32545 0.35757 0.00032 MINI INTERN> 5.34662 25.94622 0.00000 16.48778 4.52711 MINI EXTERN> -46.12508 -12.97297 0.00000 0.00000 0.00000 MINI CONSTR> 68.39195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9801 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 61.47740 0.12423 1.21345 0.00080 MINI INTERN> 5.65293 25.95921 0.00000 16.38647 4.60015 MINI EXTERN> -46.56691 -13.10485 0.00000 0.00000 0.00000 MINI CONSTR> 68.55040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 61.29516 0.18224 1.41684 0.00083 MINI INTERN> 5.53858 25.86676 0.00000 16.40436 4.57124 MINI EXTERN> -46.69618 -13.06652 0.00000 0.00000 0.00000 MINI CONSTR> 68.67694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9801 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 60.95339 0.34178 0.39200 0.00036 MINI INTERN> 5.27082 25.73121 0.00000 16.46901 4.48520 MINI EXTERN> -46.65634 -13.11947 0.00000 0.00000 0.00000 MINI CONSTR> 68.77296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 60.77761 0.17578 0.31079 0.00037 MINI INTERN> 5.27227 25.68995 0.00000 16.44702 4.48722 MINI EXTERN> -46.82339 -13.16814 0.00000 0.00000 0.00000 MINI CONSTR> 68.87267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9799 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 60.59780 0.17981 0.32124 0.00039 MINI INTERN> 5.24151 25.63459 0.00000 16.43781 4.47504 MINI EXTERN> -46.95917 -13.20787 0.00000 0.00000 0.00000 MINI CONSTR> 68.97588 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 60.42600 0.17180 0.54318 0.00040 MINI INTERN> 5.16301 25.57222 0.00000 16.44832 4.44357 MINI EXTERN> -47.04590 -13.23666 0.00000 0.00000 0.00000 MINI CONSTR> 69.08144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9796 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 60.25951 0.16648 0.40781 0.00042 MINI INTERN> 5.19551 25.51910 0.00000 16.41665 4.44871 MINI EXTERN> -47.20623 -13.28521 0.00000 0.00000 0.00000 MINI CONSTR> 69.17098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 60.12611 0.13340 0.63424 0.00043 MINI INTERN> 5.10398 25.48275 0.00000 16.42721 4.42172 MINI EXTERN> -47.26458 -13.30250 0.00000 0.00000 0.00000 MINI CONSTR> 69.25754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9794 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 59.98625 0.13986 0.69115 0.00045 MINI INTERN> 5.12754 25.43209 0.00000 16.40646 4.41495 MINI EXTERN> -47.38071 -13.35406 0.00000 0.00000 0.00000 MINI CONSTR> 69.33997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 59.86040 0.12585 0.71768 0.00046 MINI INTERN> 5.04028 25.41907 0.00000 16.40521 4.40190 MINI EXTERN> -47.44855 -13.37250 0.00000 0.00000 0.00000 MINI CONSTR> 69.41499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9790 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 59.73453 0.12586 0.76538 0.00048 MINI INTERN> 5.01419 25.37582 0.00000 16.39201 4.39286 MINI EXTERN> -47.53982 -13.39223 0.00000 0.00000 0.00000 MINI CONSTR> 69.49170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 59.61675 0.11778 0.72214 0.00050 MINI INTERN> 5.00355 25.35071 0.00000 16.37339 4.39039 MINI EXTERN> -47.62816 -13.43012 0.00000 0.00000 0.00000 MINI CONSTR> 69.55700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9789 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 59.49971 0.11705 0.76783 0.00052 MINI INTERN> 5.00592 25.29084 0.00000 16.35238 4.38643 MINI EXTERN> -47.72971 -13.43619 0.00000 0.00000 0.00000 MINI CONSTR> 69.63003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 59.35599 0.14372 0.23965 0.00022 MINI INTERN> 5.22231 25.19467 0.00000 16.26579 4.43103 MINI EXTERN> -47.96450 -13.48733 0.00000 0.00000 0.00000 MINI CONSTR> 69.69402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9789 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 59.30678 0.04921 0.81821 0.00056 MINI INTERN> 4.92437 25.26503 0.00000 16.33408 4.36953 MINI EXTERN> -47.84296 -13.49313 0.00000 0.00000 0.00000 MINI CONSTR> 69.74986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 59.21531 0.09147 0.91587 0.00058 MINI INTERN> 5.00695 25.20835 0.00000 16.30347 4.36796 MINI EXTERN> -47.93976 -13.54355 0.00000 0.00000 0.00000 MINI CONSTR> 69.81189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9789 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 59.06177 0.15354 0.27855 0.00025 MINI INTERN> 5.23837 25.07325 0.00000 16.20554 4.42127 MINI EXTERN> -48.20022 -13.55279 0.00000 0.00000 0.00000 MINI CONSTR> 69.87634 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 58.98314 0.07863 0.20276 0.00026 MINI INTERN> 5.18962 25.05277 0.00000 16.20342 4.40819 MINI EXTERN> -48.22603 -13.56721 0.00000 0.00000 0.00000 MINI CONSTR> 69.92237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 58.89634 0.08679 0.21258 0.00027 MINI INTERN> 5.19789 25.01418 0.00000 16.18265 4.40596 MINI EXTERN> -48.29750 -13.58571 0.00000 0.00000 0.00000 MINI CONSTR> 69.97886 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 58.81888 0.07746 0.39018 0.00028 MINI INTERN> 5.29044 24.95593 0.00000 16.14137 4.41687 MINI EXTERN> -48.41342 -13.61089 0.00000 0.00000 0.00000 MINI CONSTR> 70.03857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 58.73961 0.07927 0.25542 0.00029 MINI INTERN> 5.21430 24.94465 0.00000 16.14252 4.40233 MINI EXTERN> -48.42786 -13.62096 0.00000 0.00000 0.00000 MINI CONSTR> 70.08464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 58.67053 0.06908 0.33532 0.00030 MINI INTERN> 5.26147 24.90089 0.00000 16.11533 4.40463 MINI EXTERN> -48.50417 -13.64321 0.00000 0.00000 0.00000 MINI CONSTR> 70.13559 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 58.61437 0.05616 0.44949 0.00031 MINI INTERN> 5.31779 24.85325 0.00000 16.08779 4.40899 MINI EXTERN> -48.58048 -13.65498 0.00000 0.00000 0.00000 MINI CONSTR> 70.18201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 58.54991 0.06446 0.48878 0.00032 MINI INTERN> 5.32405 24.83058 0.00000 16.06986 4.40635 MINI EXTERN> -48.63085 -13.68002 0.00000 0.00000 0.00000 MINI CONSTR> 70.22994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 58.49552 0.05439 0.53757 0.00033 MINI INTERN> 5.33928 24.79110 0.00000 16.05121 4.40617 MINI EXTERN> -48.68652 -13.67990 0.00000 0.00000 0.00000 MINI CONSTR> 70.27417 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 58.44070 0.05481 0.50147 0.00034 MINI INTERN> 5.34929 24.76168 0.00000 16.03747 4.40150 MINI EXTERN> -48.72278 -13.69846 0.00000 0.00000 0.00000 MINI CONSTR> 70.31200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 58.38468 0.05603 0.52571 0.00036 MINI INTERN> 5.32730 24.74379 0.00000 16.02473 4.39849 MINI EXTERN> -48.76172 -13.70458 0.00000 0.00000 0.00000 MINI CONSTR> 70.35666 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 58.31583 0.06885 0.16875 0.00015 MINI INTERN> 5.10366 24.79225 0.00000 16.06381 4.36203 MINI EXTERN> -48.67800 -13.71506 0.00000 0.00000 0.00000 MINI CONSTR> 70.38714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 58.29366 0.02217 0.56459 0.00038 MINI INTERN> 5.38063 24.68070 0.00000 15.98990 4.39543 MINI EXTERN> -48.84734 -13.73745 0.00000 0.00000 0.00000 MINI CONSTR> 70.43179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 58.25043 0.04323 0.63509 0.00040 MINI INTERN> 5.32967 24.67222 0.00000 15.98490 4.38988 MINI EXTERN> -48.86869 -13.72991 0.00000 0.00000 0.00000 MINI CONSTR> 70.47235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 58.17723 0.07320 0.19335 0.00017 MINI INTERN> 5.07425 24.74010 0.00000 16.02954 4.35071 MINI EXTERN> -48.76872 -13.74938 0.00000 0.00000 0.00000 MINI CONSTR> 70.50072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 58.13984 0.03739 0.13964 0.00018 MINI INTERN> 5.10555 24.71217 0.00000 16.00997 4.35437 MINI EXTERN> -48.81509 -13.75943 0.00000 0.00000 0.00000 MINI CONSTR> 70.53230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 58.09802 0.04182 0.14540 0.00019 MINI INTERN> 5.09509 24.69669 0.00000 15.99918 4.35047 MINI EXTERN> -48.84143 -13.77096 0.00000 0.00000 0.00000 MINI CONSTR> 70.56898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 58.06117 0.03685 0.27233 0.00019 MINI INTERN> 5.02652 24.70359 0.00000 16.00285 4.33768 MINI EXTERN> -48.83582 -13.77892 0.00000 0.00000 0.00000 MINI CONSTR> 70.60526 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 58.02275 0.03842 0.16892 0.00020 MINI INTERN> 5.07211 24.66848 0.00000 15.97961 4.34287 MINI EXTERN> -48.88808 -13.79029 0.00000 0.00000 0.00000 MINI CONSTR> 70.63806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 57.98656 0.03619 0.19374 0.00021 MINI INTERN> 5.05910 24.65326 0.00000 15.97001 4.33898 MINI EXTERN> -48.91098 -13.79703 0.00000 0.00000 0.00000 MINI CONSTR> 70.67323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9787 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 57.95995 0.02661 0.30955 0.00021 MINI INTERN> 5.00573 24.66154 0.00000 15.97249 4.32881 MINI EXTERN> -48.90568 -13.80627 0.00000 0.00000 0.00000 MINI CONSTR> 70.70332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 57.92777 0.03218 0.32248 0.00022 MINI INTERN> 5.00674 24.64309 0.00000 15.96149 4.32563 MINI EXTERN> -48.92949 -13.81593 0.00000 0.00000 0.00000 MINI CONSTR> 70.73624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9786 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 57.89954 0.02823 0.36972 0.00023 MINI INTERN> 4.99561 24.62698 0.00000 15.95303 4.32215 MINI EXTERN> -48.94971 -13.81700 0.00000 0.00000 0.00000 MINI CONSTR> 70.76847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 57.87317 0.02637 0.34630 0.00024 MINI INTERN> 4.99387 24.62147 0.00000 15.94334 4.32082 MINI EXTERN> -48.96812 -13.83295 0.00000 0.00000 0.00000 MINI CONSTR> 70.79474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9786 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 57.84676 0.02640 0.36791 0.00025 MINI INTERN> 4.99565 24.60097 0.00000 15.93154 4.32059 MINI EXTERN> -48.99560 -13.83167 0.00000 0.00000 0.00000 MINI CONSTR> 70.82528 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 57.81422 0.03254 0.11339 0.00011 MINI INTERN> 5.11668 24.54878 0.00000 15.89055 4.33934 MINI EXTERN> -49.08015 -13.85314 0.00000 0.00000 0.00000 MINI CONSTR> 70.85216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 57.80290 0.01132 0.39102 0.00027 MINI INTERN> 4.96173 24.59814 0.00000 15.92022 4.31420 MINI EXTERN> -49.01653 -13.85144 0.00000 0.00000 0.00000 MINI CONSTR> 70.87659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 57.78172 0.02119 0.43415 0.00028 MINI INTERN> 4.99362 24.57917 0.00000 15.90560 4.31388 MINI EXTERN> -49.04277 -13.87165 0.00000 0.00000 0.00000 MINI CONSTR> 70.90388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 57.74666 0.03506 0.13459 0.00012 MINI INTERN> 5.13030 24.50711 0.00000 15.85865 4.33738 MINI EXTERN> -49.14363 -13.87578 0.00000 0.00000 0.00000 MINI CONSTR> 70.93263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 57.72850 0.01816 0.09718 0.00012 MINI INTERN> 5.10580 24.50526 0.00000 15.85721 4.33225 MINI EXTERN> -49.14506 -13.88047 0.00000 0.00000 0.00000 MINI CONSTR> 70.95350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 57.70803 0.02047 0.10003 0.00013 MINI INTERN> 5.10850 24.49248 0.00000 15.84720 4.33157 MINI EXTERN> -49.16436 -13.88708 0.00000 0.00000 0.00000 MINI CONSTR> 70.97972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 57.69001 0.01802 0.18788 0.00013 MINI INTERN> 5.15517 24.46521 0.00000 15.82680 4.33713 MINI EXTERN> -49.20486 -13.89688 0.00000 0.00000 0.00000 MINI CONSTR> 71.00745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 57.67141 0.01860 0.11854 0.00014 MINI INTERN> 5.12171 24.46743 0.00000 15.82689 4.33108 MINI EXTERN> -49.20231 -13.90235 0.00000 0.00000 0.00000 MINI CONSTR> 71.02896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 57.65454 0.01687 0.15061 0.00014 MINI INTERN> 5.13162 24.45246 0.00000 15.81571 4.33188 MINI EXTERN> -49.22402 -13.90688 0.00000 0.00000 0.00000 MINI CONSTR> 71.05376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 57.64161 0.01293 0.21431 0.00015 MINI INTERN> 5.16668 24.43062 0.00000 15.80079 4.33504 MINI EXTERN> -49.25253 -13.91479 0.00000 0.00000 0.00000 MINI CONSTR> 71.07581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 57.62647 0.01514 0.23434 0.00015 MINI INTERN> 5.17034 24.42323 0.00000 15.79235 4.33398 MINI EXTERN> -49.26614 -13.92595 0.00000 0.00000 0.00000 MINI CONSTR> 71.09865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 57.61351 0.01296 0.25269 0.00016 MINI INTERN> 5.18082 24.40662 0.00000 15.78262 4.33483 MINI EXTERN> -49.28544 -13.92596 0.00000 0.00000 0.00000 MINI CONSTR> 71.12001 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 57.60043 0.01308 0.23857 0.00016 MINI INTERN> 5.18142 24.39854 0.00000 15.77668 4.33298 MINI EXTERN> -49.29461 -13.93337 0.00000 0.00000 0.00000 MINI CONSTR> 71.13880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 57.58737 0.01306 0.25472 0.00017 MINI INTERN> 5.16995 24.39252 0.00000 15.77111 4.33178 MINI EXTERN> -49.30484 -13.93361 0.00000 0.00000 0.00000 MINI CONSTR> 71.16046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 57.57123 0.01614 0.08073 0.00007 MINI INTERN> 5.07456 24.42237 0.00000 15.78742 4.31724 MINI EXTERN> -49.26798 -13.93806 0.00000 0.00000 0.00000 MINI CONSTR> 71.17566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 57.56540 0.00583 0.26910 0.00018 MINI INTERN> 5.19490 24.36777 0.00000 15.75406 4.33175 MINI EXTERN> -49.33397 -13.94702 0.00000 0.00000 0.00000 MINI CONSTR> 71.19790 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 57.55403 0.01137 0.28225 0.00019 MINI INTERN> 5.19695 24.36255 0.00000 15.74708 4.33073 MINI EXTERN> -49.34408 -13.95712 0.00000 0.00000 0.00000 MINI CONSTR> 71.21791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 57.53697 0.01706 0.09403 0.00008 MINI INTERN> 5.06261 24.40427 0.00000 15.77060 4.31297 MINI EXTERN> -49.29466 -13.95273 0.00000 0.00000 0.00000 MINI CONSTR> 71.23391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 57.52796 0.00901 0.06891 0.00009 MINI INTERN> 5.07734 24.39277 0.00000 15.76161 4.31477 MINI EXTERN> -49.31089 -13.95735 0.00000 0.00000 0.00000 MINI CONSTR> 71.24972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 57.51803 0.00994 0.07156 0.00009 MINI INTERN> 5.07282 24.38800 0.00000 15.75660 4.31337 MINI EXTERN> -49.31836 -13.96227 0.00000 0.00000 0.00000 MINI CONSTR> 71.26787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 57.50880 0.00922 0.12560 0.00009 MINI INTERN> 5.04405 24.39234 0.00000 15.75716 4.30855 MINI EXTERN> -49.31461 -13.96520 0.00000 0.00000 0.00000 MINI CONSTR> 71.28651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 57.49973 0.00908 0.08530 0.00010 MINI INTERN> 5.06338 24.37903 0.00000 15.74723 4.31056 MINI EXTERN> -49.33199 -13.97135 0.00000 0.00000 0.00000 MINI CONSTR> 71.30287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 57.49149 0.00824 0.10606 0.00010 MINI INTERN> 5.05060 24.37745 0.00000 15.74436 4.30852 MINI EXTERN> -49.33568 -13.97360 0.00000 0.00000 0.00000 MINI CONSTR> 71.31982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 57.48481 0.00668 0.14933 0.00010 MINI INTERN> 5.03173 24.38119 0.00000 15.74383 4.30523 MINI EXTERN> -49.33401 -13.97820 0.00000 0.00000 0.00000 MINI CONSTR> 71.33504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 57.47701 0.00780 0.15568 0.00011 MINI INTERN> 5.02998 24.37438 0.00000 15.73865 4.30462 MINI EXTERN> -49.34251 -13.97988 0.00000 0.00000 0.00000 MINI CONSTR> 71.35177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 57.47053 0.00648 0.18045 0.00011 MINI INTERN> 5.03014 24.37238 0.00000 15.73430 4.30322 MINI EXTERN> -49.34742 -13.98885 0.00000 0.00000 0.00000 MINI CONSTR> 71.36676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 57.46396 0.00657 0.16450 0.00011 MINI INTERN> 5.02259 24.36980 0.00000 15.73085 4.30271 MINI EXTERN> -49.35291 -13.98955 0.00000 0.00000 0.00000 MINI CONSTR> 71.38046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9785 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 57.45733 0.00663 0.17609 0.00012 MINI INTERN> 5.01866 24.36465 0.00000 15.72665 4.30174 MINI EXTERN> -49.35936 -13.99122 0.00000 0.00000 0.00000 MINI CONSTR> 71.39622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 57.44890 0.00843 0.05615 0.00005 MINI INTERN> 5.08775 24.33130 0.00000 15.70588 4.31053 MINI EXTERN> -49.39776 -13.99988 0.00000 0.00000 0.00000 MINI CONSTR> 71.41108 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9784 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 57.44574 0.00316 0.18645 0.00013 MINI INTERN> 5.01420 24.35877 0.00000 15.71886 4.29997 MINI EXTERN> -49.36974 -14.00030 0.00000 0.00000 0.00000 MINI CONSTR> 71.42397 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 57.43999 0.00575 0.19408 0.00013 MINI INTERN> 5.01278 24.35240 0.00000 15.71434 4.29963 MINI EXTERN> -49.37718 -14.00063 0.00000 0.00000 0.00000 MINI CONSTR> 71.43865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9784 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 57.43157 0.00843 0.06276 0.00006 MINI INTERN> 5.09275 24.31522 0.00000 15.69105 4.30993 MINI EXTERN> -49.41987 -14.01103 0.00000 0.00000 0.00000 MINI CONSTR> 71.45351 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 57.42697 0.00460 0.04866 0.00006 MINI INTERN> 5.08333 24.31491 0.00000 15.68975 4.30813 MINI EXTERN> -49.42049 -14.01332 0.00000 0.00000 0.00000 MINI CONSTR> 71.46466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9784 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 57.42561 0.00136 0.22397 0.00015 MINI INTERN> 5.00483 24.34239 0.00000 15.70360 4.29749 MINI EXTERN> -49.39219 -14.00867 0.00000 0.00000 0.00000 MINI CONSTR> 71.47815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 57.41706 0.00855 0.08029 0.00006 MINI INTERN> 5.10134 24.29878 0.00000 15.67682 4.30984 MINI EXTERN> -49.44106 -14.02105 0.00000 0.00000 0.00000 MINI CONSTR> 71.49238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 57.41260 0.00445 0.06189 0.00007 MINI INTERN> 5.09316 24.29854 0.00000 15.67522 4.30817 MINI EXTERN> -49.44196 -14.02427 0.00000 0.00000 0.00000 MINI CONSTR> 71.50373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 57.40848 0.00412 0.07285 0.00007 MINI INTERN> 5.09833 24.29187 0.00000 15.67018 4.30860 MINI EXTERN> -49.44988 -14.02657 0.00000 0.00000 0.00000 MINI CONSTR> 71.51595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 57.40499 0.00349 0.10440 0.00007 MINI INTERN> 5.11323 24.28265 0.00000 15.66337 4.30994 MINI EXTERN> -49.46073 -14.03124 0.00000 0.00000 0.00000 MINI CONSTR> 71.52778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 57.40116 0.00383 0.11079 0.00007 MINI INTERN> 5.10897 24.27943 0.00000 15.66039 4.30951 MINI EXTERN> -49.46504 -14.03165 0.00000 0.00000 0.00000 MINI CONSTR> 71.53954 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 57.39779 0.00338 0.11842 0.00008 MINI INTERN> 5.11947 24.27278 0.00000 15.65513 4.30989 MINI EXTERN> -49.47255 -14.03730 0.00000 0.00000 0.00000 MINI CONSTR> 71.55037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 57.39446 0.00333 0.12679 0.00008 MINI INTERN> 5.11903 24.26813 0.00000 15.65165 4.30984 MINI EXTERN> -49.47788 -14.03777 0.00000 0.00000 0.00000 MINI CONSTR> 71.56145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 57.39124 0.00322 0.11817 0.00008 MINI INTERN> 5.12047 24.26511 0.00000 15.64868 4.30928 MINI EXTERN> -49.48138 -14.04192 0.00000 0.00000 0.00000 MINI CONSTR> 71.57101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 57.38799 0.00325 0.12606 0.00008 MINI INTERN> 5.11684 24.26217 0.00000 15.64574 4.30901 MINI EXTERN> -49.48555 -14.04245 0.00000 0.00000 0.00000 MINI CONSTR> 71.58224 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 57.38396 0.00403 0.04061 0.00004 MINI INTERN> 5.06981 24.27983 0.00000 15.65368 4.30256 MINI EXTERN> -49.46835 -14.04391 0.00000 0.00000 0.00000 MINI CONSTR> 71.59033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 57.38252 0.00144 0.13375 0.00009 MINI INTERN> 5.12709 24.25298 0.00000 15.63813 4.30902 MINI EXTERN> -49.49590 -14.05024 0.00000 0.00000 0.00000 MINI CONSTR> 71.60143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 57.37988 0.00264 0.14859 0.00009 MINI INTERN> 5.11546 24.25252 0.00000 15.63705 4.30817 MINI EXTERN> -49.49723 -14.04787 0.00000 0.00000 0.00000 MINI CONSTR> 71.61178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 57.37564 0.00424 0.04559 0.00004 MINI INTERN> 5.06505 24.27302 0.00000 15.64584 4.30121 MINI EXTERN> -49.47804 -14.05102 0.00000 0.00000 0.00000 MINI CONSTR> 71.61957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 57.37336 0.00227 0.03444 0.00004 MINI INTERN> 5.07228 24.26739 0.00000 15.64172 4.30198 MINI EXTERN> -49.48446 -14.05331 0.00000 0.00000 0.00000 MINI CONSTR> 71.62777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 57.37083 0.00253 0.03523 0.00004 MINI INTERN> 5.07102 24.26520 0.00000 15.63916 4.30155 MINI EXTERN> -49.48753 -14.05584 0.00000 0.00000 0.00000 MINI CONSTR> 71.63727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 57.36851 0.00232 0.06241 0.00005 MINI INTERN> 5.05618 24.26873 0.00000 15.63956 4.29947 MINI EXTERN> -49.48505 -14.05730 0.00000 0.00000 0.00000 MINI CONSTR> 71.64692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 57.36620 0.00231 0.04021 0.00005 MINI INTERN> 5.06621 24.26172 0.00000 15.63477 4.30055 MINI EXTERN> -49.49262 -14.05984 0.00000 0.00000 0.00000 MINI CONSTR> 71.65540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 57.36418 0.00202 0.03266 0.00005 MINI INTERN> 5.07102 24.25733 0.00000 15.63131 4.30096 MINI EXTERN> -49.49767 -14.06220 0.00000 0.00000 0.00000 MINI CONSTR> 71.66343 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 57.36418 0.00202 0.03266 0.00006 STPD INTERN> 5.07102 24.25733 0.00000 15.63131 4.30096 STPD EXTERN> -49.49767 -14.06220 0.00000 0.00000 0.00000 STPD CONSTR> 71.66343 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 9783 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9783 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 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 57.36418 0.00202 0.03266 0.00000 MINI INTERN> 5.07102 24.25733 0.00000 15.63131 4.30096 MINI EXTERN> -49.49767 -14.06220 0.00000 0.00000 0.00000 MINI CONSTR> 71.66343 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 57.31889 0.04529 0.00984 0.02000 CONJ INTERN> 5.07455 24.14443 0.00000 15.52338 4.29368 CONJ EXTERN> -49.65015 -14.14937 0.00000 0.00000 0.00000 CONJ CONSTR> 72.08235 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 ALA 1 HT1 ) 1.7502 ( PROT ALA 1 HT2 ) 1.7502 ( PROT ALA 1 N ) 2.1877 ( PROT ALA 1 HT3 ) 1.7502 ( PROT ALA 1 CA ) 2.1877 ( PROT ALA 1 CB ) 1.7502 ( PROT ALA 1 C ) 2.1877 ( PROT ALA 1 O ) 2.1877 ( PROT LEU 2 N ) 2.1877 ( PROT LEU 2 H ) 1.7502 ( PROT LEU 2 CA ) 2.1877 ( PROT LEU 2 CB ) 1.7502 ( PROT LEU 2 CG ) 1.7502 ( PROT LEU 2 CD1 ) 1.7502 ( PROT LEU 2 CD2 ) 1.7502 ( PROT LEU 2 C ) 2.1877 ( PROT LEU 2 O ) 2.1877 ( PROT GLN 3 N ) 2.1877 ( PROT GLN 3 H ) 1.7502 ( PROT GLN 3 CA ) 2.1877 ( PROT GLN 3 CB ) 1.7502 ( PROT GLN 3 CG ) 1.7502 ( PROT GLN 3 CD ) 1.7502 ( PROT GLN 3 OE1 ) 1.7502 ( PROT GLN 3 NE2 ) 1.7502 ( PROT GLN 3 HE21 ) 1.7502 ( PROT GLN 3 HE22 ) 1.7502 ( PROT GLN 3 C ) 2.1877 ( PROT GLN 3 O ) 2.1877 ( PROT ALA 4 N ) 2.1877 ( PROT ALA 4 H ) 1.7502 ( PROT ALA 4 CA ) 2.1877 ( PROT ALA 4 CB ) 1.7502 ( PROT ALA 4 C ) 2.1877 ( PROT ALA 4 O ) 2.1877 ( PROT PHE 5 N ) 2.1877 ( PROT PHE 5 H ) 1.7502 ( PROT PHE 5 CA ) 2.1877 ( PROT PHE 5 CB ) 1.7502 ( PROT PHE 5 CG ) 1.7502 ( PROT PHE 5 CD1 ) 1.7502 ( PROT PHE 5 CD2 ) 1.7502 ( PROT PHE 5 CE1 ) 1.7502 ( PROT PHE 5 CE2 ) 1.7502 ( PROT PHE 5 CZ ) 1.7502 ( PROT PHE 5 C ) 2.1877 ( PROT PHE 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 ILE 7 N ) 2.1877 ( PROT ILE 7 H ) 1.7502 ( PROT ILE 7 CA ) 2.1877 ( PROT ILE 7 CB ) 1.7502 ( PROT ILE 7 CG2 ) 1.7502 ( PROT ILE 7 CG1 ) 1.7502 ( PROT ILE 7 CD ) 1.7502 ( PROT ILE 7 C ) 2.1877 ( PROT ILE 7 O ) 2.1877 ( PROT ALA 8 N ) 2.1877 ( PROT ALA 8 H ) 1.7502 ( PROT ALA 8 CA ) 2.1877 ( PROT ALA 8 CB ) 1.7502 ( PROT ALA 8 C ) 2.1877 ( PROT ALA 8 O ) 2.1877 ( PROT LEU 9 N ) 2.1877 ( PROT LEU 9 H ) 1.7502 ( PROT LEU 9 CA ) 2.1877 ( PROT LEU 9 CB ) 1.7502 ( PROT LEU 9 CG ) 1.7502 ( PROT LEU 9 CD1 ) 1.7502 ( PROT LEU 9 CD2 ) 1.7502 ( PROT LEU 9 C ) 2.1877 ( PROT LEU 9 O ) 2.1877 ( PROT SER 10 N ) 2.1877 ( PROT SER 10 H ) 1.7502 ( PROT SER 10 CA ) 2.1877 ( PROT SER 10 CB ) 1.7502 ( PROT SER 10 OG ) 1.7502 ( PROT SER 10 HG ) 1.7502 ( PROT SER 10 C ) 2.1877 ( PROT SER 10 O ) 2.1877 ( PROT SER 11 N ) 2.1877 ( PROT SER 11 H ) 1.7502 ( PROT SER 11 CA ) 2.1877 ( PROT SER 11 CB ) 1.7502 ( PROT SER 11 OG ) 1.7502 ( PROT SER 11 HG ) 1.7502 ( PROT SER 11 C ) 2.1877 ( PROT SER 11 O ) 2.1877 ( PROT PHE 12 N ) 2.1877 ( PROT PHE 12 H ) 1.7502 ( PROT PHE 12 CA ) 2.1877 ( PROT PHE 12 CB ) 1.7502 ( PROT PHE 12 CG ) 1.7502 ( PROT PHE 12 CD1 ) 1.7502 ( PROT PHE 12 CD2 ) 1.7502 ( PROT PHE 12 CE1 ) 1.7502 ( PROT PHE 12 CE2 ) 1.7502 ( PROT PHE 12 CZ ) 1.7502 ( PROT PHE 12 C ) 2.1877 ( PROT PHE 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 SER 14 N ) 2.1877 ( PROT SER 14 H ) 1.7502 ( PROT SER 14 CA ) 2.1877 ( PROT SER 14 CB ) 1.7502 ( PROT SER 14 OG ) 1.7502 ( PROT SER 14 HG ) 1.7502 ( PROT SER 14 C ) 2.1877 ( PROT SER 14 O ) 2.1877 ( PROT LYS 15 N ) 2.1877 ( PROT LYS 15 H ) 1.7502 ( PROT LYS 15 CA ) 2.1877 ( PROT LYS 15 CB ) 1.7502 ( PROT LYS 15 CG ) 1.7502 ( PROT LYS 15 CD ) 1.7502 ( PROT LYS 15 CE ) 1.7502 ( PROT LYS 15 NZ ) 1.7502 ( PROT LYS 15 HZ1 ) 1.7502 ( PROT LYS 15 HZ2 ) 1.7502 ( PROT LYS 15 HZ3 ) 1.7502 ( PROT LYS 15 C ) 2.1877 ( PROT LYS 15 O ) 2.1877 ( PROT LEU 16 N ) 2.1877 ( PROT LEU 16 H ) 1.7502 ( PROT LEU 16 CA ) 2.1877 ( PROT LEU 16 CB ) 1.7502 ( PROT LEU 16 CG ) 1.7502 ( PROT LEU 16 CD1 ) 1.7502 ( PROT LEU 16 CD2 ) 1.7502 ( PROT LEU 16 C ) 2.1877 ( PROT LEU 16 O ) 2.1877 ( PROT ALA 17 N ) 2.1877 ( PROT ALA 17 H ) 1.7502 ( PROT ALA 17 CA ) 2.1877 ( PROT ALA 17 CB ) 1.7502 ( PROT ALA 17 C ) 2.1877 ( PROT ALA 17 O ) 2.1877 ( PROT CYS 18 N ) 2.1877 ( PROT CYS 18 H ) 1.7502 ( PROT CYS 18 CA ) 2.1877 ( PROT CYS 18 CB ) 1.7502 ( PROT CYS 18 SG ) 1.7502 ( PROT CYS 18 C ) 2.1877 ( PROT CYS 18 O ) 2.1877 ( PROT GLU 19 N ) 2.1877 ( PROT GLU 19 H ) 1.7502 ( PROT GLU 19 CA ) 2.1877 ( PROT GLU 19 CB ) 1.7502 ( PROT GLU 19 CG ) 1.7502 ( PROT GLU 19 CD ) 1.7502 ( PROT GLU 19 OE1 ) 1.7502 ( PROT GLU 19 OE2 ) 1.7502 ( PROT GLU 19 C ) 2.1877 ( PROT GLU 19 OT1 ) 1.7502 ( PROT GLU 19 OT2 ) 1.7502 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43134 4.57614 -7.52895 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00336 -0.00091 -0.00368 ROTATION MATRIX 1.000000 -0.000158 -0.000250 0.000158 1.000000 0.000408 0.000250 -0.000408 1.000000 AXIS OF ROTATION IS 0.809353 0.496958 -0.313018 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 23.4896 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.373924 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3739" Parameter: A <- "0.3739" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.93615 4.27017 -7.72706 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.00394 0.01009 -0.00520 ROTATION MATRIX 0.999767 0.016595 0.013822 -0.016268 0.999594 -0.023407 -0.014204 0.023177 0.999630 AXIS OF ROTATION IS -0.733312 -0.441179 0.517314 ANGLE IS 1.82 CENTER OF ROTATION 8.842131 4.090942 -8.017302 SHIFT IS -0.004252 TOTAL SQUARE DIFF IS 1.2099 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.252345 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3739" RDCMND substituted energy or value "?RMS" to " 0.2523" Parameter: A <- "0.3739 0.2523" 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 0.3739 0.2523 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 " 72.08" Parameter: H <- "72.08" 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 -14.76346 72.08235 1.33165 ENER INTERN> 5.07455 24.14443 0.00000 15.52338 4.29368 ENER EXTERN> -49.65015 -14.14937 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 " -14.76" Parameter: B <- "-14.76" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -14.15" Parameter: C <- "-14.15" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -49.65" Parameter: C <- " -63.80" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -63.80" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.07" Parameter: D <- "5.07" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 24.14" Parameter: D <- " 29.21" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 15.52" Parameter: D <- " 44.73" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.29" Parameter: D <- " 49.02" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 49.02" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 6600 ENER= -14.76 GRMS= 1.33 ELEC= -14.15 VDW= -49.65 RDTITL> *EXTERNAL= -63.80 INTERNAL= 49.02 USER= 0.00 HARM= 72.08 RDTITL> *BOND= 5.07 ANGL= 24.14 DIHE= 15.52 IMPR= 4.29 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9783 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9782 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 36.55271 -51.31617 0.53027 0.02000 MINI INTERN> 5.07455 24.14443 0.00000 15.52338 4.29368 MINI EXTERN> -49.65015 -14.14937 0.00000 0.00000 0.00000 MINI CONSTR> 51.31617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 57.67160 -21.11889 16.70449 0.00864 MINI INTERN> 30.48114 20.32626 0.00000 16.84191 3.65367 MINI EXTERN> -56.92851 -10.93866 0.00000 0.00000 0.00000 MINI CONSTR> 54.23579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9771 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 34.31661 23.35499 0.72769 0.00156 MINI INTERN> 5.22100 23.29518 0.00000 16.39843 4.25976 MINI EXTERN> -56.71908 -12.65140 0.00000 0.00000 0.00000 MINI CONSTR> 54.51271 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 34.03433 0.28227 0.65906 0.00067 MINI INTERN> 5.00345 23.58656 0.00000 16.33245 4.29788 MINI EXTERN> -56.99754 -12.86883 0.00000 0.00000 0.00000 MINI CONSTR> 54.68037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9765 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 33.89132 0.14301 0.98802 0.00070 MINI INTERN> 5.10460 23.52080 0.00000 16.30566 4.30381 MINI EXTERN> -57.18041 -12.96429 0.00000 0.00000 0.00000 MINI CONSTR> 54.80115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 33.63190 0.25942 0.31128 0.00030 MINI INTERN> 4.96706 23.35431 0.00000 16.33548 4.23601 MINI EXTERN> -57.15519 -13.01805 0.00000 0.00000 0.00000 MINI CONSTR> 54.91229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9761 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 33.54082 0.09108 1.06983 0.00075 MINI INTERN> 4.97106 23.54172 0.00000 16.27979 4.29701 MINI EXTERN> -57.42339 -13.17469 0.00000 0.00000 0.00000 MINI CONSTR> 55.04932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 33.27906 0.26176 0.35158 0.00032 MINI INTERN> 4.98450 23.19648 0.00000 16.31762 4.20830 MINI EXTERN> -57.43921 -13.14490 0.00000 0.00000 0.00000 MINI CONSTR> 55.15627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9757 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 33.12991 0.14915 0.27999 0.00034 MINI INTERN> 4.92990 23.20304 0.00000 16.30542 4.20928 MINI EXTERN> -57.56729 -13.21013 0.00000 0.00000 0.00000 MINI CONSTR> 55.25969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 32.98231 0.14760 0.28681 0.00035 MINI INTERN> 4.91975 23.15234 0.00000 16.29601 4.19997 MINI EXTERN> -57.69255 -13.25856 0.00000 0.00000 0.00000 MINI CONSTR> 55.36534 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9753 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 32.84230 0.14001 0.49129 0.00036 MINI INTERN> 4.96701 23.03858 0.00000 16.28872 4.17673 MINI EXTERN> -57.80686 -13.29742 0.00000 0.00000 0.00000 MINI CONSTR> 55.47553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 32.70918 0.13312 0.38219 0.00037 MINI INTERN> 4.90060 23.04349 0.00000 16.27943 4.17634 MINI EXTERN> -57.91618 -13.34061 0.00000 0.00000 0.00000 MINI CONSTR> 55.56611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9753 ATOM PAIRS WERE FOUND FOR ATOM LIST 265 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 32.58354 0.12564 0.42713 0.00039 MINI INTERN> 4.86759 23.00934 0.00000 16.27274 4.16587 MINI EXTERN> -58.01459 -13.37708 0.00000 0.00000 0.00000 MINI CONSTR> 55.65967 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 32.47099 0.11255 0.57033 0.00040 MINI INTERN> 4.88751 22.91613 0.00000 16.27170 4.14541 MINI EXTERN> -58.11130 -13.38830 0.00000 0.00000 0.00000 MINI CONSTR> 55.74984 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9750 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 32.35511 0.11588 0.64771 0.00042 MINI INTERN> 4.95542 22.83672 0.00000 16.25486 4.13819 MINI EXTERN> -58.23882 -13.42842 0.00000 0.00000 0.00000 MINI CONSTR> 55.83716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 32.24919 0.10593 0.67853 0.00043 MINI INTERN> 4.91211 22.81168 0.00000 16.25248 4.12703 MINI EXTERN> -58.31835 -13.45267 0.00000 0.00000 0.00000 MINI CONSTR> 55.91691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9750 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 32.14181 0.10737 0.65072 0.00045 MINI INTERN> 4.83373 22.81066 0.00000 16.24330 4.12482 MINI EXTERN> -58.39832 -13.46680 0.00000 0.00000 0.00000 MINI CONSTR> 55.99442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 32.04210 0.09971 0.69938 0.00046 MINI INTERN> 4.84110 22.79744 0.00000 16.22555 4.12229 MINI EXTERN> -58.48767 -13.52600 0.00000 0.00000 0.00000 MINI CONSTR> 56.06940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9749 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 31.94188 0.10022 0.66390 0.00048 MINI INTERN> 4.76637 22.78284 0.00000 16.22548 4.11087 MINI EXTERN> -58.54805 -13.53713 0.00000 0.00000 0.00000 MINI CONSTR> 56.14148 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 31.81262 0.12926 0.22381 0.00021 MINI INTERN> 4.81033 22.78438 0.00000 16.16425 4.15152 MINI EXTERN> -58.72443 -13.58716 0.00000 0.00000 0.00000 MINI CONSTR> 56.21374 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9749 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 31.76426 0.04836 0.78368 0.00052 MINI INTERN> 4.76659 22.71949 0.00000 16.19843 4.09939 MINI EXTERN> -58.70602 -13.59471 0.00000 0.00000 0.00000 MINI CONSTR> 56.28109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 31.68797 0.07628 0.90200 0.00054 MINI INTERN> 4.73868 22.69699 0.00000 16.17920 4.10496 MINI EXTERN> -58.79860 -13.58252 0.00000 0.00000 0.00000 MINI CONSTR> 56.34927 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9749 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 31.54537 0.14260 0.24811 0.00023 MINI INTERN> 4.81175 22.67685 0.00000 16.11657 4.14097 MINI EXTERN> -58.95973 -13.65227 0.00000 0.00000 0.00000 MINI CONSTR> 56.41123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 31.46952 0.07585 0.20542 0.00024 MINI INTERN> 4.80226 22.64019 0.00000 16.10856 4.13178 MINI EXTERN> -59.01128 -13.66724 0.00000 0.00000 0.00000 MINI CONSTR> 56.46525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9749 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 31.39083 0.07869 0.21069 0.00025 MINI INTERN> 4.80598 22.60535 0.00000 16.09247 4.12874 MINI EXTERN> -59.08054 -13.68507 0.00000 0.00000 0.00000 MINI CONSTR> 56.52390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 31.31439 0.07644 0.20503 0.00026 MINI INTERN> 4.80045 22.57341 0.00000 16.07893 4.12409 MINI EXTERN> -59.14238 -13.70074 0.00000 0.00000 0.00000 MINI CONSTR> 56.58064 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9748 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 31.23950 0.07490 0.36917 0.00027 MINI INTERN> 4.85775 22.53193 0.00000 16.04538 4.13255 MINI EXTERN> -59.24501 -13.72770 0.00000 0.00000 0.00000 MINI CONSTR> 56.64460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 31.16358 0.07592 0.25033 0.00028 MINI INTERN> 4.80631 22.51052 0.00000 16.04418 4.11993 MINI EXTERN> -59.27735 -13.73567 0.00000 0.00000 0.00000 MINI CONSTR> 56.69565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9747 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 31.09575 0.06782 0.31636 0.00029 MINI INTERN> 4.83786 22.47242 0.00000 16.02145 4.12092 MINI EXTERN> -59.35042 -13.75647 0.00000 0.00000 0.00000 MINI CONSTR> 56.74999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 31.03783 0.05792 0.43537 0.00030 MINI INTERN> 4.87623 22.43423 0.00000 15.99728 4.12433 MINI EXTERN> -59.42452 -13.77100 0.00000 0.00000 0.00000 MINI CONSTR> 56.80128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9747 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 30.97246 0.06537 0.46356 0.00031 MINI INTERN> 4.87404 22.41293 0.00000 15.98319 4.11996 MINI EXTERN> -59.47566 -13.79431 0.00000 0.00000 0.00000 MINI CONSTR> 56.85229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 30.91569 0.05676 0.50401 0.00032 MINI INTERN> 4.88863 22.37429 0.00000 15.96522 4.11978 MINI EXTERN> -59.53578 -13.79637 0.00000 0.00000 0.00000 MINI CONSTR> 56.89993 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9746 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 30.85801 0.05769 0.47907 0.00033 MINI INTERN> 4.89651 22.34524 0.00000 15.95246 4.11461 MINI EXTERN> -59.57809 -13.81498 0.00000 0.00000 0.00000 MINI CONSTR> 56.94226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 30.80296 0.05505 0.52872 0.00034 MINI INTERN> 4.86029 22.32696 0.00000 15.94546 4.10890 MINI EXTERN> -59.61573 -13.81113 0.00000 0.00000 0.00000 MINI CONSTR> 56.98822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9742 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 30.74797 0.05499 0.49481 0.00036 MINI INTERN> 4.90402 22.28648 0.00000 15.92371 4.10906 MINI EXTERN> -59.67281 -13.83261 0.00000 0.00000 0.00000 MINI CONSTR> 57.03012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 30.67750 0.07048 0.16561 0.00015 MINI INTERN> 4.72976 22.31579 0.00000 15.95310 4.07917 MINI EXTERN> -59.63251 -13.83478 0.00000 0.00000 0.00000 MINI CONSTR> 57.06697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9741 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 30.65077 0.02673 0.56349 0.00038 MINI INTERN> 4.92538 22.23109 0.00000 15.89305 4.10560 MINI EXTERN> -59.76524 -13.85229 0.00000 0.00000 0.00000 MINI CONSTR> 57.11320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 30.60318 0.04759 0.62311 0.00040 MINI INTERN> 4.91950 22.22189 0.00000 15.88349 4.09886 MINI EXTERN> -59.79498 -13.87951 0.00000 0.00000 0.00000 MINI CONSTR> 57.15393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9741 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 30.52719 0.07599 0.19144 0.00017 MINI INTERN> 4.70538 22.25660 0.00000 15.91869 4.06746 MINI EXTERN> -59.74470 -13.86475 0.00000 0.00000 0.00000 MINI CONSTR> 57.18852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 30.48553 0.04166 0.14793 0.00018 MINI INTERN> 4.72318 22.23320 0.00000 15.90182 4.06913 MINI EXTERN> -59.78811 -13.87557 0.00000 0.00000 0.00000 MINI CONSTR> 57.22188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9739 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 30.43971 0.04581 0.15289 0.00019 MINI INTERN> 4.71346 22.21563 0.00000 15.89093 4.06543 MINI EXTERN> -59.82168 -13.88389 0.00000 0.00000 0.00000 MINI CONSTR> 57.25985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 30.39517 0.04455 0.24977 0.00019 MINI INTERN> 4.67830 22.20743 0.00000 15.88748 4.05579 MINI EXTERN> -59.84070 -13.89252 0.00000 0.00000 0.00000 MINI CONSTR> 57.29939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9739 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 30.35363 0.04153 0.19273 0.00020 MINI INTERN> 4.69122 22.18311 0.00000 15.87088 4.05735 MINI EXTERN> -59.88288 -13.89899 0.00000 0.00000 0.00000 MINI CONSTR> 57.33294 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 30.31504 0.03860 0.21969 0.00021 MINI INTERN> 4.67507 22.17337 0.00000 15.86299 4.05270 MINI EXTERN> -59.90708 -13.90848 0.00000 0.00000 0.00000 MINI CONSTR> 57.36646 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9739 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 30.27519 0.03985 0.20810 0.00021 MINI INTERN> 4.67797 22.15394 0.00000 15.85002 4.05091 MINI EXTERN> -59.94067 -13.91737 0.00000 0.00000 0.00000 MINI CONSTR> 57.40039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 30.24254 0.03265 0.32490 0.00022 MINI INTERN> 4.64004 22.15272 0.00000 15.84832 4.04275 MINI EXTERN> -59.95319 -13.92148 0.00000 0.00000 0.00000 MINI CONSTR> 57.43339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9738 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 30.20589 0.03665 0.34392 0.00023 MINI INTERN> 4.65167 22.13267 0.00000 15.83482 4.04057 MINI EXTERN> -59.98532 -13.93468 0.00000 0.00000 0.00000 MINI CONSTR> 57.46616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 30.17392 0.03197 0.37424 0.00024 MINI INTERN> 4.62395 22.12626 0.00000 15.82896 4.03682 MINI EXTERN> -60.00558 -13.93328 0.00000 0.00000 0.00000 MINI CONSTR> 57.49679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9738 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 30.14145 0.03247 0.35591 0.00025 MINI INTERN> 4.63006 22.11300 0.00000 15.81721 4.03544 MINI EXTERN> -60.03211 -13.94675 0.00000 0.00000 0.00000 MINI CONSTR> 57.52459 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 30.11056 0.03089 0.39436 0.00026 MINI INTERN> 4.62852 22.09282 0.00000 15.80503 4.03545 MINI EXTERN> -60.06415 -13.94224 0.00000 0.00000 0.00000 MINI CONSTR> 57.55513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9738 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 30.07939 0.03116 0.36835 0.00027 MINI INTERN> 4.61149 22.09073 0.00000 15.79902 4.03070 MINI EXTERN> -60.07888 -13.95595 0.00000 0.00000 0.00000 MINI CONSTR> 57.58228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 30.03955 0.03984 0.12329 0.00011 MINI INTERN> 4.71721 22.02716 0.00000 15.76105 4.04496 MINI EXTERN> -60.15397 -13.96722 0.00000 0.00000 0.00000 MINI CONSTR> 57.61036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9738 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 30.02373 0.01582 0.41965 0.00029 MINI INTERN> 4.59486 22.07027 0.00000 15.78210 4.02528 MINI EXTERN> -60.12119 -13.96528 0.00000 0.00000 0.00000 MINI CONSTR> 57.63771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 29.99697 0.02677 0.46647 0.00030 MINI INTERN> 4.63237 22.04711 0.00000 15.76536 4.02529 MINI EXTERN> -60.15365 -13.98460 0.00000 0.00000 0.00000 MINI CONSTR> 57.66509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9737 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 29.95407 0.04290 0.13963 0.00013 MINI INTERN> 4.72261 21.98256 0.00000 15.72848 4.04064 MINI EXTERN> -60.22782 -13.98455 0.00000 0.00000 0.00000 MINI CONSTR> 57.69215 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 29.93025 0.02382 0.11303 0.00013 MINI INTERN> 4.70832 21.97669 0.00000 15.72337 4.03696 MINI EXTERN> -60.24041 -13.98913 0.00000 0.00000 0.00000 MINI CONSTR> 57.71445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9737 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 29.90487 0.02538 0.11625 0.00014 MINI INTERN> 4.71089 21.96249 0.00000 15.71304 4.03575 MINI EXTERN> -60.26293 -13.99395 0.00000 0.00000 0.00000 MINI CONSTR> 57.73958 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 29.88016 0.02471 0.11128 0.00014 MINI INTERN> 4.70672 21.95170 0.00000 15.70446 4.03368 MINI EXTERN> -60.28186 -13.99861 0.00000 0.00000 0.00000 MINI CONSTR> 57.76407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9737 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 29.85474 0.02542 0.19637 0.00015 MINI INTERN> 4.74037 21.92493 0.00000 15.68583 4.03627 MINI EXTERN> -60.31895 -14.00638 0.00000 0.00000 0.00000 MINI CONSTR> 57.79267 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 29.83089 0.02385 0.13881 0.00015 MINI INTERN> 4.71483 21.92284 0.00000 15.68252 4.03187 MINI EXTERN> -60.32786 -14.00830 0.00000 0.00000 0.00000 MINI CONSTR> 57.81499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9736 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 29.80886 0.02203 0.16986 0.00016 MINI INTERN> 4.72873 21.90648 0.00000 15.67044 4.03163 MINI EXTERN> -60.35162 -14.01559 0.00000 0.00000 0.00000 MINI CONSTR> 57.83879 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 29.79023 0.01863 0.24119 0.00016 MINI INTERN> 4.74895 21.88632 0.00000 15.65703 4.03301 MINI EXTERN> -60.37862 -14.01814 0.00000 0.00000 0.00000 MINI CONSTR> 57.86168 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9736 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 29.76988 0.02035 0.26310 0.00017 MINI INTERN> 4.75170 21.87778 0.00000 15.64848 4.03079 MINI EXTERN> -60.39446 -14.02820 0.00000 0.00000 0.00000 MINI CONSTR> 57.88378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 29.75119 0.01869 0.27128 0.00018 MINI INTERN> 4.76154 21.86078 0.00000 15.63776 4.03105 MINI EXTERN> -60.41637 -14.02860 0.00000 0.00000 0.00000 MINI CONSTR> 57.90503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9736 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 29.73193 0.01926 0.28835 0.00018 MINI INTERN> 4.75904 21.85010 0.00000 15.62932 4.02987 MINI EXTERN> -60.43373 -14.02982 0.00000 0.00000 0.00000 MINI CONSTR> 57.92715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 29.71368 0.01825 0.27351 0.00019 MINI INTERN> 4.76033 21.84170 0.00000 15.62195 4.02789 MINI EXTERN> -60.44716 -14.03722 0.00000 0.00000 0.00000 MINI CONSTR> 57.94619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9736 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 29.69604 0.01764 0.30130 0.00020 MINI INTERN> 4.73957 21.83710 0.00000 15.61737 4.02550 MINI EXTERN> -60.45847 -14.03241 0.00000 0.00000 0.00000 MINI CONSTR> 57.96738 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 29.67362 0.02242 0.09304 0.00009 MINI INTERN> 4.67576 21.85728 0.00000 15.62485 4.01577 MINI EXTERN> -60.44448 -14.03903 0.00000 0.00000 0.00000 MINI CONSTR> 57.98347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9736 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 29.66376 0.00986 0.30974 0.00021 MINI INTERN> 4.77044 21.80897 0.00000 15.59657 4.02510 MINI EXTERN> -60.49553 -14.04708 0.00000 0.00000 0.00000 MINI CONSTR> 58.00529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 29.63908 0.02468 0.09545 0.00009 MINI INTERN> 4.67147 21.84038 0.00000 15.60981 4.01272 MINI EXTERN> -60.47289 -14.04584 0.00000 0.00000 0.00000 MINI CONSTR> 58.02344 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9735 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 29.63206 0.00702 0.32994 0.00023 MINI INTERN> 4.77164 21.79107 0.00000 15.58099 4.02274 MINI EXTERN> -60.52425 -14.05407 0.00000 0.00000 0.00000 MINI CONSTR> 58.04394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 29.61704 0.01502 0.36532 0.00024 MINI INTERN> 4.75249 21.78751 0.00000 15.57634 4.02066 MINI EXTERN> -60.53463 -14.04967 0.00000 0.00000 0.00000 MINI CONSTR> 58.06434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 29.59213 0.02490 0.11773 0.00010 MINI INTERN> 4.66077 21.81919 0.00000 15.58953 4.00776 MINI EXTERN> -60.51020 -14.05502 0.00000 0.00000 0.00000 MINI CONSTR> 58.08009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 29.57912 0.01301 0.08176 0.00011 MINI INTERN> 4.67326 21.80640 0.00000 15.58026 4.00860 MINI EXTERN> -60.52670 -14.05816 0.00000 0.00000 0.00000 MINI CONSTR> 58.09546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 29.56383 0.01529 0.08145 0.00011 MINI INTERN> 4.67271 21.79812 0.00000 15.57274 4.00728 MINI EXTERN> -60.53999 -14.06153 0.00000 0.00000 0.00000 MINI CONSTR> 58.11451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 29.54940 0.01443 0.15651 0.00011 MINI INTERN> 4.65224 21.79805 0.00000 15.56971 4.00306 MINI EXTERN> -60.54564 -14.06272 0.00000 0.00000 0.00000 MINI CONSTR> 58.13469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 263 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 29.53584 0.01356 0.11003 0.00012 MINI INTERN> 4.66449 21.78602 0.00000 15.56025 4.00363 MINI EXTERN> -60.56161 -14.06763 0.00000 0.00000 0.00000 MINI CONSTR> 58.15069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 29.52388 0.01196 0.13782 0.00012 MINI INTERN> 4.65495 21.78309 0.00000 15.55580 4.00149 MINI EXTERN> -60.56940 -14.06913 0.00000 0.00000 0.00000 MINI CONSTR> 58.16709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 29.51329 0.01060 0.18503 0.00013 MINI INTERN> 4.64388 21.78104 0.00000 15.55202 3.99920 MINI EXTERN> -60.57616 -14.06964 0.00000 0.00000 0.00000 MINI CONSTR> 58.18295 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 29.50168 0.01160 0.20289 0.00013 MINI INTERN> 4.65119 21.77313 0.00000 15.54445 3.99824 MINI EXTERN> -60.58797 -14.07634 0.00000 0.00000 0.00000 MINI CONSTR> 58.19899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 29.49117 0.01052 0.20956 0.00014 MINI INTERN> 4.63946 21.77092 0.00000 15.54066 3.99651 MINI EXTERN> -60.59490 -14.07543 0.00000 0.00000 0.00000 MINI CONSTR> 58.21395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 29.48037 0.01079 0.20003 0.00014 MINI INTERN> 4.63893 21.76431 0.00000 15.53463 3.99589 MINI EXTERN> -60.60516 -14.07664 0.00000 0.00000 0.00000 MINI CONSTR> 58.22841 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 29.47013 0.01025 0.24195 0.00015 MINI INTERN> 4.64600 21.75700 0.00000 15.52738 3.99457 MINI EXTERN> -60.61610 -14.08337 0.00000 0.00000 0.00000 MINI CONSTR> 58.24465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 29.46007 0.01006 0.21956 0.00015 MINI INTERN> 4.63806 21.75327 0.00000 15.52308 3.99363 MINI EXTERN> -60.62372 -14.08225 0.00000 0.00000 0.00000 MINI CONSTR> 58.25800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 29.44969 0.01038 0.23368 0.00016 MINI INTERN> 4.63852 21.74358 0.00000 15.51613 3.99355 MINI EXTERN> -60.63630 -14.07960 0.00000 0.00000 0.00000 MINI CONSTR> 58.27382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 29.43682 0.01287 0.07074 0.00007 MINI INTERN> 4.67306 21.72324 0.00000 15.50253 3.99718 MINI EXTERN> -60.65777 -14.08779 0.00000 0.00000 0.00000 MINI CONSTR> 58.28638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 29.43231 0.00451 0.24750 0.00017 MINI INTERN> 4.63140 21.73770 0.00000 15.50714 3.99074 MINI EXTERN> -60.64987 -14.08520 0.00000 0.00000 0.00000 MINI CONSTR> 58.30040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 29.42439 0.00792 0.29029 0.00018 MINI INTERN> 4.65396 21.72744 0.00000 15.49786 3.99074 MINI EXTERN> -60.66268 -14.09697 0.00000 0.00000 0.00000 MINI CONSTR> 58.31404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 29.40969 0.01470 0.08087 0.00008 MINI INTERN> 4.67477 21.70551 0.00000 15.48542 3.99493 MINI EXTERN> -60.68468 -14.09366 0.00000 0.00000 0.00000 MINI CONSTR> 58.32740 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 29.40200 0.00769 0.06367 0.00008 MINI INTERN> 4.66893 21.70303 0.00000 15.48201 3.99354 MINI EXTERN> -60.68988 -14.09451 0.00000 0.00000 0.00000 MINI CONSTR> 58.33887 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 29.39367 0.00832 0.06709 0.00008 MINI INTERN> 4.67047 21.69710 0.00000 15.47633 3.99291 MINI EXTERN> -60.69859 -14.09655 0.00000 0.00000 0.00000 MINI CONSTR> 58.35200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 29.38552 0.00815 0.10999 0.00008 MINI INTERN> 4.67890 21.68794 0.00000 15.46870 3.99312 MINI EXTERN> -60.71048 -14.09891 0.00000 0.00000 0.00000 MINI CONSTR> 58.36624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 29.37754 0.00798 0.07534 0.00009 MINI INTERN> 4.67132 21.68631 0.00000 15.46549 3.99149 MINI EXTERN> -60.71504 -14.10009 0.00000 0.00000 0.00000 MINI CONSTR> 58.37806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 29.37041 0.00712 0.06097 0.00009 MINI INTERN> 4.66706 21.68344 0.00000 15.46179 3.99030 MINI EXTERN> -60.72049 -14.10107 0.00000 0.00000 0.00000 MINI CONSTR> 58.38938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 29.36330 0.00711 0.13726 0.00009 MINI INTERN> 4.68017 21.67265 0.00000 15.45314 3.99108 MINI EXTERN> -60.73381 -14.10373 0.00000 0.00000 0.00000 MINI CONSTR> 58.40379 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 29.35524 0.00806 0.08116 0.00010 MINI INTERN> 4.67047 21.67217 0.00000 15.45050 3.98914 MINI EXTERN> -60.73718 -14.10514 0.00000 0.00000 0.00000 MINI CONSTR> 58.41529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9734 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 29.34944 0.00581 0.14680 0.00010 MINI INTERN> 4.67708 21.66422 0.00000 15.44388 3.98951 MINI EXTERN> -60.74749 -14.10563 0.00000 0.00000 0.00000 MINI CONSTR> 58.42787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 29.34354 0.00589 0.17389 0.00011 MINI INTERN> 4.68250 21.66008 0.00000 15.43871 3.98861 MINI EXTERN> -60.75408 -14.11137 0.00000 0.00000 0.00000 MINI CONSTR> 58.43909 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9733 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 29.33746 0.00608 0.15576 0.00011 MINI INTERN> 4.68089 21.65518 0.00000 15.43464 3.98823 MINI EXTERN> -60.76051 -14.11022 0.00000 0.00000 0.00000 MINI CONSTR> 58.44925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 29.33208 0.00538 0.19475 0.00011 MINI INTERN> 4.67534 21.65120 0.00000 15.43070 3.98766 MINI EXTERN> -60.76703 -14.10690 0.00000 0.00000 0.00000 MINI CONSTR> 58.46111 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9733 ATOM PAIRS WERE FOUND FOR ATOM LIST 264 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 29.32645 0.00563 0.17842 0.00012 MINI INTERN> 4.67583 21.64724 0.00000 15.42686 3.98700 MINI EXTERN> -60.77239 -14.10847 0.00000 0.00000 0.00000 MINI CONSTR> 58.47038 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 29.32645 0.00563 0.17842 0.00014 STPD INTERN> 4.67583 21.64724 0.00000 15.42686 3.98700 STPD EXTERN> -60.77239 -14.10847 0.00000 0.00000 0.00000 STPD CONSTR> 58.47038 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 9733 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9733 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 29.32645 0.00563 0.17842 0.00000 MINI INTERN> 4.67583 21.64724 0.00000 15.42686 3.98700 MINI EXTERN> -60.77239 -14.10847 0.00000 0.00000 0.00000 MINI CONSTR> 58.47038 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 29.14605 0.18041 0.01628 0.00182 MINI INTERN> 4.63800 21.42425 0.00000 15.18073 3.94688 MINI EXTERN> -61.17380 -14.16530 0.00000 0.00000 0.00000 MINI CONSTR> 59.29529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 29.14488 0.00117 0.03348 0.00306 MINI INTERN> 4.63373 21.41511 0.00000 15.16607 3.93255 MINI EXTERN> -60.99754 -14.18777 0.00000 0.00000 0.00000 MINI CONSTR> 59.18272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 29.14336 0.00152 0.02257 0.00362 MINI INTERN> 4.64725 21.46914 0.00000 15.16213 3.94697 MINI EXTERN> -60.97837 -14.15258 0.00000 0.00000 0.00000 MINI CONSTR> 59.04881 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 29.14271 0.00065 0.01767 0.00160 MINI INTERN> 4.65109 21.47810 0.00000 15.17557 3.94669 MINI EXTERN> -61.00307 -14.12550 0.00000 0.00000 0.00000 MINI CONSTR> 59.01983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 29.14241 0.00030 0.01124 0.00085 MINI INTERN> 4.64775 21.46681 0.00000 15.18764 3.94899 MINI EXTERN> -61.02257 -14.10869 0.00000 0.00000 0.00000 MINI CONSTR> 59.02247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 29.14215 0.00026 0.01380 0.00151 MINI INTERN> 4.65025 21.47346 0.00000 15.18649 3.94708 MINI EXTERN> -61.04278 -14.11168 0.00000 0.00000 0.00000 MINI CONSTR> 59.03932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 29.14188 0.00027 0.01173 0.00146 MINI INTERN> 4.64707 21.45727 0.00000 15.18394 3.94991 MINI EXTERN> -61.04152 -14.11979 0.00000 0.00000 0.00000 MINI CONSTR> 59.06501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 36 29.14184 0.00004 0.00981 0.02000 CONJ INTERN> 4.64450 21.45804 0.00000 15.18276 3.94871 CONJ EXTERN> -61.04549 -14.11660 0.00000 0.00000 0.00000 CONJ CONSTR> 59.06993 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 ALA 1 HT1 ) 1.1376 ( PROT ALA 1 HT2 ) 1.1376 ( PROT ALA 1 N ) 1.4220 ( PROT ALA 1 HT3 ) 1.1376 ( PROT ALA 1 CA ) 1.4220 ( PROT ALA 1 CB ) 1.1376 ( PROT ALA 1 C ) 1.4220 ( PROT ALA 1 O ) 1.4220 ( PROT LEU 2 N ) 1.4220 ( PROT LEU 2 H ) 1.1376 ( PROT LEU 2 CA ) 1.4220 ( PROT LEU 2 CB ) 1.1376 ( PROT LEU 2 CG ) 1.1376 ( PROT LEU 2 CD1 ) 1.1376 ( PROT LEU 2 CD2 ) 1.1376 ( PROT LEU 2 C ) 1.4220 ( PROT LEU 2 O ) 1.4220 ( PROT GLN 3 N ) 1.4220 ( PROT GLN 3 H ) 1.1376 ( PROT GLN 3 CA ) 1.4220 ( PROT GLN 3 CB ) 1.1376 ( PROT GLN 3 CG ) 1.1376 ( PROT GLN 3 CD ) 1.1376 ( PROT GLN 3 OE1 ) 1.1376 ( PROT GLN 3 NE2 ) 1.1376 ( PROT GLN 3 HE21 ) 1.1376 ( PROT GLN 3 HE22 ) 1.1376 ( PROT GLN 3 C ) 1.4220 ( PROT GLN 3 O ) 1.4220 ( PROT ALA 4 N ) 1.4220 ( PROT ALA 4 H ) 1.1376 ( PROT ALA 4 CA ) 1.4220 ( PROT ALA 4 CB ) 1.1376 ( PROT ALA 4 C ) 1.4220 ( PROT ALA 4 O ) 1.4220 ( PROT PHE 5 N ) 1.4220 ( PROT PHE 5 H ) 1.1376 ( PROT PHE 5 CA ) 1.4220 ( PROT PHE 5 CB ) 1.1376 ( PROT PHE 5 CG ) 1.1376 ( PROT PHE 5 CD1 ) 1.1376 ( PROT PHE 5 CD2 ) 1.1376 ( PROT PHE 5 CE1 ) 1.1376 ( PROT PHE 5 CE2 ) 1.1376 ( PROT PHE 5 CZ ) 1.1376 ( PROT PHE 5 C ) 1.4220 ( PROT PHE 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 ILE 7 N ) 1.4220 ( PROT ILE 7 H ) 1.1376 ( PROT ILE 7 CA ) 1.4220 ( PROT ILE 7 CB ) 1.1376 ( PROT ILE 7 CG2 ) 1.1376 ( PROT ILE 7 CG1 ) 1.1376 ( PROT ILE 7 CD ) 1.1376 ( PROT ILE 7 C ) 1.4220 ( PROT ILE 7 O ) 1.4220 ( PROT ALA 8 N ) 1.4220 ( PROT ALA 8 H ) 1.1376 ( PROT ALA 8 CA ) 1.4220 ( PROT ALA 8 CB ) 1.1376 ( PROT ALA 8 C ) 1.4220 ( PROT ALA 8 O ) 1.4220 ( PROT LEU 9 N ) 1.4220 ( PROT LEU 9 H ) 1.1376 ( PROT LEU 9 CA ) 1.4220 ( PROT LEU 9 CB ) 1.1376 ( PROT LEU 9 CG ) 1.1376 ( PROT LEU 9 CD1 ) 1.1376 ( PROT LEU 9 CD2 ) 1.1376 ( PROT LEU 9 C ) 1.4220 ( PROT LEU 9 O ) 1.4220 ( PROT SER 10 N ) 1.4220 ( PROT SER 10 H ) 1.1376 ( PROT SER 10 CA ) 1.4220 ( PROT SER 10 CB ) 1.1376 ( PROT SER 10 OG ) 1.1376 ( PROT SER 10 HG ) 1.1376 ( PROT SER 10 C ) 1.4220 ( PROT SER 10 O ) 1.4220 ( PROT SER 11 N ) 1.4220 ( PROT SER 11 H ) 1.1376 ( PROT SER 11 CA ) 1.4220 ( PROT SER 11 CB ) 1.1376 ( PROT SER 11 OG ) 1.1376 ( PROT SER 11 HG ) 1.1376 ( PROT SER 11 C ) 1.4220 ( PROT SER 11 O ) 1.4220 ( PROT PHE 12 N ) 1.4220 ( PROT PHE 12 H ) 1.1376 ( PROT PHE 12 CA ) 1.4220 ( PROT PHE 12 CB ) 1.1376 ( PROT PHE 12 CG ) 1.1376 ( PROT PHE 12 CD1 ) 1.1376 ( PROT PHE 12 CD2 ) 1.1376 ( PROT PHE 12 CE1 ) 1.1376 ( PROT PHE 12 CE2 ) 1.1376 ( PROT PHE 12 CZ ) 1.1376 ( PROT PHE 12 C ) 1.4220 ( PROT PHE 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 SER 14 N ) 1.4220 ( PROT SER 14 H ) 1.1376 ( PROT SER 14 CA ) 1.4220 ( PROT SER 14 CB ) 1.1376 ( PROT SER 14 OG ) 1.1376 ( PROT SER 14 HG ) 1.1376 ( PROT SER 14 C ) 1.4220 ( PROT SER 14 O ) 1.4220 ( PROT LYS 15 N ) 1.4220 ( PROT LYS 15 H ) 1.1376 ( PROT LYS 15 CA ) 1.4220 ( PROT LYS 15 CB ) 1.1376 ( PROT LYS 15 CG ) 1.1376 ( PROT LYS 15 CD ) 1.1376 ( PROT LYS 15 CE ) 1.1376 ( PROT LYS 15 NZ ) 1.1376 ( PROT LYS 15 HZ1 ) 1.1376 ( PROT LYS 15 HZ2 ) 1.1376 ( PROT LYS 15 HZ3 ) 1.1376 ( PROT LYS 15 C ) 1.4220 ( PROT LYS 15 O ) 1.4220 ( PROT LEU 16 N ) 1.4220 ( PROT LEU 16 H ) 1.1376 ( PROT LEU 16 CA ) 1.4220 ( PROT LEU 16 CB ) 1.1376 ( PROT LEU 16 CG ) 1.1376 ( PROT LEU 16 CD1 ) 1.1376 ( PROT LEU 16 CD2 ) 1.1376 ( PROT LEU 16 C ) 1.4220 ( PROT LEU 16 O ) 1.4220 ( PROT ALA 17 N ) 1.4220 ( PROT ALA 17 H ) 1.1376 ( PROT ALA 17 CA ) 1.4220 ( PROT ALA 17 CB ) 1.1376 ( PROT ALA 17 C ) 1.4220 ( PROT ALA 17 O ) 1.4220 ( PROT CYS 18 N ) 1.4220 ( PROT CYS 18 H ) 1.1376 ( PROT CYS 18 CA ) 1.4220 ( PROT CYS 18 CB ) 1.1376 ( PROT CYS 18 SG ) 1.1376 ( PROT CYS 18 C ) 1.4220 ( PROT CYS 18 O ) 1.4220 ( PROT GLU 19 N ) 1.4220 ( PROT GLU 19 H ) 1.1376 ( PROT GLU 19 CA ) 1.4220 ( PROT GLU 19 CB ) 1.1376 ( PROT GLU 19 CG ) 1.1376 ( PROT GLU 19 CD ) 1.1376 ( PROT GLU 19 OE1 ) 1.1376 ( PROT GLU 19 OE2 ) 1.1376 ( PROT GLU 19 C ) 1.4220 ( PROT GLU 19 OT1 ) 1.1376 ( PROT GLU 19 OT2 ) 1.1376 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43086 4.57564 -7.52825 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00384 -0.00041 -0.00437 ROTATION MATRIX 1.000000 -0.000230 -0.000345 0.000230 1.000000 0.000567 0.000345 -0.000568 1.000000 AXIS OF ROTATION IS 0.807644 0.490553 -0.327214 ANGLE IS 0.04 TOTAL SQUARE DIFF IS 29.7914 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.421105 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4211" Parameter: A <- "0.4211" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.94006 4.27357 -7.73106 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.00785 0.00670 -0.00120 ROTATION MATRIX 0.999734 0.017662 0.014804 -0.017282 0.999527 -0.025423 -0.015246 0.025160 0.999567 AXIS OF ROTATION IS -0.739189 -0.439132 0.510649 ANGLE IS 1.96 CENTER OF ROTATION 8.851618 4.133812 -7.977069 SHIFT IS 0.002250 TOTAL SQUARE DIFF IS 1.7734 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.305509 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4211" RDCMND substituted energy or value "?RMS" to " 0.3055" Parameter: A <- "0.4211 0.3055" 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 0.4211 0.3055 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 59.07" Parameter: H <- "59.07" 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 -29.92809 59.06993 0.97048 ENER INTERN> 4.64450 21.45804 0.00000 15.18276 3.94871 ENER EXTERN> -61.04549 -14.11660 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 " -29.93" Parameter: B <- "-29.93" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -14.12" Parameter: C <- "-14.12" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -61.05" Parameter: C <- " -75.17" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -75.17" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.64" Parameter: D <- "4.64" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 21.46" Parameter: D <- " 26.10" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 15.18" Parameter: D <- " 41.28" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.95" Parameter: D <- " 45.23" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 45.23" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 7200 ENER= -29.93 GRMS= 0.97 ELEC= -14.12 VDW= -61.05 RDTITL> *EXTERNAL= -75.17 INTERNAL= 45.23 USER= 0.00 HARM= 59.07 RDTITL> *BOND= 4.64 ANGL= 21.46 DIHE= 15.18 IMPR= 3.95 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= -29.93 GRMS= 0.97 ELEC= -14.12 VDW= -61.05 RDTITL> *EXTERNAL= -75.17 INTERNAL= 45.23 USER= 0.00 HARM= 59.07 RDTITL> *BOND= 4.64 ANGL= 21.46 DIHE= 15.18 IMPR= 3.95 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= -29.93 GRMS= 0.97 ELEC= -14.12 VDW= -61.05 RDTITL> *EXTERNAL= -75.17 INTERNAL= 45.23 USER= 0.00 HARM= 59.07 RDTITL> *BOND= 4.64 ANGL= 21.46 DIHE= 15.18 IMPR= 3.95 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 7200 0.4211 0.3055 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "7200" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9733 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9732 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 11.84230 -41.77039 0.38407 0.02000 MINI INTERN> 4.64450 21.45804 0.00000 15.18276 3.94871 MINI EXTERN> -61.04549 -14.11660 0.00000 0.00000 0.00000 MINI CONSTR> 41.77039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 34.60208 -22.75978 17.06173 0.00864 MINI INTERN> 29.48192 19.12942 0.00000 16.38809 3.38777 MINI EXTERN> -66.55771 -11.16938 0.00000 0.00000 0.00000 MINI CONSTR> 43.94197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9724 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 10.34963 24.25245 0.98232 0.00156 MINI INTERN> 4.91539 20.77411 0.00000 15.90542 3.91955 MINI EXTERN> -66.45797 -12.81994 0.00000 0.00000 0.00000 MINI CONSTR> 44.11308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 10.16652 0.18311 0.39934 0.00067 MINI INTERN> 4.61091 21.15860 0.00000 15.81869 3.96635 MINI EXTERN> -66.54406 -13.02974 0.00000 0.00000 0.00000 MINI CONSTR> 44.18577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9723 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 10.03771 0.12881 0.34289 0.00029 MINI INTERN> 4.65974 20.98108 0.00000 15.83403 3.92196 MINI EXTERN> -66.54264 -13.07409 0.00000 0.00000 0.00000 MINI CONSTR> 44.25764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 9.93905 0.09867 0.23740 0.00030 MINI INTERN> 4.62398 20.99799 0.00000 15.81145 3.92388 MINI EXTERN> -66.57750 -13.16355 0.00000 0.00000 0.00000 MINI CONSTR> 44.32280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9722 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 9.82270 0.11634 0.41543 0.00031 MINI INTERN> 4.58167 20.94625 0.00000 15.81634 3.89889 MINI EXTERN> -66.60274 -13.23320 0.00000 0.00000 0.00000 MINI CONSTR> 44.41550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 9.71592 0.10678 0.29753 0.00032 MINI INTERN> 4.56012 20.94644 0.00000 15.79282 3.90152 MINI EXTERN> -66.67502 -13.30456 0.00000 0.00000 0.00000 MINI CONSTR> 44.49461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9720 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 9.60933 0.10660 0.29616 0.00034 MINI INTERN> 4.56902 20.89523 0.00000 15.78063 3.89323 MINI EXTERN> -66.75953 -13.35077 0.00000 0.00000 0.00000 MINI CONSTR> 44.58151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 9.50651 0.10282 0.32602 0.00035 MINI INTERN> 4.53907 20.87344 0.00000 15.77077 3.88550 MINI EXTERN> -66.83370 -13.39861 0.00000 0.00000 0.00000 MINI CONSTR> 44.67003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9720 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 9.42537 0.08114 0.52214 0.00036 MINI INTERN> 4.50117 20.84192 0.00000 15.77800 3.86586 MINI EXTERN> -66.88433 -13.42959 0.00000 0.00000 0.00000 MINI CONSTR> 44.75235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 9.33392 0.09145 0.55995 0.00037 MINI INTERN> 4.50541 20.79311 0.00000 15.76671 3.85966 MINI EXTERN> -66.97616 -13.45036 0.00000 0.00000 0.00000 MINI CONSTR> 44.83556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9718 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 9.25434 0.07959 0.60829 0.00039 MINI INTERN> 4.48127 20.78143 0.00000 15.76201 3.85099 MINI EXTERN> -67.04138 -13.49025 0.00000 0.00000 0.00000 MINI CONSTR> 44.91026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 9.17309 0.08124 0.57844 0.00040 MINI INTERN> 4.44949 20.76776 0.00000 15.75212 3.84940 MINI EXTERN> -67.11751 -13.50865 0.00000 0.00000 0.00000 MINI CONSTR> 44.98048 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9716 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 9.09506 0.07803 0.63428 0.00042 MINI INTERN> 4.48802 20.73195 0.00000 15.73235 3.84833 MINI EXTERN> -67.20969 -13.54971 0.00000 0.00000 0.00000 MINI CONSTR> 45.05381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 8.99570 0.09936 0.19659 0.00018 MINI INTERN> 4.57138 20.68300 0.00000 15.67929 3.87708 MINI EXTERN> -67.36261 -13.57023 0.00000 0.00000 0.00000 MINI CONSTR> 45.11780 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9715 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 8.95242 0.04328 0.66051 0.00045 MINI INTERN> 4.38442 20.71610 0.00000 15.72954 3.83322 MINI EXTERN> -67.32432 -13.57444 0.00000 0.00000 0.00000 MINI CONSTR> 45.18790 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 8.88226 0.07016 0.72529 0.00046 MINI INTERN> 4.44147 20.67212 0.00000 15.70697 3.83293 MINI EXTERN> -67.41608 -13.61105 0.00000 0.00000 0.00000 MINI CONSTR> 45.25590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9715 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 8.81920 0.06306 0.78100 0.00048 MINI INTERN> 4.38241 20.66146 0.00000 15.70358 3.82899 MINI EXTERN> -67.47851 -13.59983 0.00000 0.00000 0.00000 MINI CONSTR> 45.32110 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 8.70673 0.11247 0.22076 0.00021 MINI INTERN> 4.57739 20.55985 0.00000 15.62705 3.86486 MINI EXTERN> -67.66308 -13.64101 0.00000 0.00000 0.00000 MINI CONSTR> 45.38167 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9715 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 8.64575 0.06098 0.17730 0.00022 MINI INTERN> 4.54809 20.54119 0.00000 15.62436 3.85635 MINI EXTERN> -67.70790 -13.65185 0.00000 0.00000 0.00000 MINI CONSTR> 45.43552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 8.57672 0.06903 0.17576 0.00022 MINI INTERN> 4.54320 20.51422 0.00000 15.61200 3.85243 MINI EXTERN> -67.77612 -13.66763 0.00000 0.00000 0.00000 MINI CONSTR> 45.49862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9714 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 8.51250 0.06423 0.18783 0.00023 MINI INTERN> 4.55267 20.48289 0.00000 15.59641 3.85085 MINI EXTERN> -67.84688 -13.68146 0.00000 0.00000 0.00000 MINI CONSTR> 45.55802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 8.45209 0.06040 0.33060 0.00024 MINI INTERN> 4.61491 20.43641 0.00000 15.56570 3.85840 MINI EXTERN> -67.94690 -13.69715 0.00000 0.00000 0.00000 MINI CONSTR> 45.62072 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9713 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 8.39003 0.06206 0.22395 0.00025 MINI INTERN> 4.56583 20.42601 0.00000 15.56663 3.84708 MINI EXTERN> -67.97909 -13.70835 0.00000 0.00000 0.00000 MINI CONSTR> 45.67192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 8.33299 0.05704 0.27712 0.00026 MINI INTERN> 4.58742 20.39097 0.00000 15.54789 3.84770 MINI EXTERN> -68.05059 -13.71753 0.00000 0.00000 0.00000 MINI CONSTR> 45.72713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9713 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 8.28482 0.04817 0.39245 0.00027 MINI INTERN> 4.64274 20.34906 0.00000 15.52321 3.85152 MINI EXTERN> -68.12817 -13.73207 0.00000 0.00000 0.00000 MINI CONSTR> 45.77853 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 8.22990 0.05492 0.41485 0.00028 MINI INTERN> 4.62573 20.32928 0.00000 15.51320 3.84793 MINI EXTERN> -68.18055 -13.73635 0.00000 0.00000 0.00000 MINI CONSTR> 45.83065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9710 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 8.18107 0.04883 0.44857 0.00029 MINI INTERN> 4.66495 20.29252 0.00000 15.49404 3.84749 MINI EXTERN> -68.24291 -13.75338 0.00000 0.00000 0.00000 MINI CONSTR> 45.87836 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 8.13250 0.04857 0.47658 0.00030 MINI INTERN> 4.66663 20.26455 0.00000 15.48123 3.84545 MINI EXTERN> -68.29644 -13.75474 0.00000 0.00000 0.00000 MINI CONSTR> 45.92582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9711 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 8.08420 0.04830 0.44649 0.00031 MINI INTERN> 4.67076 20.24067 0.00000 15.47048 3.84115 MINI EXTERN> -68.33932 -13.76754 0.00000 0.00000 0.00000 MINI CONSTR> 45.96800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 8.03587 0.04833 0.48640 0.00032 MINI INTERN> 4.65052 20.22461 0.00000 15.46106 3.83782 MINI EXTERN> -68.38536 -13.76855 0.00000 0.00000 0.00000 MINI CONSTR> 46.01578 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9711 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 7.97490 0.06097 0.15539 0.00014 MINI INTERN> 4.47100 20.27272 0.00000 15.49309 3.81017 MINI EXTERN> -68.34577 -13.77904 0.00000 0.00000 0.00000 MINI CONSTR> 46.05272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 7.94901 0.02589 0.50961 0.00034 MINI INTERN> 4.68905 20.16616 0.00000 15.43090 3.83510 MINI EXTERN> -68.48536 -13.78614 0.00000 0.00000 0.00000 MINI CONSTR> 46.09931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9711 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 7.88446 0.06455 0.16298 0.00015 MINI INTERN> 4.45544 20.23866 0.00000 15.47247 3.80336 MINI EXTERN> -68.42862 -13.79413 0.00000 0.00000 0.00000 MINI CONSTR> 46.13727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 7.86675 0.01770 0.56121 0.00037 MINI INTERN> 4.70658 20.12421 0.00000 15.40672 3.82871 MINI EXTERN> -68.56833 -13.81076 0.00000 0.00000 0.00000 MINI CONSTR> 46.17963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9711 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 7.80045 0.06631 0.18142 0.00016 MINI INTERN> 4.43580 20.21010 0.00000 15.45363 3.79627 MINI EXTERN> -68.50290 -13.80888 0.00000 0.00000 0.00000 MINI CONSTR> 46.21643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 7.78893 0.01152 0.58520 0.00040 MINI INTERN> 4.72629 20.07111 0.00000 15.37901 3.82728 MINI EXTERN> -68.65990 -13.81162 0.00000 0.00000 0.00000 MINI CONSTR> 46.25676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9711 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 7.71899 0.06994 0.20655 0.00017 MINI INTERN> 4.41500 20.18250 0.00000 15.43481 3.78918 MINI EXTERN> -68.57457 -13.82187 0.00000 0.00000 0.00000 MINI CONSTR> 46.29394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 7.68371 0.03528 0.13763 0.00018 MINI INTERN> 4.45715 20.14806 0.00000 15.41445 3.79291 MINI EXTERN> -68.62592 -13.82849 0.00000 0.00000 0.00000 MINI CONSTR> 46.32555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9709 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 7.64211 0.04160 0.24725 0.00019 MINI INTERN> 4.39054 20.15857 0.00000 15.41742 3.78156 MINI EXTERN> -68.64015 -13.83409 0.00000 0.00000 0.00000 MINI CONSTR> 46.36826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 7.60405 0.03806 0.17969 0.00019 MINI INTERN> 4.42436 20.12692 0.00000 15.39823 3.78374 MINI EXTERN> -68.68914 -13.84214 0.00000 0.00000 0.00000 MINI CONSTR> 46.40209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9708 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 7.56839 0.03567 0.21096 0.00020 MINI INTERN> 4.39950 20.12148 0.00000 15.39240 3.77901 MINI EXTERN> -68.71511 -13.84611 0.00000 0.00000 0.00000 MINI CONSTR> 46.43720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 7.53283 0.03556 0.21789 0.00021 MINI INTERN> 4.39710 20.10747 0.00000 15.38195 3.77630 MINI EXTERN> -68.74771 -13.85368 0.00000 0.00000 0.00000 MINI CONSTR> 46.47140 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9708 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 7.50336 0.02947 0.31229 0.00021 MINI INTERN> 4.34980 20.11588 0.00000 15.38247 3.76877 MINI EXTERN> -68.76034 -13.85721 0.00000 0.00000 0.00000 MINI CONSTR> 46.50399 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 7.46815 0.03520 0.32184 0.00022 MINI INTERN> 4.35646 20.09804 0.00000 15.37025 3.76640 MINI EXTERN> -68.79507 -13.86609 0.00000 0.00000 0.00000 MINI CONSTR> 46.53817 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9705 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 7.43808 0.03008 0.37410 0.00023 MINI INTERN> 4.33513 20.09053 0.00000 15.36343 3.76334 MINI EXTERN> -68.82172 -13.86324 0.00000 0.00000 0.00000 MINI CONSTR> 46.57060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 7.40709 0.03099 0.34197 0.00024 MINI INTERN> 4.33080 20.08191 0.00000 15.35479 3.76060 MINI EXTERN> -68.84623 -13.87358 0.00000 0.00000 0.00000 MINI CONSTR> 46.59880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9706 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 7.37466 0.03243 0.38228 0.00025 MINI INTERN> 4.31506 20.07329 0.00000 15.34724 3.75611 MINI EXTERN> -68.87275 -13.87732 0.00000 0.00000 0.00000 MINI CONSTR> 46.63303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 7.34465 0.03001 0.36949 0.00026 MINI INTERN> 4.31986 20.05872 0.00000 15.33608 3.75478 MINI EXTERN> -68.90209 -13.88416 0.00000 0.00000 0.00000 MINI CONSTR> 46.66147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9705 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 7.31409 0.03056 0.38807 0.00027 MINI INTERN> 4.31771 20.04226 0.00000 15.32505 3.75342 MINI EXTERN> -68.93419 -13.88295 0.00000 0.00000 0.00000 MINI CONSTR> 46.69281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 7.27605 0.03804 0.12449 0.00011 MINI INTERN> 4.46812 19.95520 0.00000 15.27920 3.77002 MINI EXTERN> -69.02316 -13.89264 0.00000 0.00000 0.00000 MINI CONSTR> 46.71930 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9704 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 7.26175 0.01430 0.41830 0.00029 MINI INTERN> 4.29099 20.03409 0.00000 15.31211 3.74666 MINI EXTERN> -68.97387 -13.89511 0.00000 0.00000 0.00000 MINI CONSTR> 46.74690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 7.23404 0.02772 0.44739 0.00030 MINI INTERN> 4.31098 20.01522 0.00000 15.29868 3.74512 MINI EXTERN> -69.00524 -13.90661 0.00000 0.00000 0.00000 MINI CONSTR> 46.77587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9703 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 7.19197 0.04207 0.14557 0.00013 MINI INTERN> 4.48046 19.91032 0.00000 15.24591 3.76597 MINI EXTERN> -69.10845 -13.90599 0.00000 0.00000 0.00000 MINI CONSTR> 46.80375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 7.18499 0.00698 0.47123 0.00032 MINI INTERN> 4.27119 20.00732 0.00000 15.28722 3.73956 MINI EXTERN> -69.04358 -13.90462 0.00000 0.00000 0.00000 MINI CONSTR> 46.82790 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9703 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 7.14111 0.04388 0.16957 0.00014 MINI INTERN> 4.49068 19.88102 0.00000 15.22447 3.76376 MINI EXTERN> -69.16162 -13.91306 0.00000 0.00000 0.00000 MINI CONSTR> 46.85587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 7.11895 0.02217 0.11332 0.00014 MINI INTERN> 4.45437 19.88829 0.00000 15.22498 3.75796 MINI EXTERN> -69.16626 -13.91691 0.00000 0.00000 0.00000 MINI CONSTR> 46.87651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9702 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 7.09413 0.02482 0.20325 0.00015 MINI INTERN> 4.50875 19.85052 0.00000 15.20256 3.76208 MINI EXTERN> -69.21337 -13.92140 0.00000 0.00000 0.00000 MINI CONSTR> 46.90497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 7.07198 0.02214 0.10917 0.00015 MINI INTERN> 4.44861 19.86852 0.00000 15.20817 3.75428 MINI EXTERN> -69.20882 -13.92322 0.00000 0.00000 0.00000 MINI CONSTR> 46.92445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9701 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 7.04860 0.02338 0.23257 0.00016 MINI INTERN> 4.51800 19.82355 0.00000 15.18238 3.76000 MINI EXTERN> -69.26155 -13.92694 0.00000 0.00000 0.00000 MINI CONSTR> 46.95316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 7.02446 0.02415 0.16636 0.00016 MINI INTERN> 4.48315 19.83054 0.00000 15.18171 3.75424 MINI EXTERN> -69.26734 -13.93299 0.00000 0.00000 0.00000 MINI CONSTR> 46.97515 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9701 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 7.00581 0.01865 0.24897 0.00017 MINI INTERN> 4.52793 19.79952 0.00000 15.16347 3.75741 MINI EXTERN> -69.30505 -13.93578 0.00000 0.00000 0.00000 MINI CONSTR> 46.99831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 6.98415 0.02166 0.27124 0.00018 MINI INTERN> 4.51812 19.79154 0.00000 15.15601 3.75561 MINI EXTERN> -69.32462 -13.93461 0.00000 0.00000 0.00000 MINI CONSTR> 47.02211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9700 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 6.96436 0.01979 0.28402 0.00018 MINI INTERN> 4.54308 19.77189 0.00000 15.14279 3.75596 MINI EXTERN> -69.35170 -13.94151 0.00000 0.00000 0.00000 MINI CONSTR> 47.04386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 6.94361 0.02076 0.29855 0.00019 MINI INTERN> 4.54739 19.75957 0.00000 15.13296 3.75498 MINI EXTERN> -69.37383 -13.94421 0.00000 0.00000 0.00000 MINI CONSTR> 47.06676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9699 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 6.92382 0.01979 0.28317 0.00020 MINI INTERN> 4.54084 19.75378 0.00000 15.12659 3.75270 MINI EXTERN> -69.38885 -13.94806 0.00000 0.00000 0.00000 MINI CONSTR> 47.08683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 6.90370 0.02012 0.30406 0.00020 MINI INTERN> 4.54166 19.74262 0.00000 15.11720 3.75175 MINI EXTERN> -69.41014 -13.94909 0.00000 0.00000 0.00000 MINI CONSTR> 47.10970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9698 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 6.88663 0.01707 0.35855 0.00021 MINI INTERN> 4.56295 19.72788 0.00000 15.10552 3.75102 MINI EXTERN> -69.43292 -13.95892 0.00000 0.00000 0.00000 MINI CONSTR> 47.13110 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 6.86813 0.01850 0.32772 0.00022 MINI INTERN> 4.55637 19.72084 0.00000 15.09926 3.74944 MINI EXTERN> -69.44780 -13.95936 0.00000 0.00000 0.00000 MINI CONSTR> 47.14938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9698 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 6.85086 0.01727 0.36195 0.00023 MINI INTERN> 4.52268 19.72398 0.00000 15.09744 3.74613 MINI EXTERN> -69.45677 -13.95268 0.00000 0.00000 0.00000 MINI CONSTR> 47.17007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 6.83382 0.01704 0.36709 0.00024 MINI INTERN> 4.56297 19.70258 0.00000 15.08267 3.74676 MINI EXTERN> -69.48289 -13.96746 0.00000 0.00000 0.00000 MINI CONSTR> 47.18919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9698 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 6.80626 0.02756 0.11191 0.00010 MINI INTERN> 4.38942 19.77211 0.00000 15.11108 3.72874 MINI EXTERN> -69.43741 -13.96436 0.00000 0.00000 0.00000 MINI CONSTR> 47.20666 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 6.80118 0.00507 0.37726 0.00025 MINI INTERN> 4.57392 19.68071 0.00000 15.06537 3.74545 MINI EXTERN> -69.51930 -13.97145 0.00000 0.00000 0.00000 MINI CONSTR> 47.22648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9697 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 6.77285 0.02833 0.13451 0.00011 MINI INTERN> 4.37550 19.76359 0.00000 15.09912 3.72452 MINI EXTERN> -69.46379 -13.97038 0.00000 0.00000 0.00000 MINI CONSTR> 47.24429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 6.75835 0.01450 0.09222 0.00011 MINI INTERN> 4.39996 19.74386 0.00000 15.08715 3.72638 MINI EXTERN> -69.48700 -13.97181 0.00000 0.00000 0.00000 MINI CONSTR> 47.25981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9697 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 6.74185 0.01650 0.15872 0.00012 MINI INTERN> 4.35972 19.75644 0.00000 15.08812 3.72048 MINI EXTERN> -69.48796 -13.97486 0.00000 0.00000 0.00000 MINI CONSTR> 47.27992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 6.72728 0.01457 0.08658 0.00012 MINI INTERN> 4.40225 19.72794 0.00000 15.07236 3.72418 MINI EXTERN> -69.51732 -13.97705 0.00000 0.00000 0.00000 MINI CONSTR> 47.29492 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9696 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 6.70998 0.01731 0.17712 0.00013 MINI INTERN> 4.35007 19.74604 0.00000 15.07525 3.71680 MINI EXTERN> -69.51508 -13.98003 0.00000 0.00000 0.00000 MINI CONSTR> 47.31692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 6.69371 0.01627 0.11499 0.00013 MINI INTERN> 4.37820 19.72360 0.00000 15.06167 3.71894 MINI EXTERN> -69.54078 -13.98191 0.00000 0.00000 0.00000 MINI CONSTR> 47.33398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9696 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 6.67867 0.01504 0.14467 0.00014 MINI INTERN> 4.36664 19.72308 0.00000 15.05707 3.71609 MINI EXTERN> -69.55039 -13.98591 0.00000 0.00000 0.00000 MINI CONSTR> 47.35209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 6.66670 0.01197 0.20436 0.00014 MINI INTERN> 4.33590 19.73240 0.00000 15.05738 3.71170 MINI EXTERN> -69.55185 -13.98706 0.00000 0.00000 0.00000 MINI CONSTR> 47.36823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9696 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 6.65170 0.01500 0.20859 0.00015 MINI INTERN> 4.33377 19.72536 0.00000 15.05035 3.71044 MINI EXTERN> -69.56634 -13.98801 0.00000 0.00000 0.00000 MINI CONSTR> 47.38614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 6.63881 0.01289 0.25143 0.00015 MINI INTERN> 4.34048 19.71875 0.00000 15.04278 3.70886 MINI EXTERN> -69.57963 -13.99539 0.00000 0.00000 0.00000 MINI CONSTR> 47.40297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9696 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 6.62585 0.01296 0.22777 0.00016 MINI INTERN> 4.32741 19.71739 0.00000 15.03902 3.70712 MINI EXTERN> -69.58818 -13.99455 0.00000 0.00000 0.00000 MINI CONSTR> 47.41764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 6.61406 0.01179 0.27990 0.00016 MINI INTERN> 4.31596 19.71445 0.00000 15.03427 3.70551 MINI EXTERN> -69.59945 -13.99136 0.00000 0.00000 0.00000 MINI CONSTR> 47.43467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9697 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 6.60178 0.01228 0.25589 0.00017 MINI INTERN> 4.31793 19.70804 0.00000 15.02804 3.70476 MINI EXTERN> -69.61083 -13.99439 0.00000 0.00000 0.00000 MINI CONSTR> 47.44823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 6.58523 0.01655 0.08190 0.00007 MINI INTERN> 4.41809 19.65091 0.00000 14.99946 3.71447 MINI EXTERN> -69.65976 -14.00042 0.00000 0.00000 0.00000 MINI CONSTR> 47.46248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9697 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 6.57865 0.00658 0.26614 0.00018 MINI INTERN> 4.30651 19.70469 0.00000 15.01892 3.70087 MINI EXTERN> -69.62745 -14.00196 0.00000 0.00000 0.00000 MINI CONSTR> 47.47706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 6.56057 0.01808 0.08140 0.00008 MINI INTERN> 4.41727 19.63914 0.00000 14.98689 3.71230 MINI EXTERN> -69.68333 -14.00454 0.00000 0.00000 0.00000 MINI CONSTR> 47.49283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9697 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 6.55544 0.00513 0.28514 0.00020 MINI INTERN> 4.29948 19.69705 0.00000 15.00811 3.69790 MINI EXTERN> -69.64797 -14.00610 0.00000 0.00000 0.00000 MINI CONSTR> 47.50698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 6.54415 0.01129 0.31238 0.00020 MINI INTERN> 4.29816 19.68919 0.00000 15.00137 3.69748 MINI EXTERN> -69.66206 -14.00292 0.00000 0.00000 0.00000 MINI CONSTR> 47.52292 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9697 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 6.52554 0.01861 0.10193 0.00009 MINI INTERN> 4.42932 19.61569 0.00000 14.96556 3.71055 MINI EXTERN> -69.72216 -14.01069 0.00000 0.00000 0.00000 MINI CONSTR> 47.53729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 6.51570 0.00984 0.07162 0.00009 MINI INTERN> 4.40719 19.62192 0.00000 14.96537 3.70736 MINI EXTERN> -69.72311 -14.01204 0.00000 0.00000 0.00000 MINI CONSTR> 47.54901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9697 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 6.50409 0.01161 0.07234 0.00009 MINI INTERN> 4.40718 19.61593 0.00000 14.95902 3.70641 MINI EXTERN> -69.73465 -14.01372 0.00000 0.00000 0.00000 MINI CONSTR> 47.56392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 6.49316 0.01093 0.13458 0.00010 MINI INTERN> 4.44296 19.59252 0.00000 14.94463 3.70911 MINI EXTERN> -69.75946 -14.01643 0.00000 0.00000 0.00000 MINI CONSTR> 47.57984 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9697 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 6.48253 0.01064 0.09036 0.00010 MINI INTERN> 4.42023 19.59901 0.00000 14.94425 3.70572 MINI EXTERN> -69.76042 -14.01850 0.00000 0.00000 0.00000 MINI CONSTR> 47.59225 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 6.47250 0.01002 0.10930 0.00011 MINI INTERN> 4.42773 19.58943 0.00000 14.93669 3.70581 MINI EXTERN> -69.77398 -14.01916 0.00000 0.00000 0.00000 MINI CONSTR> 47.60598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9696 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 6.46402 0.00848 0.15993 0.00011 MINI INTERN> 4.45320 19.57318 0.00000 14.92596 3.70731 MINI EXTERN> -69.79193 -14.02264 0.00000 0.00000 0.00000 MINI CONSTR> 47.61895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 6.45352 0.01050 0.11273 0.00011 MINI INTERN> 4.42535 19.58072 0.00000 14.92641 3.70391 MINI EXTERN> -69.79213 -14.02195 0.00000 0.00000 0.00000 MINI CONSTR> 47.63121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9696 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 6.44604 0.00749 0.17109 0.00012 MINI INTERN> 4.45158 19.56358 0.00000 14.91568 3.70582 MINI EXTERN> -69.81045 -14.02366 0.00000 0.00000 0.00000 MINI CONSTR> 47.64349 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 6.44604 0.00749 0.17109 0.00014 STPD INTERN> 4.45158 19.56358 0.00000 14.91568 3.70582 STPD EXTERN> -69.81045 -14.02366 0.00000 0.00000 0.00000 STPD CONSTR> 47.64349 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 9696 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9696 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 6.44604 0.00749 0.17109 0.00000 MINI INTERN> 4.45158 19.56358 0.00000 14.91568 3.70582 MINI EXTERN> -69.81045 -14.02366 0.00000 0.00000 0.00000 MINI CONSTR> 47.64349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 6.02926 0.41678 0.02759 0.00383 MINI INTERN> 4.35712 19.22091 0.00000 14.48534 3.62387 MINI EXTERN> -70.65856 -14.14100 0.00000 0.00000 0.00000 MINI CONSTR> 49.14156 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 6.02612 0.00314 0.06169 0.00537 MINI INTERN> 4.31955 19.18835 0.00000 14.47281 3.61096 MINI EXTERN> -70.36960 -14.18838 0.00000 0.00000 0.00000 MINI CONSTR> 48.99243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 6.02044 0.00568 0.04539 0.00825 MINI INTERN> 4.33523 19.27395 0.00000 14.47144 3.62207 MINI EXTERN> -70.21336 -14.16869 0.00000 0.00000 0.00000 MINI CONSTR> 48.69980 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 6.01833 0.00211 0.03150 0.00251 MINI INTERN> 4.35901 19.32908 0.00000 14.49553 3.63001 MINI EXTERN> -70.26142 -14.14589 0.00000 0.00000 0.00000 MINI CONSTR> 48.61200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 6.01750 0.00083 0.01737 0.00133 MINI INTERN> 4.35834 19.31987 0.00000 14.51722 3.63284 MINI EXTERN> -70.29303 -14.10887 0.00000 0.00000 0.00000 MINI CONSTR> 48.59113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 6.01705 0.00045 0.01740 0.00161 MINI INTERN> 4.36443 19.33423 0.00000 14.52934 3.63313 MINI EXTERN> -70.32646 -14.10812 0.00000 0.00000 0.00000 MINI CONSTR> 48.59049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 6.01661 0.00044 0.01620 0.00186 MINI INTERN> 4.36167 19.32435 0.00000 14.53446 3.63654 MINI EXTERN> -70.31355 -14.12107 0.00000 0.00000 0.00000 MINI CONSTR> 48.59422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 6.01626 0.00035 0.01297 0.00181 MINI INTERN> 4.36338 19.32879 0.00000 14.53743 3.63891 MINI EXTERN> -70.32819 -14.12878 0.00000 0.00000 0.00000 MINI CONSTR> 48.60471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 6.01606 0.00020 0.00921 0.00096 MINI INTERN> 4.36526 19.32267 0.00000 14.53964 3.63677 MINI EXTERN> -70.33374 -14.12700 0.00000 0.00000 0.00000 MINI CONSTR> 48.61246 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 45 6.01606 0.00020 0.00921 0.02000 CONJ INTERN> 4.36526 19.32267 0.00000 14.53964 3.63677 CONJ EXTERN> -70.33374 -14.12700 0.00000 0.00000 0.00000 CONJ CONSTR> 48.61246 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 ALA 1 HT1 ) 0.73944 ( PROT ALA 1 HT2 ) 0.73944 ( PROT ALA 1 N ) 0.92430 ( PROT ALA 1 HT3 ) 0.73944 ( PROT ALA 1 CA ) 0.92430 ( PROT ALA 1 CB ) 0.73944 ( PROT ALA 1 C ) 0.92430 ( PROT ALA 1 O ) 0.92430 ( PROT LEU 2 N ) 0.92430 ( PROT LEU 2 H ) 0.73944 ( PROT LEU 2 CA ) 0.92430 ( PROT LEU 2 CB ) 0.73944 ( PROT LEU 2 CG ) 0.73944 ( PROT LEU 2 CD1 ) 0.73944 ( PROT LEU 2 CD2 ) 0.73944 ( PROT LEU 2 C ) 0.92430 ( PROT LEU 2 O ) 0.92430 ( PROT GLN 3 N ) 0.92430 ( PROT GLN 3 H ) 0.73944 ( PROT GLN 3 CA ) 0.92430 ( PROT GLN 3 CB ) 0.73944 ( PROT GLN 3 CG ) 0.73944 ( PROT GLN 3 CD ) 0.73944 ( PROT GLN 3 OE1 ) 0.73944 ( PROT GLN 3 NE2 ) 0.73944 ( PROT GLN 3 HE21 ) 0.73944 ( PROT GLN 3 HE22 ) 0.73944 ( PROT GLN 3 C ) 0.92430 ( PROT GLN 3 O ) 0.92430 ( PROT ALA 4 N ) 0.92430 ( PROT ALA 4 H ) 0.73944 ( PROT ALA 4 CA ) 0.92430 ( PROT ALA 4 CB ) 0.73944 ( PROT ALA 4 C ) 0.92430 ( PROT ALA 4 O ) 0.92430 ( PROT PHE 5 N ) 0.92430 ( PROT PHE 5 H ) 0.73944 ( PROT PHE 5 CA ) 0.92430 ( PROT PHE 5 CB ) 0.73944 ( PROT PHE 5 CG ) 0.73944 ( PROT PHE 5 CD1 ) 0.73944 ( PROT PHE 5 CD2 ) 0.73944 ( PROT PHE 5 CE1 ) 0.73944 ( PROT PHE 5 CE2 ) 0.73944 ( PROT PHE 5 CZ ) 0.73944 ( PROT PHE 5 C ) 0.92430 ( PROT PHE 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 ILE 7 N ) 0.92430 ( PROT ILE 7 H ) 0.73944 ( PROT ILE 7 CA ) 0.92430 ( PROT ILE 7 CB ) 0.73944 ( PROT ILE 7 CG2 ) 0.73944 ( PROT ILE 7 CG1 ) 0.73944 ( PROT ILE 7 CD ) 0.73944 ( PROT ILE 7 C ) 0.92430 ( PROT ILE 7 O ) 0.92430 ( PROT ALA 8 N ) 0.92430 ( PROT ALA 8 H ) 0.73944 ( PROT ALA 8 CA ) 0.92430 ( PROT ALA 8 CB ) 0.73944 ( PROT ALA 8 C ) 0.92430 ( PROT ALA 8 O ) 0.92430 ( PROT LEU 9 N ) 0.92430 ( PROT LEU 9 H ) 0.73944 ( PROT LEU 9 CA ) 0.92430 ( PROT LEU 9 CB ) 0.73944 ( PROT LEU 9 CG ) 0.73944 ( PROT LEU 9 CD1 ) 0.73944 ( PROT LEU 9 CD2 ) 0.73944 ( PROT LEU 9 C ) 0.92430 ( PROT LEU 9 O ) 0.92430 ( PROT SER 10 N ) 0.92430 ( PROT SER 10 H ) 0.73944 ( PROT SER 10 CA ) 0.92430 ( PROT SER 10 CB ) 0.73944 ( PROT SER 10 OG ) 0.73944 ( PROT SER 10 HG ) 0.73944 ( PROT SER 10 C ) 0.92430 ( PROT SER 10 O ) 0.92430 ( PROT SER 11 N ) 0.92430 ( PROT SER 11 H ) 0.73944 ( PROT SER 11 CA ) 0.92430 ( PROT SER 11 CB ) 0.73944 ( PROT SER 11 OG ) 0.73944 ( PROT SER 11 HG ) 0.73944 ( PROT SER 11 C ) 0.92430 ( PROT SER 11 O ) 0.92430 ( PROT PHE 12 N ) 0.92430 ( PROT PHE 12 H ) 0.73944 ( PROT PHE 12 CA ) 0.92430 ( PROT PHE 12 CB ) 0.73944 ( PROT PHE 12 CG ) 0.73944 ( PROT PHE 12 CD1 ) 0.73944 ( PROT PHE 12 CD2 ) 0.73944 ( PROT PHE 12 CE1 ) 0.73944 ( PROT PHE 12 CE2 ) 0.73944 ( PROT PHE 12 CZ ) 0.73944 ( PROT PHE 12 C ) 0.92430 ( PROT PHE 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 SER 14 N ) 0.92430 ( PROT SER 14 H ) 0.73944 ( PROT SER 14 CA ) 0.92430 ( PROT SER 14 CB ) 0.73944 ( PROT SER 14 OG ) 0.73944 ( PROT SER 14 HG ) 0.73944 ( PROT SER 14 C ) 0.92430 ( PROT SER 14 O ) 0.92430 ( PROT LYS 15 N ) 0.92430 ( PROT LYS 15 H ) 0.73944 ( PROT LYS 15 CA ) 0.92430 ( PROT LYS 15 CB ) 0.73944 ( PROT LYS 15 CG ) 0.73944 ( PROT LYS 15 CD ) 0.73944 ( PROT LYS 15 CE ) 0.73944 ( PROT LYS 15 NZ ) 0.73944 ( PROT LYS 15 HZ1 ) 0.73944 ( PROT LYS 15 HZ2 ) 0.73944 ( PROT LYS 15 HZ3 ) 0.73944 ( PROT LYS 15 C ) 0.92430 ( PROT LYS 15 O ) 0.92430 ( PROT LEU 16 N ) 0.92430 ( PROT LEU 16 H ) 0.73944 ( PROT LEU 16 CA ) 0.92430 ( PROT LEU 16 CB ) 0.73944 ( PROT LEU 16 CG ) 0.73944 ( PROT LEU 16 CD1 ) 0.73944 ( PROT LEU 16 CD2 ) 0.73944 ( PROT LEU 16 C ) 0.92430 ( PROT LEU 16 O ) 0.92430 ( PROT ALA 17 N ) 0.92430 ( PROT ALA 17 H ) 0.73944 ( PROT ALA 17 CA ) 0.92430 ( PROT ALA 17 CB ) 0.73944 ( PROT ALA 17 C ) 0.92430 ( PROT ALA 17 O ) 0.92430 ( PROT CYS 18 N ) 0.92430 ( PROT CYS 18 H ) 0.73944 ( PROT CYS 18 CA ) 0.92430 ( PROT CYS 18 CB ) 0.73944 ( PROT CYS 18 SG ) 0.73944 ( PROT CYS 18 C ) 0.92430 ( PROT CYS 18 O ) 0.92430 ( PROT GLU 19 N ) 0.92430 ( PROT GLU 19 H ) 0.73944 ( PROT GLU 19 CA ) 0.92430 ( PROT GLU 19 CB ) 0.73944 ( PROT GLU 19 CG ) 0.73944 ( PROT GLU 19 CD ) 0.73944 ( PROT GLU 19 OE1 ) 0.73944 ( PROT GLU 19 OE2 ) 0.73944 ( PROT GLU 19 C ) 0.92430 ( PROT GLU 19 OT1 ) 0.73944 ( PROT GLU 19 OT2 ) 0.73944 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.43023 4.57504 -7.52739 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00447 0.00019 -0.00523 ROTATION MATRIX 1.000000 -0.000224 -0.000340 0.000224 1.000000 0.000578 0.000339 -0.000578 1.000000 AXIS OF ROTATION IS 0.817818 0.480481 -0.316722 ANGLE IS 0.04 TOTAL SQUARE DIFF IS 37.9392 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.475214 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4752" Parameter: A <- "0.4752" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.94462 4.27693 -7.73595 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.01241 0.00333 0.00369 ROTATION MATRIX 0.999720 0.018140 0.015224 -0.017728 0.999486 -0.026720 -0.015701 0.026443 0.999527 AXIS OF ROTATION IS -0.746687 -0.434362 0.503775 ANGLE IS 2.04 CENTER OF ROTATION 8.846309 4.180284 -7.955392 SHIFT IS 0.009677 TOTAL SQUARE DIFF IS 2.5601 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.367070 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4752" RDCMND substituted energy or value "?RMS" to " 0.3671" Parameter: A <- "0.4752 0.3671" 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 0.4752 0.3671 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 48.61" Parameter: H <- "48.61" 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 -42.59640 48.61246 0.70706 ENER INTERN> 4.36526 19.32267 0.00000 14.53964 3.63677 ENER EXTERN> -70.33374 -14.12700 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 " -42.60" Parameter: B <- "-42.60" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -14.13" Parameter: C <- "-14.13" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -70.33" Parameter: C <- " -84.46" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -84.46" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.37" Parameter: D <- "4.37" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 19.32" Parameter: D <- " 23.69" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 14.54" Parameter: D <- " 38.23" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.64" Parameter: D <- " 41.87" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 41.87" 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= 7800 ENER= -42.60 GRMS= 0.71 ELEC= -14.13 VDW= -70.33 RDTITL> *EXTERNAL= -84.46 INTERNAL= 41.87 USER= 0.00 HARM= 48.61 RDTITL> *BOND= 4.37 ANGL= 19.32 DIHE= 14.54 IMPR= 3.64 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9696 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9688 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 -8.59163 -34.00478 0.27566 0.02000 MINI INTERN> 4.36526 19.32267 0.00000 14.53964 3.63677 MINI EXTERN> -70.33374 -14.12700 0.00000 0.00000 0.00000 MINI CONSTR> 34.00478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 16.09554 -24.68716 17.67732 0.00864 MINI INTERN> 30.45979 17.97804 0.00000 15.55694 3.19826 MINI EXTERN> -75.08024 -11.67559 0.00000 0.00000 0.00000 MINI CONSTR> 35.65833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9681 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -9.51614 25.61168 1.32028 0.00156 MINI INTERN> 4.82979 18.76804 0.00000 15.13042 3.60929 MINI EXTERN> -74.65612 -12.95615 0.00000 0.00000 0.00000 MINI CONSTR> 35.75859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -9.60326 0.08712 1.30076 0.00067 MINI INTERN> 4.33958 19.43517 0.00000 14.98600 3.69684 MINI EXTERN> -74.57731 -13.29984 0.00000 0.00000 0.00000 MINI CONSTR> 35.81631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9680 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -9.79154 0.18829 0.44012 0.00029 MINI INTERN> 4.46159 19.00044 0.00000 15.05085 3.61904 MINI EXTERN> -74.54964 -13.21679 0.00000 0.00000 0.00000 MINI CONSTR> 35.84297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -9.85795 0.06641 0.44145 0.00030 MINI INTERN> 4.40677 19.00961 0.00000 15.03564 3.61156 MINI EXTERN> -74.50414 -13.30895 0.00000 0.00000 0.00000 MINI CONSTR> 35.89155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9678 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -9.92209 0.06414 0.45993 0.00031 MINI INTERN> 4.33240 19.04300 0.00000 15.02079 3.60629 MINI EXTERN> -74.47211 -13.39841 0.00000 0.00000 0.00000 MINI CONSTR> 35.94594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -9.98493 0.06284 0.48844 0.00032 MINI INTERN> 4.32763 19.01123 0.00000 15.00763 3.59860 MINI EXTERN> -74.48622 -13.44777 0.00000 0.00000 0.00000 MINI CONSTR> 36.00396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9676 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -10.04169 0.05676 0.53663 0.00034 MINI INTERN> 4.31895 18.99831 0.00000 14.99571 3.59319 MINI EXTERN> -74.50894 -13.50030 0.00000 0.00000 0.00000 MINI CONSTR> 36.06138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -10.09801 0.05632 0.49995 0.00035 MINI INTERN> 4.28504 18.99639 0.00000 14.98600 3.59177 MINI EXTERN> -74.54096 -13.53042 0.00000 0.00000 0.00000 MINI CONSTR> 36.11418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9676 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -10.15490 0.05689 0.53610 0.00036 MINI INTERN> 4.31408 18.96110 0.00000 14.96986 3.58890 MINI EXTERN> -74.59362 -13.56947 0.00000 0.00000 0.00000 MINI CONSTR> 36.17425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -10.22604 0.07115 0.16718 0.00016 MINI INTERN> 4.37221 18.93787 0.00000 14.92333 3.61505 MINI EXTERN> -74.70092 -13.59977 0.00000 0.00000 0.00000 MINI CONSTR> 36.22618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9676 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -10.25357 0.02753 0.57494 0.00039 MINI INTERN> 4.25505 18.95371 0.00000 14.95965 3.58017 MINI EXTERN> -74.66881 -13.61668 0.00000 0.00000 0.00000 MINI CONSTR> 36.28333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -10.29895 0.04538 0.66145 0.00040 MINI INTERN> 4.26221 18.92887 0.00000 14.94281 3.58436 MINI EXTERN> -74.73721 -13.62061 0.00000 0.00000 0.00000 MINI CONSTR> 36.34063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9676 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -10.37957 0.08062 0.18297 0.00017 MINI INTERN> 4.37460 18.87219 0.00000 14.89051 3.60948 MINI EXTERN> -74.85938 -13.65969 0.00000 0.00000 0.00000 MINI CONSTR> 36.39272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -10.42424 0.04467 0.15268 0.00018 MINI INTERN> 4.35931 18.85508 0.00000 14.88706 3.60361 MINI EXTERN> -74.89782 -13.67230 0.00000 0.00000 0.00000 MINI CONSTR> 36.44081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9676 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -10.47269 0.04845 0.15676 0.00019 MINI INTERN> 4.36035 18.83320 0.00000 14.87650 3.60202 MINI EXTERN> -74.95357 -13.68622 0.00000 0.00000 0.00000 MINI CONSTR> 36.49503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -10.51856 0.04587 0.16002 0.00019 MINI INTERN> 4.36331 18.81124 0.00000 14.86649 3.60014 MINI EXTERN> -75.00694 -13.69941 0.00000 0.00000 0.00000 MINI CONSTR> 36.54661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9675 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -10.56468 0.04612 0.26388 0.00020 MINI INTERN> 4.40283 18.77811 0.00000 14.84443 3.60556 MINI EXTERN> -75.08540 -13.71403 0.00000 0.00000 0.00000 MINI CONSTR> 36.60382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -10.60957 0.04489 0.19471 0.00021 MINI INTERN> 4.37476 18.76709 0.00000 14.84378 3.59808 MINI EXTERN> -75.11953 -13.72469 0.00000 0.00000 0.00000 MINI CONSTR> 36.65094 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9675 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -10.65180 0.04223 0.22686 0.00022 MINI INTERN> 4.38976 18.74014 0.00000 14.83049 3.59839 MINI EXTERN> -75.17811 -13.73321 0.00000 0.00000 0.00000 MINI CONSTR> 36.70074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -10.69430 0.04250 0.23058 0.00022 MINI INTERN> 4.39115 18.72008 0.00000 14.82127 3.59600 MINI EXTERN> -75.22788 -13.74429 0.00000 0.00000 0.00000 MINI CONSTR> 36.74937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9673 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -10.72960 0.03530 0.33821 0.00023 MINI INTERN> 4.43422 18.68453 0.00000 14.80172 3.60011 MINI EXTERN> -75.29524 -13.75177 0.00000 0.00000 0.00000 MINI CONSTR> 36.79683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -10.77075 0.04115 0.35459 0.00024 MINI INTERN> 4.43312 18.66861 0.00000 14.79306 3.59726 MINI EXTERN> -75.34219 -13.76540 0.00000 0.00000 0.00000 MINI CONSTR> 36.84479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9672 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -10.80698 0.03623 0.39179 0.00025 MINI INTERN> 4.44463 18.64207 0.00000 14.78093 3.59751 MINI EXTERN> -75.39569 -13.76641 0.00000 0.00000 0.00000 MINI CONSTR> 36.88998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -10.84312 0.03614 0.40561 0.00026 MINI INTERN> 4.46640 18.61496 0.00000 14.76891 3.59609 MINI EXTERN> -75.44455 -13.77780 0.00000 0.00000 0.00000 MINI CONSTR> 36.93285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9672 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -10.87964 0.03652 0.38518 0.00027 MINI INTERN> 4.45583 18.59901 0.00000 14.76285 3.59299 MINI EXTERN> -75.48305 -13.78069 0.00000 0.00000 0.00000 MINI CONSTR> 36.97342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -10.91595 0.03630 0.42044 0.00028 MINI INTERN> 4.45767 18.58478 0.00000 14.75438 3.58986 MINI EXTERN> -75.52500 -13.79509 0.00000 0.00000 0.00000 MINI CONSTR> 37.01746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9671 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -10.96196 0.04601 0.13455 0.00012 MINI INTERN> 4.29836 18.63048 0.00000 14.78266 3.56901 MINI EXTERN> -75.50143 -13.79467 0.00000 0.00000 0.00000 MINI CONSTR> 37.05365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -10.98215 0.02020 0.44416 0.00030 MINI INTERN> 4.48196 18.53824 0.00000 14.73247 3.58817 MINI EXTERN> -75.61507 -13.80508 0.00000 0.00000 0.00000 MINI CONSTR> 37.09715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9670 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -11.03060 0.04844 0.14273 0.00013 MINI INTERN> 4.28551 18.60449 0.00000 14.76797 3.56393 MINI EXTERN> -75.57786 -13.80821 0.00000 0.00000 0.00000 MINI CONSTR> 37.13358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -11.04451 0.01392 0.49233 0.00032 MINI INTERN> 4.46859 18.50818 0.00000 14.71816 3.58394 MINI EXTERN> -75.69067 -13.80676 0.00000 0.00000 0.00000 MINI CONSTR> 37.17404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9669 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -11.09537 0.05086 0.15373 0.00014 MINI INTERN> 4.27133 18.58100 0.00000 14.75377 3.55909 MINI EXTERN> -75.64947 -13.82045 0.00000 0.00000 0.00000 MINI CONSTR> 37.20935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -11.10585 0.01048 0.50252 0.00034 MINI INTERN> 4.51106 18.45867 0.00000 14.69320 3.58327 MINI EXTERN> -75.77801 -13.82191 0.00000 0.00000 0.00000 MINI CONSTR> 37.24786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9669 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -11.16094 0.05509 0.16308 0.00015 MINI INTERN> 4.26147 18.55463 0.00000 14.73807 3.55432 MINI EXTERN> -75.72297 -13.83267 0.00000 0.00000 0.00000 MINI CONSTR> 37.28621 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -11.18898 0.02804 0.12284 0.00015 MINI INTERN> 4.28539 18.52981 0.00000 14.72430 3.55618 MINI EXTERN> -75.76546 -13.83712 0.00000 0.00000 0.00000 MINI CONSTR> 37.31793 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9669 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -11.22020 0.03122 0.13078 0.00016 MINI INTERN> 4.27449 18.52051 0.00000 14.71793 3.55316 MINI EXTERN> -75.79772 -13.84323 0.00000 0.00000 0.00000 MINI CONSTR> 37.35466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -11.25050 0.03030 0.22338 0.00017 MINI INTERN> 4.22567 18.53009 0.00000 14.72040 3.54522 MINI EXTERN> -75.81581 -13.84960 0.00000 0.00000 0.00000 MINI CONSTR> 37.39353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9667 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -11.28111 0.03061 0.14908 0.00017 MINI INTERN> 4.25775 18.49955 0.00000 14.70405 3.54773 MINI EXTERN> -75.86253 -13.85430 0.00000 0.00000 0.00000 MINI CONSTR> 37.42664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -11.30853 0.02742 0.12050 0.00018 MINI INTERN> 4.27566 18.47789 0.00000 14.69176 3.54841 MINI EXTERN> -75.90103 -13.85933 0.00000 0.00000 0.00000 MINI CONSTR> 37.45811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9666 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -11.33640 0.02787 0.27283 0.00019 MINI INTERN> 4.20077 18.50185 0.00000 14.70038 3.53716 MINI EXTERN> -75.90773 -13.86593 0.00000 0.00000 0.00000 MINI CONSTR> 37.49710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -11.36800 0.03160 0.16530 0.00019 MINI INTERN> 4.24376 18.46463 0.00000 14.68085 3.54133 MINI EXTERN> -75.95876 -13.86927 0.00000 0.00000 0.00000 MINI CONSTR> 37.52946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9666 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -11.39121 0.02321 0.28909 0.00020 MINI INTERN> 4.19215 18.48041 0.00000 14.68542 3.53288 MINI EXTERN> -75.96833 -13.87642 0.00000 0.00000 0.00000 MINI CONSTR> 37.56268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -11.41788 0.02667 0.31909 0.00021 MINI INTERN> 4.18515 18.46895 0.00000 14.67790 3.53099 MINI EXTERN> -75.99967 -13.87730 0.00000 0.00000 0.00000 MINI CONSTR> 37.59610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9664 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -11.44197 0.02409 0.33591 0.00021 MINI INTERN> 4.17095 18.46734 0.00000 14.67383 3.52728 MINI EXTERN> -76.02094 -13.88627 0.00000 0.00000 0.00000 MINI CONSTR> 37.62583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -11.46683 0.02486 0.31836 0.00022 MINI INTERN> 4.17182 18.45486 0.00000 14.66524 3.52670 MINI EXTERN> -76.05012 -13.88944 0.00000 0.00000 0.00000 MINI CONSTR> 37.65412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9664 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -11.49211 0.02528 0.34343 0.00023 MINI INTERN> 4.17411 18.44306 0.00000 14.65711 3.52432 MINI EXTERN> -76.07901 -13.89725 0.00000 0.00000 0.00000 MINI CONSTR> 37.68556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -11.52426 0.03215 0.11256 0.00010 MINI INTERN> 4.29505 18.36577 0.00000 14.61911 3.53850 MINI EXTERN> -76.15718 -13.89861 0.00000 0.00000 0.00000 MINI CONSTR> 37.71311 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9664 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -11.53811 0.01385 0.36258 0.00025 MINI INTERN> 4.15105 18.43171 0.00000 14.64597 3.52004 MINI EXTERN> -76.12644 -13.90249 0.00000 0.00000 0.00000 MINI CONSTR> 37.74205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -11.57243 0.03432 0.11369 0.00011 MINI INTERN> 4.29458 18.34298 0.00000 14.60318 3.53553 MINI EXTERN> -76.21173 -13.90746 0.00000 0.00000 0.00000 MINI CONSTR> 37.77048 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9664 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -11.58357 0.01114 0.38697 0.00027 MINI INTERN> 4.13942 18.41698 0.00000 14.63315 3.51565 MINI EXTERN> -76.17464 -13.91234 0.00000 0.00000 0.00000 MINI CONSTR> 37.79822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -11.60750 0.02393 0.39961 0.00028 MINI INTERN> 4.13747 18.40647 0.00000 14.62572 3.51331 MINI EXTERN> -76.20109 -13.91723 0.00000 0.00000 0.00000 MINI CONSTR> 37.82784 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9664 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -11.63030 0.02280 0.42861 0.00029 MINI INTERN> 4.13242 18.39569 0.00000 14.61808 3.51171 MINI EXTERN> -76.22877 -13.91707 0.00000 0.00000 0.00000 MINI CONSTR> 37.85763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -11.66689 0.03659 0.14610 0.00012 MINI INTERN> 4.30880 18.29133 0.00000 14.56712 3.53155 MINI EXTERN> -76.32476 -13.92544 0.00000 0.00000 0.00000 MINI CONSTR> 37.88450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9664 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -11.68617 0.01928 0.10176 0.00013 MINI INTERN> 4.27944 18.29643 0.00000 14.56761 3.52678 MINI EXTERN> -76.33371 -13.92894 0.00000 0.00000 0.00000 MINI CONSTR> 37.90622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -11.70798 0.02181 0.10815 0.00013 MINI INTERN> 4.28538 18.28297 0.00000 14.55846 3.52613 MINI EXTERN> -76.36065 -13.93290 0.00000 0.00000 0.00000 MINI CONSTR> 37.93264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9663 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -11.72923 0.02125 0.18349 0.00014 MINI INTERN> 4.32478 18.25357 0.00000 14.54132 3.52910 MINI EXTERN> -76.40128 -13.93767 0.00000 0.00000 0.00000 MINI CONSTR> 37.96094 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -11.75050 0.02127 0.12332 0.00014 MINI INTERN> 4.29359 18.25886 0.00000 14.54121 3.52439 MINI EXTERN> -76.41155 -13.94135 0.00000 0.00000 0.00000 MINI CONSTR> 37.98436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9663 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -11.76970 0.01920 0.10082 0.00015 MINI INTERN> 4.27662 18.25796 0.00000 14.53826 3.52126 MINI EXTERN> -76.42612 -13.94461 0.00000 0.00000 0.00000 MINI CONSTR> 38.00692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -11.78938 0.01968 0.22524 0.00015 MINI INTERN> 4.33940 18.21776 0.00000 14.51581 3.52672 MINI EXTERN> -76.47501 -13.94977 0.00000 0.00000 0.00000 MINI CONSTR> 38.03570 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9663 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -11.81158 0.02220 0.13215 0.00016 MINI INTERN> 4.29517 18.22936 0.00000 14.51849 3.52059 MINI EXTERN> -76.47997 -13.95379 0.00000 0.00000 0.00000 MINI CONSTR> 38.05859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -11.82861 0.01703 0.24660 0.00016 MINI INTERN> 4.33945 18.19893 0.00000 14.50065 3.52457 MINI EXTERN> -76.51997 -13.95676 0.00000 0.00000 0.00000 MINI CONSTR> 38.08452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9663 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -11.84623 0.01762 0.27187 0.00017 MINI INTERN> 4.34985 18.18723 0.00000 14.49248 3.52333 MINI EXTERN> -76.54168 -13.96454 0.00000 0.00000 0.00000 MINI CONSTR> 38.10711 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -11.86346 0.01723 0.27500 0.00018 MINI INTERN> 4.35746 18.17356 0.00000 14.48383 3.52334 MINI EXTERN> -76.56498 -13.96543 0.00000 0.00000 0.00000 MINI CONSTR> 38.12876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9662 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -11.88115 0.01769 0.26193 0.00018 MINI INTERN> 4.35099 18.16798 0.00000 14.47874 3.52149 MINI EXTERN> -76.58151 -13.96840 0.00000 0.00000 0.00000 MINI CONSTR> 38.14957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -11.89912 0.01796 0.28237 0.00019 MINI INTERN> 4.35810 18.15673 0.00000 14.47016 3.52086 MINI EXTERN> -76.60419 -13.97360 0.00000 0.00000 0.00000 MINI CONSTR> 38.17282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9661 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -11.91528 0.01616 0.33058 0.00020 MINI INTERN> 4.36351 18.14499 0.00000 14.46131 3.52091 MINI EXTERN> -76.62786 -13.97420 0.00000 0.00000 0.00000 MINI CONSTR> 38.19606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -11.93209 0.01682 0.30094 0.00020 MINI INTERN> 4.36084 18.13836 0.00000 14.45631 3.51905 MINI EXTERN> -76.64291 -13.97842 0.00000 0.00000 0.00000 MINI CONSTR> 38.21469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9661 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -11.95600 0.02391 0.09575 0.00009 MINI INTERN> 4.23680 18.18977 0.00000 14.47710 3.50439 MINI EXTERN> -76.61628 -13.98189 0.00000 0.00000 0.00000 MINI CONSTR> 38.23411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -11.96428 0.00828 0.32103 0.00022 MINI INTERN> 4.37221 18.11834 0.00000 14.44150 3.51735 MINI EXTERN> -76.68181 -13.98769 0.00000 0.00000 0.00000 MINI CONSTR> 38.25581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9661 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -11.98070 0.01641 0.34399 0.00023 MINI INTERN> 4.35679 18.11656 0.00000 14.43703 3.51560 MINI EXTERN> -76.69723 -13.98705 0.00000 0.00000 0.00000 MINI CONSTR> 38.27761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -12.00567 0.02498 0.11185 0.00010 MINI INTERN> 4.22306 18.17336 0.00000 14.46048 3.49945 MINI EXTERN> -76.66569 -13.99228 0.00000 0.00000 0.00000 MINI CONSTR> 38.29593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9660 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -12.01005 0.00437 0.36212 0.00025 MINI INTERN> 4.38362 18.09166 0.00000 14.42083 3.51453 MINI EXTERN> -76.73638 -13.99986 0.00000 0.00000 0.00000 MINI CONSTR> 38.31556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -12.03634 0.02629 0.12905 0.00011 MINI INTERN> 4.21366 18.16412 0.00000 14.45031 3.49618 MINI EXTERN> -76.69569 -13.99942 0.00000 0.00000 0.00000 MINI CONSTR> 38.33452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9660 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -12.04984 0.01350 0.08818 0.00011 MINI INTERN> 4.23438 18.14696 0.00000 14.44007 3.49792 MINI EXTERN> -76.71769 -14.00198 0.00000 0.00000 0.00000 MINI CONSTR> 38.35050 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -12.06527 0.01543 0.15291 0.00011 MINI INTERN> 4.19992 18.15759 0.00000 14.44131 3.49277 MINI EXTERN> -76.72288 -14.00544 0.00000 0.00000 0.00000 MINI CONSTR> 38.37146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9660 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -12.07889 0.01363 0.08432 0.00012 MINI INTERN> 4.23547 18.13296 0.00000 14.42808 3.49595 MINI EXTERN> -76.74930 -14.00886 0.00000 0.00000 0.00000 MINI CONSTR> 38.38681 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -12.09462 0.01573 0.17319 0.00012 MINI INTERN> 4.19045 18.14872 0.00000 14.43121 3.48961 MINI EXTERN> -76.75179 -14.01191 0.00000 0.00000 0.00000 MINI CONSTR> 38.40910 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9659 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -12.11006 0.01544 0.11115 0.00013 MINI INTERN> 4.21756 18.12773 0.00000 14.41926 3.49159 MINI EXTERN> -76.77664 -14.01614 0.00000 0.00000 0.00000 MINI CONSTR> 38.42658 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -12.12412 0.01406 0.14341 0.00013 MINI INTERN> 4.20061 18.12942 0.00000 14.41670 3.48894 MINI EXTERN> -76.78697 -14.01816 0.00000 0.00000 0.00000 MINI CONSTR> 38.44532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9659 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -12.13591 0.01179 0.19812 0.00014 MINI INTERN> 4.17966 18.13547 0.00000 14.41631 3.48532 MINI EXTERN> -76.79295 -14.02206 0.00000 0.00000 0.00000 MINI CONSTR> 38.46234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -12.15022 0.01430 0.20372 0.00014 MINI INTERN> 4.17831 18.12851 0.00000 14.41015 3.48451 MINI EXTERN> -76.80900 -14.02353 0.00000 0.00000 0.00000 MINI CONSTR> 38.48082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9659 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -12.16248 0.01226 0.23854 0.00015 MINI INTERN> 4.18056 18.12383 0.00000 14.40516 3.48266 MINI EXTERN> -76.82166 -14.03086 0.00000 0.00000 0.00000 MINI CONSTR> 38.49783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -12.17524 0.01277 0.21721 0.00015 MINI INTERN> 4.16992 18.12211 0.00000 14.40155 3.48147 MINI EXTERN> -76.83267 -14.03103 0.00000 0.00000 0.00000 MINI CONSTR> 38.51341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9659 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -12.18886 0.01362 0.23977 0.00016 MINI INTERN> 4.16296 18.11933 0.00000 14.39704 3.47949 MINI EXTERN> -76.84558 -14.03418 0.00000 0.00000 0.00000 MINI CONSTR> 38.53208 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -12.20160 0.01274 0.23249 0.00016 MINI INTERN> 4.16519 18.11217 0.00000 14.39130 3.47884 MINI EXTERN> -76.85983 -14.03731 0.00000 0.00000 0.00000 MINI CONSTR> 38.54804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9658 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -12.21452 0.01292 0.24357 0.00017 MINI INTERN> 4.16167 18.10810 0.00000 14.38588 3.47758 MINI EXTERN> -76.87290 -14.04016 0.00000 0.00000 0.00000 MINI CONSTR> 38.56531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -12.23113 0.01661 0.07988 0.00007 MINI INTERN> 4.24551 18.05648 0.00000 14.36143 3.48631 MINI EXTERN> -76.91665 -14.04502 0.00000 0.00000 0.00000 MINI CONSTR> 38.58081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9658 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -12.23772 0.00659 0.26737 0.00018 MINI INTERN> 4.15275 18.10206 0.00000 14.37737 3.47483 MINI EXTERN> -76.89565 -14.04588 0.00000 0.00000 0.00000 MINI CONSTR> 38.59680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -12.24939 0.01166 0.29077 0.00019 MINI INTERN> 4.17074 18.08696 0.00000 14.37035 3.47485 MINI EXTERN> -76.91449 -14.05070 0.00000 0.00000 0.00000 MINI CONSTR> 38.61289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9658 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -12.25974 0.01036 0.31961 0.00020 MINI INTERN> 4.15949 18.08858 0.00000 14.36394 3.47428 MINI EXTERN> -76.92384 -14.05064 0.00000 0.00000 0.00000 MINI CONSTR> 38.62845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -12.27857 0.01883 0.08993 0.00008 MINI INTERN> 4.25028 18.03177 0.00000 14.33949 3.48331 MINI EXTERN> -76.96910 -14.05716 0.00000 0.00000 0.00000 MINI CONSTR> 38.64284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9658 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -12.28899 0.01041 0.07339 0.00009 MINI INTERN> 4.23832 18.03300 0.00000 14.33768 3.48123 MINI EXTERN> -76.97579 -14.05953 0.00000 0.00000 0.00000 MINI CONSTR> 38.65610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -12.29245 0.00347 0.33470 0.00022 MINI INTERN> 4.14043 18.08378 0.00000 14.35388 3.46932 MINI EXTERN> -76.95276 -14.05998 0.00000 0.00000 0.00000 MINI CONSTR> 38.67287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9658 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -12.31228 0.01982 0.11387 0.00009 MINI INTERN> 4.25971 18.01110 0.00000 14.32224 3.48176 MINI EXTERN> -77.00865 -14.06629 0.00000 0.00000 0.00000 MINI CONSTR> 38.68785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -12.32215 0.00987 0.07216 0.00010 MINI INTERN> 4.23651 18.01835 0.00000 14.32331 3.47853 MINI EXTERN> -77.01046 -14.06821 0.00000 0.00000 0.00000 MINI CONSTR> 38.69983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9658 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -12.33399 0.01183 0.13762 0.00010 MINI INTERN> 4.26701 17.99721 0.00000 14.31059 3.48088 MINI EXTERN> -77.03470 -14.07240 0.00000 0.00000 0.00000 MINI CONSTR> 38.71744 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -12.34488 0.01090 0.09921 0.00011 MINI INTERN> 4.25048 18.00046 0.00000 14.31001 3.47821 MINI EXTERN> -77.03979 -14.07495 0.00000 0.00000 0.00000 MINI CONSTR> 38.73070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9659 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -12.35498 0.01009 0.11848 0.00011 MINI INTERN> 4.25920 17.99123 0.00000 14.30309 3.47842 MINI EXTERN> -77.05391 -14.07782 0.00000 0.00000 0.00000 MINI CONSTR> 38.74481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -12.36402 0.00905 0.16538 0.00011 MINI INTERN> 4.27691 17.97792 0.00000 14.29474 3.47942 MINI EXTERN> -77.07056 -14.08115 0.00000 0.00000 0.00000 MINI CONSTR> 38.75871 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9659 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -12.37572 0.01170 0.09701 0.00012 MINI INTERN> 4.24814 17.98715 0.00000 14.29611 3.47574 MINI EXTERN> -77.07182 -14.08310 0.00000 0.00000 0.00000 MINI CONSTR> 38.77206 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 -12.37572 0.01170 0.09701 0.00014 STPD INTERN> 4.24814 17.98715 0.00000 14.29611 3.47574 STPD EXTERN> -77.07182 -14.08310 0.00000 0.00000 0.00000 STPD CONSTR> 38.77206 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 9659 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9659 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 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 -12.37572 0.01170 0.09701 0.00000 MINI INTERN> 4.24814 17.98715 0.00000 14.29611 3.47574 MINI EXTERN> -77.07182 -14.08310 0.00000 0.00000 0.00000 MINI CONSTR> 38.77206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -13.02395 0.64823 0.07507 0.01002 MINI INTERN> 4.17629 17.47255 0.00000 13.76475 3.37746 MINI EXTERN> -78.50822 -14.38749 0.00000 0.00000 0.00000 MINI CONSTR> 41.08070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -13.03000 0.00605 0.08467 0.00431 MINI INTERN> 4.13925 17.46169 0.00000 13.75778 3.36594 MINI EXTERN> -78.31512 -14.45436 0.00000 0.00000 0.00000 MINI CONSTR> 41.01482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -13.05152 0.02152 0.11635 0.01717 MINI INTERN> 4.09334 17.43706 0.00000 13.73773 3.37093 MINI EXTERN> -77.72075 -14.56062 0.00000 0.00000 0.00000 MINI CONSTR> 40.59080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -13.06559 0.01408 0.06892 0.00967 MINI INTERN> 4.15102 17.62865 0.00000 13.79714 3.37450 MINI EXTERN> -77.74627 -14.60677 0.00000 0.00000 0.00000 MINI CONSTR> 40.33614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -13.07157 0.00597 0.05253 0.00519 MINI INTERN> 4.17223 17.62610 0.00000 13.83730 3.37452 MINI EXTERN> -77.79489 -14.53697 0.00000 0.00000 0.00000 MINI CONSTR> 40.25015 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -13.07485 0.00328 0.04436 0.00481 MINI INTERN> 4.18338 17.63353 0.00000 13.87935 3.39185 MINI EXTERN> -77.85760 -14.52991 0.00000 0.00000 0.00000 MINI CONSTR> 40.22454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -13.07769 0.00284 0.04690 0.00440 MINI INTERN> 4.18829 17.63554 0.00000 13.91253 3.39753 MINI EXTERN> -77.87621 -14.55332 0.00000 0.00000 0.00000 MINI CONSTR> 40.21794 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -13.08083 0.00314 0.04832 0.00544 MINI INTERN> 4.16856 17.63577 0.00000 13.92504 3.40239 MINI EXTERN> -77.86390 -14.57584 0.00000 0.00000 0.00000 MINI CONSTR> 40.22715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -13.08407 0.00323 0.04429 0.00753 MINI INTERN> 4.18264 17.60885 0.00000 13.95249 3.40671 MINI EXTERN> -77.85528 -14.63382 0.00000 0.00000 0.00000 MINI CONSTR> 40.25435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -13.08675 0.00268 0.04640 0.00608 MINI INTERN> 4.17921 17.59622 0.00000 13.96220 3.39928 MINI EXTERN> -77.89514 -14.61245 0.00000 0.00000 0.00000 MINI CONSTR> 40.28392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -13.08896 0.00221 0.03541 0.00465 MINI INTERN> 4.16780 17.56224 0.00000 13.97947 3.40579 MINI EXTERN> -77.85193 -14.65745 0.00000 0.00000 0.00000 MINI CONSTR> 40.30514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -13.09097 0.00202 0.03371 0.00576 MINI INTERN> 4.16899 17.54572 0.00000 13.99270 3.40478 MINI EXTERN> -77.80561 -14.72279 0.00000 0.00000 0.00000 MINI CONSTR> 40.32524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -13.09332 0.00235 0.04359 0.00864 MINI INTERN> 4.17257 17.53958 0.00000 13.99213 3.40117 MINI EXTERN> -77.82220 -14.73201 0.00000 0.00000 0.00000 MINI CONSTR> 40.35543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -13.09621 0.00288 0.05072 0.00869 MINI INTERN> 4.17001 17.51186 0.00000 14.00551 3.39590 MINI EXTERN> -77.83604 -14.74702 0.00000 0.00000 0.00000 MINI CONSTR> 40.40357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -13.09929 0.00308 0.04073 0.00775 MINI INTERN> 4.17413 17.51146 0.00000 14.00279 3.39155 MINI EXTERN> -77.85142 -14.79318 0.00000 0.00000 0.00000 MINI CONSTR> 40.46538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -13.10167 0.00238 0.04148 0.00846 MINI INTERN> 4.17696 17.48995 0.00000 13.99804 3.39880 MINI EXTERN> -77.85465 -14.83391 0.00000 0.00000 0.00000 MINI CONSTR> 40.52314 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -13.10443 0.00276 0.04865 0.01076 MINI INTERN> 4.17446 17.46409 0.00000 13.97383 3.39591 MINI EXTERN> -77.83190 -14.88742 0.00000 0.00000 0.00000 MINI CONSTR> 40.60660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -13.10846 0.00403 0.05762 0.01297 MINI INTERN> 4.15589 17.43715 0.00000 13.97823 3.38945 MINI EXTERN> -77.84072 -14.98562 0.00000 0.00000 0.00000 MINI CONSTR> 40.75715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -13.11589 0.00743 0.10343 0.02862 MINI INTERN> 4.16100 17.34266 0.00000 13.95077 3.38064 MINI EXTERN> -77.88775 -15.13107 0.00000 0.00000 0.00000 MINI CONSTR> 41.06786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -13.13437 0.01848 0.24538 0.05774 MINI INTERN> 4.06891 17.20039 0.00000 13.84954 3.40323 MINI EXTERN> -77.98826 -15.52485 0.00000 0.00000 0.00000 MINI CONSTR> 41.85668 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 -13.13437 0.01848 0.24538 0.02000 CONJ INTERN> 4.06891 17.20039 0.00000 13.84954 3.40323 CONJ EXTERN> -77.98826 -15.52485 0.00000 0.00000 0.00000 CONJ CONSTR> 41.85668 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 ALA 1 HT1 ) 0.48064 ( PROT ALA 1 HT2 ) 0.48064 ( PROT ALA 1 N ) 0.60080 ( PROT ALA 1 HT3 ) 0.48064 ( PROT ALA 1 CA ) 0.60080 ( PROT ALA 1 CB ) 0.48064 ( PROT ALA 1 C ) 0.60080 ( PROT ALA 1 O ) 0.60080 ( PROT LEU 2 N ) 0.60080 ( PROT LEU 2 H ) 0.48064 ( PROT LEU 2 CA ) 0.60080 ( PROT LEU 2 CB ) 0.48064 ( PROT LEU 2 CG ) 0.48064 ( PROT LEU 2 CD1 ) 0.48064 ( PROT LEU 2 CD2 ) 0.48064 ( PROT LEU 2 C ) 0.60080 ( PROT LEU 2 O ) 0.60080 ( PROT GLN 3 N ) 0.60080 ( PROT GLN 3 H ) 0.48064 ( PROT GLN 3 CA ) 0.60080 ( PROT GLN 3 CB ) 0.48064 ( PROT GLN 3 CG ) 0.48064 ( PROT GLN 3 CD ) 0.48064 ( PROT GLN 3 OE1 ) 0.48064 ( PROT GLN 3 NE2 ) 0.48064 ( PROT GLN 3 HE21 ) 0.48064 ( PROT GLN 3 HE22 ) 0.48064 ( PROT GLN 3 C ) 0.60080 ( PROT GLN 3 O ) 0.60080 ( PROT ALA 4 N ) 0.60080 ( PROT ALA 4 H ) 0.48064 ( PROT ALA 4 CA ) 0.60080 ( PROT ALA 4 CB ) 0.48064 ( PROT ALA 4 C ) 0.60080 ( PROT ALA 4 O ) 0.60080 ( PROT PHE 5 N ) 0.60080 ( PROT PHE 5 H ) 0.48064 ( PROT PHE 5 CA ) 0.60080 ( PROT PHE 5 CB ) 0.48064 ( PROT PHE 5 CG ) 0.48064 ( PROT PHE 5 CD1 ) 0.48064 ( PROT PHE 5 CD2 ) 0.48064 ( PROT PHE 5 CE1 ) 0.48064 ( PROT PHE 5 CE2 ) 0.48064 ( PROT PHE 5 CZ ) 0.48064 ( PROT PHE 5 C ) 0.60080 ( PROT PHE 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 ILE 7 N ) 0.60080 ( PROT ILE 7 H ) 0.48064 ( PROT ILE 7 CA ) 0.60080 ( PROT ILE 7 CB ) 0.48064 ( PROT ILE 7 CG2 ) 0.48064 ( PROT ILE 7 CG1 ) 0.48064 ( PROT ILE 7 CD ) 0.48064 ( PROT ILE 7 C ) 0.60080 ( PROT ILE 7 O ) 0.60080 ( PROT ALA 8 N ) 0.60080 ( PROT ALA 8 H ) 0.48064 ( PROT ALA 8 CA ) 0.60080 ( PROT ALA 8 CB ) 0.48064 ( PROT ALA 8 C ) 0.60080 ( PROT ALA 8 O ) 0.60080 ( PROT LEU 9 N ) 0.60080 ( PROT LEU 9 H ) 0.48064 ( PROT LEU 9 CA ) 0.60080 ( PROT LEU 9 CB ) 0.48064 ( PROT LEU 9 CG ) 0.48064 ( PROT LEU 9 CD1 ) 0.48064 ( PROT LEU 9 CD2 ) 0.48064 ( PROT LEU 9 C ) 0.60080 ( PROT LEU 9 O ) 0.60080 ( PROT SER 10 N ) 0.60080 ( PROT SER 10 H ) 0.48064 ( PROT SER 10 CA ) 0.60080 ( PROT SER 10 CB ) 0.48064 ( PROT SER 10 OG ) 0.48064 ( PROT SER 10 HG ) 0.48064 ( PROT SER 10 C ) 0.60080 ( PROT SER 10 O ) 0.60080 ( PROT SER 11 N ) 0.60080 ( PROT SER 11 H ) 0.48064 ( PROT SER 11 CA ) 0.60080 ( PROT SER 11 CB ) 0.48064 ( PROT SER 11 OG ) 0.48064 ( PROT SER 11 HG ) 0.48064 ( PROT SER 11 C ) 0.60080 ( PROT SER 11 O ) 0.60080 ( PROT PHE 12 N ) 0.60080 ( PROT PHE 12 H ) 0.48064 ( PROT PHE 12 CA ) 0.60080 ( PROT PHE 12 CB ) 0.48064 ( PROT PHE 12 CG ) 0.48064 ( PROT PHE 12 CD1 ) 0.48064 ( PROT PHE 12 CD2 ) 0.48064 ( PROT PHE 12 CE1 ) 0.48064 ( PROT PHE 12 CE2 ) 0.48064 ( PROT PHE 12 CZ ) 0.48064 ( PROT PHE 12 C ) 0.60080 ( PROT PHE 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 SER 14 N ) 0.60080 ( PROT SER 14 H ) 0.48064 ( PROT SER 14 CA ) 0.60080 ( PROT SER 14 CB ) 0.48064 ( PROT SER 14 OG ) 0.48064 ( PROT SER 14 HG ) 0.48064 ( PROT SER 14 C ) 0.60080 ( PROT SER 14 O ) 0.60080 ( PROT LYS 15 N ) 0.60080 ( PROT LYS 15 H ) 0.48064 ( PROT LYS 15 CA ) 0.60080 ( PROT LYS 15 CB ) 0.48064 ( PROT LYS 15 CG ) 0.48064 ( PROT LYS 15 CD ) 0.48064 ( PROT LYS 15 CE ) 0.48064 ( PROT LYS 15 NZ ) 0.48064 ( PROT LYS 15 HZ1 ) 0.48064 ( PROT LYS 15 HZ2 ) 0.48064 ( PROT LYS 15 HZ3 ) 0.48064 ( PROT LYS 15 C ) 0.60080 ( PROT LYS 15 O ) 0.60080 ( PROT LEU 16 N ) 0.60080 ( PROT LEU 16 H ) 0.48064 ( PROT LEU 16 CA ) 0.60080 ( PROT LEU 16 CB ) 0.48064 ( PROT LEU 16 CG ) 0.48064 ( PROT LEU 16 CD1 ) 0.48064 ( PROT LEU 16 CD2 ) 0.48064 ( PROT LEU 16 C ) 0.60080 ( PROT LEU 16 O ) 0.60080 ( PROT ALA 17 N ) 0.60080 ( PROT ALA 17 H ) 0.48064 ( PROT ALA 17 CA ) 0.60080 ( PROT ALA 17 CB ) 0.48064 ( PROT ALA 17 C ) 0.60080 ( PROT ALA 17 O ) 0.60080 ( PROT CYS 18 N ) 0.60080 ( PROT CYS 18 H ) 0.48064 ( PROT CYS 18 CA ) 0.60080 ( PROT CYS 18 CB ) 0.48064 ( PROT CYS 18 SG ) 0.48064 ( PROT CYS 18 C ) 0.60080 ( PROT CYS 18 O ) 0.60080 ( PROT GLU 19 N ) 0.60080 ( PROT GLU 19 H ) 0.48064 ( PROT GLU 19 CA ) 0.60080 ( PROT GLU 19 CB ) 0.48064 ( PROT GLU 19 CG ) 0.48064 ( PROT GLU 19 CD ) 0.48064 ( PROT GLU 19 OE1 ) 0.48064 ( PROT GLU 19 OE2 ) 0.48064 ( PROT GLU 19 C ) 0.60080 ( PROT GLU 19 OT1 ) 0.48064 ( PROT GLU 19 OT2 ) 0.48064 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.42849 4.57402 -7.52668 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00621 0.00120 -0.00594 ROTATION MATRIX 1.000000 -0.000599 -0.000677 0.000600 0.999999 0.001358 0.000676 -0.001358 0.999999 AXIS OF ROTATION IS 0.832356 0.414762 -0.367636 ANGLE IS 0.09 TOTAL SQUARE DIFF IS 50.7406 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.549570 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.5496" Parameter: A <- "0.5496" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.95362 4.28362 -7.74442 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.02141 -0.00336 0.01216 ROTATION MATRIX 0.999713 0.018610 0.015055 -0.018187 0.999448 -0.027815 -0.015564 0.027533 0.999500 AXIS OF ROTATION IS -0.756352 -0.418421 0.502848 ANGLE IS 2.10 CENTER OF ROTATION 8.849995 4.239116 -7.913744 SHIFT IS 0.023712 TOTAL SQUARE DIFF IS 3.6064 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.435672 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.5496" RDCMND substituted energy or value "?RMS" to " 0.4357" Parameter: A <- "0.5496 0.4357" 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 0.5496 0.4357 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 " 41.86" Parameter: H <- "41.86" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -54.99105 41.85668 0.56101 ENER INTERN> 4.06891 17.20039 0.00000 13.84954 3.40323 ENER EXTERN> -77.98826 -15.52485 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 " -54.99" Parameter: B <- "-54.99" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -15.52" Parameter: C <- "-15.52" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -77.99" Parameter: C <- " -93.51" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -93.51" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.07" Parameter: D <- "4.07" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 17.20" Parameter: D <- " 21.27" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 13.85" Parameter: D <- " 35.12" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.40" Parameter: D <- " 38.52" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 38.52" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 8400 ENER= -54.99 GRMS= 0.56 ELEC= -15.52 VDW= -77.99 RDTITL> *EXTERNAL= -93.51 INTERNAL= 38.52 USER= 0.00 HARM= 41.86 RDTITL> *BOND= 4.07 ANGL= 17.20 DIHE= 13.85 IMPR= 3.40 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= -54.99 GRMS= 0.56 ELEC= -15.52 VDW= -77.99 RDTITL> *EXTERNAL= -93.51 INTERNAL= 38.52 USER= 0.00 HARM= 41.86 RDTITL> *BOND= 4.07 ANGL= 17.20 DIHE= 13.85 IMPR= 3.40 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= -54.99 GRMS= 0.56 ELEC= -15.52 VDW= -77.99 RDTITL> *EXTERNAL= -93.51 INTERNAL= 38.52 USER= 0.00 HARM= 41.86 RDTITL> *BOND= 4.07 ANGL= 17.20 DIHE= 13.85 IMPR= 3.40 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 8400 0.5496 0.4357 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "8400" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9659 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9648 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 -26.07443 -28.91661 0.30491 0.02000 MINI INTERN> 4.06891 17.20039 0.00000 13.84954 3.40323 MINI EXTERN> -77.98826 -15.52485 0.00000 0.00000 0.00000 MINI CONSTR> 28.91661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -23.26937 -2.80507 5.89368 0.00360 MINI INTERN> 7.08352 18.04537 0.00000 14.30044 3.30106 MINI EXTERN> -80.67448 -15.13764 0.00000 0.00000 0.00000 MINI CONSTR> 29.81237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9640 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -26.74186 3.47249 0.38846 0.00065 MINI INTERN> 4.32198 17.33310 0.00000 14.10026 3.38846 MINI EXTERN> -80.54697 -15.20510 0.00000 0.00000 0.00000 MINI CONSTR> 29.86642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -26.83009 0.08823 0.20943 0.00028 MINI INTERN> 4.25177 17.26502 0.00000 14.04898 3.39695 MINI EXTERN> -80.47606 -15.24172 0.00000 0.00000 0.00000 MINI CONSTR> 29.92497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9641 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -26.89862 0.06853 0.32594 0.00029 MINI INTERN> 4.27328 17.19810 0.00000 14.02045 3.39436 MINI EXTERN> -80.47603 -15.30099 0.00000 0.00000 0.00000 MINI CONSTR> 29.99220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -26.95203 0.05341 0.42873 0.00030 MINI INTERN> 4.30639 17.15447 0.00000 14.00276 3.38621 MINI EXTERN> -80.49235 -15.35916 0.00000 0.00000 0.00000 MINI CONSTR> 30.04965 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9641 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -27.00740 0.05537 0.45284 0.00031 MINI INTERN> 4.31887 17.12136 0.00000 13.98273 3.38288 MINI EXTERN> -80.52034 -15.39924 0.00000 0.00000 0.00000 MINI CONSTR> 30.10634 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -27.06106 0.05366 0.47839 0.00032 MINI INTERN> 4.33592 17.09087 0.00000 13.96610 3.37975 MINI EXTERN> -80.55544 -15.44005 0.00000 0.00000 0.00000 MINI CONSTR> 30.16179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9639 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -27.11213 0.05108 0.51771 0.00034 MINI INTERN> 4.30180 17.09053 0.00000 13.94649 3.38381 MINI EXTERN> -80.59102 -15.45831 0.00000 0.00000 0.00000 MINI CONSTR> 30.21457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -27.16469 0.05256 0.51114 0.00035 MINI INTERN> 4.31781 17.06413 0.00000 13.92784 3.38154 MINI EXTERN> -80.63180 -15.49168 0.00000 0.00000 0.00000 MINI CONSTR> 30.26746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9637 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -27.21753 0.05284 0.48980 0.00036 MINI INTERN> 4.34460 17.03097 0.00000 13.90903 3.37790 MINI EXTERN> -80.67450 -15.52566 0.00000 0.00000 0.00000 MINI CONSTR> 30.32013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -27.28534 0.06780 0.16717 0.00016 MINI INTERN> 4.17971 17.13024 0.00000 13.90399 3.39339 MINI EXTERN> -80.69901 -15.56130 0.00000 0.00000 0.00000 MINI CONSTR> 30.36765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9637 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -27.30869 0.02336 0.64131 0.00039 MINI INTERN> 4.31358 17.02967 0.00000 13.87172 3.38205 MINI EXTERN> -80.75652 -15.57236 0.00000 0.00000 0.00000 MINI CONSTR> 30.42318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -27.36097 0.05228 0.61692 0.00040 MINI INTERN> 4.36384 16.97828 0.00000 13.85006 3.37604 MINI EXTERN> -80.80260 -15.60165 0.00000 0.00000 0.00000 MINI CONSTR> 30.47505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9637 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -27.40654 0.04556 0.67657 0.00042 MINI INTERN> 4.36764 16.97531 0.00000 13.83898 3.37391 MINI EXTERN> -80.84057 -15.64678 0.00000 0.00000 0.00000 MINI CONSTR> 30.52498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -27.46034 0.05381 0.61755 0.00043 MINI INTERN> 4.41545 16.91611 0.00000 13.81190 3.36892 MINI EXTERN> -80.88762 -15.66110 0.00000 0.00000 0.00000 MINI CONSTR> 30.57599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9637 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -27.54567 0.08533 0.19444 0.00019 MINI INTERN> 4.15124 17.08597 0.00000 13.80242 3.39394 MINI EXTERN> -80.91359 -15.69256 0.00000 0.00000 0.00000 MINI CONSTR> 30.62692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -27.59087 0.04520 0.16457 0.00019 MINI INTERN> 4.16489 17.06343 0.00000 13.78288 3.39170 MINI EXTERN> -80.95140 -15.71229 0.00000 0.00000 0.00000 MINI CONSTR> 30.66992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9636 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -27.64090 0.05003 0.16975 0.00020 MINI INTERN> 4.15766 17.05703 0.00000 13.76169 3.39185 MINI EXTERN> -80.99171 -15.73600 0.00000 0.00000 0.00000 MINI CONSTR> 30.71857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -27.69195 0.05105 0.16190 0.00021 MINI INTERN> 4.16399 17.03902 0.00000 13.73847 3.39069 MINI EXTERN> -81.03342 -15.75813 0.00000 0.00000 0.00000 MINI CONSTR> 30.76744 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9636 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -27.74408 0.05213 0.26801 0.00022 MINI INTERN> 4.10640 17.07513 0.00000 13.71717 3.39676 MINI EXTERN> -81.07254 -15.78875 0.00000 0.00000 0.00000 MINI CONSTR> 30.82174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -27.79377 0.04969 0.23744 0.00022 MINI INTERN> 4.13217 17.04112 0.00000 13.69179 3.39361 MINI EXTERN> -81.11380 -15.80585 0.00000 0.00000 0.00000 MINI CONSTR> 30.86719 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9633 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -27.83897 0.04520 0.26415 0.00023 MINI INTERN> 4.13236 17.03074 0.00000 13.66949 3.39324 MINI EXTERN> -81.15052 -15.82516 0.00000 0.00000 0.00000 MINI CONSTR> 30.91088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -27.87738 0.03840 0.38805 0.00024 MINI INTERN> 4.11963 17.03566 0.00000 13.64762 3.39514 MINI EXTERN> -81.18461 -15.84408 0.00000 0.00000 0.00000 MINI CONSTR> 30.95327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9634 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -27.91967 0.04229 0.42786 0.00025 MINI INTERN> 4.13175 17.01714 0.00000 13.62473 3.39357 MINI EXTERN> -81.22095 -15.86095 0.00000 0.00000 0.00000 MINI CONSTR> 30.99502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -27.95906 0.03939 0.48256 0.00026 MINI INTERN> 4.15338 16.99223 0.00000 13.60180 3.39116 MINI EXTERN> -81.25670 -15.87604 0.00000 0.00000 0.00000 MINI CONSTR> 31.03510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9632 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -27.99770 0.03864 0.46219 0.00027 MINI INTERN> 4.17816 16.96171 0.00000 13.58223 3.38778 MINI EXTERN> -81.28781 -15.88913 0.00000 0.00000 0.00000 MINI CONSTR> 31.06935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -28.03852 0.04082 0.47869 0.00028 MINI INTERN> 4.18416 16.94765 0.00000 13.56090 3.38676 MINI EXTERN> -81.32091 -15.90534 0.00000 0.00000 0.00000 MINI CONSTR> 31.10826 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9630 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -28.09226 0.05374 0.14990 0.00012 MINI INTERN> 4.17988 16.92934 0.00000 13.54679 3.38378 MINI EXTERN> -81.34883 -15.92615 0.00000 0.00000 0.00000 MINI CONSTR> 31.14293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -28.11313 0.02087 0.52650 0.00030 MINI INTERN> 4.19350 16.92408 0.00000 13.52075 3.38528 MINI EXTERN> -81.38210 -15.93525 0.00000 0.00000 0.00000 MINI CONSTR> 31.18060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9627 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -28.15177 0.03864 0.53816 0.00031 MINI INTERN> 4.19483 16.91414 0.00000 13.50055 3.38475 MINI EXTERN> -81.41276 -15.95037 0.00000 0.00000 0.00000 MINI CONSTR> 31.21710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -28.19102 0.03926 0.55437 0.00032 MINI INTERN> 4.19587 16.90448 0.00000 13.47970 3.38429 MINI EXTERN> -81.44428 -15.96559 0.00000 0.00000 0.00000 MINI CONSTR> 31.25452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9627 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -28.24925 0.05822 0.17235 0.00014 MINI INTERN> 4.17407 16.89668 0.00000 13.46761 3.38220 MINI EXTERN> -81.46962 -15.98827 0.00000 0.00000 0.00000 MINI CONSTR> 31.28808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -28.28219 0.03294 0.14287 0.00014 MINI INTERN> 4.17263 16.88928 0.00000 13.45046 3.38200 MINI EXTERN> -81.49482 -15.99946 0.00000 0.00000 0.00000 MINI CONSTR> 31.31772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9627 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -28.29422 0.01203 0.63022 0.00036 MINI INTERN> 4.20202 16.87809 0.00000 13.42239 3.38306 MINI EXTERN> -81.52992 -16.00581 0.00000 0.00000 0.00000 MINI CONSTR> 31.35595 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -28.35856 0.06434 0.22759 0.00015 MINI INTERN> 4.17232 16.87259 0.00000 13.41137 3.38070 MINI EXTERN> -81.55539 -16.03044 0.00000 0.00000 0.00000 MINI CONSTR> 31.39030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9627 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -28.38987 0.03131 0.13943 0.00016 MINI INTERN> 4.17025 16.86466 0.00000 13.39503 3.38067 MINI EXTERN> -81.57865 -16.03867 0.00000 0.00000 0.00000 MINI CONSTR> 31.41684 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -28.42790 0.03803 0.14312 0.00017 MINI INTERN> 4.16944 16.85591 0.00000 13.37550 3.38013 MINI EXTERN> -81.60856 -16.05236 0.00000 0.00000 0.00000 MINI CONSTR> 31.45204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9627 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -28.46234 0.03444 0.29777 0.00017 MINI INTERN> 4.17183 16.84899 0.00000 13.35714 3.37910 MINI EXTERN> -81.63898 -16.06926 0.00000 0.00000 0.00000 MINI CONSTR> 31.48883 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -28.49865 0.03631 0.17845 0.00018 MINI INTERN> 4.16827 16.83973 0.00000 13.33918 3.37897 MINI EXTERN> -81.66510 -16.07809 0.00000 0.00000 0.00000 MINI CONSTR> 31.51839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9626 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -28.53436 0.03571 0.19035 0.00019 MINI INTERN> 4.16766 16.83136 0.00000 13.32074 3.37840 MINI EXTERN> -81.69393 -16.09051 0.00000 0.00000 0.00000 MINI CONSTR> 31.55191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -28.56308 0.02871 0.34150 0.00019 MINI INTERN> 4.17102 16.82532 0.00000 13.30450 3.37748 MINI EXTERN> -81.72123 -16.10467 0.00000 0.00000 0.00000 MINI CONSTR> 31.58451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9626 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -28.59608 0.03301 0.34509 0.00020 MINI INTERN> 4.17030 16.81735 0.00000 13.28746 3.37695 MINI EXTERN> -81.74820 -16.11546 0.00000 0.00000 0.00000 MINI CONSTR> 31.61553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -28.62889 0.03281 0.36053 0.00021 MINI INTERN> 4.16990 16.80948 0.00000 13.27035 3.37637 MINI EXTERN> -81.77561 -16.12643 0.00000 0.00000 0.00000 MINI CONSTR> 31.64706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9626 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -28.66025 0.03136 0.39175 0.00021 MINI INTERN> 4.17014 16.80196 0.00000 13.25368 3.37575 MINI EXTERN> -81.80274 -16.13732 0.00000 0.00000 0.00000 MINI CONSTR> 31.67827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -28.68981 0.02955 0.37854 0.00022 MINI INTERN> 4.16906 16.79428 0.00000 13.23889 3.37527 MINI EXTERN> -81.82684 -16.14584 0.00000 0.00000 0.00000 MINI CONSTR> 31.70538 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9626 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -28.71961 0.02980 0.40047 0.00023 MINI INTERN> 4.16908 16.78689 0.00000 13.22327 3.37466 MINI EXTERN> -81.85273 -16.15561 0.00000 0.00000 0.00000 MINI CONSTR> 31.73484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -28.75011 0.03050 0.41583 0.00024 MINI INTERN> 4.16859 16.77940 0.00000 13.20746 3.37405 MINI EXTERN> -81.87908 -16.16527 0.00000 0.00000 0.00000 MINI CONSTR> 31.76474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9626 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -28.78084 0.03073 0.42038 0.00025 MINI INTERN> 4.16756 16.77177 0.00000 13.19182 3.37345 MINI EXTERN> -81.90532 -16.17444 0.00000 0.00000 0.00000 MINI CONSTR> 31.79433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -28.82001 0.03917 0.13496 0.00011 MINI INTERN> 4.16348 16.75528 0.00000 13.17386 3.37378 MINI EXTERN> -81.93242 -16.17396 0.00000 0.00000 0.00000 MINI CONSTR> 31.81997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9626 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -28.83267 0.01266 0.46380 0.00027 MINI INTERN> 4.16866 16.75772 0.00000 13.16478 3.37220 MINI EXTERN> -81.95251 -16.19043 0.00000 0.00000 0.00000 MINI CONSTR> 31.84691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -28.86064 0.02797 0.48060 0.00028 MINI INTERN> 4.16805 16.75078 0.00000 13.15035 3.37156 MINI EXTERN> -81.97765 -16.19884 0.00000 0.00000 0.00000 MINI CONSTR> 31.87511 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9625 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -28.88757 0.02693 0.50684 0.00029 MINI INTERN> 4.16774 16.74426 0.00000 13.13619 3.37090 MINI EXTERN> -82.00262 -16.20723 0.00000 0.00000 0.00000 MINI CONSTR> 31.90320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -28.93205 0.04448 0.16766 0.00012 MINI INTERN> 4.16400 16.72181 0.00000 13.11724 3.37129 MINI EXTERN> -82.03267 -16.20283 0.00000 0.00000 0.00000 MINI CONSTR> 31.92910 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9624 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -28.95482 0.02277 0.11921 0.00013 MINI INTERN> 4.16026 16.71773 0.00000 13.10738 3.37063 MINI EXTERN> -82.05107 -16.21005 0.00000 0.00000 0.00000 MINI CONSTR> 31.95031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -28.98196 0.02714 0.11838 0.00013 MINI INTERN> 4.15986 16.70965 0.00000 13.09408 3.36994 MINI EXTERN> -82.07571 -16.21673 0.00000 0.00000 0.00000 MINI CONSTR> 31.97696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9624 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -29.00882 0.02685 0.12024 0.00014 MINI INTERN> 4.15976 16.70130 0.00000 13.08089 3.36923 MINI EXTERN> -82.10046 -16.22303 0.00000 0.00000 0.00000 MINI CONSTR> 32.00350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -29.03391 0.02509 0.24227 0.00014 MINI INTERN> 4.16824 16.68732 0.00000 13.06555 3.36862 MINI EXTERN> -82.12945 -16.22600 0.00000 0.00000 0.00000 MINI CONSTR> 32.03181 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9623 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -29.05931 0.02541 0.14943 0.00015 MINI INTERN> 4.16162 16.68369 0.00000 13.05563 3.36784 MINI EXTERN> -82.14875 -16.23367 0.00000 0.00000 0.00000 MINI CONSTR> 32.05432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -29.08461 0.02530 0.15409 0.00015 MINI INTERN> 4.16211 16.67505 0.00000 13.04336 3.36707 MINI EXTERN> -82.17290 -16.23909 0.00000 0.00000 0.00000 MINI CONSTR> 32.07978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9623 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -29.10907 0.02445 0.17690 0.00016 MINI INTERN> 4.16402 16.66555 0.00000 13.03113 3.36630 MINI EXTERN> -82.19732 -16.24374 0.00000 0.00000 0.00000 MINI CONSTR> 32.10499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -29.12781 0.01875 0.28519 0.00016 MINI INTERN> 4.17230 16.65381 0.00000 13.01929 3.36567 MINI EXTERN> -82.22113 -16.24566 0.00000 0.00000 0.00000 MINI CONSTR> 32.12791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9622 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -29.15103 0.02322 0.29398 0.00017 MINI INTERN> 4.17424 16.64445 0.00000 13.00807 3.36483 MINI EXTERN> -82.24457 -16.24996 0.00000 0.00000 0.00000 MINI CONSTR> 32.15192 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -29.17359 0.02256 0.31481 0.00018 MINI INTERN> 4.17797 16.63392 0.00000 12.99686 3.36393 MINI EXTERN> -82.26860 -16.25365 0.00000 0.00000 0.00000 MINI CONSTR> 32.17598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9621 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -29.19450 0.02091 0.34752 0.00018 MINI INTERN> 4.18264 16.62339 0.00000 12.98603 3.36306 MINI EXTERN> -82.29202 -16.25678 0.00000 0.00000 0.00000 MINI CONSTR> 32.19918 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -29.21450 0.02000 0.32914 0.00019 MINI INTERN> 4.17875 16.61932 0.00000 12.97712 3.36245 MINI EXTERN> -82.30956 -16.26141 0.00000 0.00000 0.00000 MINI CONSTR> 32.21883 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9621 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -29.23568 0.02118 0.34327 0.00020 MINI INTERN> 4.18244 16.60896 0.00000 12.96688 3.36151 MINI EXTERN> -82.33246 -16.26455 0.00000 0.00000 0.00000 MINI CONSTR> 32.24155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -29.25711 0.02143 0.34961 0.00020 MINI INTERN> 4.18608 16.59828 0.00000 12.95685 3.36050 MINI EXTERN> -82.35545 -16.26760 0.00000 0.00000 0.00000 MINI CONSTR> 32.26423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9621 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -29.28477 0.02766 0.11042 0.00009 MINI INTERN> 4.14686 16.61927 0.00000 12.95012 3.36024 MINI EXTERN> -82.36171 -16.28389 0.00000 0.00000 0.00000 MINI CONSTR> 32.28434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -29.29420 0.00943 0.38326 0.00022 MINI INTERN> 4.19073 16.58163 0.00000 12.93852 3.35886 MINI EXTERN> -82.39588 -16.27322 0.00000 0.00000 0.00000 MINI CONSTR> 32.30517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9621 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -29.31380 0.01960 0.39506 0.00023 MINI INTERN> 4.19595 16.57015 0.00000 12.92928 3.35779 MINI EXTERN> -82.41826 -16.27534 0.00000 0.00000 0.00000 MINI CONSTR> 32.32662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -29.33299 0.01920 0.41290 0.00024 MINI INTERN> 4.20379 16.55665 0.00000 12.92015 3.35660 MINI EXTERN> -82.44163 -16.27674 0.00000 0.00000 0.00000 MINI CONSTR> 32.34819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9621 ATOM PAIRS WERE FOUND FOR ATOM LIST 255 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -29.36418 0.03119 0.12959 0.00010 MINI INTERN> 4.13748 16.59835 0.00000 12.91296 3.35719 MINI EXTERN> -82.43903 -16.30008 0.00000 0.00000 0.00000 MINI CONSTR> 32.36894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -29.38046 0.01628 0.10022 0.00011 MINI INTERN> 4.14475 16.58533 0.00000 12.90563 3.35621 MINI EXTERN> -82.45830 -16.29984 0.00000 0.00000 0.00000 MINI CONSTR> 32.38576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9621 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -29.39946 0.01899 0.09902 0.00011 MINI INTERN> 4.14392 16.57875 0.00000 12.89684 3.35536 MINI EXTERN> -82.47762 -16.30290 0.00000 0.00000 0.00000 MINI CONSTR> 32.40619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -29.41856 0.01910 0.09915 0.00011 MINI INTERN> 4.14234 16.57274 0.00000 12.88799 3.35451 MINI EXTERN> -82.49686 -16.30615 0.00000 0.00000 0.00000 MINI CONSTR> 32.42687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9619 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -29.43804 0.01948 0.17879 0.00012 MINI INTERN> 4.11869 16.58710 0.00000 12.87765 3.35449 MINI EXTERN> -82.50924 -16.31693 0.00000 0.00000 0.00000 MINI CONSTR> 32.45020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -29.45563 0.01759 0.12620 0.00012 MINI INTERN> 4.12962 16.56975 0.00000 12.87035 3.35319 MINI EXTERN> -82.53104 -16.31541 0.00000 0.00000 0.00000 MINI CONSTR> 32.46790 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9618 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -29.47366 0.01804 0.12307 0.00013 MINI INTERN> 4.12879 16.56326 0.00000 12.86198 3.35233 MINI EXTERN> -82.54968 -16.31798 0.00000 0.00000 0.00000 MINI CONSTR> 32.48764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -29.49185 0.01819 0.12568 0.00013 MINI INTERN> 4.12651 16.55801 0.00000 12.85345 3.35150 MINI EXTERN> -82.56808 -16.32103 0.00000 0.00000 0.00000 MINI CONSTR> 32.50778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9618 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -29.50965 0.01780 0.14036 0.00014 MINI INTERN> 4.12103 16.55588 0.00000 12.84487 3.35080 MINI EXTERN> -82.58509 -16.32505 0.00000 0.00000 0.00000 MINI CONSTR> 32.52791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -29.52349 0.01383 0.23642 0.00014 MINI INTERN> 4.09662 16.57352 0.00000 12.83603 3.35116 MINI EXTERN> -82.59253 -16.33512 0.00000 0.00000 0.00000 MINI CONSTR> 32.54683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9618 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -29.54021 0.01672 0.24175 0.00015 MINI INTERN> 4.09428 16.56887 0.00000 12.82811 3.35036 MINI EXTERN> -82.60967 -16.33794 0.00000 0.00000 0.00000 MINI CONSTR> 32.56579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -29.55665 0.01644 0.25591 0.00015 MINI INTERN> 4.09005 16.56616 0.00000 12.82009 3.34964 MINI EXTERN> -82.62613 -16.34142 0.00000 0.00000 0.00000 MINI CONSTR> 32.58496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9617 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -29.57211 0.01545 0.28129 0.00016 MINI INTERN> 4.08360 16.56605 0.00000 12.81220 3.34904 MINI EXTERN> -82.64110 -16.34563 0.00000 0.00000 0.00000 MINI CONSTR> 32.60372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -29.58675 0.01464 0.26894 0.00016 MINI INTERN> 4.08590 16.55759 0.00000 12.80590 3.34803 MINI EXTERN> -82.65736 -16.34648 0.00000 0.00000 0.00000 MINI CONSTR> 32.61966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9617 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -29.60195 0.01520 0.28238 0.00017 MINI INTERN> 4.08222 16.55481 0.00000 12.79851 3.34730 MINI EXTERN> -82.67290 -16.34961 0.00000 0.00000 0.00000 MINI CONSTR> 32.63771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -29.61743 0.01548 0.29052 0.00018 MINI INTERN> 4.07969 16.55070 0.00000 12.79119 3.34649 MINI EXTERN> -82.68909 -16.35229 0.00000 0.00000 0.00000 MINI CONSTR> 32.65589 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9617 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -29.63771 0.02028 0.08988 0.00008 MINI INTERN> 4.15033 16.47525 0.00000 12.78833 3.34162 MINI EXTERN> -82.73381 -16.33082 0.00000 0.00000 0.00000 MINI CONSTR> 32.67139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -29.64506 0.00735 0.31720 0.00019 MINI INTERN> 4.07290 16.54560 0.00000 12.77767 3.34505 MINI EXTERN> -82.71773 -16.35790 0.00000 0.00000 0.00000 MINI CONSTR> 32.68935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9617 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -29.65925 0.01419 0.32597 0.00020 MINI INTERN> 4.07037 16.54186 0.00000 12.77094 3.34425 MINI EXTERN> -82.73277 -16.36028 0.00000 0.00000 0.00000 MINI CONSTR> 32.70639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -29.67333 0.01407 0.33919 0.00020 MINI INTERN> 4.06694 16.53897 0.00000 12.76412 3.34348 MINI EXTERN> -82.74763 -16.36290 0.00000 0.00000 0.00000 MINI CONSTR> 32.72369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9616 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -29.69601 0.02268 0.10211 0.00009 MINI INTERN> 4.15598 16.44475 0.00000 12.76190 3.33733 MINI EXTERN> -82.80026 -16.33513 0.00000 0.00000 0.00000 MINI CONSTR> 32.73941 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -29.70804 0.01204 0.08435 0.00009 MINI INTERN> 4.14628 16.44787 0.00000 12.75618 3.33700 MINI EXTERN> -82.80975 -16.33895 0.00000 0.00000 0.00000 MINI CONSTR> 32.75333 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9616 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -29.72178 0.01373 0.08307 0.00009 MINI INTERN> 4.14519 16.44269 0.00000 12.74988 3.33607 MINI EXTERN> -82.82458 -16.34057 0.00000 0.00000 0.00000 MINI CONSTR> 32.76955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -29.73570 0.01392 0.08275 0.00010 MINI INTERN> 4.14488 16.43671 0.00000 12.74351 3.33506 MINI EXTERN> -82.83996 -16.34198 0.00000 0.00000 0.00000 MINI CONSTR> 32.78608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9616 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -29.74948 0.01378 0.08432 0.00010 MINI INTERN> 4.14589 16.42962 0.00000 12.73724 3.33397 MINI EXTERN> -82.85572 -16.34300 0.00000 0.00000 0.00000 MINI CONSTR> 32.80253 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -29.76243 0.01295 0.16773 0.00011 MINI INTERN> 4.17431 16.39989 0.00000 12.73139 3.33134 MINI EXTERN> -82.88195 -16.33733 0.00000 0.00000 0.00000 MINI CONSTR> 32.81993 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9615 ATOM PAIRS WERE FOUND FOR ATOM LIST 257 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -29.77555 0.01312 0.10471 0.00011 MINI INTERN> 4.15409 16.41089 0.00000 12.72539 3.33150 MINI EXTERN> -82.88811 -16.34347 0.00000 0.00000 0.00000 MINI CONSTR> 32.83416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -29.78871 0.01316 0.10690 0.00011 MINI INTERN> 4.15369 16.40548 0.00000 12.71926 3.33049 MINI EXTERN> -82.90266 -16.34509 0.00000 0.00000 0.00000 MINI CONSTR> 32.85012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9615 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -29.80161 0.01291 0.11893 0.00012 MINI INTERN> 4.15607 16.39794 0.00000 12.71322 3.32932 MINI EXTERN> -82.91808 -16.34614 0.00000 0.00000 0.00000 MINI CONSTR> 32.86606 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 -29.80161 0.01291 0.11893 0.00014 STPD INTERN> 4.15607 16.39794 0.00000 12.71322 3.32932 STPD EXTERN> -82.91808 -16.34614 0.00000 0.00000 0.00000 STPD CONSTR> 32.86606 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 9615 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9615 ATOM PAIRS WERE FOUND FOR ATOM LIST 256 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 -29.80161 0.01291 0.11893 0.00000 MINI INTERN> 4.15607 16.39794 0.00000 12.71322 3.32932 MINI EXTERN> -82.91808 -16.34614 0.00000 0.00000 0.00000 MINI CONSTR> 32.86606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -30.53420 0.73259 0.42196 0.12239 MINI INTERN> 4.07141 15.92040 0.00000 12.33447 3.23364 MINI EXTERN> -84.55358 -16.35246 0.00000 0.00000 0.00000 MINI CONSTR> 34.81193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -30.60385 0.06965 0.20349 0.01822 MINI INTERN> 4.15946 15.85099 0.00000 12.30186 3.25231 MINI EXTERN> -84.72744 -16.45300 0.00000 0.00000 0.00000 MINI CONSTR> 35.01197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -30.64272 0.03886 0.24459 0.01231 MINI INTERN> 4.07169 15.77887 0.00000 12.30229 3.19883 MINI EXTERN> -84.53923 -16.53493 0.00000 0.00000 0.00000 MINI CONSTR> 35.07976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -30.69066 0.04795 0.25682 0.01759 MINI INTERN> 3.99887 15.67386 0.00000 12.21006 3.20983 MINI EXTERN> -84.37593 -16.52810 0.00000 0.00000 0.00000 MINI CONSTR> 35.12075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -30.75043 0.05977 0.23445 0.02684 MINI INTERN> 4.07589 15.76414 0.00000 12.14868 3.18208 MINI EXTERN> -84.54789 -16.53601 0.00000 0.00000 0.00000 MINI CONSTR> 35.16268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -30.81126 0.06083 0.26570 0.02851 MINI INTERN> 4.15588 15.69130 0.00000 12.10423 3.12934 MINI EXTERN> -84.44980 -16.65588 0.00000 0.00000 0.00000 MINI CONSTR> 35.21366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -30.86779 0.05653 0.22809 0.02155 MINI INTERN> 4.07304 15.67998 0.00000 11.99532 3.11519 MINI EXTERN> -84.48204 -16.51976 0.00000 0.00000 0.00000 MINI CONSTR> 35.27047 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -30.91328 0.04549 0.18939 0.02310 MINI INTERN> 4.06864 15.69345 0.00000 11.94358 3.11407 MINI EXTERN> -84.48392 -16.56370 0.00000 0.00000 0.00000 MINI CONSTR> 35.31460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -30.94210 0.02882 0.15745 0.01501 MINI INTERN> 4.10147 15.69651 0.00000 11.95149 3.07942 MINI EXTERN> -84.47803 -16.63810 0.00000 0.00000 0.00000 MINI CONSTR> 35.34513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -30.96312 0.02102 0.14289 0.01152 MINI INTERN> 4.06421 15.66594 0.00000 11.94635 3.10028 MINI EXTERN> -84.41436 -16.69195 0.00000 0.00000 0.00000 MINI CONSTR> 35.36639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -30.97762 0.01450 0.11462 0.00796 MINI INTERN> 4.08038 15.67162 0.00000 11.94984 3.13074 MINI EXTERN> -84.47949 -16.71280 0.00000 0.00000 0.00000 MINI CONSTR> 35.38211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -30.99093 0.01331 0.10703 0.00825 MINI INTERN> 4.10879 15.71365 0.00000 11.98392 3.14209 MINI EXTERN> -84.56324 -16.77460 0.00000 0.00000 0.00000 MINI CONSTR> 35.39847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -31.00107 0.01014 0.10979 0.00829 MINI INTERN> 4.08674 15.71683 0.00000 12.03192 3.12058 MINI EXTERN> -84.57031 -16.79718 0.00000 0.00000 0.00000 MINI CONSTR> 35.41034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -31.01235 0.01128 0.09925 0.00911 MINI INTERN> 4.07048 15.68967 0.00000 12.08764 3.14769 MINI EXTERN> -84.58658 -16.84162 0.00000 0.00000 0.00000 MINI CONSTR> 35.42037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -31.02158 0.00924 0.10693 0.00907 MINI INTERN> 4.08739 15.68065 0.00000 12.13582 3.12661 MINI EXTERN> -84.58123 -16.89164 0.00000 0.00000 0.00000 MINI CONSTR> 35.42081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -31.03311 0.01153 0.10475 0.01082 MINI INTERN> 4.11667 15.67640 0.00000 12.14644 3.13834 MINI EXTERN> -84.52333 -17.00087 0.00000 0.00000 0.00000 MINI CONSTR> 35.41324 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -31.04236 0.00925 0.10319 0.00893 MINI INTERN> 4.08591 15.68236 0.00000 12.15417 3.14045 MINI EXTERN> -84.44567 -17.06191 0.00000 0.00000 0.00000 MINI CONSTR> 35.40232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -31.05044 0.00808 0.08879 0.00838 MINI INTERN> 4.08135 15.68216 0.00000 12.15347 3.13350 MINI EXTERN> -84.39754 -17.09735 0.00000 0.00000 0.00000 MINI CONSTR> 35.39398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -31.05668 0.00624 0.09075 0.00700 MINI INTERN> 4.08154 15.67755 0.00000 12.17759 3.13152 MINI EXTERN> -84.38657 -17.13028 0.00000 0.00000 0.00000 MINI CONSTR> 35.39196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -31.06358 0.00690 0.08144 0.00804 MINI INTERN> 4.07205 15.69625 0.00000 12.17972 3.12847 MINI EXTERN> -84.37086 -17.16384 0.00000 0.00000 0.00000 MINI CONSTR> 35.39462 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 -31.06358 0.00690 0.08144 0.02000 CONJ INTERN> 4.07205 15.69625 0.00000 12.17972 3.12847 CONJ EXTERN> -84.37086 -17.16384 0.00000 0.00000 0.00000 CONJ CONSTR> 35.39462 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 ALA 1 HT1 ) 0.31241 ( PROT ALA 1 HT2 ) 0.31241 ( PROT ALA 1 N ) 0.39052 ( PROT ALA 1 HT3 ) 0.31241 ( PROT ALA 1 CA ) 0.39052 ( PROT ALA 1 CB ) 0.31241 ( PROT ALA 1 C ) 0.39052 ( PROT ALA 1 O ) 0.39052 ( PROT LEU 2 N ) 0.39052 ( PROT LEU 2 H ) 0.31241 ( PROT LEU 2 CA ) 0.39052 ( PROT LEU 2 CB ) 0.31241 ( PROT LEU 2 CG ) 0.31241 ( PROT LEU 2 CD1 ) 0.31241 ( PROT LEU 2 CD2 ) 0.31241 ( PROT LEU 2 C ) 0.39052 ( PROT LEU 2 O ) 0.39052 ( PROT GLN 3 N ) 0.39052 ( PROT GLN 3 H ) 0.31241 ( PROT GLN 3 CA ) 0.39052 ( PROT GLN 3 CB ) 0.31241 ( PROT GLN 3 CG ) 0.31241 ( PROT GLN 3 CD ) 0.31241 ( PROT GLN 3 OE1 ) 0.31241 ( PROT GLN 3 NE2 ) 0.31241 ( PROT GLN 3 HE21 ) 0.31241 ( PROT GLN 3 HE22 ) 0.31241 ( PROT GLN 3 C ) 0.39052 ( PROT GLN 3 O ) 0.39052 ( PROT ALA 4 N ) 0.39052 ( PROT ALA 4 H ) 0.31241 ( PROT ALA 4 CA ) 0.39052 ( PROT ALA 4 CB ) 0.31241 ( PROT ALA 4 C ) 0.39052 ( PROT ALA 4 O ) 0.39052 ( PROT PHE 5 N ) 0.39052 ( PROT PHE 5 H ) 0.31241 ( PROT PHE 5 CA ) 0.39052 ( PROT PHE 5 CB ) 0.31241 ( PROT PHE 5 CG ) 0.31241 ( PROT PHE 5 CD1 ) 0.31241 ( PROT PHE 5 CD2 ) 0.31241 ( PROT PHE 5 CE1 ) 0.31241 ( PROT PHE 5 CE2 ) 0.31241 ( PROT PHE 5 CZ ) 0.31241 ( PROT PHE 5 C ) 0.39052 ( PROT PHE 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 ILE 7 N ) 0.39052 ( PROT ILE 7 H ) 0.31241 ( PROT ILE 7 CA ) 0.39052 ( PROT ILE 7 CB ) 0.31241 ( PROT ILE 7 CG2 ) 0.31241 ( PROT ILE 7 CG1 ) 0.31241 ( PROT ILE 7 CD ) 0.31241 ( PROT ILE 7 C ) 0.39052 ( PROT ILE 7 O ) 0.39052 ( PROT ALA 8 N ) 0.39052 ( PROT ALA 8 H ) 0.31241 ( PROT ALA 8 CA ) 0.39052 ( PROT ALA 8 CB ) 0.31241 ( PROT ALA 8 C ) 0.39052 ( PROT ALA 8 O ) 0.39052 ( PROT LEU 9 N ) 0.39052 ( PROT LEU 9 H ) 0.31241 ( PROT LEU 9 CA ) 0.39052 ( PROT LEU 9 CB ) 0.31241 ( PROT LEU 9 CG ) 0.31241 ( PROT LEU 9 CD1 ) 0.31241 ( PROT LEU 9 CD2 ) 0.31241 ( PROT LEU 9 C ) 0.39052 ( PROT LEU 9 O ) 0.39052 ( PROT SER 10 N ) 0.39052 ( PROT SER 10 H ) 0.31241 ( PROT SER 10 CA ) 0.39052 ( PROT SER 10 CB ) 0.31241 ( PROT SER 10 OG ) 0.31241 ( PROT SER 10 HG ) 0.31241 ( PROT SER 10 C ) 0.39052 ( PROT SER 10 O ) 0.39052 ( PROT SER 11 N ) 0.39052 ( PROT SER 11 H ) 0.31241 ( PROT SER 11 CA ) 0.39052 ( PROT SER 11 CB ) 0.31241 ( PROT SER 11 OG ) 0.31241 ( PROT SER 11 HG ) 0.31241 ( PROT SER 11 C ) 0.39052 ( PROT SER 11 O ) 0.39052 ( PROT PHE 12 N ) 0.39052 ( PROT PHE 12 H ) 0.31241 ( PROT PHE 12 CA ) 0.39052 ( PROT PHE 12 CB ) 0.31241 ( PROT PHE 12 CG ) 0.31241 ( PROT PHE 12 CD1 ) 0.31241 ( PROT PHE 12 CD2 ) 0.31241 ( PROT PHE 12 CE1 ) 0.31241 ( PROT PHE 12 CE2 ) 0.31241 ( PROT PHE 12 CZ ) 0.31241 ( PROT PHE 12 C ) 0.39052 ( PROT PHE 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 SER 14 N ) 0.39052 ( PROT SER 14 H ) 0.31241 ( PROT SER 14 CA ) 0.39052 ( PROT SER 14 CB ) 0.31241 ( PROT SER 14 OG ) 0.31241 ( PROT SER 14 HG ) 0.31241 ( PROT SER 14 C ) 0.39052 ( PROT SER 14 O ) 0.39052 ( PROT LYS 15 N ) 0.39052 ( PROT LYS 15 H ) 0.31241 ( PROT LYS 15 CA ) 0.39052 ( PROT LYS 15 CB ) 0.31241 ( PROT LYS 15 CG ) 0.31241 ( PROT LYS 15 CD ) 0.31241 ( PROT LYS 15 CE ) 0.31241 ( PROT LYS 15 NZ ) 0.31241 ( PROT LYS 15 HZ1 ) 0.31241 ( PROT LYS 15 HZ2 ) 0.31241 ( PROT LYS 15 HZ3 ) 0.31241 ( PROT LYS 15 C ) 0.39052 ( PROT LYS 15 O ) 0.39052 ( PROT LEU 16 N ) 0.39052 ( PROT LEU 16 H ) 0.31241 ( PROT LEU 16 CA ) 0.39052 ( PROT LEU 16 CB ) 0.31241 ( PROT LEU 16 CG ) 0.31241 ( PROT LEU 16 CD1 ) 0.31241 ( PROT LEU 16 CD2 ) 0.31241 ( PROT LEU 16 C ) 0.39052 ( PROT LEU 16 O ) 0.39052 ( PROT ALA 17 N ) 0.39052 ( PROT ALA 17 H ) 0.31241 ( PROT ALA 17 CA ) 0.39052 ( PROT ALA 17 CB ) 0.31241 ( PROT ALA 17 C ) 0.39052 ( PROT ALA 17 O ) 0.39052 ( PROT CYS 18 N ) 0.39052 ( PROT CYS 18 H ) 0.31241 ( PROT CYS 18 CA ) 0.39052 ( PROT CYS 18 CB ) 0.31241 ( PROT CYS 18 SG ) 0.31241 ( PROT CYS 18 C ) 0.39052 ( PROT CYS 18 O ) 0.39052 ( PROT GLU 19 N ) 0.39052 ( PROT GLU 19 H ) 0.31241 ( PROT GLU 19 CA ) 0.39052 ( PROT GLU 19 CB ) 0.31241 ( PROT GLU 19 CG ) 0.31241 ( PROT GLU 19 CD ) 0.31241 ( PROT GLU 19 OE1 ) 0.31241 ( PROT GLU 19 OE2 ) 0.31241 ( PROT GLU 19 C ) 0.39052 ( PROT GLU 19 OT1 ) 0.31241 ( PROT GLU 19 OT2 ) 0.31241 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.42968 4.57298 -7.52439 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00502 0.00225 -0.00824 ROTATION MATRIX 0.999999 0.001086 0.000818 -0.001085 0.999999 -0.001304 -0.000820 0.001303 0.999999 AXIS OF ROTATION IS -0.692037 -0.434771 0.576245 ANGLE IS 0.11 TOTAL SQUARE DIFF IS 66.6451 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.629839 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.6298" Parameter: A <- "0.6298" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.96083 4.29436 -7.75013 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.02862 -0.01410 0.01787 ROTATION MATRIX 0.999761 0.017035 0.013712 -0.016674 0.999522 -0.026018 -0.014149 0.025783 0.999567 AXIS OF ROTATION IS -0.764114 -0.410965 0.497229 ANGLE IS 1.94 CENTER OF ROTATION 8.936705 4.270263 -7.770370 SHIFT IS 0.036545 TOTAL SQUARE DIFF IS 4.7630 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.500682 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.6298" RDCMND substituted energy or value "?RMS" to " 0.5007" Parameter: A <- "0.6298 0.5007" 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 0.6298 0.5007 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 " 35.39" Parameter: H <- "35.39" 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 -66.45820 35.39462 0.39862 ENER INTERN> 4.07205 15.69625 0.00000 12.17972 3.12847 ENER EXTERN> -84.37086 -17.16384 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 " -66.46" Parameter: B <- "-66.46" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -17.16" Parameter: C <- "-17.16" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -84.37" Parameter: C <- " -101.53" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -101.53" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.07" Parameter: D <- "4.07" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 15.70" Parameter: D <- " 19.77" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 12.18" Parameter: D <- " 31.95" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.13" Parameter: D <- " 35.08" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 35.08" 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= -66.46 GRMS= 0.40 ELEC= -17.16 VDW= -84.37 RDTITL> *EXTERNAL= -101.53 INTERNAL= 35.08 USER= 0.00 HARM= 35.39 RDTITL> *BOND= 4.07 ANGL= 15.70 DIHE= 12.18 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 "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9615 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9607 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 -42.45088 -24.00732 0.16791 0.02000 MINI INTERN> 4.07205 15.69625 0.00000 12.17972 3.12847 MINI EXTERN> -84.37086 -17.16384 0.00000 0.00000 0.00000 MINI CONSTR> 24.00732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -40.34442 -2.10646 5.39589 0.00360 MINI INTERN> 5.46818 17.16780 0.00000 12.64930 3.12770 MINI EXTERN> -87.32479 -16.37120 0.00000 0.00000 0.00000 MINI CONSTR> 24.93860 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9596 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -42.94170 2.59728 0.25860 0.00065 MINI INTERN> 4.18968 15.72283 0.00000 12.46648 3.15548 MINI EXTERN> -86.98644 -16.43769 0.00000 0.00000 0.00000 MINI CONSTR> 24.94795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -42.98469 0.04299 0.28276 0.00028 MINI INTERN> 4.14080 15.69600 0.00000 12.43764 3.13767 MINI EXTERN> -86.86479 -16.50978 0.00000 0.00000 0.00000 MINI CONSTR> 24.97777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9596 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -43.01896 0.03426 0.12173 0.00012 MINI INTERN> 4.17695 15.64589 0.00000 12.40468 3.14302 MINI EXTERN> -86.82973 -16.56362 0.00000 0.00000 0.00000 MINI CONSTR> 25.00384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -43.04272 0.02376 0.12946 0.00013 MINI INTERN> 4.17635 15.62223 0.00000 12.39035 3.14108 MINI EXTERN> -86.80122 -16.60090 0.00000 0.00000 0.00000 MINI CONSTR> 25.02939 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9596 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -43.06120 0.01848 0.10685 0.00013 MINI INTERN> 4.16677 15.61620 0.00000 12.37880 3.14102 MINI EXTERN> -86.78389 -16.63076 0.00000 0.00000 0.00000 MINI CONSTR> 25.05065 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -43.07996 0.01876 0.22913 0.00013 MINI INTERN> 4.18913 15.57643 0.00000 12.36754 3.13936 MINI EXTERN> -86.78696 -16.64376 0.00000 0.00000 0.00000 MINI CONSTR> 25.07829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9595 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -43.10041 0.02045 0.13624 0.00014 MINI INTERN> 4.16943 15.58367 0.00000 12.35673 3.13958 MINI EXTERN> -86.77819 -16.67341 0.00000 0.00000 0.00000 MINI CONSTR> 25.10178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -43.11959 0.01918 0.16029 0.00014 MINI INTERN> 4.17371 15.56646 0.00000 12.34695 3.13871 MINI EXTERN> -86.78598 -16.68830 0.00000 0.00000 0.00000 MINI CONSTR> 25.12887 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9594 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -43.13429 0.01470 0.24941 0.00015 MINI INTERN> 4.19206 15.53807 0.00000 12.33954 3.13732 MINI EXTERN> -86.80357 -16.69153 0.00000 0.00000 0.00000 MINI CONSTR> 25.15382 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -43.15262 0.01833 0.25828 0.00016 MINI INTERN> 4.19469 15.52478 0.00000 12.33119 3.13644 MINI EXTERN> -86.81809 -16.70259 0.00000 0.00000 0.00000 MINI CONSTR> 25.18095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9593 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -43.17038 0.01776 0.27768 0.00016 MINI INTERN> 4.19901 15.51037 0.00000 12.32339 3.13546 MINI EXTERN> -86.83638 -16.71075 0.00000 0.00000 0.00000 MINI CONSTR> 25.20852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -43.18690 0.01652 0.30518 0.00017 MINI INTERN> 4.20476 15.49542 0.00000 12.31631 3.13443 MINI EXTERN> -86.85710 -16.71611 0.00000 0.00000 0.00000 MINI CONSTR> 25.23540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9592 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -43.20281 0.01591 0.28795 0.00017 MINI INTERN> 4.19929 15.49220 0.00000 12.30988 3.13398 MINI EXTERN> -86.87232 -16.72433 0.00000 0.00000 0.00000 MINI CONSTR> 25.25849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -43.21974 0.01693 0.30084 0.00018 MINI INTERN> 4.20177 15.48056 0.00000 12.30315 3.13302 MINI EXTERN> -86.89478 -16.72911 0.00000 0.00000 0.00000 MINI CONSTR> 25.28564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9592 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -43.23692 0.01718 0.30758 0.00019 MINI INTERN> 4.20264 15.47044 0.00000 12.29652 3.13209 MINI EXTERN> -86.91798 -16.73368 0.00000 0.00000 0.00000 MINI CONSTR> 25.31305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -43.25929 0.02237 0.09612 0.00008 MINI INTERN> 4.12934 15.53514 0.00000 12.28610 3.13478 MINI EXTERN> -86.90769 -16.77473 0.00000 0.00000 0.00000 MINI CONSTR> 25.33777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9591 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -43.26701 0.00772 0.33597 0.00020 MINI INTERN> 4.20801 15.44928 0.00000 12.28508 3.13016 MINI EXTERN> -86.96426 -16.73840 0.00000 0.00000 0.00000 MINI CONSTR> 25.36312 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -43.28280 0.01579 0.34628 0.00021 MINI INTERN> 4.20974 15.43918 0.00000 12.27927 3.12915 MINI EXTERN> -86.98888 -16.74060 0.00000 0.00000 0.00000 MINI CONSTR> 25.38935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9590 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -43.29837 0.01557 0.36171 0.00022 MINI INTERN> 4.21281 15.42789 0.00000 12.27355 3.12804 MINI EXTERN> -87.01474 -16.74185 0.00000 0.00000 0.00000 MINI CONSTR> 25.41593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -43.32364 0.02526 0.11215 0.00009 MINI INTERN> 4.11937 15.51285 0.00000 12.26199 3.13163 MINI EXTERN> -86.99912 -16.79214 0.00000 0.00000 0.00000 MINI CONSTR> 25.44179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9590 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -43.33688 0.01325 0.08883 0.00010 MINI INTERN> 4.12761 15.49660 0.00000 12.25806 3.13038 MINI EXTERN> -87.02320 -16.78905 0.00000 0.00000 0.00000 MINI CONSTR> 25.46273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -43.35228 0.01540 0.08776 0.00010 MINI INTERN> 4.12722 15.48913 0.00000 12.25260 3.12944 MINI EXTERN> -87.04738 -16.79123 0.00000 0.00000 0.00000 MINI CONSTR> 25.48796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9590 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -43.36785 0.01557 0.08776 0.00010 MINI INTERN> 4.12611 15.48240 0.00000 12.24702 3.12850 MINI EXTERN> -87.07181 -16.79369 0.00000 0.00000 0.00000 MINI CONSTR> 25.51362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -43.38319 0.01534 0.09014 0.00011 MINI INTERN> 4.12377 15.47724 0.00000 12.24142 3.12763 MINI EXTERN> -87.09558 -16.79676 0.00000 0.00000 0.00000 MINI CONSTR> 25.53908 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9590 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -43.39735 0.01416 0.18210 0.00011 MINI INTERN> 4.09980 15.49825 0.00000 12.23382 3.12794 MINI EXTERN> -87.11012 -16.81324 0.00000 0.00000 0.00000 MINI CONSTR> 25.56620 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -43.41216 0.01481 0.11109 0.00012 MINI INTERN> 4.11500 15.47268 0.00000 12.23038 3.12616 MINI EXTERN> -87.13928 -16.80505 0.00000 0.00000 0.00000 MINI CONSTR> 25.58795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9589 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -43.42695 0.01479 0.11478 0.00012 MINI INTERN> 4.11340 15.46712 0.00000 12.22497 3.12523 MINI EXTERN> -87.16303 -16.80747 0.00000 0.00000 0.00000 MINI CONSTR> 25.61284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -43.44134 0.01439 0.13107 0.00012 MINI INTERN> 4.10891 15.46524 0.00000 12.21934 3.12447 MINI EXTERN> -87.18523 -16.81167 0.00000 0.00000 0.00000 MINI CONSTR> 25.63761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9588 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -43.45252 0.01118 0.21321 0.00013 MINI INTERN> 4.09220 15.48010 0.00000 12.21310 3.12455 MINI EXTERN> -87.19900 -16.82396 0.00000 0.00000 0.00000 MINI CONSTR> 25.66049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -43.46633 0.01381 0.21794 0.00013 MINI INTERN> 4.09108 15.47465 0.00000 12.20794 3.12361 MINI EXTERN> -87.22180 -16.82597 0.00000 0.00000 0.00000 MINI CONSTR> 25.68415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9588 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -43.48000 0.01367 0.22986 0.00014 MINI INTERN> 4.08900 15.47058 0.00000 12.20260 3.12269 MINI EXTERN> -87.24439 -16.82860 0.00000 0.00000 0.00000 MINI CONSTR> 25.70811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -43.49297 0.01297 0.25168 0.00014 MINI INTERN> 4.08551 15.46875 0.00000 12.19720 3.12187 MINI EXTERN> -87.26576 -16.83222 0.00000 0.00000 0.00000 MINI CONSTR> 25.73169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9588 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -43.50530 0.01233 0.24193 0.00015 MINI INTERN> 4.08650 15.46132 0.00000 12.19295 3.12095 MINI EXTERN> -87.28614 -16.83289 0.00000 0.00000 0.00000 MINI CONSTR> 25.75202 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -43.51798 0.01268 0.25448 0.00015 MINI INTERN> 4.08481 15.45742 0.00000 12.18785 3.12005 MINI EXTERN> -87.30745 -16.83529 0.00000 0.00000 0.00000 MINI CONSTR> 25.77462 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9587 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -43.53101 0.01302 0.26262 0.00016 MINI INTERN> 4.08466 15.45151 0.00000 12.18275 3.11900 MINI EXTERN> -87.33001 -16.83651 0.00000 0.00000 0.00000 MINI CONSTR> 25.79759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -43.54419 0.01318 0.26446 0.00017 MINI INTERN> 4.08621 15.44337 0.00000 12.17779 3.11783 MINI EXTERN> -87.35333 -16.83648 0.00000 0.00000 0.00000 MINI CONSTR> 25.82042 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9588 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -43.56105 0.01686 0.08461 0.00007 MINI INTERN> 4.12806 15.38328 0.00000 12.17748 3.11474 MINI EXTERN> -87.39195 -16.81269 0.00000 0.00000 0.00000 MINI CONSTR> 25.84004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -43.56704 0.00599 0.29144 0.00018 MINI INTERN> 4.08338 15.43643 0.00000 12.16829 3.11614 MINI EXTERN> -87.39213 -16.84121 0.00000 0.00000 0.00000 MINI CONSTR> 25.86206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9587 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -43.57944 0.01240 0.29745 0.00019 MINI INTERN> 4.08693 15.42641 0.00000 12.16353 3.11480 MINI EXTERN> -87.41564 -16.83960 0.00000 0.00000 0.00000 MINI CONSTR> 25.88412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -43.59190 0.01247 0.30522 0.00019 MINI INTERN> 4.09469 15.41134 0.00000 12.15894 3.11311 MINI EXTERN> -87.44174 -16.83480 0.00000 0.00000 0.00000 MINI CONSTR> 25.90657 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9587 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -43.60407 0.01217 0.31774 0.00020 MINI INTERN> 4.10481 15.39352 0.00000 12.15454 3.11125 MINI EXTERN> -87.46882 -16.82837 0.00000 0.00000 0.00000 MINI CONSTR> 25.92899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -43.62404 0.01997 0.10108 0.00009 MINI INTERN> 4.12405 15.35755 0.00000 12.15314 3.11020 MINI EXTERN> -87.49470 -16.82405 0.00000 0.00000 0.00000 MINI CONSTR> 25.94976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9587 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -43.63460 0.01056 0.07690 0.00009 MINI INTERN> 4.12119 15.35522 0.00000 12.14883 3.10932 MINI EXTERN> -87.51135 -16.82538 0.00000 0.00000 0.00000 MINI CONSTR> 25.96756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -43.63818 0.00358 0.34829 0.00022 MINI INTERN> 4.11654 15.36289 0.00000 12.14136 3.10734 MINI EXTERN> -87.53489 -16.82309 0.00000 0.00000 0.00000 MINI CONSTR> 25.99167 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9587 ATOM PAIRS WERE FOUND FOR ATOM LIST 258 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -43.65964 0.02146 0.12891 0.00010 MINI INTERN> 4.12358 15.34167 0.00000 12.13898 3.10753 MINI EXTERN> -87.55351 -16.83092 0.00000 0.00000 0.00000 MINI CONSTR> 26.01303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -43.66997 0.01033 0.07556 0.00010 MINI INTERN> 4.11984 15.33965 0.00000 12.13481 3.10651 MINI EXTERN> -87.56943 -16.83087 0.00000 0.00000 0.00000 MINI CONSTR> 26.02952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9586 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -43.68299 0.01302 0.14621 0.00010 MINI INTERN> 4.12402 15.33064 0.00000 12.12951 3.10570 MINI EXTERN> -87.59233 -16.83534 0.00000 0.00000 0.00000 MINI CONSTR> 26.05482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -43.69467 0.01168 0.10103 0.00011 MINI INTERN> 4.12102 15.32724 0.00000 12.12495 3.10463 MINI EXTERN> -87.61024 -16.83598 0.00000 0.00000 0.00000 MINI CONSTR> 26.07370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9586 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -43.70641 0.01174 0.10463 0.00011 MINI INTERN> 4.12093 15.32185 0.00000 12.12018 3.10368 MINI EXTERN> -87.62952 -16.83810 0.00000 0.00000 0.00000 MINI CONSTR> 26.09457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -43.71787 0.01145 0.11806 0.00011 MINI INTERN> 4.12143 15.31619 0.00000 12.11549 3.10277 MINI EXTERN> -87.64855 -16.84050 0.00000 0.00000 0.00000 MINI CONSTR> 26.11531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9586 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -43.72697 0.00910 0.18414 0.00012 MINI INTERN> 4.12526 15.30954 0.00000 12.11136 3.10212 MINI EXTERN> -87.66578 -16.84399 0.00000 0.00000 0.00000 MINI CONSTR> 26.13453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -43.73830 0.01133 0.18596 0.00012 MINI INTERN> 4.12535 15.30425 0.00000 12.10666 3.10118 MINI EXTERN> -87.68436 -16.84615 0.00000 0.00000 0.00000 MINI CONSTR> 26.15477 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9586 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -43.75059 0.01229 0.12764 0.00013 MINI INTERN> 4.12118 15.30128 0.00000 12.10198 3.10005 MINI EXTERN> -87.70214 -16.84675 0.00000 0.00000 0.00000 MINI CONSTR> 26.17381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -43.75866 0.00807 0.20124 0.00013 MINI INTERN> 4.12576 15.29470 0.00000 12.09806 3.09947 MINI EXTERN> -87.71823 -16.85040 0.00000 0.00000 0.00000 MINI CONSTR> 26.19197 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9585 ATOM PAIRS WERE FOUND FOR ATOM LIST 259 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -43.76937 0.01071 0.22452 0.00014 MINI INTERN> 4.12753 15.28870 0.00000 12.09333 3.09857 MINI EXTERN> -87.73689 -16.85325 0.00000 0.00000 0.00000 MINI CONSTR> 26.21265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -43.77940 0.01003 0.21750 0.00014 MINI INTERN> 4.12676 15.28463 0.00000 12.08919 3.09771 MINI EXTERN> -87.75277 -16.85502 0.00000 0.00000 0.00000 MINI CONSTR> 26.23010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9585 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -43.78981 0.01041 0.22568 0.00015 MINI INTERN> 4.12715 15.27963 0.00000 12.08473 3.09681 MINI EXTERN> -87.77005 -16.85739 0.00000 0.00000 0.00000 MINI CONSTR> 26.24932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -43.80032 0.01051 0.22886 0.00015 MINI INTERN> 4.12716 15.27484 0.00000 12.08027 3.09589 MINI EXTERN> -87.78719 -16.85968 0.00000 0.00000 0.00000 MINI CONSTR> 26.26841 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9585 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -43.81375 0.01343 0.07496 0.00007 MINI INTERN> 4.11255 15.27880 0.00000 12.07524 3.09418 MINI EXTERN> -87.80366 -16.85606 0.00000 0.00000 0.00000 MINI CONSTR> 26.28522 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -43.81849 0.00475 0.25568 0.00016 MINI INTERN> 4.12872 15.26576 0.00000 12.07216 3.09429 MINI EXTERN> -87.81820 -16.86438 0.00000 0.00000 0.00000 MINI CONSTR> 26.30316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9585 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -43.82855 0.01006 0.26282 0.00017 MINI INTERN> 4.12928 15.26085 0.00000 12.06776 3.09340 MINI EXTERN> -87.83484 -16.86688 0.00000 0.00000 0.00000 MINI CONSTR> 26.32188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -43.83863 0.01008 0.27279 0.00018 MINI INTERN> 4.13009 15.25576 0.00000 12.06332 3.09248 MINI EXTERN> -87.85167 -16.86953 0.00000 0.00000 0.00000 MINI CONSTR> 26.34093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9584 ATOM PAIRS WERE FOUND FOR ATOM LIST 260 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -43.84834 0.00972 0.28834 0.00018 MINI INTERN> 4.13137 15.25053 0.00000 12.05891 3.09159 MINI EXTERN> -87.86831 -16.87232 0.00000 0.00000 0.00000 MINI CONSTR> 26.35989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -43.86450 0.01616 0.09619 0.00008 MINI INTERN> 4.10914 15.25874 0.00000 12.05310 3.08951 MINI EXTERN> -87.88589 -16.86656 0.00000 0.00000 0.00000 MINI CONSTR> 26.37746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9583 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -43.87277 0.00827 0.06774 0.00008 MINI INTERN> 4.11098 15.25332 0.00000 12.04995 3.08896 MINI EXTERN> -87.89806 -16.86961 0.00000 0.00000 0.00000 MINI CONSTR> 26.39169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -43.88272 0.00995 0.06755 0.00009 MINI INTERN> 4.11062 15.24916 0.00000 12.04561 3.08806 MINI EXTERN> -87.91394 -16.87199 0.00000 0.00000 0.00000 MINI CONSTR> 26.40976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9583 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -43.89264 0.00992 0.06871 0.00009 MINI INTERN> 4.11009 15.24518 0.00000 12.04124 3.08714 MINI EXTERN> -87.92981 -16.87433 0.00000 0.00000 0.00000 MINI CONSTR> 26.42784 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -43.90213 0.00949 0.13589 0.00009 MINI INTERN> 4.10635 15.24477 0.00000 12.03596 3.08590 MINI EXTERN> -87.94768 -16.87483 0.00000 0.00000 0.00000 MINI CONSTR> 26.44739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9583 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -43.91158 0.00945 0.08579 0.00010 MINI INTERN> 4.10810 15.23860 0.00000 12.03261 3.08529 MINI EXTERN> -87.96058 -16.87843 0.00000 0.00000 0.00000 MINI CONSTR> 26.46282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -43.92117 0.00959 0.08594 0.00010 MINI INTERN> 4.10779 15.23468 0.00000 12.02835 3.08442 MINI EXTERN> -87.97583 -16.88092 0.00000 0.00000 0.00000 MINI CONSTR> 26.48033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9583 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -43.93074 0.00957 0.09200 0.00010 MINI INTERN> 4.10721 15.23111 0.00000 12.02399 3.08352 MINI EXTERN> -87.99129 -16.88330 0.00000 0.00000 0.00000 MINI CONSTR> 26.49802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -43.93852 0.00778 0.16587 0.00011 MINI INTERN> 4.10451 15.23120 0.00000 12.01914 3.08249 MINI EXTERN> -88.00732 -16.88396 0.00000 0.00000 0.00000 MINI CONSTR> 26.51541 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9583 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -43.94746 0.00894 0.16659 0.00011 MINI INTERN> 4.10442 15.22755 0.00000 12.01508 3.08170 MINI EXTERN> -88.02162 -16.88647 0.00000 0.00000 0.00000 MINI CONSTR> 26.53186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -43.95648 0.00901 0.17190 0.00011 MINI INTERN> 4.10444 15.22406 0.00000 12.01083 3.08091 MINI EXTERN> -88.03644 -16.88899 0.00000 0.00000 0.00000 MINI CONSTR> 26.54873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9583 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -43.96531 0.00884 0.18342 0.00012 MINI INTERN> 4.10455 15.22083 0.00000 12.00645 3.08014 MINI EXTERN> -88.05150 -16.89146 0.00000 0.00000 0.00000 MINI CONSTR> 26.56569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -43.97365 0.00833 0.20106 0.00012 MINI INTERN> 4.10460 15.21800 0.00000 12.00214 3.07937 MINI EXTERN> -88.06617 -16.89377 0.00000 0.00000 0.00000 MINI CONSTR> 26.58218 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9582 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -43.98167 0.00803 0.19098 0.00013 MINI INTERN> 4.10418 15.21442 0.00000 11.99889 3.07860 MINI EXTERN> -88.07779 -16.89629 0.00000 0.00000 0.00000 MINI CONSTR> 26.59631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -43.99013 0.00845 0.20029 0.00013 MINI INTERN> 4.10451 15.21127 0.00000 11.99467 3.07789 MINI EXTERN> -88.09214 -16.89887 0.00000 0.00000 0.00000 MINI CONSTR> 26.61255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9580 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -43.99881 0.00868 0.20674 0.00014 MINI INTERN> 4.10534 15.20776 0.00000 11.99033 3.07724 MINI EXTERN> -88.10688 -16.90166 0.00000 0.00000 0.00000 MINI CONSTR> 26.62907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -44.00761 0.00881 0.20865 0.00014 MINI INTERN> 4.10639 15.20391 0.00000 11.98602 3.07660 MINI EXTERN> -88.12148 -16.90460 0.00000 0.00000 0.00000 MINI CONSTR> 26.64554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9580 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -44.01896 0.01134 0.06616 0.00006 MINI INTERN> 4.10701 15.19138 0.00000 11.98564 3.07514 MINI EXTERN> -88.12688 -16.91104 0.00000 0.00000 0.00000 MINI CONSTR> 26.65979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -44.02288 0.00393 0.22843 0.00015 MINI INTERN> 4.10683 15.19823 0.00000 11.97837 3.07523 MINI EXTERN> -88.14732 -16.90957 0.00000 0.00000 0.00000 MINI CONSTR> 26.67533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9579 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -44.03111 0.00823 0.23451 0.00016 MINI INTERN> 4.10829 15.19450 0.00000 11.97413 3.07465 MINI EXTERN> -88.16141 -16.91242 0.00000 0.00000 0.00000 MINI CONSTR> 26.69113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -44.03934 0.00823 0.24333 0.00016 MINI INTERN> 4.11027 15.19057 0.00000 11.96970 3.07412 MINI EXTERN> -88.17594 -16.91527 0.00000 0.00000 0.00000 MINI CONSTR> 26.70719 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9579 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -44.04726 0.00792 0.25709 0.00017 MINI INTERN> 4.11238 15.18684 0.00000 11.96521 3.07360 MINI EXTERN> -88.19044 -16.91798 0.00000 0.00000 0.00000 MINI CONSTR> 26.72314 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -44.06053 0.01327 0.08515 0.00007 MINI INTERN> 4.10445 15.17440 0.00000 11.96752 3.07070 MINI EXTERN> -88.18956 -16.92553 0.00000 0.00000 0.00000 MINI CONSTR> 26.73750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9579 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -44.06739 0.00686 0.06046 0.00008 MINI INTERN> 4.10481 15.17278 0.00000 11.96360 3.07040 MINI EXTERN> -88.20164 -16.92707 0.00000 0.00000 0.00000 MINI CONSTR> 26.74971 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -44.07564 0.00825 0.06013 0.00008 MINI INTERN> 4.10443 15.16961 0.00000 11.95987 3.06958 MINI EXTERN> -88.21422 -16.93000 0.00000 0.00000 0.00000 MINI CONSTR> 26.76510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9578 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -44.08392 0.00829 0.06073 0.00008 MINI INTERN> 4.10398 15.16637 0.00000 11.95618 3.06872 MINI EXTERN> -88.22670 -16.93306 0.00000 0.00000 0.00000 MINI CONSTR> 26.78059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -44.09212 0.00820 0.11714 0.00008 MINI INTERN> 4.10131 15.16205 0.00000 11.95413 3.06699 MINI EXTERN> -88.23609 -16.93808 0.00000 0.00000 0.00000 MINI CONSTR> 26.79757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9578 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -44.09989 0.00777 0.07720 0.00009 MINI INTERN> 4.10209 15.15994 0.00000 11.94969 3.06676 MINI EXTERN> -88.24944 -16.93976 0.00000 0.00000 0.00000 MINI CONSTR> 26.81084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -44.10783 0.00794 0.07656 0.00009 MINI INTERN> 4.10146 15.15715 0.00000 11.94615 3.06593 MINI EXTERN> -88.26132 -16.94288 0.00000 0.00000 0.00000 MINI CONSTR> 26.82569 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9578 ATOM PAIRS WERE FOUND FOR ATOM LIST 262 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -44.11580 0.00797 0.08092 0.00009 MINI INTERN> 4.10032 15.15436 0.00000 11.94276 3.06503 MINI EXTERN> -88.27296 -16.94607 0.00000 0.00000 0.00000 MINI CONSTR> 26.84075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -44.12335 0.00755 0.09962 0.00010 MINI INTERN> 4.09905 15.15162 0.00000 11.93992 3.06388 MINI EXTERN> -88.28316 -16.95013 0.00000 0.00000 0.00000 MINI CONSTR> 26.85548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9577 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -44.12923 0.00588 0.14810 0.00010 MINI INTERN> 4.09634 15.14921 0.00000 11.93842 3.06255 MINI EXTERN> -88.29024 -16.95408 0.00000 0.00000 0.00000 MINI CONSTR> 26.86857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -44.13673 0.00749 0.15312 0.00011 MINI INTERN> 4.09452 15.14699 0.00000 11.93529 3.06172 MINI EXTERN> -88.30118 -16.95699 0.00000 0.00000 0.00000 MINI CONSTR> 26.88293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9576 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -44.14366 0.00694 0.17334 0.00011 MINI INTERN> 4.09449 15.14498 0.00000 11.93237 3.06052 MINI EXTERN> -88.31101 -16.96199 0.00000 0.00000 0.00000 MINI CONSTR> 26.89698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -44.15039 0.00673 0.16418 0.00011 MINI INTERN> 4.09259 15.14246 0.00000 11.92945 3.06010 MINI EXTERN> -88.32107 -16.96320 0.00000 0.00000 0.00000 MINI CONSTR> 26.90928 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9576 ATOM PAIRS WERE FOUND FOR ATOM LIST 261 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -44.15717 0.00677 0.17750 0.00012 MINI INTERN> 4.09355 15.14003 0.00000 11.92637 3.05900 MINI EXTERN> -88.33089 -16.96791 0.00000 0.00000 0.00000 MINI CONSTR> 26.92269 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 -44.15717 0.00677 0.17750 0.00014 STPD INTERN> 4.09355 15.14003 0.00000 11.92637 3.05900 STPD EXTERN> -88.33089 -16.96791 0.00000 0.00000 0.00000 STPD CONSTR> 26.92269 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 9576 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9576 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 -44.15717 0.00677 0.17750 0.00000 MINI INTERN> 4.09355 15.14003 0.00000 11.92637 3.05900 MINI EXTERN> -88.33089 -16.96791 0.00000 0.00000 0.00000 MINI CONSTR> 26.92269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -44.81819 0.66102 0.45359 0.13322 MINI INTERN> 4.08787 14.66432 0.00000 11.43735 2.95329 MINI EXTERN> -90.06890 -17.25486 0.00000 0.00000 0.00000 MINI CONSTR> 29.36273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -44.91557 0.09738 0.08722 0.01074 MINI INTERN> 4.08901 14.73251 0.00000 11.35429 2.93457 MINI EXTERN> -90.29881 -17.51533 0.00000 0.00000 0.00000 MINI CONSTR> 29.78820 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -44.95300 0.03743 0.23735 0.02864 MINI INTERN> 3.96814 14.67816 0.00000 11.34080 2.92696 MINI EXTERN> -89.97678 -17.65428 0.00000 0.00000 0.00000 MINI CONSTR> 29.76400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -45.04663 0.09363 0.19046 0.06387 MINI INTERN> 3.96503 14.85221 0.00000 11.27733 2.91443 MINI EXTERN> -89.54285 -18.15995 0.00000 0.00000 0.00000 MINI CONSTR> 29.64717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -45.10028 0.05364 0.14487 0.02304 MINI INTERN> 4.08035 14.87339 0.00000 11.36105 2.92776 MINI EXTERN> -89.57429 -18.36302 0.00000 0.00000 0.00000 MINI CONSTR> 29.59448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -45.11986 0.01958 0.10273 0.00912 MINI INTERN> 4.10415 14.86231 0.00000 11.40650 2.92533 MINI EXTERN> -89.58161 -18.41638 0.00000 0.00000 0.00000 MINI CONSTR> 29.57985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -45.13079 0.01094 0.08489 0.00912 MINI INTERN> 4.07784 14.87456 0.00000 11.43267 2.92706 MINI EXTERN> -89.58857 -18.42572 0.00000 0.00000 0.00000 MINI CONSTR> 29.57138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -45.14237 0.01158 0.08969 0.01090 MINI INTERN> 4.07058 14.89364 0.00000 11.46445 2.91949 MINI EXTERN> -89.62086 -18.43179 0.00000 0.00000 0.00000 MINI CONSTR> 29.56212 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -45.15607 0.01370 0.10103 0.01750 MINI INTERN> 4.06887 14.86879 0.00000 11.51504 2.92123 MINI EXTERN> -89.62347 -18.45044 0.00000 0.00000 0.00000 MINI CONSTR> 29.54391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -45.16552 0.00945 0.07483 0.01076 MINI INTERN> 4.07876 14.82951 0.00000 11.52612 2.92597 MINI EXTERN> -89.63307 -18.42067 0.00000 0.00000 0.00000 MINI CONSTR> 29.52787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -45.17246 0.00694 0.05304 0.00848 MINI INTERN> 4.08381 14.86048 0.00000 11.54707 2.91800 MINI EXTERN> -89.59366 -18.49177 0.00000 0.00000 0.00000 MINI CONSTR> 29.50362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -45.17738 0.00492 0.05009 0.00574 MINI INTERN> 4.07144 14.85694 0.00000 11.55187 2.92885 MINI EXTERN> -89.51794 -18.54875 0.00000 0.00000 0.00000 MINI CONSTR> 29.48021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -45.18121 0.00383 0.05274 0.00647 MINI INTERN> 4.07850 14.84581 0.00000 11.57709 2.92328 MINI EXTERN> -89.47763 -18.58383 0.00000 0.00000 0.00000 MINI CONSTR> 29.45557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -45.18461 0.00339 0.04566 0.00549 MINI INTERN> 4.06224 14.84483 0.00000 11.60544 2.92306 MINI EXTERN> -89.47125 -18.58081 0.00000 0.00000 0.00000 MINI CONSTR> 29.43189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -45.18719 0.00259 0.03606 0.00637 MINI INTERN> 4.06351 14.84319 0.00000 11.61127 2.92471 MINI EXTERN> -89.47123 -18.57145 0.00000 0.00000 0.00000 MINI CONSTR> 29.41281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -45.18928 0.00209 0.03625 0.00426 MINI INTERN> 4.08278 14.85025 0.00000 11.61660 2.91893 MINI EXTERN> -89.47993 -18.57516 0.00000 0.00000 0.00000 MINI CONSTR> 29.39725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -45.19090 0.00162 0.02960 0.00320 MINI INTERN> 4.07777 14.85275 0.00000 11.60414 2.91914 MINI EXTERN> -89.47314 -18.55979 0.00000 0.00000 0.00000 MINI CONSTR> 29.38822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -45.19221 0.00131 0.02523 0.00361 MINI INTERN> 4.07370 14.84335 0.00000 11.60055 2.92024 MINI EXTERN> -89.45407 -18.55974 0.00000 0.00000 0.00000 MINI CONSTR> 29.38376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -45.19312 0.00091 0.02671 0.00319 MINI INTERN> 4.06821 14.82697 0.00000 11.60295 2.91823 MINI EXTERN> -89.44805 -18.54697 0.00000 0.00000 0.00000 MINI CONSTR> 29.38554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -45.19389 0.00077 0.02034 0.00248 MINI INTERN> 4.07633 14.83896 0.00000 11.60265 2.92217 MINI EXTERN> -89.45774 -18.56566 0.00000 0.00000 0.00000 MINI CONSTR> 29.38939 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 -45.19389 0.00077 0.02034 0.02000 CONJ INTERN> 4.07633 14.83896 0.00000 11.60265 2.92217 CONJ EXTERN> -89.45774 -18.56566 0.00000 0.00000 0.00000 CONJ CONSTR> 29.38939 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 ALA 1 HT1 ) 0.20307 ( PROT ALA 1 HT2 ) 0.20307 ( PROT ALA 1 N ) 0.25384 ( PROT ALA 1 HT3 ) 0.20307 ( PROT ALA 1 CA ) 0.25384 ( PROT ALA 1 CB ) 0.20307 ( PROT ALA 1 C ) 0.25384 ( PROT ALA 1 O ) 0.25384 ( PROT LEU 2 N ) 0.25384 ( PROT LEU 2 H ) 0.20307 ( PROT LEU 2 CA ) 0.25384 ( PROT LEU 2 CB ) 0.20307 ( PROT LEU 2 CG ) 0.20307 ( PROT LEU 2 CD1 ) 0.20307 ( PROT LEU 2 CD2 ) 0.20307 ( PROT LEU 2 C ) 0.25384 ( PROT LEU 2 O ) 0.25384 ( PROT GLN 3 N ) 0.25384 ( PROT GLN 3 H ) 0.20307 ( PROT GLN 3 CA ) 0.25384 ( PROT GLN 3 CB ) 0.20307 ( PROT GLN 3 CG ) 0.20307 ( PROT GLN 3 CD ) 0.20307 ( PROT GLN 3 OE1 ) 0.20307 ( PROT GLN 3 NE2 ) 0.20307 ( PROT GLN 3 HE21 ) 0.20307 ( PROT GLN 3 HE22 ) 0.20307 ( PROT GLN 3 C ) 0.25384 ( PROT GLN 3 O ) 0.25384 ( PROT ALA 4 N ) 0.25384 ( PROT ALA 4 H ) 0.20307 ( PROT ALA 4 CA ) 0.25384 ( PROT ALA 4 CB ) 0.20307 ( PROT ALA 4 C ) 0.25384 ( PROT ALA 4 O ) 0.25384 ( PROT PHE 5 N ) 0.25384 ( PROT PHE 5 H ) 0.20307 ( PROT PHE 5 CA ) 0.25384 ( PROT PHE 5 CB ) 0.20307 ( PROT PHE 5 CG ) 0.20307 ( PROT PHE 5 CD1 ) 0.20307 ( PROT PHE 5 CD2 ) 0.20307 ( PROT PHE 5 CE1 ) 0.20307 ( PROT PHE 5 CE2 ) 0.20307 ( PROT PHE 5 CZ ) 0.20307 ( PROT PHE 5 C ) 0.25384 ( PROT PHE 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 ILE 7 N ) 0.25384 ( PROT ILE 7 H ) 0.20307 ( PROT ILE 7 CA ) 0.25384 ( PROT ILE 7 CB ) 0.20307 ( PROT ILE 7 CG2 ) 0.20307 ( PROT ILE 7 CG1 ) 0.20307 ( PROT ILE 7 CD ) 0.20307 ( PROT ILE 7 C ) 0.25384 ( PROT ILE 7 O ) 0.25384 ( PROT ALA 8 N ) 0.25384 ( PROT ALA 8 H ) 0.20307 ( PROT ALA 8 CA ) 0.25384 ( PROT ALA 8 CB ) 0.20307 ( PROT ALA 8 C ) 0.25384 ( PROT ALA 8 O ) 0.25384 ( PROT LEU 9 N ) 0.25384 ( PROT LEU 9 H ) 0.20307 ( PROT LEU 9 CA ) 0.25384 ( PROT LEU 9 CB ) 0.20307 ( PROT LEU 9 CG ) 0.20307 ( PROT LEU 9 CD1 ) 0.20307 ( PROT LEU 9 CD2 ) 0.20307 ( PROT LEU 9 C ) 0.25384 ( PROT LEU 9 O ) 0.25384 ( PROT SER 10 N ) 0.25384 ( PROT SER 10 H ) 0.20307 ( PROT SER 10 CA ) 0.25384 ( PROT SER 10 CB ) 0.20307 ( PROT SER 10 OG ) 0.20307 ( PROT SER 10 HG ) 0.20307 ( PROT SER 10 C ) 0.25384 ( PROT SER 10 O ) 0.25384 ( PROT SER 11 N ) 0.25384 ( PROT SER 11 H ) 0.20307 ( PROT SER 11 CA ) 0.25384 ( PROT SER 11 CB ) 0.20307 ( PROT SER 11 OG ) 0.20307 ( PROT SER 11 HG ) 0.20307 ( PROT SER 11 C ) 0.25384 ( PROT SER 11 O ) 0.25384 ( PROT PHE 12 N ) 0.25384 ( PROT PHE 12 H ) 0.20307 ( PROT PHE 12 CA ) 0.25384 ( PROT PHE 12 CB ) 0.20307 ( PROT PHE 12 CG ) 0.20307 ( PROT PHE 12 CD1 ) 0.20307 ( PROT PHE 12 CD2 ) 0.20307 ( PROT PHE 12 CE1 ) 0.20307 ( PROT PHE 12 CE2 ) 0.20307 ( PROT PHE 12 CZ ) 0.20307 ( PROT PHE 12 C ) 0.25384 ( PROT PHE 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 SER 14 N ) 0.25384 ( PROT SER 14 H ) 0.20307 ( PROT SER 14 CA ) 0.25384 ( PROT SER 14 CB ) 0.20307 ( PROT SER 14 OG ) 0.20307 ( PROT SER 14 HG ) 0.20307 ( PROT SER 14 C ) 0.25384 ( PROT SER 14 O ) 0.25384 ( PROT LYS 15 N ) 0.25384 ( PROT LYS 15 H ) 0.20307 ( PROT LYS 15 CA ) 0.25384 ( PROT LYS 15 CB ) 0.20307 ( PROT LYS 15 CG ) 0.20307 ( PROT LYS 15 CD ) 0.20307 ( PROT LYS 15 CE ) 0.20307 ( PROT LYS 15 NZ ) 0.20307 ( PROT LYS 15 HZ1 ) 0.20307 ( PROT LYS 15 HZ2 ) 0.20307 ( PROT LYS 15 HZ3 ) 0.20307 ( PROT LYS 15 C ) 0.25384 ( PROT LYS 15 O ) 0.25384 ( PROT LEU 16 N ) 0.25384 ( PROT LEU 16 H ) 0.20307 ( PROT LEU 16 CA ) 0.25384 ( PROT LEU 16 CB ) 0.20307 ( PROT LEU 16 CG ) 0.20307 ( PROT LEU 16 CD1 ) 0.20307 ( PROT LEU 16 CD2 ) 0.20307 ( PROT LEU 16 C ) 0.25384 ( PROT LEU 16 O ) 0.25384 ( PROT ALA 17 N ) 0.25384 ( PROT ALA 17 H ) 0.20307 ( PROT ALA 17 CA ) 0.25384 ( PROT ALA 17 CB ) 0.20307 ( PROT ALA 17 C ) 0.25384 ( PROT ALA 17 O ) 0.25384 ( PROT CYS 18 N ) 0.25384 ( PROT CYS 18 H ) 0.20307 ( PROT CYS 18 CA ) 0.25384 ( PROT CYS 18 CB ) 0.20307 ( PROT CYS 18 SG ) 0.20307 ( PROT CYS 18 C ) 0.25384 ( PROT CYS 18 O ) 0.25384 ( PROT GLU 19 N ) 0.25384 ( PROT GLU 19 H ) 0.20307 ( PROT GLU 19 CA ) 0.25384 ( PROT GLU 19 CB ) 0.20307 ( PROT GLU 19 CG ) 0.20307 ( PROT GLU 19 CD ) 0.20307 ( PROT GLU 19 OE1 ) 0.20307 ( PROT GLU 19 OE2 ) 0.20307 ( PROT GLU 19 C ) 0.25384 ( PROT GLU 19 OT1 ) 0.20307 ( PROT GLU 19 OT2 ) 0.20307 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.42802 4.57247 -7.52445 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00668 0.00276 -0.00817 ROTATION MATRIX 1.000000 0.000433 0.000156 -0.000433 1.000000 -0.000259 -0.000156 0.000259 1.000000 AXIS OF ROTATION IS -0.489879 -0.295425 0.820209 ANGLE IS 0.03 TOTAL SQUARE DIFF IS 85.7471 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.714422 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.7144" Parameter: A <- "0.7144" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.96786 4.29742 -7.75486 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.03565 -0.01716 0.02260 ROTATION MATRIX 0.999840 0.013632 0.011618 -0.013371 0.999663 -0.022245 -0.011917 0.022086 0.999685 AXIS OF ROTATION IS -0.777821 -0.412942 0.473785 ANGLE IS 1.63 CENTER OF ROTATION 8.907866 4.313023 -7.791714 SHIFT IS 0.045518 TOTAL SQUARE DIFF IS 6.1498 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.568924 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.7144" RDCMND substituted energy or value "?RMS" to " 0.5689" Parameter: A <- "0.7144 0.5689" 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 0.7144 0.5689 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 29.39" Parameter: H <- "29.39" 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 -74.58328 29.38939 0.28627 ENER INTERN> 4.07633 14.83896 0.00000 11.60265 2.92217 ENER EXTERN> -89.45774 -18.56566 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 " -74.58" Parameter: B <- "-74.58" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -18.57" Parameter: C <- "-18.57" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -89.46" Parameter: C <- " -108.03" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -108.03" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.08" Parameter: D <- "4.08" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.84" Parameter: D <- " 18.92" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.60" Parameter: D <- " 30.52" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.92" Parameter: D <- " 33.44" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 33.44" 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= -74.58 GRMS= 0.29 ELEC= -18.57 VDW= -89.46 RDTITL> *EXTERNAL= -108.03 INTERNAL= 33.44 USER= 0.00 HARM= 29.39 RDTITL> *BOND= 4.08 ANGL= 14.84 DIHE= 11.60 IMPR= 2.92 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 "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= -74.58 GRMS= 0.29 ELEC= -18.57 VDW= -89.46 RDTITL> *EXTERNAL= -108.03 INTERNAL= 33.44 USER= 0.00 HARM= 29.39 RDTITL> *BOND= 4.08 ANGL= 14.84 DIHE= 11.60 IMPR= 2.92 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= -74.58 GRMS= 0.29 ELEC= -18.57 VDW= -89.46 RDTITL> *EXTERNAL= -108.03 INTERNAL= 33.44 USER= 0.00 HARM= 29.39 RDTITL> *BOND= 4.08 ANGL= 14.84 DIHE= 11.60 IMPR= 2.92 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 9600 0.7144 0.5689 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "9600" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9576 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9557 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 -54.97623 -19.60705 0.10688 0.02000 MINI INTERN> 4.07633 14.83896 0.00000 11.60265 2.92217 MINI EXTERN> -89.45774 -18.56566 0.00000 0.00000 0.00000 MINI CONSTR> 19.60705 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -54.90999 -0.06624 1.60234 0.00150 MINI INTERN> 4.49574 15.25865 0.00000 11.87336 2.93241 MINI EXTERN> -92.53831 -17.31810 0.00000 0.00000 0.00000 MINI CONSTR> 20.38626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9549 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -55.24427 0.33427 0.65047 0.00065 MINI INTERN> 4.26593 15.05351 0.00000 11.85360 2.92263 MINI EXTERN> -92.09108 -17.61932 0.00000 0.00000 0.00000 MINI CONSTR> 20.37048 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -55.31837 0.07410 0.32392 0.00028 MINI INTERN> 4.22215 14.94079 0.00000 11.79436 2.92394 MINI EXTERN> -91.75338 -17.82481 0.00000 0.00000 0.00000 MINI CONSTR> 20.37858 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9549 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -55.34545 0.02708 0.12850 0.00012 MINI INTERN> 4.18294 14.91750 0.00000 11.78071 2.92269 MINI EXTERN> -91.62187 -17.91350 0.00000 0.00000 0.00000 MINI CONSTR> 20.38609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -55.35989 0.01444 0.11928 0.00013 MINI INTERN> 4.17049 14.89683 0.00000 11.75975 2.92406 MINI EXTERN> -91.53093 -17.97635 0.00000 0.00000 0.00000 MINI CONSTR> 20.39625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9549 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -55.37068 0.01079 0.19358 0.00013 MINI INTERN> 4.16352 14.88158 0.00000 11.74069 2.92494 MINI EXTERN> -91.47007 -18.01947 0.00000 0.00000 0.00000 MINI CONSTR> 20.40812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -55.38239 0.01171 0.20288 0.00013 MINI INTERN> 4.15708 14.86825 0.00000 11.72445 2.92586 MINI EXTERN> -91.42199 -18.05739 0.00000 0.00000 0.00000 MINI CONSTR> 20.42134 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9548 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -55.39295 0.01055 0.22311 0.00014 MINI INTERN> 4.15521 14.85598 0.00000 11.71023 2.92626 MINI EXTERN> -91.38819 -18.08789 0.00000 0.00000 0.00000 MINI CONSTR> 20.43545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -55.40280 0.00985 0.21068 0.00014 MINI INTERN> 4.14974 14.84855 0.00000 11.70006 2.92679 MINI EXTERN> -91.36570 -18.11053 0.00000 0.00000 0.00000 MINI CONSTR> 20.44827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9547 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -55.41298 0.01018 0.22027 0.00015 MINI INTERN> 4.14937 14.83926 0.00000 11.68874 2.92685 MINI EXTERN> -91.34852 -18.13233 0.00000 0.00000 0.00000 MINI CONSTR> 20.46364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -55.42591 0.01292 0.07116 0.00006 MINI INTERN> 4.14034 14.83149 0.00000 11.68560 2.92687 MINI EXTERN> -91.32079 -18.16666 0.00000 0.00000 0.00000 MINI CONSTR> 20.47725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9547 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -55.43062 0.00472 0.23724 0.00016 MINI INTERN> 4.14445 14.82734 0.00000 11.67094 2.92717 MINI EXTERN> -91.33484 -18.15845 0.00000 0.00000 0.00000 MINI CONSTR> 20.49277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -55.43999 0.00936 0.24518 0.00017 MINI INTERN> 4.14619 14.81975 0.00000 11.66241 2.92678 MINI EXTERN> -91.33293 -18.17105 0.00000 0.00000 0.00000 MINI CONSTR> 20.50887 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9546 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -55.45340 0.01341 0.07632 0.00007 MINI INTERN> 4.13537 14.81403 0.00000 11.66217 2.92655 MINI EXTERN> -91.31271 -18.20193 0.00000 0.00000 0.00000 MINI CONSTR> 20.52312 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -55.46130 0.00790 0.06486 0.00007 MINI INTERN> 4.13438 14.80973 0.00000 11.65560 2.92636 MINI EXTERN> -91.31759 -18.20654 0.00000 0.00000 0.00000 MINI CONSTR> 20.53675 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9546 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -55.46993 0.00863 0.06609 0.00008 MINI INTERN> 4.13373 14.80475 0.00000 11.64929 2.92599 MINI EXTERN> -91.32236 -18.21353 0.00000 0.00000 0.00000 MINI CONSTR> 20.55218 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -55.47829 0.00836 0.06725 0.00008 MINI INTERN> 4.13263 14.80038 0.00000 11.64343 2.92565 MINI EXTERN> -91.32871 -18.21907 0.00000 0.00000 0.00000 MINI CONSTR> 20.56740 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9545 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -55.48684 0.00855 0.10892 0.00008 MINI INTERN> 4.13175 14.79550 0.00000 11.63853 2.92512 MINI EXTERN> -91.33277 -18.22935 0.00000 0.00000 0.00000 MINI CONSTR> 20.58438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -55.49427 0.00743 0.06348 0.00009 MINI INTERN> 4.13150 14.79215 0.00000 11.63238 2.92483 MINI EXTERN> -91.34573 -18.22634 0.00000 0.00000 0.00000 MINI CONSTR> 20.59694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9545 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -55.50260 0.00833 0.12906 0.00009 MINI INTERN> 4.12984 14.78786 0.00000 11.62843 2.92427 MINI EXTERN> -91.34989 -18.23794 0.00000 0.00000 0.00000 MINI CONSTR> 20.61482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -55.51101 0.00840 0.08709 0.00009 MINI INTERN> 4.13103 14.78333 0.00000 11.62224 2.92368 MINI EXTERN> -91.36418 -18.23632 0.00000 0.00000 0.00000 MINI CONSTR> 20.62923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9544 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -55.51858 0.00758 0.10804 0.00010 MINI INTERN> 4.12976 14.77994 0.00000 11.61803 2.92321 MINI EXTERN> -91.37284 -18.24123 0.00000 0.00000 0.00000 MINI CONSTR> 20.64454 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -55.52533 0.00674 0.14741 0.00010 MINI INTERN> 4.12882 14.77684 0.00000 11.61439 2.92273 MINI EXTERN> -91.38060 -18.24691 0.00000 0.00000 0.00000 MINI CONSTR> 20.65940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9543 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -55.53347 0.00814 0.14530 0.00010 MINI INTERN> 4.12933 14.77267 0.00000 11.60930 2.92208 MINI EXTERN> -91.39330 -18.24871 0.00000 0.00000 0.00000 MINI CONSTR> 20.67516 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -55.54161 0.00813 0.11814 0.00011 MINI INTERN> 4.12749 14.76994 0.00000 11.60404 2.92174 MINI EXTERN> -91.40783 -18.24686 0.00000 0.00000 0.00000 MINI CONSTR> 20.68987 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9542 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -55.54759 0.00599 0.16034 0.00011 MINI INTERN> 4.12731 14.76700 0.00000 11.60100 2.92119 MINI EXTERN> -91.41535 -18.25260 0.00000 0.00000 0.00000 MINI CONSTR> 20.70385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -55.55469 0.00710 0.18979 0.00012 MINI INTERN> 4.13099 14.76189 0.00000 11.59630 2.92023 MINI EXTERN> -91.42782 -18.25585 0.00000 0.00000 0.00000 MINI CONSTR> 20.71957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9542 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -55.56176 0.00707 0.17391 0.00012 MINI INTERN> 4.12810 14.76006 0.00000 11.59260 2.91996 MINI EXTERN> -91.43860 -18.25680 0.00000 0.00000 0.00000 MINI CONSTR> 20.73291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -55.56907 0.00731 0.18707 0.00012 MINI INTERN> 4.12519 14.75835 0.00000 11.58814 2.91971 MINI EXTERN> -91.45189 -18.25696 0.00000 0.00000 0.00000 MINI CONSTR> 20.74838 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9540 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -55.57838 0.00931 0.06075 0.00005 MINI INTERN> 4.13033 14.75250 0.00000 11.57955 2.91889 MINI EXTERN> -91.47835 -18.24280 0.00000 0.00000 0.00000 MINI CONSTR> 20.76151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -55.58241 0.00403 0.19610 0.00013 MINI INTERN> 4.12697 14.75151 0.00000 11.58047 2.91837 MINI EXTERN> -91.47407 -18.26178 0.00000 0.00000 0.00000 MINI CONSTR> 20.77612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9538 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -55.59268 0.01026 0.05912 0.00006 MINI INTERN> 4.13011 14.74635 0.00000 11.57111 2.91776 MINI EXTERN> -91.50356 -18.24494 0.00000 0.00000 0.00000 MINI CONSTR> 20.79050 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -55.59611 0.00343 0.21392 0.00014 MINI INTERN> 4.12791 14.74523 0.00000 11.57211 2.91713 MINI EXTERN> -91.49896 -18.26484 0.00000 0.00000 0.00000 MINI CONSTR> 20.80533 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9537 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -55.60235 0.00625 0.23906 0.00015 MINI INTERN> 4.12286 14.74533 0.00000 11.56758 2.91730 MINI EXTERN> -91.51386 -18.26138 0.00000 0.00000 0.00000 MINI CONSTR> 20.81980 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -55.61319 0.01084 0.06960 0.00006 MINI INTERN> 4.13095 14.73736 0.00000 11.55821 2.91607 MINI EXTERN> -91.54286 -18.24577 0.00000 0.00000 0.00000 MINI CONSTR> 20.83286 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9537 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -55.61510 0.00191 0.23376 0.00016 MINI INTERN> 4.12468 14.73886 0.00000 11.56095 2.91588 MINI EXTERN> -91.53329 -18.26845 0.00000 0.00000 0.00000 MINI CONSTR> 20.84627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -55.62664 0.01154 0.07921 0.00007 MINI INTERN> 4.13152 14.73158 0.00000 11.54967 2.91493 MINI EXTERN> -91.56907 -18.24629 0.00000 0.00000 0.00000 MINI CONSTR> 20.86101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9535 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -55.63249 0.00585 0.05532 0.00007 MINI INTERN> 4.12975 14.72976 0.00000 11.54733 2.91453 MINI EXTERN> -91.57600 -18.25042 0.00000 0.00000 0.00000 MINI CONSTR> 20.87255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -55.63952 0.00703 0.05567 0.00007 MINI INTERN> 4.12996 14.72679 0.00000 11.54300 2.91393 MINI EXTERN> -91.58923 -18.25122 0.00000 0.00000 0.00000 MINI CONSTR> 20.88724 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9535 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -55.64652 0.00700 0.10377 0.00008 MINI INTERN> 4.13260 14.72317 0.00000 11.53666 2.91322 MINI EXTERN> -91.60907 -18.24655 0.00000 0.00000 0.00000 MINI CONSTR> 20.90346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -55.65291 0.00639 0.07712 0.00008 MINI INTERN> 4.13202 14.72058 0.00000 11.53380 2.91266 MINI EXTERN> -91.61742 -18.25045 0.00000 0.00000 0.00000 MINI CONSTR> 20.91590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9535 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -55.65891 0.00601 0.08979 0.00008 MINI INTERN> 4.13225 14.71824 0.00000 11.52949 2.91218 MINI EXTERN> -91.63071 -18.24939 0.00000 0.00000 0.00000 MINI CONSTR> 20.92902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -55.66522 0.00630 0.08526 0.00009 MINI INTERN> 4.13216 14.71574 0.00000 11.52575 2.91164 MINI EXTERN> -91.64196 -18.25073 0.00000 0.00000 0.00000 MINI CONSTR> 20.94220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9534 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -55.67051 0.00529 0.13053 0.00009 MINI INTERN> 4.13456 14.71290 0.00000 11.52069 2.91104 MINI EXTERN> -91.65760 -18.24750 0.00000 0.00000 0.00000 MINI CONSTR> 20.95540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -55.67692 0.00641 0.12861 0.00009 MINI INTERN> 4.13521 14.70999 0.00000 11.51681 2.91039 MINI EXTERN> -91.66911 -18.24912 0.00000 0.00000 0.00000 MINI CONSTR> 20.96891 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9533 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -55.68332 0.00640 0.10512 0.00010 MINI INTERN> 4.13207 14.70887 0.00000 11.51381 2.91012 MINI EXTERN> -91.67802 -18.25164 0.00000 0.00000 0.00000 MINI CONSTR> 20.98147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -55.68803 0.00471 0.14214 0.00010 MINI INTERN> 4.13476 14.70608 0.00000 11.50924 2.90953 MINI EXTERN> -91.69194 -18.24912 0.00000 0.00000 0.00000 MINI CONSTR> 20.99343 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9533 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -55.69355 0.00552 0.17026 0.00010 MINI INTERN> 4.13910 14.70181 0.00000 11.50506 2.90857 MINI EXTERN> -91.70390 -18.25092 0.00000 0.00000 0.00000 MINI CONSTR> 21.00674 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -55.69913 0.00558 0.15496 0.00011 MINI INTERN> 4.13732 14.70058 0.00000 11.50156 2.90831 MINI EXTERN> -91.71443 -18.25048 0.00000 0.00000 0.00000 MINI CONSTR> 21.01800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9533 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -55.70476 0.00564 0.16881 0.00011 MINI INTERN> 4.13300 14.70069 0.00000 11.49826 2.90824 MINI EXTERN> -91.72444 -18.25135 0.00000 0.00000 0.00000 MINI CONSTR> 21.03083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -55.71043 0.00566 0.15920 0.00011 MINI INTERN> 4.13743 14.69630 0.00000 11.49406 2.90731 MINI EXTERN> -91.73639 -18.25182 0.00000 0.00000 0.00000 MINI CONSTR> 21.04270 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9533 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -55.71770 0.00727 0.05395 0.00005 MINI INTERN> 4.12873 14.69665 0.00000 11.49441 2.90734 MINI EXTERN> -91.73370 -18.26498 0.00000 0.00000 0.00000 MINI CONSTR> 21.05385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -55.72067 0.00297 0.18096 0.00012 MINI INTERN> 4.13915 14.69180 0.00000 11.48642 2.90625 MINI EXTERN> -91.75857 -18.25212 0.00000 0.00000 0.00000 MINI CONSTR> 21.06641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9532 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -55.72606 0.00539 0.19544 0.00013 MINI INTERN> 4.13437 14.69226 0.00000 11.48325 2.90623 MINI EXTERN> -91.76795 -18.25318 0.00000 0.00000 0.00000 MINI CONSTR> 21.07895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -55.73427 0.00821 0.06059 0.00006 MINI INTERN> 4.12853 14.69049 0.00000 11.48366 2.90590 MINI EXTERN> -91.76420 -18.26872 0.00000 0.00000 0.00000 MINI CONSTR> 21.09009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -55.73617 0.00191 0.20053 0.00014 MINI INTERN> 4.13824 14.68674 0.00000 11.47541 2.90497 MINI EXTERN> -91.79028 -18.25306 0.00000 0.00000 0.00000 MINI CONSTR> 21.10181 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -55.74507 0.00889 0.06530 0.00006 MINI INTERN> 4.12845 14.68650 0.00000 11.47650 2.90495 MINI EXTERN> -91.78422 -18.27111 0.00000 0.00000 0.00000 MINI CONSTR> 21.11386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -55.74981 0.00475 0.05010 0.00006 MINI INTERN> 4.12915 14.68453 0.00000 11.47283 2.90446 MINI EXTERN> -91.79482 -18.26990 0.00000 0.00000 0.00000 MINI CONSTR> 21.12394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -55.75523 0.00542 0.05221 0.00006 MINI INTERN> 4.12929 14.68243 0.00000 11.46924 2.90396 MINI EXTERN> -91.80466 -18.27141 0.00000 0.00000 0.00000 MINI CONSTR> 21.13592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -55.76055 0.00531 0.08682 0.00007 MINI INTERN> 4.12771 14.68114 0.00000 11.46625 2.90364 MINI EXTERN> -91.81222 -18.27571 0.00000 0.00000 0.00000 MINI CONSTR> 21.14864 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -55.76520 0.00465 0.05046 0.00007 MINI INTERN> 4.12955 14.67869 0.00000 11.46233 2.90303 MINI EXTERN> -91.82363 -18.27306 0.00000 0.00000 0.00000 MINI CONSTR> 21.15789 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -55.77032 0.00513 0.10177 0.00007 MINI INTERN> 4.12833 14.67724 0.00000 11.45958 2.90269 MINI EXTERN> -91.83007 -18.27895 0.00000 0.00000 0.00000 MINI CONSTR> 21.17085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -55.77550 0.00518 0.07346 0.00007 MINI INTERN> 4.12782 14.67576 0.00000 11.45566 2.90228 MINI EXTERN> -91.84132 -18.27704 0.00000 0.00000 0.00000 MINI CONSTR> 21.18133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -55.77984 0.00434 0.11136 0.00008 MINI INTERN> 4.12787 14.67405 0.00000 11.45305 2.90187 MINI EXTERN> -91.84748 -18.28164 0.00000 0.00000 0.00000 MINI CONSTR> 21.19245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -55.78536 0.00552 0.06981 0.00008 MINI INTERN> 4.12821 14.67203 0.00000 11.44870 2.90134 MINI EXTERN> -91.85991 -18.27894 0.00000 0.00000 0.00000 MINI CONSTR> 21.20320 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -55.78958 0.00422 0.11963 0.00008 MINI INTERN> 4.12827 14.67036 0.00000 11.44612 2.90096 MINI EXTERN> -91.86573 -18.28415 0.00000 0.00000 0.00000 MINI CONSTR> 21.21458 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -55.79442 0.00485 0.12989 0.00009 MINI INTERN> 4.12648 14.66966 0.00000 11.44252 2.90075 MINI EXTERN> -91.87549 -18.28424 0.00000 0.00000 0.00000 MINI CONSTR> 21.22590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -55.79887 0.00445 0.13663 0.00009 MINI INTERN> 4.12822 14.66710 0.00000 11.43949 2.90013 MINI EXTERN> -91.88282 -18.28732 0.00000 0.00000 0.00000 MINI CONSTR> 21.23633 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -55.80350 0.00463 0.13037 0.00009 MINI INTERN> 4.12742 14.66590 0.00000 11.43620 2.89979 MINI EXTERN> -91.89155 -18.28764 0.00000 0.00000 0.00000 MINI CONSTR> 21.24639 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -55.80803 0.00453 0.15589 0.00010 MINI INTERN> 4.13095 14.66253 0.00000 11.43241 2.89903 MINI EXTERN> -91.90095 -18.28988 0.00000 0.00000 0.00000 MINI CONSTR> 21.25789 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -55.81255 0.00453 0.14214 0.00010 MINI INTERN> 4.12859 14.66212 0.00000 11.42954 2.89885 MINI EXTERN> -91.90838 -18.29073 0.00000 0.00000 0.00000 MINI CONSTR> 21.26745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -55.81727 0.00472 0.15273 0.00010 MINI INTERN> 4.12667 14.66160 0.00000 11.42582 2.89867 MINI EXTERN> -91.91826 -18.29041 0.00000 0.00000 0.00000 MINI CONSTR> 21.27865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -55.82324 0.00597 0.04907 0.00004 MINI INTERN> 4.13090 14.65767 0.00000 11.42050 2.89744 MINI EXTERN> -91.93387 -18.28372 0.00000 0.00000 0.00000 MINI CONSTR> 21.28785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 266 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -55.82573 0.00250 0.15965 0.00011 MINI INTERN> 4.12793 14.65795 0.00000 11.41977 2.89773 MINI EXTERN> -91.93294 -18.29459 0.00000 0.00000 0.00000 MINI CONSTR> 21.29842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -55.83238 0.00664 0.04944 0.00005 MINI INTERN> 4.13101 14.65448 0.00000 11.41376 2.89655 MINI EXTERN> -91.95076 -18.28601 0.00000 0.00000 0.00000 MINI CONSTR> 21.30860 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -55.83445 0.00208 0.17140 0.00012 MINI INTERN> 4.12805 14.65493 0.00000 11.41309 2.89695 MINI EXTERN> -91.94949 -18.29706 0.00000 0.00000 0.00000 MINI CONSTR> 21.31906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -55.83869 0.00423 0.19122 0.00012 MINI INTERN> 4.13387 14.65059 0.00000 11.40902 2.89593 MINI EXTERN> -91.95946 -18.29834 0.00000 0.00000 0.00000 MINI CONSTR> 21.32970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -55.84574 0.00705 0.05866 0.00005 MINI INTERN> 4.13140 14.64985 0.00000 11.40355 2.89517 MINI EXTERN> -91.97618 -18.28879 0.00000 0.00000 0.00000 MINI CONSTR> 21.33926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -55.84964 0.00390 0.04533 0.00005 MINI INTERN> 4.13104 14.64854 0.00000 11.40105 2.89489 MINI EXTERN> -91.98184 -18.29117 0.00000 0.00000 0.00000 MINI CONSTR> 21.34785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9531 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -55.85406 0.00443 0.04714 0.00006 MINI INTERN> 4.13094 14.64715 0.00000 11.39764 2.89446 MINI EXTERN> -91.99020 -18.29207 0.00000 0.00000 0.00000 MINI CONSTR> 21.35802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -55.85825 0.00418 0.04898 0.00006 MINI INTERN> 4.13130 14.64559 0.00000 11.39439 2.89400 MINI EXTERN> -91.99810 -18.29307 0.00000 0.00000 0.00000 MINI CONSTR> 21.36765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9530 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -55.86256 0.00431 0.07893 0.00006 MINI INTERN> 4.13214 14.64403 0.00000 11.39034 2.89338 MINI EXTERN> -92.00846 -18.29237 0.00000 0.00000 0.00000 MINI CONSTR> 21.37839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -55.86639 0.00383 0.04523 0.00006 MINI INTERN> 4.13132 14.64281 0.00000 11.38832 2.89321 MINI EXTERN> -92.01241 -18.29593 0.00000 0.00000 0.00000 MINI CONSTR> 21.38628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9529 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -55.87065 0.00426 0.09388 0.00007 MINI INTERN> 4.13318 14.64095 0.00000 11.38378 2.89241 MINI EXTERN> -92.02418 -18.29435 0.00000 0.00000 0.00000 MINI CONSTR> 21.39756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -55.87498 0.00433 0.06603 0.00007 MINI INTERN> 4.13109 14.64033 0.00000 11.38126 2.89231 MINI EXTERN> -92.02959 -18.29694 0.00000 0.00000 0.00000 MINI CONSTR> 21.40657 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9529 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -55.87851 0.00353 0.10203 0.00007 MINI INTERN> 4.13310 14.63852 0.00000 11.37751 2.89160 MINI EXTERN> -92.03903 -18.29626 0.00000 0.00000 0.00000 MINI CONSTR> 21.41605 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -55.88314 0.00463 0.06048 0.00007 MINI INTERN> 4.13177 14.63728 0.00000 11.37500 2.89141 MINI EXTERN> -92.04404 -18.29984 0.00000 0.00000 0.00000 MINI CONSTR> 21.42529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9529 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -55.88679 0.00365 0.11158 0.00008 MINI INTERN> 4.13316 14.63589 0.00000 11.37095 2.89069 MINI EXTERN> -92.05421 -18.29894 0.00000 0.00000 0.00000 MINI CONSTR> 21.43567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -55.89097 0.00418 0.11370 0.00008 MINI INTERN> 4.13270 14.63481 0.00000 11.36771 2.89030 MINI EXTERN> -92.06159 -18.30037 0.00000 0.00000 0.00000 MINI CONSTR> 21.44547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9529 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -55.89497 0.00401 0.12468 0.00008 MINI INTERN> 4.13444 14.63263 0.00000 11.36438 2.88968 MINI EXTERN> -92.06899 -18.30237 0.00000 0.00000 0.00000 MINI CONSTR> 21.45525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -55.89859 0.00362 0.13274 0.00008 MINI INTERN> 4.13238 14.63274 0.00000 11.36131 2.88949 MINI EXTERN> -92.07631 -18.30240 0.00000 0.00000 0.00000 MINI CONSTR> 21.46420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9529 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -55.90236 0.00376 0.12547 0.00009 MINI INTERN> 4.13405 14.63054 0.00000 11.35844 2.88895 MINI EXTERN> -92.08258 -18.30430 0.00000 0.00000 0.00000 MINI CONSTR> 21.47254 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -55.90611 0.00376 0.13827 0.00009 MINI INTERN> 4.13066 14.63118 0.00000 11.35556 2.88898 MINI EXTERN> -92.08905 -18.30529 0.00000 0.00000 0.00000 MINI CONSTR> 21.48185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9528 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -55.90992 0.00381 0.12933 0.00009 MINI INTERN> 4.13367 14.62842 0.00000 11.35233 2.88819 MINI EXTERN> -92.09628 -18.30667 0.00000 0.00000 0.00000 MINI CONSTR> 21.49043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -55.91487 0.00495 0.04374 0.00004 MINI INTERN> 4.13161 14.62684 0.00000 11.35056 2.88843 MINI EXTERN> -92.09844 -18.31257 0.00000 0.00000 0.00000 MINI CONSTR> 21.49871 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9528 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -55.91693 0.00207 0.14777 0.00010 MINI INTERN> 4.13482 14.62580 0.00000 11.34622 2.88726 MINI EXTERN> -92.10984 -18.30911 0.00000 0.00000 0.00000 MINI CONSTR> 21.50792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -55.92047 0.00353 0.16431 0.00011 MINI INTERN> 4.13050 14.62698 0.00000 11.34350 2.88747 MINI EXTERN> -92.11578 -18.31011 0.00000 0.00000 0.00000 MINI CONSTR> 21.51698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9528 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -55.92381 0.00334 0.17306 0.00011 MINI INTERN> 4.13764 14.62223 0.00000 11.34022 2.88626 MINI EXTERN> -92.12250 -18.31303 0.00000 0.00000 0.00000 MINI CONSTR> 21.52539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -55.92961 0.00580 0.04984 0.00005 MINI INTERN> 4.13185 14.62205 0.00000 11.33864 2.88694 MINI EXTERN> -92.12430 -18.31820 0.00000 0.00000 0.00000 MINI CONSTR> 21.53341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9528 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -55.93290 0.00329 0.04185 0.00005 MINI INTERN> 4.13208 14.62097 0.00000 11.33589 2.88651 MINI EXTERN> -92.13038 -18.31895 0.00000 0.00000 0.00000 MINI CONSTR> 21.54098 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 -55.93290 0.00329 0.04185 0.00006 STPD INTERN> 4.13208 14.62097 0.00000 11.33589 2.88651 STPD EXTERN> -92.13038 -18.31895 0.00000 0.00000 0.00000 STPD CONSTR> 21.54098 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 9528 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9528 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 -55.93290 0.00329 0.04185 0.00000 MINI INTERN> 4.13208 14.62097 0.00000 11.33589 2.88651 MINI EXTERN> -92.13038 -18.31895 0.00000 0.00000 0.00000 MINI CONSTR> 21.54098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -56.29909 0.36618 0.48635 0.06953 MINI INTERN> 4.11435 14.36865 0.00000 10.80546 2.82256 MINI EXTERN> -93.33955 -18.35772 0.00000 0.00000 0.00000 MINI CONSTR> 23.28716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -56.36944 0.07035 0.13454 0.02651 MINI INTERN> 4.17601 14.40950 0.00000 10.68547 2.80697 MINI EXTERN> -93.56761 -18.51965 0.00000 0.00000 0.00000 MINI CONSTR> 23.63988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -56.37538 0.00594 0.07078 0.00317 MINI INTERN> 4.17318 14.41733 0.00000 10.67702 2.80861 MINI EXTERN> -93.55511 -18.55487 0.00000 0.00000 0.00000 MINI CONSTR> 23.65848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -56.39672 0.02134 0.21441 0.02107 MINI INTERN> 4.10027 14.29746 0.00000 10.65207 2.80189 MINI EXTERN> -93.35663 -18.53230 0.00000 0.00000 0.00000 MINI CONSTR> 23.64052 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -56.44638 0.04966 0.26501 0.04196 MINI INTERN> 4.06808 14.35376 0.00000 10.56661 2.79224 MINI EXTERN> -93.00604 -18.78050 0.00000 0.00000 0.00000 MINI CONSTR> 23.55947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -56.47846 0.03208 0.19437 0.02197 MINI INTERN> 4.11146 14.41651 0.00000 10.54747 2.80163 MINI EXTERN> -92.87280 -18.99153 0.00000 0.00000 0.00000 MINI CONSTR> 23.50880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -56.50436 0.02590 0.17583 0.01711 MINI INTERN> 4.13512 14.49955 0.00000 10.50526 2.80822 MINI EXTERN> -92.91255 -19.01720 0.00000 0.00000 0.00000 MINI CONSTR> 23.47724 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -56.51528 0.01092 0.10209 0.00767 MINI INTERN> 4.18084 14.52403 0.00000 10.48935 2.80482 MINI EXTERN> -92.90665 -19.06867 0.00000 0.00000 0.00000 MINI CONSTR> 23.46100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -56.52356 0.00828 0.08787 0.00838 MINI INTERN> 4.17299 14.53613 0.00000 10.48497 2.78849 MINI EXTERN> -92.88076 -19.07388 0.00000 0.00000 0.00000 MINI CONSTR> 23.44850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -56.53003 0.00647 0.08754 0.00714 MINI INTERN> 4.13994 14.52718 0.00000 10.47512 2.78923 MINI EXTERN> -92.85902 -19.04462 0.00000 0.00000 0.00000 MINI CONSTR> 23.44214 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -56.53773 0.00771 0.09710 0.01032 MINI INTERN> 4.14938 14.51477 0.00000 10.45590 2.78285 MINI EXTERN> -92.83548 -19.03981 0.00000 0.00000 0.00000 MINI CONSTR> 23.43465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -56.54399 0.00625 0.09012 0.00629 MINI INTERN> 4.14533 14.54019 0.00000 10.44714 2.79254 MINI EXTERN> -92.84234 -19.05577 0.00000 0.00000 0.00000 MINI CONSTR> 23.42893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -56.55110 0.00711 0.09544 0.00931 MINI INTERN> 4.15395 14.47987 0.00000 10.44859 2.78591 MINI EXTERN> -92.84290 -19.00347 0.00000 0.00000 0.00000 MINI CONSTR> 23.42694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -56.55757 0.00647 0.07475 0.00723 MINI INTERN> 4.13577 14.45986 0.00000 10.44030 2.78882 MINI EXTERN> -92.82859 -18.97975 0.00000 0.00000 0.00000 MINI CONSTR> 23.42601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -56.56224 0.00467 0.06397 0.00766 MINI INTERN> 4.14668 14.45742 0.00000 10.45349 2.77965 MINI EXTERN> -92.78302 -19.03718 0.00000 0.00000 0.00000 MINI CONSTR> 23.42071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -56.56510 0.00286 0.04912 0.00414 MINI INTERN> 4.13065 14.47092 0.00000 10.44640 2.78814 MINI EXTERN> -92.77145 -19.04946 0.00000 0.00000 0.00000 MINI CONSTR> 23.41969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -56.56738 0.00228 0.04990 0.00402 MINI INTERN> 4.14049 14.45383 0.00000 10.45886 2.78763 MINI EXTERN> -92.74467 -19.08025 0.00000 0.00000 0.00000 MINI CONSTR> 23.41673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -56.56955 0.00217 0.05003 0.00426 MINI INTERN> 4.13800 14.46234 0.00000 10.47454 2.79475 MINI EXTERN> -92.75100 -19.10054 0.00000 0.00000 0.00000 MINI CONSTR> 23.41235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -56.57182 0.00227 0.05297 0.00431 MINI INTERN> 4.13737 14.45148 0.00000 10.49693 2.79792 MINI EXTERN> -92.76771 -19.09558 0.00000 0.00000 0.00000 MINI CONSTR> 23.40777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -56.57366 0.00184 0.04371 0.00390 MINI INTERN> 4.13786 14.43882 0.00000 10.50682 2.80529 MINI EXTERN> -92.77851 -19.08774 0.00000 0.00000 0.00000 MINI CONSTR> 23.40381 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 -56.57366 0.00184 0.04371 0.02000 CONJ INTERN> 4.13786 14.43882 0.00000 10.50682 2.80529 CONJ EXTERN> -92.77851 -19.08774 0.00000 0.00000 0.00000 CONJ CONSTR> 23.40381 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 ALA 1 HT1 ) 0.13199 ( PROT ALA 1 HT2 ) 0.13199 ( PROT ALA 1 N ) 0.16499 ( PROT ALA 1 HT3 ) 0.13199 ( PROT ALA 1 CA ) 0.16499 ( PROT ALA 1 CB ) 0.13199 ( PROT ALA 1 C ) 0.16499 ( PROT ALA 1 O ) 0.16499 ( PROT LEU 2 N ) 0.16499 ( PROT LEU 2 H ) 0.13199 ( PROT LEU 2 CA ) 0.16499 ( PROT LEU 2 CB ) 0.13199 ( PROT LEU 2 CG ) 0.13199 ( PROT LEU 2 CD1 ) 0.13199 ( PROT LEU 2 CD2 ) 0.13199 ( PROT LEU 2 C ) 0.16499 ( PROT LEU 2 O ) 0.16499 ( PROT GLN 3 N ) 0.16499 ( PROT GLN 3 H ) 0.13199 ( PROT GLN 3 CA ) 0.16499 ( PROT GLN 3 CB ) 0.13199 ( PROT GLN 3 CG ) 0.13199 ( PROT GLN 3 CD ) 0.13199 ( PROT GLN 3 OE1 ) 0.13199 ( PROT GLN 3 NE2 ) 0.13199 ( PROT GLN 3 HE21 ) 0.13199 ( PROT GLN 3 HE22 ) 0.13199 ( PROT GLN 3 C ) 0.16499 ( PROT GLN 3 O ) 0.16499 ( PROT ALA 4 N ) 0.16499 ( PROT ALA 4 H ) 0.13199 ( PROT ALA 4 CA ) 0.16499 ( PROT ALA 4 CB ) 0.13199 ( PROT ALA 4 C ) 0.16499 ( PROT ALA 4 O ) 0.16499 ( PROT PHE 5 N ) 0.16499 ( PROT PHE 5 H ) 0.13199 ( PROT PHE 5 CA ) 0.16499 ( PROT PHE 5 CB ) 0.13199 ( PROT PHE 5 CG ) 0.13199 ( PROT PHE 5 CD1 ) 0.13199 ( PROT PHE 5 CD2 ) 0.13199 ( PROT PHE 5 CE1 ) 0.13199 ( PROT PHE 5 CE2 ) 0.13199 ( PROT PHE 5 CZ ) 0.13199 ( PROT PHE 5 C ) 0.16499 ( PROT PHE 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 ILE 7 N ) 0.16499 ( PROT ILE 7 H ) 0.13199 ( PROT ILE 7 CA ) 0.16499 ( PROT ILE 7 CB ) 0.13199 ( PROT ILE 7 CG2 ) 0.13199 ( PROT ILE 7 CG1 ) 0.13199 ( PROT ILE 7 CD ) 0.13199 ( PROT ILE 7 C ) 0.16499 ( PROT ILE 7 O ) 0.16499 ( PROT ALA 8 N ) 0.16499 ( PROT ALA 8 H ) 0.13199 ( PROT ALA 8 CA ) 0.16499 ( PROT ALA 8 CB ) 0.13199 ( PROT ALA 8 C ) 0.16499 ( PROT ALA 8 O ) 0.16499 ( PROT LEU 9 N ) 0.16499 ( PROT LEU 9 H ) 0.13199 ( PROT LEU 9 CA ) 0.16499 ( PROT LEU 9 CB ) 0.13199 ( PROT LEU 9 CG ) 0.13199 ( PROT LEU 9 CD1 ) 0.13199 ( PROT LEU 9 CD2 ) 0.13199 ( PROT LEU 9 C ) 0.16499 ( PROT LEU 9 O ) 0.16499 ( PROT SER 10 N ) 0.16499 ( PROT SER 10 H ) 0.13199 ( PROT SER 10 CA ) 0.16499 ( PROT SER 10 CB ) 0.13199 ( PROT SER 10 OG ) 0.13199 ( PROT SER 10 HG ) 0.13199 ( PROT SER 10 C ) 0.16499 ( PROT SER 10 O ) 0.16499 ( PROT SER 11 N ) 0.16499 ( PROT SER 11 H ) 0.13199 ( PROT SER 11 CA ) 0.16499 ( PROT SER 11 CB ) 0.13199 ( PROT SER 11 OG ) 0.13199 ( PROT SER 11 HG ) 0.13199 ( PROT SER 11 C ) 0.16499 ( PROT SER 11 O ) 0.16499 ( PROT PHE 12 N ) 0.16499 ( PROT PHE 12 H ) 0.13199 ( PROT PHE 12 CA ) 0.16499 ( PROT PHE 12 CB ) 0.13199 ( PROT PHE 12 CG ) 0.13199 ( PROT PHE 12 CD1 ) 0.13199 ( PROT PHE 12 CD2 ) 0.13199 ( PROT PHE 12 CE1 ) 0.13199 ( PROT PHE 12 CE2 ) 0.13199 ( PROT PHE 12 CZ ) 0.13199 ( PROT PHE 12 C ) 0.16499 ( PROT PHE 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 SER 14 N ) 0.16499 ( PROT SER 14 H ) 0.13199 ( PROT SER 14 CA ) 0.16499 ( PROT SER 14 CB ) 0.13199 ( PROT SER 14 OG ) 0.13199 ( PROT SER 14 HG ) 0.13199 ( PROT SER 14 C ) 0.16499 ( PROT SER 14 O ) 0.16499 ( PROT LYS 15 N ) 0.16499 ( PROT LYS 15 H ) 0.13199 ( PROT LYS 15 CA ) 0.16499 ( PROT LYS 15 CB ) 0.13199 ( PROT LYS 15 CG ) 0.13199 ( PROT LYS 15 CD ) 0.13199 ( PROT LYS 15 CE ) 0.13199 ( PROT LYS 15 NZ ) 0.13199 ( PROT LYS 15 HZ1 ) 0.13199 ( PROT LYS 15 HZ2 ) 0.13199 ( PROT LYS 15 HZ3 ) 0.13199 ( PROT LYS 15 C ) 0.16499 ( PROT LYS 15 O ) 0.16499 ( PROT LEU 16 N ) 0.16499 ( PROT LEU 16 H ) 0.13199 ( PROT LEU 16 CA ) 0.16499 ( PROT LEU 16 CB ) 0.13199 ( PROT LEU 16 CG ) 0.13199 ( PROT LEU 16 CD1 ) 0.13199 ( PROT LEU 16 CD2 ) 0.13199 ( PROT LEU 16 C ) 0.16499 ( PROT LEU 16 O ) 0.16499 ( PROT ALA 17 N ) 0.16499 ( PROT ALA 17 H ) 0.13199 ( PROT ALA 17 CA ) 0.16499 ( PROT ALA 17 CB ) 0.13199 ( PROT ALA 17 C ) 0.16499 ( PROT ALA 17 O ) 0.16499 ( PROT CYS 18 N ) 0.16499 ( PROT CYS 18 H ) 0.13199 ( PROT CYS 18 CA ) 0.16499 ( PROT CYS 18 CB ) 0.13199 ( PROT CYS 18 SG ) 0.13199 ( PROT CYS 18 C ) 0.16499 ( PROT CYS 18 O ) 0.16499 ( PROT GLU 19 N ) 0.16499 ( PROT GLU 19 H ) 0.13199 ( PROT GLU 19 CA ) 0.16499 ( PROT GLU 19 CB ) 0.13199 ( PROT GLU 19 CG ) 0.13199 ( PROT GLU 19 CD ) 0.13199 ( PROT GLU 19 OE1 ) 0.13199 ( PROT GLU 19 OE2 ) 0.13199 ( PROT GLU 19 C ) 0.16499 ( PROT GLU 19 OT1 ) 0.13199 ( PROT GLU 19 OT2 ) 0.13199 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.42599 4.57108 -7.52430 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00871 0.00414 -0.00833 ROTATION MATRIX 1.000000 -0.000395 -0.000651 0.000396 0.999999 0.001165 0.000650 -0.001165 0.999999 AXIS OF ROTATION IS 0.837179 0.467262 -0.284247 ANGLE IS 0.08 TOTAL SQUARE DIFF IS 105.5523 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.792646 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.7926" Parameter: A <- "0.7926" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.97407 4.30700 -7.76350 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.04186 -0.02674 0.03124 ROTATION MATRIX 0.999881 0.011742 0.010011 -0.011539 0.999732 -0.020076 -0.010244 0.019958 0.999748 AXIS OF ROTATION IS -0.792009 -0.400723 0.460590 ANGLE IS 1.45 CENTER OF ROTATION 8.945143 4.509572 -7.573760 SHIFT IS 0.058254 TOTAL SQUARE DIFF IS 7.5132 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.628832 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.7926" RDCMND substituted energy or value "?RMS" to " 0.6288" Parameter: A <- "0.7926 0.6288" 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 0.7926 0.6288 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 " 23.40" Parameter: H <- "23.40" 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 -79.97747 23.40381 0.20641 ENER INTERN> 4.13786 14.43882 0.00000 10.50682 2.80529 ENER EXTERN> -92.77851 -19.08774 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 " -79.98" Parameter: B <- "-79.98" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -19.09" Parameter: C <- "-19.09" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -92.78" Parameter: C <- " -111.87" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -111.87" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.14" Parameter: D <- "4.14" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.44" Parameter: D <- " 18.58" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.51" Parameter: D <- " 29.09" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.81" Parameter: D <- " 31.90" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 31.90" 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= -79.98 GRMS= 0.21 ELEC= -19.09 VDW= -92.78 RDTITL> *EXTERNAL= -111.87 INTERNAL= 31.90 USER= 0.00 HARM= 23.40 RDTITL> *BOND= 4.14 ANGL= 14.44 DIHE= 10.51 IMPR= 2.81 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9528 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9505 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 -64.46982 -15.50765 0.08376 0.02000 MINI INTERN> 4.13786 14.43882 0.00000 10.50682 2.80529 MINI EXTERN> -92.77851 -19.08774 0.00000 0.00000 0.00000 MINI CONSTR> 15.50765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -60.70583 -3.76399 6.87808 0.00360 MINI INTERN> 7.67150 15.49813 0.00000 10.73388 2.85093 MINI EXTERN> -95.12292 -18.33755 0.00000 0.00000 0.00000 MINI CONSTR> 16.00019 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9498 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -64.62440 3.91857 0.20510 0.00065 MINI INTERN> 4.30956 14.71905 0.00000 10.67442 2.79661 MINI EXTERN> -95.04538 -18.06824 0.00000 0.00000 0.00000 MINI CONSTR> 15.98957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -64.64044 0.01604 0.49708 0.00028 MINI INTERN> 4.31792 14.59779 0.00000 10.60773 2.79375 MINI EXTERN> -94.67169 -18.27027 0.00000 0.00000 0.00000 MINI CONSTR> 15.98432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9498 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -64.67314 0.03270 0.14571 0.00012 MINI INTERN> 4.24615 14.58724 0.00000 10.60126 2.79499 MINI EXTERN> -94.49912 -18.39068 0.00000 0.00000 0.00000 MINI CONSTR> 15.98702 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -64.68362 0.01048 0.13401 0.00013 MINI INTERN> 4.23120 14.56332 0.00000 10.58475 2.79661 MINI EXTERN> -94.39702 -18.45309 0.00000 0.00000 0.00000 MINI CONSTR> 15.99060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9498 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -64.68998 0.00636 0.18317 0.00013 MINI INTERN> 4.21719 14.54824 0.00000 10.57283 2.79826 MINI EXTERN> -94.32189 -18.49963 0.00000 0.00000 0.00000 MINI CONSTR> 15.99502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -64.69943 0.00945 0.05785 0.00006 MINI INTERN> 4.22451 14.52549 0.00000 10.55711 2.79973 MINI EXTERN> -94.28108 -18.52519 0.00000 0.00000 0.00000 MINI CONSTR> 15.99999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9498 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -64.70227 0.00283 0.20422 0.00014 MINI INTERN> 4.20351 14.52195 0.00000 10.55127 2.80126 MINI EXTERN> -94.22063 -18.56581 0.00000 0.00000 0.00000 MINI CONSTR> 16.00618 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -64.71170 0.00944 0.06015 0.00006 MINI INTERN> 4.21517 14.50214 0.00000 10.53689 2.80239 MINI EXTERN> -94.20066 -18.58041 0.00000 0.00000 0.00000 MINI CONSTR> 16.01279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9498 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -64.71649 0.00479 0.04949 0.00006 MINI INTERN> 4.21141 14.49476 0.00000 10.53021 2.80324 MINI EXTERN> -94.17653 -18.59837 0.00000 0.00000 0.00000 MINI CONSTR> 16.01879 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -64.72166 0.00517 0.05022 0.00006 MINI INTERN> 4.20877 14.48747 0.00000 10.52276 2.80413 MINI EXTERN> -94.15633 -18.61454 0.00000 0.00000 0.00000 MINI CONSTR> 16.02606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9498 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -64.72637 0.00471 0.09401 0.00007 MINI INTERN> 4.21049 14.47973 0.00000 10.51459 2.80484 MINI EXTERN> -94.14407 -18.62607 0.00000 0.00000 0.00000 MINI CONSTR> 16.03412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -64.73123 0.00486 0.05879 0.00007 MINI INTERN> 4.20615 14.47560 0.00000 10.51001 2.80530 MINI EXTERN> -94.13202 -18.63742 0.00000 0.00000 0.00000 MINI CONSTR> 16.04115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9498 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -64.73609 0.00486 0.05889 0.00007 MINI INTERN> 4.20391 14.47135 0.00000 10.50439 2.80577 MINI EXTERN> -94.12452 -18.64635 0.00000 0.00000 0.00000 MINI CONSTR> 16.04937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -64.74062 0.00453 0.07651 0.00007 MINI INTERN> 4.20455 14.46637 0.00000 10.49898 2.80591 MINI EXTERN> -94.12121 -18.65291 0.00000 0.00000 0.00000 MINI CONSTR> 16.05769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9496 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -64.74405 0.00343 0.11212 0.00008 MINI INTERN> 4.20640 14.46225 0.00000 10.49409 2.80599 MINI EXTERN> -94.12202 -18.65582 0.00000 0.00000 0.00000 MINI CONSTR> 16.06507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -64.74796 0.00391 0.12940 0.00008 MINI INTERN> 4.20278 14.46117 0.00000 10.48987 2.80641 MINI EXTERN> -94.12189 -18.65928 0.00000 0.00000 0.00000 MINI CONSTR> 16.07297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9495 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -64.75190 0.00394 0.11902 0.00008 MINI INTERN> 4.20611 14.45571 0.00000 10.48616 2.80599 MINI EXTERN> -94.12385 -18.66209 0.00000 0.00000 0.00000 MINI CONSTR> 16.08008 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -64.75577 0.00387 0.14124 0.00009 MINI INTERN> 4.20273 14.45516 0.00000 10.48227 2.80632 MINI EXTERN> -94.12663 -18.66411 0.00000 0.00000 0.00000 MINI CONSTR> 16.08849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9494 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -64.75961 0.00384 0.12901 0.00009 MINI INTERN> 4.20542 14.45058 0.00000 10.47890 2.80587 MINI EXTERN> -94.13028 -18.66563 0.00000 0.00000 0.00000 MINI CONSTR> 16.09553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -64.76364 0.00403 0.13704 0.00009 MINI INTERN> 4.20557 14.44807 0.00000 10.47540 2.80561 MINI EXTERN> -94.13473 -18.66745 0.00000 0.00000 0.00000 MINI CONSTR> 16.10388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9493 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -64.76882 0.00518 0.04454 0.00004 MINI INTERN> 4.19981 14.44645 0.00000 10.47405 2.80572 MINI EXTERN> -94.13263 -18.67338 0.00000 0.00000 0.00000 MINI CONSTR> 16.11116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -64.77095 0.00213 0.14536 0.00010 MINI INTERN> 4.20452 14.44440 0.00000 10.46905 2.80537 MINI EXTERN> -94.14548 -18.66797 0.00000 0.00000 0.00000 MINI CONSTR> 16.11916 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9493 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -64.77653 0.00558 0.04425 0.00004 MINI INTERN> 4.19989 14.44207 0.00000 10.46774 2.80533 MINI EXTERN> -94.14431 -18.67414 0.00000 0.00000 0.00000 MINI CONSTR> 16.12689 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -64.77827 0.00174 0.15805 0.00011 MINI INTERN> 4.20282 14.44172 0.00000 10.46303 2.80507 MINI EXTERN> -94.15783 -18.66801 0.00000 0.00000 0.00000 MINI CONSTR> 16.13493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9494 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -64.78399 0.00572 0.04990 0.00005 MINI INTERN> 4.20018 14.43795 0.00000 10.46186 2.80487 MINI EXTERN> -94.15708 -18.67424 0.00000 0.00000 0.00000 MINI CONSTR> 16.14249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -64.78724 0.00325 0.04201 0.00005 MINI INTERN> 4.19978 14.43693 0.00000 10.45926 2.80471 MINI EXTERN> -94.16369 -18.67341 0.00000 0.00000 0.00000 MINI CONSTR> 16.14918 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9492 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -64.79074 0.00350 0.04307 0.00005 MINI INTERN> 4.19993 14.43520 0.00000 10.45657 2.80447 MINI EXTERN> -94.17041 -18.67311 0.00000 0.00000 0.00000 MINI CONSTR> 16.15660 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -64.79426 0.00353 0.04140 0.00005 MINI INTERN> 4.20009 14.43357 0.00000 10.45383 2.80422 MINI EXTERN> -94.17771 -18.67234 0.00000 0.00000 0.00000 MINI CONSTR> 16.16408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9491 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -64.79793 0.00367 0.04129 0.00005 MINI INTERN> 4.20033 14.43183 0.00000 10.45100 2.80394 MINI EXTERN> -94.18540 -18.67157 0.00000 0.00000 0.00000 MINI CONSTR> 16.17194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -64.80173 0.00379 0.07155 0.00006 MINI INTERN> 4.20100 14.42927 0.00000 10.44811 2.80370 MINI EXTERN> -94.19289 -18.67174 0.00000 0.00000 0.00000 MINI CONSTR> 16.18082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9490 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -64.80514 0.00341 0.05632 0.00006 MINI INTERN> 4.20123 14.42806 0.00000 10.44546 2.80337 MINI EXTERN> -94.20059 -18.67047 0.00000 0.00000 0.00000 MINI CONSTR> 16.18780 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -64.80838 0.00324 0.06367 0.00006 MINI INTERN> 4.20094 14.42690 0.00000 10.44305 2.80322 MINI EXTERN> -94.20764 -18.66991 0.00000 0.00000 0.00000 MINI CONSTR> 16.19507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9490 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -64.81182 0.00344 0.05909 0.00006 MINI INTERN> 4.20132 14.42536 0.00000 10.44042 2.80294 MINI EXTERN> -94.21563 -18.66871 0.00000 0.00000 0.00000 MINI CONSTR> 16.20248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -64.81521 0.00340 0.06467 0.00006 MINI INTERN> 4.20126 14.42412 0.00000 10.43775 2.80271 MINI EXTERN> -94.22344 -18.66773 0.00000 0.00000 0.00000 MINI CONSTR> 16.21011 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9489 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -64.81800 0.00279 0.09613 0.00007 MINI INTERN> 4.20237 14.42221 0.00000 10.43547 2.80249 MINI EXTERN> -94.23007 -18.66782 0.00000 0.00000 0.00000 MINI CONSTR> 16.21734 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -64.82137 0.00337 0.09992 0.00007 MINI INTERN> 4.20172 14.42152 0.00000 10.43266 2.80232 MINI EXTERN> -94.23829 -18.66624 0.00000 0.00000 0.00000 MINI CONSTR> 16.22495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9488 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -64.82430 0.00293 0.11411 0.00007 MINI INTERN> 4.20487 14.41834 0.00000 10.43040 2.80184 MINI EXTERN> -94.24600 -18.66579 0.00000 0.00000 0.00000 MINI CONSTR> 16.23205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -64.82735 0.00305 0.10575 0.00007 MINI INTERN> 4.20225 14.41915 0.00000 10.42808 2.80189 MINI EXTERN> -94.25268 -18.66466 0.00000 0.00000 0.00000 MINI CONSTR> 16.23861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9488 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -64.83024 0.00289 0.12927 0.00008 MINI INTERN> 4.20640 14.41548 0.00000 10.42552 2.80127 MINI EXTERN> -94.26110 -18.66387 0.00000 0.00000 0.00000 MINI CONSTR> 16.24606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -64.83322 0.00298 0.11732 0.00008 MINI INTERN> 4.20479 14.41560 0.00000 10.42343 2.80123 MINI EXTERN> -94.26759 -18.66298 0.00000 0.00000 0.00000 MINI CONSTR> 16.25230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9488 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -64.83710 0.00388 0.03932 0.00003 MINI INTERN> 4.20226 14.41640 0.00000 10.42086 2.80087 MINI EXTERN> -94.27749 -18.65856 0.00000 0.00000 0.00000 MINI CONSTR> 16.25856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -64.83893 0.00183 0.12486 0.00009 MINI INTERN> 4.20438 14.41415 0.00000 10.41883 2.80090 MINI EXTERN> -94.28171 -18.66121 0.00000 0.00000 0.00000 MINI CONSTR> 16.26573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9488 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -64.84314 0.00421 0.04018 0.00004 MINI INTERN> 4.20269 14.41418 0.00000 10.41613 2.80037 MINI EXTERN> -94.29259 -18.65626 0.00000 0.00000 0.00000 MINI CONSTR> 16.27234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -64.84468 0.00154 0.13323 0.00009 MINI INTERN> 4.20419 14.41256 0.00000 10.41410 2.80058 MINI EXTERN> -94.29649 -18.65898 0.00000 0.00000 0.00000 MINI CONSTR> 16.27936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9487 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -64.84919 0.00451 0.04069 0.00004 MINI INTERN> 4.20308 14.41203 0.00000 10.41136 2.79987 MINI EXTERN> -94.30779 -18.65397 0.00000 0.00000 0.00000 MINI CONSTR> 16.28622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -64.85043 0.00124 0.14266 0.00010 MINI INTERN> 4.20498 14.41037 0.00000 10.40926 2.80015 MINI EXTERN> -94.31171 -18.65664 0.00000 0.00000 0.00000 MINI CONSTR> 16.29317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -64.85327 0.00285 0.15729 0.00010 MINI INTERN> 4.20938 14.40671 0.00000 10.40659 2.79944 MINI EXTERN> -94.32039 -18.65543 0.00000 0.00000 0.00000 MINI CONSTR> 16.30044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -64.85800 0.00473 0.05114 0.00004 MINI INTERN> 4.20357 14.40916 0.00000 10.40427 2.79910 MINI EXTERN> -94.33068 -18.65026 0.00000 0.00000 0.00000 MINI CONSTR> 16.30684 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -64.86055 0.00254 0.03625 0.00005 MINI INTERN> 4.20399 14.40793 0.00000 10.40232 2.79896 MINI EXTERN> -94.33636 -18.64986 0.00000 0.00000 0.00000 MINI CONSTR> 16.31248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -64.86136 0.00082 0.16812 0.00011 MINI INTERN> 4.20939 14.40443 0.00000 10.39969 2.79904 MINI EXTERN> -94.34198 -18.65223 0.00000 0.00000 0.00000 MINI CONSTR> 16.32029 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -64.86652 0.00516 0.06341 0.00005 MINI INTERN> 4.20418 14.40637 0.00000 10.39731 2.79835 MINI EXTERN> -94.35302 -18.64677 0.00000 0.00000 0.00000 MINI CONSTR> 16.32706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -64.86930 0.00278 0.04742 0.00005 MINI INTERN> 4.20401 14.40555 0.00000 10.39514 2.79823 MINI EXTERN> -94.35930 -18.64612 0.00000 0.00000 0.00000 MINI CONSTR> 16.33319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -64.87197 0.00267 0.05475 0.00005 MINI INTERN> 4.20486 14.40425 0.00000 10.39292 2.79790 MINI EXTERN> -94.36665 -18.64492 0.00000 0.00000 0.00000 MINI CONSTR> 16.33966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -64.87462 0.00265 0.05874 0.00006 MINI INTERN> 4.20431 14.40394 0.00000 10.39068 2.79774 MINI EXTERN> -94.37359 -18.64372 0.00000 0.00000 0.00000 MINI CONSTR> 16.34603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -64.87693 0.00231 0.08310 0.00006 MINI INTERN> 4.20545 14.40272 0.00000 10.38854 2.79733 MINI EXTERN> -94.38093 -18.64233 0.00000 0.00000 0.00000 MINI CONSTR> 16.35228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -64.87978 0.00285 0.06143 0.00006 MINI INTERN> 4.20444 14.40241 0.00000 10.38638 2.79734 MINI EXTERN> -94.38701 -18.64168 0.00000 0.00000 0.00000 MINI CONSTR> 16.35834 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -64.88188 0.00210 0.08917 0.00006 MINI INTERN> 4.20457 14.40200 0.00000 10.38431 2.79704 MINI EXTERN> -94.39400 -18.64008 0.00000 0.00000 0.00000 MINI CONSTR> 16.36429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -64.88425 0.00238 0.10144 0.00006 MINI INTERN> 4.20757 14.39940 0.00000 10.38218 2.79649 MINI EXTERN> -94.40096 -18.63937 0.00000 0.00000 0.00000 MINI CONSTR> 16.37042 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -64.88673 0.00247 0.09422 0.00007 MINI INTERN> 4.20546 14.40012 0.00000 10.38015 2.79654 MINI EXTERN> -94.40711 -18.63801 0.00000 0.00000 0.00000 MINI CONSTR> 16.37612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -64.88901 0.00229 0.11578 0.00007 MINI INTERN> 4.20885 14.39742 0.00000 10.37793 2.79595 MINI EXTERN> -94.41405 -18.63756 0.00000 0.00000 0.00000 MINI CONSTR> 16.38245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -64.89142 0.00241 0.10522 0.00007 MINI INTERN> 4.20827 14.39707 0.00000 10.37601 2.79582 MINI EXTERN> -94.41999 -18.63644 0.00000 0.00000 0.00000 MINI CONSTR> 16.38783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -64.89382 0.00240 0.10981 0.00007 MINI INTERN> 4.20484 14.39874 0.00000 10.37391 2.79611 MINI EXTERN> -94.42615 -18.63505 0.00000 0.00000 0.00000 MINI CONSTR> 16.39378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -64.89619 0.00237 0.10602 0.00008 MINI INTERN> 4.20637 14.39713 0.00000 10.37187 2.79566 MINI EXTERN> -94.43269 -18.63400 0.00000 0.00000 0.00000 MINI CONSTR> 16.39947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -64.89933 0.00315 0.03596 0.00003 MINI INTERN> 4.20762 14.39494 0.00000 10.36985 2.79573 MINI EXTERN> -94.43680 -18.63551 0.00000 0.00000 0.00000 MINI CONSTR> 16.40483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -64.90062 0.00129 0.11960 0.00008 MINI INTERN> 4.20703 14.39570 0.00000 10.36779 2.79518 MINI EXTERN> -94.44537 -18.63191 0.00000 0.00000 0.00000 MINI CONSTR> 16.41095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -64.90286 0.00224 0.13553 0.00009 MINI INTERN> 4.21153 14.39225 0.00000 10.36562 2.79454 MINI EXTERN> -94.45142 -18.63234 0.00000 0.00000 0.00000 MINI CONSTR> 16.41695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -64.90514 0.00228 0.13456 0.00009 MINI INTERN> 4.20670 14.39492 0.00000 10.36363 2.79486 MINI EXTERN> -94.45809 -18.62993 0.00000 0.00000 0.00000 MINI CONSTR> 16.42278 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -64.90887 0.00373 0.04197 0.00004 MINI INTERN> 4.20868 14.39191 0.00000 10.36144 2.79492 MINI EXTERN> -94.46189 -18.63218 0.00000 0.00000 0.00000 MINI CONSTR> 16.42823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9486 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -64.90952 0.00065 0.13998 0.00010 MINI INTERN> 4.20727 14.39353 0.00000 10.35965 2.79442 MINI EXTERN> -94.47013 -18.62814 0.00000 0.00000 0.00000 MINI CONSTR> 16.43387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -64.91340 0.00388 0.05023 0.00004 MINI INTERN> 4.20892 14.39070 0.00000 10.35736 2.79460 MINI EXTERN> -94.47386 -18.63063 0.00000 0.00000 0.00000 MINI CONSTR> 16.43952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9485 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -64.91540 0.00201 0.03473 0.00004 MINI INTERN> 4.20910 14.39007 0.00000 10.35572 2.79430 MINI EXTERN> -94.47911 -18.62965 0.00000 0.00000 0.00000 MINI CONSTR> 16.44416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -64.91774 0.00234 0.05748 0.00004 MINI INTERN> 4.20953 14.38931 0.00000 10.35340 2.79423 MINI EXTERN> -94.48538 -18.62926 0.00000 0.00000 0.00000 MINI CONSTR> 16.45043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9485 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -64.91979 0.00205 0.03410 0.00005 MINI INTERN> 4.20954 14.38877 0.00000 10.35180 2.79389 MINI EXTERN> -94.49070 -18.62808 0.00000 0.00000 0.00000 MINI CONSTR> 16.45499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -64.92199 0.00220 0.06770 0.00005 MINI INTERN> 4.21081 14.38755 0.00000 10.34944 2.79378 MINI EXTERN> -94.49676 -18.62805 0.00000 0.00000 0.00000 MINI CONSTR> 16.46124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9483 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -64.92423 0.00224 0.05115 0.00005 MINI INTERN> 4.20967 14.38771 0.00000 10.34763 2.79366 MINI EXTERN> -94.50245 -18.62680 0.00000 0.00000 0.00000 MINI CONSTR> 16.46636 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -64.92630 0.00207 0.05834 0.00005 MINI INTERN> 4.21036 14.38682 0.00000 10.34566 2.79346 MINI EXTERN> -94.50794 -18.62636 0.00000 0.00000 0.00000 MINI CONSTR> 16.47170 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9481 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -64.92824 0.00194 0.07691 0.00005 MINI INTERN> 4.21134 14.38585 0.00000 10.34363 2.79329 MINI EXTERN> -94.51343 -18.62605 0.00000 0.00000 0.00000 MINI CONSTR> 16.47714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -64.93068 0.00244 0.05197 0.00005 MINI INTERN> 4.21012 14.38597 0.00000 10.34173 2.79309 MINI EXTERN> -94.51957 -18.62450 0.00000 0.00000 0.00000 MINI CONSTR> 16.48248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9481 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -64.93241 0.00172 0.08199 0.00006 MINI INTERN> 4.21079 14.38532 0.00000 10.33974 2.79305 MINI EXTERN> -94.52466 -18.62439 0.00000 0.00000 0.00000 MINI CONSTR> 16.48775 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -64.93435 0.00194 0.09493 0.00006 MINI INTERN> 4.21347 14.38325 0.00000 10.33772 2.79256 MINI EXTERN> -94.53020 -18.62422 0.00000 0.00000 0.00000 MINI CONSTR> 16.49307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -64.93639 0.00205 0.08642 0.00006 MINI INTERN> 4.21190 14.38376 0.00000 10.33596 2.79263 MINI EXTERN> -94.53527 -18.62334 0.00000 0.00000 0.00000 MINI CONSTR> 16.49796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -64.93850 0.00211 0.09992 0.00006 MINI INTERN> 4.21390 14.38213 0.00000 10.33371 2.79223 MINI EXTERN> -94.54145 -18.62282 0.00000 0.00000 0.00000 MINI CONSTR> 16.50379 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -64.94051 0.00202 0.09450 0.00007 MINI INTERN> 4.21206 14.38285 0.00000 10.33195 2.79232 MINI EXTERN> -94.54658 -18.62180 0.00000 0.00000 0.00000 MINI CONSTR> 16.50869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -64.94251 0.00200 0.10300 0.00007 MINI INTERN> 4.21506 14.38055 0.00000 10.32996 2.79167 MINI EXTERN> -94.55227 -18.62141 0.00000 0.00000 0.00000 MINI CONSTR> 16.51393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -64.94508 0.00257 0.03217 0.00003 MINI INTERN> 4.21144 14.38195 0.00000 10.32858 2.79151 MINI EXTERN> -94.55778 -18.61915 0.00000 0.00000 0.00000 MINI CONSTR> 16.51837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -64.94621 0.00112 0.10876 0.00007 MINI INTERN> 4.21238 14.38157 0.00000 10.32635 2.79188 MINI EXTERN> -94.56220 -18.61994 0.00000 0.00000 0.00000 MINI CONSTR> 16.52376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -64.94797 0.00177 0.12439 0.00008 MINI INTERN> 4.21683 14.37845 0.00000 10.32443 2.79101 MINI EXTERN> -94.56765 -18.61978 0.00000 0.00000 0.00000 MINI CONSTR> 16.52874 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -64.94996 0.00199 0.11661 0.00008 MINI INTERN> 4.21524 14.37905 0.00000 10.32253 2.79126 MINI EXTERN> -94.57241 -18.61937 0.00000 0.00000 0.00000 MINI CONSTR> 16.53375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -64.95177 0.00181 0.12910 0.00008 MINI INTERN> 4.21231 14.38068 0.00000 10.32068 2.79147 MINI EXTERN> -94.57797 -18.61785 0.00000 0.00000 0.00000 MINI CONSTR> 16.53892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -64.95495 0.00318 0.03761 0.00004 MINI INTERN> 4.21230 14.37939 0.00000 10.31920 2.79053 MINI EXTERN> -94.58401 -18.61592 0.00000 0.00000 0.00000 MINI CONSTR> 16.54357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -64.95671 0.00176 0.03074 0.00004 MINI INTERN> 4.21242 14.37894 0.00000 10.31752 2.79043 MINI EXTERN> -94.58841 -18.61557 0.00000 0.00000 0.00000 MINI CONSTR> 16.54796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -64.95862 0.00192 0.03203 0.00004 MINI INTERN> 4.21265 14.37842 0.00000 10.31567 2.79022 MINI EXTERN> -94.59352 -18.61495 0.00000 0.00000 0.00000 MINI CONSTR> 16.55289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -64.96053 0.00191 0.03089 0.00004 MINI INTERN> 4.21291 14.37788 0.00000 10.31382 2.79004 MINI EXTERN> -94.59851 -18.61444 0.00000 0.00000 0.00000 MINI CONSTR> 16.55777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -64.96250 0.00197 0.03178 0.00004 MINI INTERN> 4.21294 14.37748 0.00000 10.31192 2.78986 MINI EXTERN> -94.60373 -18.61381 0.00000 0.00000 0.00000 MINI CONSTR> 16.56284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -64.96440 0.00190 0.05761 0.00004 MINI INTERN> 4.21305 14.37714 0.00000 10.30997 2.78951 MINI EXTERN> -94.60959 -18.61277 0.00000 0.00000 0.00000 MINI CONSTR> 16.56829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -64.96615 0.00175 0.03046 0.00004 MINI INTERN> 4.21330 14.37655 0.00000 10.30836 2.78952 MINI EXTERN> -94.61328 -18.61281 0.00000 0.00000 0.00000 MINI CONSTR> 16.57222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -64.96800 0.00185 0.06551 0.00005 MINI INTERN> 4.21289 14.37661 0.00000 10.30640 2.78920 MINI EXTERN> -94.61935 -18.61156 0.00000 0.00000 0.00000 MINI CONSTR> 16.57782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -64.96993 0.00193 0.04848 0.00005 MINI INTERN> 4.21416 14.37534 0.00000 10.30459 2.78897 MINI EXTERN> -94.62373 -18.61156 0.00000 0.00000 0.00000 MINI CONSTR> 16.58232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -64.97145 0.00153 0.07014 0.00005 MINI INTERN> 4.21398 14.37529 0.00000 10.30293 2.78873 MINI EXTERN> -94.62863 -18.61067 0.00000 0.00000 0.00000 MINI CONSTR> 16.58691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -64.97145 0.00153 0.07014 0.00006 STPD INTERN> 4.21398 14.37529 0.00000 10.30293 2.78873 STPD EXTERN> -94.62863 -18.61067 0.00000 0.00000 0.00000 STPD CONSTR> 16.58691 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 9479 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9479 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -64.97145 0.00153 0.07014 0.00000 MINI INTERN> 4.21398 14.37529 0.00000 10.30293 2.78873 MINI EXTERN> -94.62863 -18.61067 0.00000 0.00000 0.00000 MINI CONSTR> 16.58691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -65.19278 0.22133 0.14352 0.04989 MINI INTERN> 4.26838 14.27873 0.00000 9.92957 2.75432 MINI EXTERN> -95.66862 -18.42480 0.00000 0.00000 0.00000 MINI CONSTR> 17.66964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -65.20159 0.00880 0.05179 0.00243 MINI INTERN> 4.26709 14.31399 0.00000 9.91300 2.75162 MINI EXTERN> -95.69630 -18.46004 0.00000 0.00000 0.00000 MINI CONSTR> 17.70906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -65.23034 0.02876 0.15202 0.06270 MINI INTERN> 4.18384 14.18021 0.00000 9.88104 2.73647 MINI EXTERN> -95.50423 -18.44000 0.00000 0.00000 0.00000 MINI CONSTR> 17.73234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -65.26859 0.03825 0.14026 0.05089 MINI INTERN> 4.19717 14.36493 0.00000 9.80838 2.73448 MINI EXTERN> -95.44040 -18.68588 0.00000 0.00000 0.00000 MINI CONSTR> 17.75273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -65.29293 0.02434 0.11003 0.01908 MINI INTERN> 4.25695 14.42868 0.00000 9.78058 2.74317 MINI EXTERN> -95.45294 -18.81888 0.00000 0.00000 0.00000 MINI CONSTR> 17.76949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -65.30365 0.01072 0.07344 0.01170 MINI INTERN> 4.26533 14.42637 0.00000 9.76377 2.73902 MINI EXTERN> -95.44760 -18.82203 0.00000 0.00000 0.00000 MINI CONSTR> 17.77150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -65.30936 0.00571 0.06974 0.00808 MINI INTERN> 4.26737 14.44797 0.00000 9.75672 2.73022 MINI EXTERN> -95.43172 -18.84690 0.00000 0.00000 0.00000 MINI CONSTR> 17.76698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -65.31692 0.00756 0.06838 0.01067 MINI INTERN> 4.25526 14.41186 0.00000 9.74208 2.72444 MINI EXTERN> -95.37147 -18.83663 0.00000 0.00000 0.00000 MINI CONSTR> 17.75754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -65.32447 0.00754 0.07862 0.01157 MINI INTERN> 4.23742 14.39907 0.00000 9.73790 2.73028 MINI EXTERN> -95.37769 -18.79502 0.00000 0.00000 0.00000 MINI CONSTR> 17.74357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -65.33224 0.00778 0.07032 0.01338 MINI INTERN> 4.25508 14.37456 0.00000 9.74139 2.72330 MINI EXTERN> -95.37636 -18.77933 0.00000 0.00000 0.00000 MINI CONSTR> 17.72911 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -65.33874 0.00650 0.05421 0.01313 MINI INTERN> 4.25276 14.35896 0.00000 9.75298 2.71263 MINI EXTERN> -95.31770 -18.81057 0.00000 0.00000 0.00000 MINI CONSTR> 17.71221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -65.34325 0.00451 0.04810 0.00772 MINI INTERN> 4.23676 14.36015 0.00000 9.75899 2.72381 MINI EXTERN> -95.31449 -18.80836 0.00000 0.00000 0.00000 MINI CONSTR> 17.69989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -65.34675 0.00350 0.04907 0.00565 MINI INTERN> 4.24990 14.36651 0.00000 9.77791 2.72833 MINI EXTERN> -95.30645 -18.85105 0.00000 0.00000 0.00000 MINI CONSTR> 17.68810 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -65.35008 0.00332 0.04939 0.00627 MINI INTERN> 4.24189 14.36039 0.00000 9.79655 2.73248 MINI EXTERN> -95.31427 -18.84159 0.00000 0.00000 0.00000 MINI CONSTR> 17.67447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -65.35325 0.00317 0.04064 0.00772 MINI INTERN> 4.23646 14.35435 0.00000 9.80626 2.74044 MINI EXTERN> -95.34831 -18.80148 0.00000 0.00000 0.00000 MINI CONSTR> 17.65903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -65.35571 0.00247 0.04254 0.00573 MINI INTERN> 4.25108 14.35523 0.00000 9.82034 2.74393 MINI EXTERN> -95.36609 -18.80271 0.00000 0.00000 0.00000 MINI CONSTR> 17.64251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -65.35774 0.00202 0.03138 0.00452 MINI INTERN> 4.24379 14.35355 0.00000 9.81067 2.73756 MINI EXTERN> -95.36037 -18.77034 0.00000 0.00000 0.00000 MINI CONSTR> 17.62740 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -65.35923 0.00149 0.03212 0.00539 MINI INTERN> 4.24231 14.35096 0.00000 9.81011 2.73225 MINI EXTERN> -95.34786 -18.75966 0.00000 0.00000 0.00000 MINI CONSTR> 17.61265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -65.36083 0.00161 0.02931 0.00498 MINI INTERN> 4.23948 14.33368 0.00000 9.80394 2.73259 MINI EXTERN> -95.29451 -18.77150 0.00000 0.00000 0.00000 MINI CONSTR> 17.59549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -65.36184 0.00100 0.02275 0.00273 MINI INTERN> 4.24095 14.32185 0.00000 9.80403 2.74031 MINI EXTERN> -95.27672 -18.77702 0.00000 0.00000 0.00000 MINI CONSTR> 17.58476 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 -65.36184 0.00100 0.02275 0.02000 CONJ INTERN> 4.24095 14.32185 0.00000 9.80403 2.74031 CONJ EXTERN> -95.27672 -18.77702 0.00000 0.00000 0.00000 CONJ CONSTR> 17.58476 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 ALA 1 HT1 ) 0.85797E-01 ( PROT ALA 1 HT2 ) 0.85797E-01 ( PROT ALA 1 N ) 0.10725 ( PROT ALA 1 HT3 ) 0.85797E-01 ( PROT ALA 1 CA ) 0.10725 ( PROT ALA 1 CB ) 0.85797E-01 ( PROT ALA 1 C ) 0.10725 ( PROT ALA 1 O ) 0.10725 ( PROT LEU 2 N ) 0.10725 ( PROT LEU 2 H ) 0.85797E-01 ( PROT LEU 2 CA ) 0.10725 ( PROT LEU 2 CB ) 0.85797E-01 ( PROT LEU 2 CG ) 0.85797E-01 ( PROT LEU 2 CD1 ) 0.85797E-01 ( PROT LEU 2 CD2 ) 0.85797E-01 ( PROT LEU 2 C ) 0.10725 ( PROT LEU 2 O ) 0.10725 ( PROT GLN 3 N ) 0.10725 ( PROT GLN 3 H ) 0.85797E-01 ( PROT GLN 3 CA ) 0.10725 ( PROT GLN 3 CB ) 0.85797E-01 ( PROT GLN 3 CG ) 0.85797E-01 ( PROT GLN 3 CD ) 0.85797E-01 ( PROT GLN 3 OE1 ) 0.85797E-01 ( PROT GLN 3 NE2 ) 0.85797E-01 ( PROT GLN 3 HE21 ) 0.85797E-01 ( PROT GLN 3 HE22 ) 0.85797E-01 ( PROT GLN 3 C ) 0.10725 ( PROT GLN 3 O ) 0.10725 ( PROT ALA 4 N ) 0.10725 ( PROT ALA 4 H ) 0.85797E-01 ( PROT ALA 4 CA ) 0.10725 ( PROT ALA 4 CB ) 0.85797E-01 ( PROT ALA 4 C ) 0.10725 ( PROT ALA 4 O ) 0.10725 ( PROT PHE 5 N ) 0.10725 ( PROT PHE 5 H ) 0.85797E-01 ( PROT PHE 5 CA ) 0.10725 ( PROT PHE 5 CB ) 0.85797E-01 ( PROT PHE 5 CG ) 0.85797E-01 ( PROT PHE 5 CD1 ) 0.85797E-01 ( PROT PHE 5 CD2 ) 0.85797E-01 ( PROT PHE 5 CE1 ) 0.85797E-01 ( PROT PHE 5 CE2 ) 0.85797E-01 ( PROT PHE 5 CZ ) 0.85797E-01 ( PROT PHE 5 C ) 0.10725 ( PROT PHE 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 ILE 7 N ) 0.10725 ( PROT ILE 7 H ) 0.85797E-01 ( PROT ILE 7 CA ) 0.10725 ( PROT ILE 7 CB ) 0.85797E-01 ( PROT ILE 7 CG2 ) 0.85797E-01 ( PROT ILE 7 CG1 ) 0.85797E-01 ( PROT ILE 7 CD ) 0.85797E-01 ( PROT ILE 7 C ) 0.10725 ( PROT ILE 7 O ) 0.10725 ( PROT ALA 8 N ) 0.10725 ( PROT ALA 8 H ) 0.85797E-01 ( PROT ALA 8 CA ) 0.10725 ( PROT ALA 8 CB ) 0.85797E-01 ( PROT ALA 8 C ) 0.10725 ( PROT ALA 8 O ) 0.10725 ( PROT LEU 9 N ) 0.10725 ( PROT LEU 9 H ) 0.85797E-01 ( PROT LEU 9 CA ) 0.10725 ( PROT LEU 9 CB ) 0.85797E-01 ( PROT LEU 9 CG ) 0.85797E-01 ( PROT LEU 9 CD1 ) 0.85797E-01 ( PROT LEU 9 CD2 ) 0.85797E-01 ( PROT LEU 9 C ) 0.10725 ( PROT LEU 9 O ) 0.10725 ( PROT SER 10 N ) 0.10725 ( PROT SER 10 H ) 0.85797E-01 ( PROT SER 10 CA ) 0.10725 ( PROT SER 10 CB ) 0.85797E-01 ( PROT SER 10 OG ) 0.85797E-01 ( PROT SER 10 HG ) 0.85797E-01 ( PROT SER 10 C ) 0.10725 ( PROT SER 10 O ) 0.10725 ( PROT SER 11 N ) 0.10725 ( PROT SER 11 H ) 0.85797E-01 ( PROT SER 11 CA ) 0.10725 ( PROT SER 11 CB ) 0.85797E-01 ( PROT SER 11 OG ) 0.85797E-01 ( PROT SER 11 HG ) 0.85797E-01 ( PROT SER 11 C ) 0.10725 ( PROT SER 11 O ) 0.10725 ( PROT PHE 12 N ) 0.10725 ( PROT PHE 12 H ) 0.85797E-01 ( PROT PHE 12 CA ) 0.10725 ( PROT PHE 12 CB ) 0.85797E-01 ( PROT PHE 12 CG ) 0.85797E-01 ( PROT PHE 12 CD1 ) 0.85797E-01 ( PROT PHE 12 CD2 ) 0.85797E-01 ( PROT PHE 12 CE1 ) 0.85797E-01 ( PROT PHE 12 CE2 ) 0.85797E-01 ( PROT PHE 12 CZ ) 0.85797E-01 ( PROT PHE 12 C ) 0.10725 ( PROT PHE 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 SER 14 N ) 0.10725 ( PROT SER 14 H ) 0.85797E-01 ( PROT SER 14 CA ) 0.10725 ( PROT SER 14 CB ) 0.85797E-01 ( PROT SER 14 OG ) 0.85797E-01 ( PROT SER 14 HG ) 0.85797E-01 ( PROT SER 14 C ) 0.10725 ( PROT SER 14 O ) 0.10725 ( PROT LYS 15 N ) 0.10725 ( PROT LYS 15 H ) 0.85797E-01 ( PROT LYS 15 CA ) 0.10725 ( PROT LYS 15 CB ) 0.85797E-01 ( PROT LYS 15 CG ) 0.85797E-01 ( PROT LYS 15 CD ) 0.85797E-01 ( PROT LYS 15 CE ) 0.85797E-01 ( PROT LYS 15 NZ ) 0.85797E-01 ( PROT LYS 15 HZ1 ) 0.85797E-01 ( PROT LYS 15 HZ2 ) 0.85797E-01 ( PROT LYS 15 HZ3 ) 0.85797E-01 ( PROT LYS 15 C ) 0.10725 ( PROT LYS 15 O ) 0.10725 ( PROT LEU 16 N ) 0.10725 ( PROT LEU 16 H ) 0.85797E-01 ( PROT LEU 16 CA ) 0.10725 ( PROT LEU 16 CB ) 0.85797E-01 ( PROT LEU 16 CG ) 0.85797E-01 ( PROT LEU 16 CD1 ) 0.85797E-01 ( PROT LEU 16 CD2 ) 0.85797E-01 ( PROT LEU 16 C ) 0.10725 ( PROT LEU 16 O ) 0.10725 ( PROT ALA 17 N ) 0.10725 ( PROT ALA 17 H ) 0.85797E-01 ( PROT ALA 17 CA ) 0.10725 ( PROT ALA 17 CB ) 0.85797E-01 ( PROT ALA 17 C ) 0.10725 ( PROT ALA 17 O ) 0.10725 ( PROT CYS 18 N ) 0.10725 ( PROT CYS 18 H ) 0.85797E-01 ( PROT CYS 18 CA ) 0.10725 ( PROT CYS 18 CB ) 0.85797E-01 ( PROT CYS 18 SG ) 0.85797E-01 ( PROT CYS 18 C ) 0.10725 ( PROT CYS 18 O ) 0.10725 ( PROT GLU 19 N ) 0.10725 ( PROT GLU 19 H ) 0.85797E-01 ( PROT GLU 19 CA ) 0.10725 ( PROT GLU 19 CB ) 0.85797E-01 ( PROT GLU 19 CG ) 0.85797E-01 ( PROT GLU 19 CD ) 0.85797E-01 ( PROT GLU 19 OE1 ) 0.85797E-01 ( PROT GLU 19 OE2 ) 0.85797E-01 ( PROT GLU 19 C ) 0.10725 ( PROT GLU 19 OT1 ) 0.85797E-01 ( PROT GLU 19 OT2 ) 0.85797E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.42489 4.56954 -7.52307 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.00982 0.00568 -0.00955 ROTATION MATRIX 1.000000 -0.000436 -0.000664 0.000437 0.999999 0.001199 0.000664 -0.001200 0.999999 AXIS OF ROTATION IS 0.833680 0.461590 -0.303171 ANGLE IS 0.08 TOTAL SQUARE DIFF IS 122.2538 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.853054 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.8531" Parameter: A <- "0.8531" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.97839 4.31508 -7.77241 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.04618 -0.03482 0.04015 ROTATION MATRIX 0.999909 0.010291 0.008668 -0.010137 0.999793 -0.017657 -0.008848 0.017568 0.999807 AXIS OF ROTATION IS -0.794662 -0.395140 0.460844 ANGLE IS 1.27 CENTER OF ROTATION 8.963565 4.776884 -7.327197 SHIFT IS 0.068957 TOTAL SQUARE DIFF IS 8.7531 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.678740 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.8531" RDCMND substituted energy or value "?RMS" to " 0.6787" Parameter: A <- "0.8531 0.6787" 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 0.8531 0.6787 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 " 17.58" Parameter: H <- "17.58" 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 -82.94660 17.58476 0.14468 ENER INTERN> 4.24095 14.32185 0.00000 9.80403 2.74031 ENER EXTERN> -95.27672 -18.77702 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 " -82.95" Parameter: B <- "-82.95" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -18.78" Parameter: C <- "-18.78" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -95.28" Parameter: C <- " -114.06" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -114.06" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.24" Parameter: D <- "4.24" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.32" Parameter: D <- " 18.56" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 9.80" Parameter: D <- " 28.36" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.74" Parameter: D <- " 31.10" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 31.10" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 10800 ENER= -82.95 GRMS= 0.14 ELEC= -18.78 VDW= -95.28 RDTITL> *EXTERNAL= -114.06 INTERNAL= 31.10 USER= 0.00 HARM= 17.58 RDTITL> *BOND= 4.24 ANGL= 14.32 DIHE= 9.80 IMPR= 2.74 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "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= -82.95 GRMS= 0.14 ELEC= -18.78 VDW= -95.28 RDTITL> *EXTERNAL= -114.06 INTERNAL= 31.10 USER= 0.00 HARM= 17.58 RDTITL> *BOND= 4.24 ANGL= 14.32 DIHE= 9.80 IMPR= 2.74 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= -82.95 GRMS= 0.14 ELEC= -18.78 VDW= -95.28 RDTITL> *EXTERNAL= -114.06 INTERNAL= 31.10 USER= 0.00 HARM= 17.58 RDTITL> *BOND= 4.24 ANGL= 14.32 DIHE= 9.80 IMPR= 2.74 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 10800 0.8531 0.6787 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "10800" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9479 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9469 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 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 -71.34409 -11.60250 0.05636 0.02000 MINI INTERN> 4.24095 14.32185 0.00000 9.80403 2.74031 MINI EXTERN> -95.27672 -18.77702 0.00000 0.00000 0.00000 MINI CONSTR> 11.60250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -66.81117 -4.53292 7.46835 0.00360 MINI INTERN> 8.36237 15.30609 0.00000 10.10526 2.68637 MINI EXTERN> -97.70080 -17.53845 0.00000 0.00000 0.00000 MINI CONSTR> 11.96798 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9464 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -71.38609 4.57492 0.60734 0.00065 MINI INTERN> 4.43229 14.69158 0.00000 10.01515 2.71651 MINI EXTERN> -97.49616 -17.70566 0.00000 0.00000 0.00000 MINI CONSTR> 11.96020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -71.42759 0.04151 0.52807 0.00028 MINI INTERN> 4.43276 14.61027 0.00000 9.97216 2.73058 MINI EXTERN> -97.21451 -17.91257 0.00000 0.00000 0.00000 MINI CONSTR> 11.95371 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9464 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -71.46260 0.03501 0.08772 0.00012 MINI INTERN> 4.38452 14.57835 0.00000 9.96176 2.73131 MINI EXTERN> -97.03988 -18.02968 0.00000 0.00000 0.00000 MINI CONSTR> 11.95102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -71.47180 0.00920 0.20129 0.00013 MINI INTERN> 4.36232 14.53687 0.00000 9.94165 2.73492 MINI EXTERN> -96.86090 -18.13606 0.00000 0.00000 0.00000 MINI CONSTR> 11.94942 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9464 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -71.47836 0.00656 0.23293 0.00013 MINI INTERN> 4.34739 14.50720 0.00000 9.92534 2.73794 MINI EXTERN> -96.74563 -18.19996 0.00000 0.00000 0.00000 MINI CONSTR> 11.94936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -71.48401 0.00566 0.21494 0.00013 MINI INTERN> 4.33949 14.48615 0.00000 9.91293 2.74040 MINI EXTERN> -96.67573 -18.23720 0.00000 0.00000 0.00000 MINI CONSTR> 11.94995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9464 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -71.49229 0.00828 0.07353 0.00006 MINI INTERN> 4.33948 14.45855 0.00000 9.89696 2.74325 MINI EXTERN> -96.61625 -18.26554 0.00000 0.00000 0.00000 MINI CONSTR> 11.95126 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -71.49620 0.00391 0.05671 0.00006 MINI INTERN> 4.33255 14.44463 0.00000 9.88725 2.74475 MINI EXTERN> -96.56465 -18.29349 0.00000 0.00000 0.00000 MINI CONSTR> 11.95276 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9464 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -71.49973 0.00354 0.05875 0.00006 MINI INTERN> 4.32783 14.43105 0.00000 9.87733 2.74625 MINI EXTERN> -96.51901 -18.31800 0.00000 0.00000 0.00000 MINI CONSTR> 11.95482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -71.50224 0.00250 0.09730 0.00006 MINI INTERN> 4.32716 14.41848 0.00000 9.86820 2.74760 MINI EXTERN> -96.48505 -18.33576 0.00000 0.00000 0.00000 MINI CONSTR> 11.95714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -71.50494 0.00270 0.10531 0.00007 MINI INTERN> 4.32534 14.40837 0.00000 9.86029 2.74866 MINI EXTERN> -96.45561 -18.35178 0.00000 0.00000 0.00000 MINI CONSTR> 11.95979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -71.50735 0.00241 0.10169 0.00007 MINI INTERN> 4.32288 14.40157 0.00000 9.85430 2.74921 MINI EXTERN> -96.43391 -18.36375 0.00000 0.00000 0.00000 MINI CONSTR> 11.96235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -71.50970 0.00235 0.10498 0.00007 MINI INTERN> 4.32199 14.39429 0.00000 9.84814 2.74979 MINI EXTERN> -96.41506 -18.37417 0.00000 0.00000 0.00000 MINI CONSTR> 11.96532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -71.51270 0.00299 0.03346 0.00003 MINI INTERN> 4.30934 14.39704 0.00000 9.84568 2.74901 MINI EXTERN> -96.39547 -18.38644 0.00000 0.00000 0.00000 MINI CONSTR> 11.96813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -71.51373 0.00104 0.11592 0.00008 MINI INTERN> 4.32113 14.38322 0.00000 9.83818 2.75037 MINI EXTERN> -96.38963 -18.38833 0.00000 0.00000 0.00000 MINI CONSTR> 11.97132 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -71.51580 0.00206 0.11961 0.00008 MINI INTERN> 4.32179 14.37780 0.00000 9.83339 2.75060 MINI EXTERN> -96.38045 -18.39361 0.00000 0.00000 0.00000 MINI CONSTR> 11.97468 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -71.51777 0.00198 0.12570 0.00008 MINI INTERN> 4.32322 14.37258 0.00000 9.82880 2.75078 MINI EXTERN> -96.37370 -18.39762 0.00000 0.00000 0.00000 MINI CONSTR> 11.97818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -71.52102 0.00324 0.04120 0.00004 MINI INTERN> 4.30208 14.38393 0.00000 9.82962 2.74883 MINI EXTERN> -96.35952 -18.40746 0.00000 0.00000 0.00000 MINI CONSTR> 11.98151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -71.52268 0.00166 0.02960 0.00004 MINI INTERN> 4.30447 14.37954 0.00000 9.82622 2.74900 MINI EXTERN> -96.35763 -18.40862 0.00000 0.00000 0.00000 MINI CONSTR> 11.98435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -71.52465 0.00197 0.02937 0.00004 MINI INTERN> 4.30378 14.37713 0.00000 9.82305 2.74879 MINI EXTERN> -96.35467 -18.41070 0.00000 0.00000 0.00000 MINI CONSTR> 11.98798 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -71.52660 0.00195 0.02980 0.00004 MINI INTERN> 4.30288 14.37520 0.00000 9.82015 2.74852 MINI EXTERN> -96.35275 -18.41227 0.00000 0.00000 0.00000 MINI CONSTR> 11.99168 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -71.52844 0.00185 0.05922 0.00004 MINI INTERN> 4.29508 14.37848 0.00000 9.81885 2.74752 MINI EXTERN> -96.34881 -18.41530 0.00000 0.00000 0.00000 MINI CONSTR> 11.99574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -71.53029 0.00185 0.03707 0.00004 MINI INTERN> 4.29938 14.37354 0.00000 9.81547 2.74772 MINI EXTERN> -96.35096 -18.41446 0.00000 0.00000 0.00000 MINI CONSTR> 11.99902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -71.53216 0.00186 0.03764 0.00004 MINI INTERN> 4.29867 14.37223 0.00000 9.81310 2.74737 MINI EXTERN> -96.35160 -18.41472 0.00000 0.00000 0.00000 MINI CONSTR> 12.00279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -71.53399 0.00183 0.04162 0.00005 MINI INTERN> 4.29704 14.37176 0.00000 9.81105 2.74693 MINI EXTERN> -96.35249 -18.41489 0.00000 0.00000 0.00000 MINI CONSTR> 12.00661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -71.53543 0.00144 0.07084 0.00005 MINI INTERN> 4.28975 14.37563 0.00000 9.81060 2.74594 MINI EXTERN> -96.35139 -18.41622 0.00000 0.00000 0.00000 MINI CONSTR> 12.01025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -71.53716 0.00173 0.07220 0.00005 MINI INTERN> 4.28857 14.37515 0.00000 9.80870 2.74561 MINI EXTERN> -96.35344 -18.41569 0.00000 0.00000 0.00000 MINI CONSTR> 12.01394 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -71.53879 0.00163 0.08056 0.00005 MINI INTERN> 4.28880 14.37382 0.00000 9.80692 2.74500 MINI EXTERN> -96.35572 -18.41524 0.00000 0.00000 0.00000 MINI CONSTR> 12.01764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9463 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -71.54027 0.00148 0.08485 0.00005 MINI INTERN> 4.28472 14.37588 0.00000 9.80575 2.74472 MINI EXTERN> -96.35742 -18.41494 0.00000 0.00000 0.00000 MINI CONSTR> 12.02103 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -71.54181 0.00154 0.08033 0.00006 MINI INTERN> 4.28591 14.37430 0.00000 9.80385 2.74453 MINI EXTERN> -96.36061 -18.41402 0.00000 0.00000 0.00000 MINI CONSTR> 12.02422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9462 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -71.54341 0.00160 0.08558 0.00006 MINI INTERN> 4.28379 14.37490 0.00000 9.80239 2.74418 MINI EXTERN> -96.36349 -18.41309 0.00000 0.00000 0.00000 MINI CONSTR> 12.02791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -71.54479 0.00138 0.10152 0.00006 MINI INTERN> 4.28325 14.37458 0.00000 9.80117 2.74341 MINI EXTERN> -96.36611 -18.41262 0.00000 0.00000 0.00000 MINI CONSTR> 12.03153 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9462 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -71.54629 0.00150 0.09268 0.00006 MINI INTERN> 4.28375 14.37375 0.00000 9.79945 2.74339 MINI EXTERN> -96.36965 -18.41153 0.00000 0.00000 0.00000 MINI CONSTR> 12.03455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -71.54841 0.00213 0.02970 0.00003 MINI INTERN> 4.30816 14.35644 0.00000 9.79227 2.74536 MINI EXTERN> -96.38264 -18.40576 0.00000 0.00000 0.00000 MINI CONSTR> 12.03776 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9462 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -71.54907 0.00066 0.10147 0.00007 MINI INTERN> 4.28123 14.37469 0.00000 9.79649 2.74326 MINI EXTERN> -96.37674 -18.40916 0.00000 0.00000 0.00000 MINI CONSTR> 12.04115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -71.55037 0.00130 0.11408 0.00007 MINI INTERN> 4.28784 14.36968 0.00000 9.79440 2.74259 MINI EXTERN> -96.38138 -18.40800 0.00000 0.00000 0.00000 MINI CONSTR> 12.04450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -71.55275 0.00238 0.03213 0.00003 MINI INTERN> 4.31003 14.35385 0.00000 9.78748 2.74471 MINI EXTERN> -96.39435 -18.40212 0.00000 0.00000 0.00000 MINI CONSTR> 12.04766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -71.55318 0.00043 0.10915 0.00007 MINI INTERN> 4.27745 14.37618 0.00000 9.79314 2.74210 MINI EXTERN> -96.38634 -18.40668 0.00000 0.00000 0.00000 MINI CONSTR> 12.05096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -71.55566 0.00248 0.03786 0.00003 MINI INTERN> 4.31280 14.35132 0.00000 9.78396 2.74442 MINI EXTERN> -96.40338 -18.39924 0.00000 0.00000 0.00000 MINI CONSTR> 12.05447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -71.55694 0.00128 0.02627 0.00003 MINI INTERN> 4.30738 14.35461 0.00000 9.78398 2.74375 MINI EXTERN> -96.40480 -18.39914 0.00000 0.00000 0.00000 MINI CONSTR> 12.05728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -71.55840 0.00147 0.02804 0.00003 MINI INTERN> 4.30898 14.35326 0.00000 9.78219 2.74363 MINI EXTERN> -96.40962 -18.39758 0.00000 0.00000 0.00000 MINI CONSTR> 12.06073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -71.55984 0.00143 0.04804 0.00004 MINI INTERN> 4.31738 14.34751 0.00000 9.77889 2.74398 MINI EXTERN> -96.41715 -18.39488 0.00000 0.00000 0.00000 MINI CONSTR> 12.06444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -71.56128 0.00145 0.03215 0.00004 MINI INTERN> 4.31168 14.35101 0.00000 9.77882 2.74334 MINI EXTERN> -96.41910 -18.39461 0.00000 0.00000 0.00000 MINI CONSTR> 12.06757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -71.56260 0.00132 0.02644 0.00004 MINI INTERN> 4.30880 14.35270 0.00000 9.77822 2.74289 MINI EXTERN> -96.42194 -18.39389 0.00000 0.00000 0.00000 MINI CONSTR> 12.07062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -71.56397 0.00137 0.05855 0.00004 MINI INTERN> 4.32202 14.34395 0.00000 9.77388 2.74358 MINI EXTERN> -96.43145 -18.39047 0.00000 0.00000 0.00000 MINI CONSTR> 12.07451 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -71.56551 0.00154 0.03427 0.00004 MINI INTERN> 4.31341 14.34935 0.00000 9.77441 2.74276 MINI EXTERN> -96.43264 -18.39049 0.00000 0.00000 0.00000 MINI CONSTR> 12.07768 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -71.56693 0.00142 0.04393 0.00004 MINI INTERN> 4.31748 14.34655 0.00000 9.77224 2.74272 MINI EXTERN> -96.43850 -18.38867 0.00000 0.00000 0.00000 MINI CONSTR> 12.08125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -71.56802 0.00109 0.06384 0.00004 MINI INTERN> 4.32490 14.34171 0.00000 9.76943 2.74308 MINI EXTERN> -96.44516 -18.38636 0.00000 0.00000 0.00000 MINI CONSTR> 12.08439 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -71.56940 0.00139 0.06791 0.00005 MINI INTERN> 4.32501 14.34165 0.00000 9.76793 2.74302 MINI EXTERN> -96.44996 -18.38491 0.00000 0.00000 0.00000 MINI CONSTR> 12.08786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -71.57060 0.00120 0.07804 0.00005 MINI INTERN> 4.32882 14.33903 0.00000 9.76623 2.74270 MINI EXTERN> -96.45487 -18.38357 0.00000 0.00000 0.00000 MINI CONSTR> 12.09107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -71.57185 0.00125 0.07127 0.00005 MINI INTERN> 4.32836 14.33924 0.00000 9.76503 2.74267 MINI EXTERN> -96.45890 -18.38221 0.00000 0.00000 0.00000 MINI CONSTR> 12.09395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -71.57314 0.00128 0.08223 0.00005 MINI INTERN> 4.33096 14.33767 0.00000 9.76302 2.74279 MINI EXTERN> -96.46462 -18.38044 0.00000 0.00000 0.00000 MINI CONSTR> 12.09748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -71.57438 0.00124 0.07737 0.00005 MINI INTERN> 4.33109 14.33741 0.00000 9.76204 2.74243 MINI EXTERN> -96.46827 -18.37943 0.00000 0.00000 0.00000 MINI CONSTR> 12.10035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -71.57571 0.00133 0.08075 0.00006 MINI INTERN> 4.33029 14.33802 0.00000 9.76074 2.74237 MINI EXTERN> -96.47281 -18.37808 0.00000 0.00000 0.00000 MINI CONSTR> 12.10375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -71.57739 0.00168 0.02634 0.00002 MINI INTERN> 4.30439 14.35439 0.00000 9.76520 2.74015 MINI EXTERN> -96.46791 -18.38018 0.00000 0.00000 0.00000 MINI CONSTR> 12.10656 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -71.57801 0.00062 0.08680 0.00006 MINI INTERN> 4.33510 14.33479 0.00000 9.75775 2.74203 MINI EXTERN> -96.48198 -18.37541 0.00000 0.00000 0.00000 MINI CONSTR> 12.10972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -71.57921 0.00120 0.09533 0.00006 MINI INTERN> 4.33011 14.33828 0.00000 9.75716 2.74197 MINI EXTERN> -96.48539 -18.37430 0.00000 0.00000 0.00000 MINI CONSTR> 12.11296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -71.58109 0.00188 0.02922 0.00003 MINI INTERN> 4.30332 14.35503 0.00000 9.76193 2.73948 MINI EXTERN> -96.48009 -18.37658 0.00000 0.00000 0.00000 MINI CONSTR> 12.11582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -71.58148 0.00039 0.09711 0.00007 MINI INTERN> 4.33731 14.33355 0.00000 9.75364 2.74189 MINI EXTERN> -96.49539 -18.37131 0.00000 0.00000 0.00000 MINI CONSTR> 12.11883 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -71.58348 0.00199 0.03329 0.00003 MINI INTERN> 4.30174 14.35609 0.00000 9.75996 2.73901 MINI EXTERN> -96.48787 -18.37429 0.00000 0.00000 0.00000 MINI CONSTR> 12.12188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -71.58454 0.00106 0.02399 0.00003 MINI INTERN> 4.30728 14.35246 0.00000 9.75786 2.73923 MINI EXTERN> -96.49311 -18.37269 0.00000 0.00000 0.00000 MINI CONSTR> 12.12443 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -71.58573 0.00120 0.02539 0.00003 MINI INTERN> 4.30611 14.35325 0.00000 9.75695 2.73898 MINI EXTERN> -96.49690 -18.37159 0.00000 0.00000 0.00000 MINI CONSTR> 12.12748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -71.58694 0.00120 0.04131 0.00003 MINI INTERN> 4.29915 14.35787 0.00000 9.75716 2.73828 MINI EXTERN> -96.49918 -18.37100 0.00000 0.00000 0.00000 MINI CONSTR> 12.13078 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -71.58800 0.00106 0.02358 0.00003 MINI INTERN> 4.30797 14.35209 0.00000 9.75442 2.73875 MINI EXTERN> -96.50534 -18.36910 0.00000 0.00000 0.00000 MINI CONSTR> 12.13322 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -71.58924 0.00125 0.04822 0.00003 MINI INTERN> 4.29711 14.35931 0.00000 9.75533 2.73778 MINI EXTERN> -96.50680 -18.36878 0.00000 0.00000 0.00000 MINI CONSTR> 12.13682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -71.59047 0.00122 0.03098 0.00004 MINI INTERN> 4.30435 14.35454 0.00000 9.75280 2.73808 MINI EXTERN> -96.51292 -18.36694 0.00000 0.00000 0.00000 MINI CONSTR> 12.13962 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -71.59161 0.00114 0.03917 0.00004 MINI INTERN> 4.30102 14.35684 0.00000 9.75226 2.73776 MINI EXTERN> -96.51621 -18.36596 0.00000 0.00000 0.00000 MINI CONSTR> 12.14269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -71.59256 0.00095 0.05536 0.00004 MINI INTERN> 4.29545 14.36057 0.00000 9.75246 2.73710 MINI EXTERN> -96.51815 -18.36551 0.00000 0.00000 0.00000 MINI CONSTR> 12.14551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -71.59385 0.00128 0.03457 0.00004 MINI INTERN> 4.30307 14.35559 0.00000 9.74972 2.73755 MINI EXTERN> -96.52465 -18.36351 0.00000 0.00000 0.00000 MINI CONSTR> 12.14838 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -71.59477 0.00093 0.05881 0.00004 MINI INTERN> 4.29477 14.36117 0.00000 9.75043 2.73671 MINI EXTERN> -96.52594 -18.36324 0.00000 0.00000 0.00000 MINI CONSTR> 12.15133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -71.59593 0.00116 0.06217 0.00004 MINI INTERN> 4.29404 14.36178 0.00000 9.74932 2.73658 MINI EXTERN> -96.53016 -18.36193 0.00000 0.00000 0.00000 MINI CONSTR> 12.15443 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -71.59694 0.00100 0.07284 0.00004 MINI INTERN> 4.29491 14.36126 0.00000 9.74836 2.73612 MINI EXTERN> -96.53393 -18.36100 0.00000 0.00000 0.00000 MINI CONSTR> 12.15734 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -71.59798 0.00104 0.06606 0.00005 MINI INTERN> 4.29370 14.36213 0.00000 9.74751 2.73607 MINI EXTERN> -96.53727 -18.35999 0.00000 0.00000 0.00000 MINI CONSTR> 12.15988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -71.59895 0.00097 0.08075 0.00005 MINI INTERN> 4.29108 14.36418 0.00000 9.74665 2.73605 MINI EXTERN> -96.54106 -18.35872 0.00000 0.00000 0.00000 MINI CONSTR> 12.16288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -71.59997 0.00102 0.07362 0.00005 MINI INTERN> 4.29212 14.36349 0.00000 9.74558 2.73592 MINI EXTERN> -96.54462 -18.35778 0.00000 0.00000 0.00000 MINI CONSTR> 12.16532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -71.60136 0.00139 0.02380 0.00002 MINI INTERN> 4.31596 14.34774 0.00000 9.73985 2.73731 MINI EXTERN> -96.55525 -18.35477 0.00000 0.00000 0.00000 MINI CONSTR> 12.16781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9461 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -71.60192 0.00056 0.07720 0.00005 MINI INTERN> 4.29094 14.36439 0.00000 9.74410 2.73524 MINI EXTERN> -96.55107 -18.35613 0.00000 0.00000 0.00000 MINI CONSTR> 12.17060 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -71.60343 0.00151 0.02459 0.00002 MINI INTERN> 4.31701 14.34725 0.00000 9.73760 2.73706 MINI EXTERN> -96.56305 -18.35259 0.00000 0.00000 0.00000 MINI CONSTR> 12.17328 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -71.60388 0.00045 0.08330 0.00006 MINI INTERN> 4.28903 14.36598 0.00000 9.74227 2.73504 MINI EXTERN> -96.55825 -18.35398 0.00000 0.00000 0.00000 MINI CONSTR> 12.17602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -71.60478 0.00090 0.09720 0.00006 MINI INTERN> 4.29750 14.36046 0.00000 9.74007 2.73481 MINI EXTERN> -96.56373 -18.35270 0.00000 0.00000 0.00000 MINI CONSTR> 12.17880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -71.60646 0.00168 0.02750 0.00003 MINI INTERN> 4.31929 14.34610 0.00000 9.73412 2.73676 MINI EXTERN> -96.57477 -18.34932 0.00000 0.00000 0.00000 MINI CONSTR> 12.18135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -71.60737 0.00091 0.02189 0.00003 MINI INTERN> 4.31588 14.34841 0.00000 9.73392 2.73641 MINI EXTERN> -96.57696 -18.34871 0.00000 0.00000 0.00000 MINI CONSTR> 12.18369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -71.60839 0.00103 0.02270 0.00003 MINI INTERN> 4.31696 14.34782 0.00000 9.73270 2.73630 MINI EXTERN> -96.58100 -18.34760 0.00000 0.00000 0.00000 MINI CONSTR> 12.18643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -71.60936 0.00097 0.02362 0.00003 MINI INTERN> 4.31786 14.34736 0.00000 9.73152 2.73624 MINI EXTERN> -96.58486 -18.34653 0.00000 0.00000 0.00000 MINI CONSTR> 12.18904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -71.61037 0.00100 0.03812 0.00003 MINI INTERN> 4.32454 14.34321 0.00000 9.72910 2.73653 MINI EXTERN> -96.59082 -18.34489 0.00000 0.00000 0.00000 MINI CONSTR> 12.19196 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -71.61126 0.00089 0.02160 0.00003 MINI INTERN> 4.31670 14.34835 0.00000 9.72986 2.73588 MINI EXTERN> -96.59142 -18.34473 0.00000 0.00000 0.00000 MINI CONSTR> 12.19410 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -71.61231 0.00105 0.04460 0.00003 MINI INTERN> 4.32722 14.34176 0.00000 9.72657 2.73641 MINI EXTERN> -96.59887 -18.34271 0.00000 0.00000 0.00000 MINI CONSTR> 12.19731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -71.61334 0.00103 0.02873 0.00003 MINI INTERN> 4.32086 14.34596 0.00000 9.72686 2.73588 MINI EXTERN> -96.60044 -18.34226 0.00000 0.00000 0.00000 MINI CONSTR> 12.19979 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -71.61429 0.00095 0.03682 0.00003 MINI INTERN> 4.32471 14.34360 0.00000 9.72515 2.73591 MINI EXTERN> -96.60511 -18.34104 0.00000 0.00000 0.00000 MINI CONSTR> 12.20248 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -71.61510 0.00081 0.05117 0.00004 MINI INTERN> 4.32975 14.34057 0.00000 9.72314 2.73621 MINI EXTERN> -96.61013 -18.33964 0.00000 0.00000 0.00000 MINI CONSTR> 12.20500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -71.61616 0.00106 0.03453 0.00004 MINI INTERN> 4.32387 14.34439 0.00000 9.72346 2.73554 MINI EXTERN> -96.61164 -18.33929 0.00000 0.00000 0.00000 MINI CONSTR> 12.20751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -71.61691 0.00075 0.05451 0.00004 MINI INTERN> 4.33137 14.33976 0.00000 9.72104 2.73592 MINI EXTERN> -96.61720 -18.33780 0.00000 0.00000 0.00000 MINI CONSTR> 12.20999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -71.61777 0.00085 0.06447 0.00004 MINI INTERN> 4.33067 14.34054 0.00000 9.71996 2.73605 MINI EXTERN> -96.62091 -18.33666 0.00000 0.00000 0.00000 MINI CONSTR> 12.21259 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -71.61865 0.00089 0.05831 0.00004 MINI INTERN> 4.33277 14.33921 0.00000 9.71882 2.73589 MINI EXTERN> -96.62439 -18.33580 0.00000 0.00000 0.00000 MINI CONSTR> 12.21485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -71.61951 0.00086 0.07013 0.00004 MINI INTERN> 4.33531 14.33768 0.00000 9.71757 2.73563 MINI EXTERN> -96.62832 -18.33492 0.00000 0.00000 0.00000 MINI CONSTR> 12.21753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -71.62039 0.00088 0.06375 0.00004 MINI INTERN> 4.33523 14.33788 0.00000 9.71661 2.73564 MINI EXTERN> -96.63152 -18.33399 0.00000 0.00000 0.00000 MINI CONSTR> 12.21976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -71.62128 0.00089 0.06879 0.00005 MINI INTERN> 4.33063 14.34119 0.00000 9.71626 2.73557 MINI EXTERN> -96.63411 -18.33312 0.00000 0.00000 0.00000 MINI CONSTR> 12.22231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -71.62242 0.00114 0.02131 0.00002 MINI INTERN> 4.31475 14.35129 0.00000 9.71885 2.73403 MINI EXTERN> -96.63193 -18.33379 0.00000 0.00000 0.00000 MINI CONSTR> 12.22439 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -71.62291 0.00049 0.07182 0.00005 MINI INTERN> 4.33836 14.33634 0.00000 9.71331 2.73542 MINI EXTERN> -96.64208 -18.33121 0.00000 0.00000 0.00000 MINI CONSTR> 12.22694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -71.62291 0.00049 0.07182 0.00002 STPD INTERN> 4.33836 14.33634 0.00000 9.71331 2.73542 STPD EXTERN> -96.64208 -18.33121 0.00000 0.00000 0.00000 STPD CONSTR> 12.22694 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 9460 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9460 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -71.62291 0.00000 0.05819 0.00000 MINI INTERN> 4.30117 14.36047 0.00000 9.72078 2.73299 MINI EXTERN> -96.63077 -18.33404 0.00000 0.00000 0.00000 MINI CONSTR> 12.22648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -71.74445 0.12154 0.04302 0.02219 MINI INTERN> 4.37694 14.37657 0.00000 9.47570 2.70530 MINI EXTERN> -97.50662 -18.06989 0.00000 0.00000 0.00000 MINI CONSTR> 12.89755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -71.74652 0.00207 0.05219 0.00235 MINI INTERN> 4.37187 14.39002 0.00000 9.47351 2.70058 MINI EXTERN> -97.50421 -18.07989 0.00000 0.00000 0.00000 MINI CONSTR> 12.90160 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -71.76765 0.02113 0.10446 0.06930 MINI INTERN> 4.30156 14.28923 0.00000 9.46452 2.68721 MINI EXTERN> -97.40028 -18.02115 0.00000 0.00000 0.00000 MINI CONSTR> 12.91126 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -71.79372 0.02607 0.11837 0.03896 MINI INTERN> 4.36097 14.46631 0.00000 9.41927 2.70914 MINI EXTERN> -97.40748 -18.26191 0.00000 0.00000 0.00000 MINI CONSTR> 12.91998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -71.80681 0.01309 0.07792 0.01551 MINI INTERN> 4.37327 14.48527 0.00000 9.39905 2.70622 MINI EXTERN> -97.39533 -18.29835 0.00000 0.00000 0.00000 MINI CONSTR> 12.92306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -71.81336 0.00656 0.05777 0.01231 MINI INTERN> 4.38516 14.49218 0.00000 9.39240 2.69851 MINI EXTERN> -97.35153 -18.35087 0.00000 0.00000 0.00000 MINI CONSTR> 12.92079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -71.81876 0.00539 0.06907 0.01092 MINI INTERN> 4.38244 14.49490 0.00000 9.38010 2.69276 MINI EXTERN> -97.29610 -18.38817 0.00000 0.00000 0.00000 MINI CONSTR> 12.91530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -71.82473 0.00598 0.05249 0.00877 MINI INTERN> 4.35924 14.46407 0.00000 9.36307 2.68277 MINI EXTERN> -97.24561 -18.35700 0.00000 0.00000 0.00000 MINI CONSTR> 12.90872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -71.82929 0.00456 0.04953 0.00977 MINI INTERN> 4.36183 14.45177 0.00000 9.36714 2.67537 MINI EXTERN> -97.26275 -18.32679 0.00000 0.00000 0.00000 MINI CONSTR> 12.90414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -71.83437 0.00508 0.05861 0.01329 MINI INTERN> 4.35459 14.44557 0.00000 9.36684 2.66907 MINI EXTERN> -97.24610 -18.32468 0.00000 0.00000 0.00000 MINI CONSTR> 12.90035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -71.83874 0.00437 0.05434 0.00900 MINI INTERN> 4.36369 14.42035 0.00000 9.36342 2.66924 MINI EXTERN> -97.23705 -18.31647 0.00000 0.00000 0.00000 MINI CONSTR> 12.89808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -71.84359 0.00485 0.05457 0.01044 MINI INTERN> 4.35232 14.43830 0.00000 9.36764 2.67577 MINI EXTERN> -97.28274 -18.29330 0.00000 0.00000 0.00000 MINI CONSTR> 12.89841 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -71.84771 0.00412 0.05241 0.00874 MINI INTERN> 4.36209 14.42016 0.00000 9.38457 2.68252 MINI EXTERN> -97.27940 -18.31714 0.00000 0.00000 0.00000 MINI CONSTR> 12.89948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -71.85126 0.00355 0.04614 0.01154 MINI INTERN> 4.35602 14.40611 0.00000 9.39619 2.68832 MINI EXTERN> -97.33771 -18.26111 0.00000 0.00000 0.00000 MINI CONSTR> 12.90091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -71.85374 0.00248 0.03630 0.00616 MINI INTERN> 4.35715 14.41311 0.00000 9.41079 2.69544 MINI EXTERN> -97.38496 -18.24576 0.00000 0.00000 0.00000 MINI CONSTR> 12.90049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -71.85604 0.00230 0.03534 0.00642 MINI INTERN> 4.36372 14.40850 0.00000 9.42076 2.69351 MINI EXTERN> -97.39375 -18.24605 0.00000 0.00000 0.00000 MINI CONSTR> 12.89727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -71.85781 0.00177 0.03182 0.00410 MINI INTERN> 4.35623 14.41894 0.00000 9.41810 2.68520 MINI EXTERN> -97.40438 -18.22441 0.00000 0.00000 0.00000 MINI CONSTR> 12.89251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -71.85974 0.00193 0.03897 0.00786 MINI INTERN> 4.35983 14.40602 0.00000 9.42365 2.69034 MINI EXTERN> -97.37712 -18.24573 0.00000 0.00000 0.00000 MINI CONSTR> 12.88327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -71.86154 0.00180 0.03092 0.00630 MINI INTERN> 4.35748 14.38332 0.00000 9.42469 2.69363 MINI EXTERN> -97.32110 -18.27273 0.00000 0.00000 0.00000 MINI CONSTR> 12.87318 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -71.86267 0.00114 0.02660 0.00394 MINI INTERN> 4.35371 14.38736 0.00000 9.42356 2.69567 MINI EXTERN> -97.31603 -18.27261 0.00000 0.00000 0.00000 MINI CONSTR> 12.86567 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 -71.86267 0.00114 0.02660 0.02000 CONJ INTERN> 4.35371 14.38736 0.00000 9.42356 2.69567 CONJ EXTERN> -97.31603 -18.27261 0.00000 0.00000 0.00000 CONJ CONSTR> 12.86567 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 ALA 1 HT1 ) 0.55768E-01 ( PROT ALA 1 HT2 ) 0.55768E-01 ( PROT ALA 1 N ) 0.69710E-01 ( PROT ALA 1 HT3 ) 0.55768E-01 ( PROT ALA 1 CA ) 0.69710E-01 ( PROT ALA 1 CB ) 0.55768E-01 ( PROT ALA 1 C ) 0.69710E-01 ( PROT ALA 1 O ) 0.69710E-01 ( PROT LEU 2 N ) 0.69710E-01 ( PROT LEU 2 H ) 0.55768E-01 ( PROT LEU 2 CA ) 0.69710E-01 ( PROT LEU 2 CB ) 0.55768E-01 ( PROT LEU 2 CG ) 0.55768E-01 ( PROT LEU 2 CD1 ) 0.55768E-01 ( PROT LEU 2 CD2 ) 0.55768E-01 ( PROT LEU 2 C ) 0.69710E-01 ( PROT LEU 2 O ) 0.69710E-01 ( PROT GLN 3 N ) 0.69710E-01 ( PROT GLN 3 H ) 0.55768E-01 ( PROT GLN 3 CA ) 0.69710E-01 ( PROT GLN 3 CB ) 0.55768E-01 ( PROT GLN 3 CG ) 0.55768E-01 ( PROT GLN 3 CD ) 0.55768E-01 ( PROT GLN 3 OE1 ) 0.55768E-01 ( PROT GLN 3 NE2 ) 0.55768E-01 ( PROT GLN 3 HE21 ) 0.55768E-01 ( PROT GLN 3 HE22 ) 0.55768E-01 ( PROT GLN 3 C ) 0.69710E-01 ( PROT GLN 3 O ) 0.69710E-01 ( PROT ALA 4 N ) 0.69710E-01 ( PROT ALA 4 H ) 0.55768E-01 ( PROT ALA 4 CA ) 0.69710E-01 ( PROT ALA 4 CB ) 0.55768E-01 ( PROT ALA 4 C ) 0.69710E-01 ( PROT ALA 4 O ) 0.69710E-01 ( PROT PHE 5 N ) 0.69710E-01 ( PROT PHE 5 H ) 0.55768E-01 ( PROT PHE 5 CA ) 0.69710E-01 ( PROT PHE 5 CB ) 0.55768E-01 ( PROT PHE 5 CG ) 0.55768E-01 ( PROT PHE 5 CD1 ) 0.55768E-01 ( PROT PHE 5 CD2 ) 0.55768E-01 ( PROT PHE 5 CE1 ) 0.55768E-01 ( PROT PHE 5 CE2 ) 0.55768E-01 ( PROT PHE 5 CZ ) 0.55768E-01 ( PROT PHE 5 C ) 0.69710E-01 ( PROT PHE 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 ILE 7 N ) 0.69710E-01 ( PROT ILE 7 H ) 0.55768E-01 ( PROT ILE 7 CA ) 0.69710E-01 ( PROT ILE 7 CB ) 0.55768E-01 ( PROT ILE 7 CG2 ) 0.55768E-01 ( PROT ILE 7 CG1 ) 0.55768E-01 ( PROT ILE 7 CD ) 0.55768E-01 ( PROT ILE 7 C ) 0.69710E-01 ( PROT ILE 7 O ) 0.69710E-01 ( PROT ALA 8 N ) 0.69710E-01 ( PROT ALA 8 H ) 0.55768E-01 ( PROT ALA 8 CA ) 0.69710E-01 ( PROT ALA 8 CB ) 0.55768E-01 ( PROT ALA 8 C ) 0.69710E-01 ( PROT ALA 8 O ) 0.69710E-01 ( PROT LEU 9 N ) 0.69710E-01 ( PROT LEU 9 H ) 0.55768E-01 ( PROT LEU 9 CA ) 0.69710E-01 ( PROT LEU 9 CB ) 0.55768E-01 ( PROT LEU 9 CG ) 0.55768E-01 ( PROT LEU 9 CD1 ) 0.55768E-01 ( PROT LEU 9 CD2 ) 0.55768E-01 ( PROT LEU 9 C ) 0.69710E-01 ( PROT LEU 9 O ) 0.69710E-01 ( PROT SER 10 N ) 0.69710E-01 ( PROT SER 10 H ) 0.55768E-01 ( PROT SER 10 CA ) 0.69710E-01 ( PROT SER 10 CB ) 0.55768E-01 ( PROT SER 10 OG ) 0.55768E-01 ( PROT SER 10 HG ) 0.55768E-01 ( PROT SER 10 C ) 0.69710E-01 ( PROT SER 10 O ) 0.69710E-01 ( PROT SER 11 N ) 0.69710E-01 ( PROT SER 11 H ) 0.55768E-01 ( PROT SER 11 CA ) 0.69710E-01 ( PROT SER 11 CB ) 0.55768E-01 ( PROT SER 11 OG ) 0.55768E-01 ( PROT SER 11 HG ) 0.55768E-01 ( PROT SER 11 C ) 0.69710E-01 ( PROT SER 11 O ) 0.69710E-01 ( PROT PHE 12 N ) 0.69710E-01 ( PROT PHE 12 H ) 0.55768E-01 ( PROT PHE 12 CA ) 0.69710E-01 ( PROT PHE 12 CB ) 0.55768E-01 ( PROT PHE 12 CG ) 0.55768E-01 ( PROT PHE 12 CD1 ) 0.55768E-01 ( PROT PHE 12 CD2 ) 0.55768E-01 ( PROT PHE 12 CE1 ) 0.55768E-01 ( PROT PHE 12 CE2 ) 0.55768E-01 ( PROT PHE 12 CZ ) 0.55768E-01 ( PROT PHE 12 C ) 0.69710E-01 ( PROT PHE 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 SER 14 N ) 0.69710E-01 ( PROT SER 14 H ) 0.55768E-01 ( PROT SER 14 CA ) 0.69710E-01 ( PROT SER 14 CB ) 0.55768E-01 ( PROT SER 14 OG ) 0.55768E-01 ( PROT SER 14 HG ) 0.55768E-01 ( PROT SER 14 C ) 0.69710E-01 ( PROT SER 14 O ) 0.69710E-01 ( PROT LYS 15 N ) 0.69710E-01 ( PROT LYS 15 H ) 0.55768E-01 ( PROT LYS 15 CA ) 0.69710E-01 ( PROT LYS 15 CB ) 0.55768E-01 ( PROT LYS 15 CG ) 0.55768E-01 ( PROT LYS 15 CD ) 0.55768E-01 ( PROT LYS 15 CE ) 0.55768E-01 ( PROT LYS 15 NZ ) 0.55768E-01 ( PROT LYS 15 HZ1 ) 0.55768E-01 ( PROT LYS 15 HZ2 ) 0.55768E-01 ( PROT LYS 15 HZ3 ) 0.55768E-01 ( PROT LYS 15 C ) 0.69710E-01 ( PROT LYS 15 O ) 0.69710E-01 ( PROT LEU 16 N ) 0.69710E-01 ( PROT LEU 16 H ) 0.55768E-01 ( PROT LEU 16 CA ) 0.69710E-01 ( PROT LEU 16 CB ) 0.55768E-01 ( PROT LEU 16 CG ) 0.55768E-01 ( PROT LEU 16 CD1 ) 0.55768E-01 ( PROT LEU 16 CD2 ) 0.55768E-01 ( PROT LEU 16 C ) 0.69710E-01 ( PROT LEU 16 O ) 0.69710E-01 ( PROT ALA 17 N ) 0.69710E-01 ( PROT ALA 17 H ) 0.55768E-01 ( PROT ALA 17 CA ) 0.69710E-01 ( PROT ALA 17 CB ) 0.55768E-01 ( PROT ALA 17 C ) 0.69710E-01 ( PROT ALA 17 O ) 0.69710E-01 ( PROT CYS 18 N ) 0.69710E-01 ( PROT CYS 18 H ) 0.55768E-01 ( PROT CYS 18 CA ) 0.69710E-01 ( PROT CYS 18 CB ) 0.55768E-01 ( PROT CYS 18 SG ) 0.55768E-01 ( PROT CYS 18 C ) 0.69710E-01 ( PROT CYS 18 O ) 0.69710E-01 ( PROT GLU 19 N ) 0.69710E-01 ( PROT GLU 19 H ) 0.55768E-01 ( PROT GLU 19 CA ) 0.69710E-01 ( PROT GLU 19 CB ) 0.55768E-01 ( PROT GLU 19 CG ) 0.55768E-01 ( PROT GLU 19 CD ) 0.55768E-01 ( PROT GLU 19 OE1 ) 0.55768E-01 ( PROT GLU 19 OE2 ) 0.55768E-01 ( PROT GLU 19 C ) 0.69710E-01 ( PROT GLU 19 OT1 ) 0.55768E-01 ( PROT GLU 19 OT2 ) 0.55768E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.42292 4.56743 -7.52126 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.01178 0.00780 -0.01137 ROTATION MATRIX 0.999999 -0.000691 -0.000851 0.000693 0.999999 0.001565 0.000850 -0.001566 0.999998 AXIS OF ROTATION IS 0.819115 0.444862 -0.362145 ANGLE IS 0.11 TOTAL SQUARE DIFF IS 137.8125 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.905711 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.9057" Parameter: A <- "0.9057" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.98388 4.32398 -7.78402 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.05167 -0.04371 0.05176 ROTATION MATRIX 0.999936 0.008747 0.007231 -0.008637 0.999848 -0.015134 -0.007362 0.015071 0.999859 AXIS OF ROTATION IS -0.799452 -0.386249 0.460095 ANGLE IS 1.08 CENTER OF ROTATION 8.964516 5.233869 -6.964695 SHIFT IS 0.082004 TOTAL SQUARE DIFF IS 9.8522 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.720096 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.9057" RDCMND substituted energy or value "?RMS" to " 0.7201" Parameter: A <- "0.9057 0.7201" 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 0.9057 0.7201 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 " 12.87" Parameter: H <- "12.87" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -84.72835 12.86567 0.10126 ENER INTERN> 4.35371 14.38736 0.00000 9.42356 2.69567 ENER EXTERN> -97.31603 -18.27261 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 " -84.73" Parameter: B <- "-84.73" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -18.27" Parameter: C <- "-18.27" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -97.32" Parameter: C <- " -115.59" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -115.59" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.35" Parameter: D <- "4.35" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.39" Parameter: D <- " 18.74" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 9.42" Parameter: D <- " 28.16" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.70" Parameter: D <- " 30.86" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 30.86" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 11400 ENER= -84.73 GRMS= 0.10 ELEC= -18.27 VDW= -97.32 RDTITL> *EXTERNAL= -115.59 INTERNAL= 30.86 USER= 0.00 HARM= 12.87 RDTITL> *BOND= 4.35 ANGL= 14.39 DIHE= 9.42 IMPR= 2.70 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 6/18/14 10:51:41 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 168 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 9460 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9444 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 -76.25834 -8.47000 0.04371 0.02000 MINI INTERN> 4.35371 14.38736 0.00000 9.42356 2.69567 MINI EXTERN> -97.31603 -18.27261 0.00000 0.00000 0.00000 MINI CONSTR> 8.47000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -72.31601 -3.94233 6.76951 0.00360 MINI INTERN> 7.97197 15.28653 0.00000 9.53271 2.66717 MINI EXTERN> -99.17260 -17.28990 0.00000 0.00000 0.00000 MINI CONSTR> 8.68811 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -76.26294 3.94693 0.45534 0.00065 MINI INTERN> 4.54366 14.75814 0.00000 9.55200 2.68979 MINI EXTERN> -98.97125 -17.51832 0.00000 0.00000 0.00000 MINI CONSTR> 8.68304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -76.30073 0.03779 0.39963 0.00028 MINI INTERN> 4.51168 14.67400 0.00000 9.53374 2.68127 MINI EXTERN> -98.72270 -17.65761 0.00000 0.00000 0.00000 MINI CONSTR> 8.67889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -76.32541 0.02468 0.12447 0.00012 MINI INTERN> 4.47376 14.63040 0.00000 9.51186 2.68432 MINI EXTERN> -98.58786 -17.71551 0.00000 0.00000 0.00000 MINI CONSTR> 8.67762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -76.33121 0.00580 0.17679 0.00013 MINI INTERN> 4.45388 14.59439 0.00000 9.49639 2.68752 MINI EXTERN> -98.47708 -17.76344 0.00000 0.00000 0.00000 MINI CONSTR> 8.67712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -76.33776 0.00655 0.05382 0.00005 MINI INTERN> 4.44946 14.56476 0.00000 9.48674 2.69065 MINI EXTERN> -98.41756 -17.78885 0.00000 0.00000 0.00000 MINI CONSTR> 8.67703 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -76.34064 0.00288 0.09073 0.00006 MINI INTERN> 4.44090 14.54505 0.00000 9.47719 2.69316 MINI EXTERN> -98.35898 -17.81525 0.00000 0.00000 0.00000 MINI CONSTR> 8.67730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -76.34297 0.00233 0.10176 0.00006 MINI INTERN> 4.43529 14.52967 0.00000 9.46962 2.69489 MINI EXTERN> -98.31314 -17.83708 0.00000 0.00000 0.00000 MINI CONSTR> 8.67777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -76.34469 0.00172 0.11801 0.00006 MINI INTERN> 4.43072 14.51773 0.00000 9.46324 2.69627 MINI EXTERN> -98.27644 -17.85463 0.00000 0.00000 0.00000 MINI CONSTR> 8.67840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -76.34626 0.00157 0.10901 0.00006 MINI INTERN> 4.42771 14.50938 0.00000 9.45870 2.69749 MINI EXTERN> -98.25165 -17.86691 0.00000 0.00000 0.00000 MINI CONSTR> 8.67902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -76.34767 0.00141 0.11340 0.00006 MINI INTERN> 4.42486 14.50080 0.00000 9.45382 2.69837 MINI EXTERN> -98.22593 -17.87942 0.00000 0.00000 0.00000 MINI CONSTR> 8.67985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -76.34987 0.00221 0.03761 0.00003 MINI INTERN> 4.42598 14.49075 0.00000 9.44985 2.70025 MINI EXTERN> -98.20658 -17.89086 0.00000 0.00000 0.00000 MINI CONSTR> 8.68073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -76.35092 0.00105 0.02498 0.00003 MINI INTERN> 4.42372 14.48609 0.00000 9.44668 2.70055 MINI EXTERN> -98.19140 -17.89810 0.00000 0.00000 0.00000 MINI CONSTR> 8.68154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -76.35216 0.00124 0.04569 0.00003 MINI INTERN> 4.42250 14.47924 0.00000 9.44251 2.70149 MINI EXTERN> -98.17289 -17.90784 0.00000 0.00000 0.00000 MINI CONSTR> 8.68282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -76.35322 0.00106 0.03257 0.00003 MINI INTERN> 4.42069 14.47528 0.00000 9.43960 2.70161 MINI EXTERN> -98.16048 -17.91379 0.00000 0.00000 0.00000 MINI CONSTR> 8.68387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -76.35423 0.00101 0.03558 0.00003 MINI INTERN> 4.41950 14.47123 0.00000 9.43670 2.70188 MINI EXTERN> -98.14905 -17.91958 0.00000 0.00000 0.00000 MINI CONSTR> 8.68509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -76.35500 0.00077 0.05623 0.00003 MINI INTERN> 4.41909 14.46770 0.00000 9.43422 2.70231 MINI EXTERN> -98.14024 -17.92436 0.00000 0.00000 0.00000 MINI CONSTR> 8.68629 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -76.35592 0.00092 0.05822 0.00003 MINI INTERN> 4.41811 14.46474 0.00000 9.43179 2.70240 MINI EXTERN> -98.13207 -17.92849 0.00000 0.00000 0.00000 MINI CONSTR> 8.68760 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -76.35679 0.00087 0.06310 0.00004 MINI INTERN> 4.41737 14.46212 0.00000 9.42955 2.70245 MINI EXTERN> -98.12524 -17.93200 0.00000 0.00000 0.00000 MINI CONSTR> 8.68896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -76.35758 0.00079 0.06925 0.00004 MINI INTERN> 4.41685 14.45987 0.00000 9.42756 2.70247 MINI EXTERN> -98.11980 -17.93484 0.00000 0.00000 0.00000 MINI CONSTR> 8.69031 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -76.35835 0.00077 0.06498 0.00004 MINI INTERN> 4.41628 14.45812 0.00000 9.42599 2.70231 MINI EXTERN> -98.11576 -17.93676 0.00000 0.00000 0.00000 MINI CONSTR> 8.69148 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -76.35917 0.00082 0.06705 0.00004 MINI INTERN> 4.41580 14.45635 0.00000 9.42420 2.70219 MINI EXTERN> -98.11184 -17.93878 0.00000 0.00000 0.00000 MINI CONSTR> 8.69291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -76.36025 0.00108 0.02061 0.00002 MINI INTERN> 4.41414 14.45494 0.00000 9.42272 2.70106 MINI EXTERN> -98.10779 -17.93953 0.00000 0.00000 0.00000 MINI CONSTR> 8.69421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9436 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -76.36064 0.00039 0.07316 0.00004 MINI INTERN> 4.41521 14.45350 0.00000 9.42119 2.70193 MINI EXTERN> -98.10656 -17.94156 0.00000 0.00000 0.00000 MINI CONSTR> 8.69565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -76.36138 0.00075 0.07525 0.00004 MINI INTERN> 4.41497 14.45230 0.00000 9.41977 2.70175 MINI EXTERN> -98.10468 -17.94257 0.00000 0.00000 0.00000 MINI CONSTR> 8.69708 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -76.36212 0.00074 0.07845 0.00005 MINI INTERN> 4.41480 14.45123 0.00000 9.41839 2.70157 MINI EXTERN> -98.10329 -17.94338 0.00000 0.00000 0.00000 MINI CONSTR> 8.69856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -76.36331 0.00119 0.02412 0.00002 MINI INTERN> 4.41305 14.45002 0.00000 9.41721 2.70014 MINI EXTERN> -98.10081 -17.94290 0.00000 0.00000 0.00000 MINI CONSTR> 8.69998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -76.36394 0.00063 0.01940 0.00002 MINI INTERN> 4.41303 14.44929 0.00000 9.41620 2.70008 MINI EXTERN> -98.10045 -17.94330 0.00000 0.00000 0.00000 MINI CONSTR> 8.70120 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -76.36467 0.00073 0.01912 0.00002 MINI INTERN> 4.41292 14.44846 0.00000 9.41505 2.69987 MINI EXTERN> -98.10012 -17.94351 0.00000 0.00000 0.00000 MINI CONSTR> 8.70266 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -76.36541 0.00074 0.01903 0.00002 MINI INTERN> 4.41283 14.44769 0.00000 9.41392 2.69963 MINI EXTERN> -98.10009 -17.94357 0.00000 0.00000 0.00000 MINI CONSTR> 8.70418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -76.36615 0.00074 0.01932 0.00002 MINI INTERN> 4.41276 14.44699 0.00000 9.41282 2.69939 MINI EXTERN> -98.10032 -17.94349 0.00000 0.00000 0.00000 MINI CONSTR> 8.70571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -76.36685 0.00071 0.03881 0.00002 MINI INTERN> 4.41244 14.44616 0.00000 9.41172 2.69879 MINI EXTERN> -98.10041 -17.94294 0.00000 0.00000 0.00000 MINI CONSTR> 8.70739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -76.36755 0.00070 0.02436 0.00002 MINI INTERN> 4.41260 14.44578 0.00000 9.41081 2.69882 MINI EXTERN> -98.10135 -17.94292 0.00000 0.00000 0.00000 MINI CONSTR> 8.70872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -76.36826 0.00071 0.02475 0.00003 MINI INTERN> 4.41260 14.44527 0.00000 9.40983 2.69859 MINI EXTERN> -98.10224 -17.94255 0.00000 0.00000 0.00000 MINI CONSTR> 8.71024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -76.36896 0.00070 0.02730 0.00003 MINI INTERN> 4.41258 14.44480 0.00000 9.40889 2.69833 MINI EXTERN> -98.10327 -17.94207 0.00000 0.00000 0.00000 MINI CONSTR> 8.71178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -76.36951 0.00055 0.04670 0.00003 MINI INTERN> 4.41243 14.44425 0.00000 9.40806 2.69786 MINI EXTERN> -98.10407 -17.94128 0.00000 0.00000 0.00000 MINI CONSTR> 8.71325 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -76.37017 0.00066 0.04721 0.00003 MINI INTERN> 4.41247 14.44390 0.00000 9.40719 2.69765 MINI EXTERN> -98.10538 -17.94073 0.00000 0.00000 0.00000 MINI CONSTR> 8.71473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -76.37084 0.00067 0.04898 0.00003 MINI INTERN> 4.41250 14.44356 0.00000 9.40633 2.69743 MINI EXTERN> -98.10682 -17.94011 0.00000 0.00000 0.00000 MINI CONSTR> 8.71625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -76.37149 0.00065 0.05272 0.00003 MINI INTERN> 4.41253 14.44326 0.00000 9.40550 2.69719 MINI EXTERN> -98.10836 -17.93941 0.00000 0.00000 0.00000 MINI CONSTR> 8.71779 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -76.37210 0.00061 0.05829 0.00003 MINI INTERN> 4.41255 14.44299 0.00000 9.40470 2.69694 MINI EXTERN> -98.10991 -17.93866 0.00000 0.00000 0.00000 MINI CONSTR> 8.71928 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -76.37268 0.00059 0.05512 0.00003 MINI INTERN> 4.41268 14.44280 0.00000 9.40398 2.69682 MINI EXTERN> -98.11145 -17.93807 0.00000 0.00000 0.00000 MINI CONSTR> 8.72056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -76.37331 0.00063 0.05763 0.00003 MINI INTERN> 4.41274 14.44260 0.00000 9.40321 2.69661 MINI EXTERN> -98.11321 -17.93732 0.00000 0.00000 0.00000 MINI CONSTR> 8.72206 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -76.37395 0.00064 0.05916 0.00004 MINI INTERN> 4.41280 14.44246 0.00000 9.40243 2.69642 MINI EXTERN> -98.11509 -17.93655 0.00000 0.00000 0.00000 MINI CONSTR> 8.72357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -76.37479 0.00084 0.01824 0.00002 MINI INTERN> 4.41369 14.44270 0.00000 9.40142 2.69692 MINI EXTERN> -98.11793 -17.93655 0.00000 0.00000 0.00000 MINI CONSTR> 8.72495 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -76.37511 0.00031 0.06444 0.00004 MINI INTERN> 4.41295 14.44221 0.00000 9.40101 2.69604 MINI EXTERN> -98.11873 -17.93499 0.00000 0.00000 0.00000 MINI CONSTR> 8.72641 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -76.37571 0.00060 0.06596 0.00004 MINI INTERN> 4.41301 14.44216 0.00000 9.40029 2.69587 MINI EXTERN> -98.12071 -17.93420 0.00000 0.00000 0.00000 MINI CONSTR> 8.72786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -76.37632 0.00061 0.06805 0.00004 MINI INTERN> 4.41305 14.44219 0.00000 9.39957 2.69570 MINI EXTERN> -98.12279 -17.93341 0.00000 0.00000 0.00000 MINI CONSTR> 8.72936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -76.37692 0.00060 0.07110 0.00004 MINI INTERN> 4.41306 14.44231 0.00000 9.39886 2.69553 MINI EXTERN> -98.12493 -17.93263 0.00000 0.00000 0.00000 MINI CONSTR> 8.73088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -76.37790 0.00098 0.02214 0.00002 MINI INTERN> 4.41460 14.44207 0.00000 9.39758 2.69615 MINI EXTERN> -98.12839 -17.93226 0.00000 0.00000 0.00000 MINI CONSTR> 8.73234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9435 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -76.37842 0.00052 0.01744 0.00002 MINI INTERN> 4.41449 14.44208 0.00000 9.39706 2.69594 MINI EXTERN> -98.13003 -17.93151 0.00000 0.00000 0.00000 MINI CONSTR> 8.73355 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -76.37902 0.00061 0.01726 0.00002 MINI INTERN> 4.41463 14.44202 0.00000 9.39634 2.69579 MINI EXTERN> -98.13221 -17.93060 0.00000 0.00000 0.00000 MINI CONSTR> 8.73501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9434 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -76.37964 0.00062 0.01722 0.00002 MINI INTERN> 4.41480 14.44197 0.00000 9.39560 2.69563 MINI EXTERN> -98.13450 -17.92965 0.00000 0.00000 0.00000 MINI CONSTR> 8.73651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -76.38026 0.00062 0.01746 0.00002 MINI INTERN> 4.41499 14.44191 0.00000 9.39485 2.69549 MINI EXTERN> -98.13685 -17.92868 0.00000 0.00000 0.00000 MINI CONSTR> 8.73803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9434 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -76.38087 0.00061 0.03381 0.00002 MINI INTERN> 4.41589 14.44135 0.00000 9.39385 2.69548 MINI EXTERN> -98.13977 -17.92739 0.00000 0.00000 0.00000 MINI CONSTR> 8.73970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -76.38146 0.00059 0.02207 0.00002 MINI INTERN> 4.41559 14.44165 0.00000 9.39334 2.69526 MINI EXTERN> -98.14164 -17.92666 0.00000 0.00000 0.00000 MINI CONSTR> 8.74100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9434 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -76.38206 0.00060 0.02180 0.00002 MINI INTERN> 4.41575 14.44163 0.00000 9.39264 2.69511 MINI EXTERN> -98.14399 -17.92568 0.00000 0.00000 0.00000 MINI CONSTR> 8.74249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -76.38267 0.00061 0.02257 0.00002 MINI INTERN> 4.41596 14.44158 0.00000 9.39191 2.69497 MINI EXTERN> -98.14644 -17.92465 0.00000 0.00000 0.00000 MINI CONSTR> 8.74400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9433 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -76.38326 0.00059 0.02577 0.00003 MINI INTERN> 4.41628 14.44146 0.00000 9.39115 2.69486 MINI EXTERN> -98.14895 -17.92358 0.00000 0.00000 0.00000 MINI CONSTR> 8.74551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -76.38373 0.00046 0.04265 0.00003 MINI INTERN> 4.41709 14.44091 0.00000 9.39034 2.69484 MINI EXTERN> -98.15148 -17.92235 0.00000 0.00000 0.00000 MINI CONSTR> 8.74692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9432 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -76.38430 0.00057 0.04349 0.00003 MINI INTERN> 4.41728 14.44091 0.00000 9.38965 2.69472 MINI EXTERN> -98.15388 -17.92134 0.00000 0.00000 0.00000 MINI CONSTR> 8.74837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -76.38487 0.00057 0.04561 0.00003 MINI INTERN> 4.41751 14.44089 0.00000 9.38894 2.69460 MINI EXTERN> -98.15638 -17.92029 0.00000 0.00000 0.00000 MINI CONSTR> 8.74985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9432 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -76.38542 0.00055 0.04971 0.00003 MINI INTERN> 4.41781 14.44084 0.00000 9.38821 2.69450 MINI EXTERN> -98.15891 -17.91922 0.00000 0.00000 0.00000 MINI CONSTR> 8.75133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -76.38595 0.00052 0.04817 0.00003 MINI INTERN> 4.41791 14.44094 0.00000 9.38762 2.69438 MINI EXTERN> -98.16105 -17.91838 0.00000 0.00000 0.00000 MINI CONSTR> 8.75262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9432 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -76.38648 0.00053 0.05101 0.00003 MINI INTERN> 4.41816 14.44095 0.00000 9.38694 2.69428 MINI EXTERN> -98.16346 -17.91737 0.00000 0.00000 0.00000 MINI CONSTR> 8.75403 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -76.38703 0.00055 0.05320 0.00003 MINI INTERN> 4.41836 14.44103 0.00000 9.38625 2.69418 MINI EXTERN> -98.16595 -17.91636 0.00000 0.00000 0.00000 MINI CONSTR> 8.75547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9432 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -76.38758 0.00056 0.05442 0.00003 MINI INTERN> 4.41852 14.44117 0.00000 9.38556 2.69406 MINI EXTERN> -98.16847 -17.91536 0.00000 0.00000 0.00000 MINI CONSTR> 8.75693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -76.38832 0.00073 0.01689 0.00001 MINI INTERN> 4.41709 14.44266 0.00000 9.38539 2.69366 MINI EXTERN> -98.16980 -17.91554 0.00000 0.00000 0.00000 MINI CONSTR> 8.75821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9432 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -76.38858 0.00026 0.05931 0.00004 MINI INTERN> 4.41895 14.44129 0.00000 9.38428 2.69388 MINI EXTERN> -98.17313 -17.91346 0.00000 0.00000 0.00000 MINI CONSTR> 8.75961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -76.38911 0.00052 0.06087 0.00004 MINI INTERN> 4.41910 14.44146 0.00000 9.38362 2.69377 MINI EXTERN> -98.17556 -17.91250 0.00000 0.00000 0.00000 MINI CONSTR> 8.76100 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9431 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -76.38963 0.00053 0.06304 0.00004 MINI INTERN> 4.41924 14.44169 0.00000 9.38294 2.69366 MINI EXTERN> -98.17808 -17.91151 0.00000 0.00000 0.00000 MINI CONSTR> 8.76243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -76.39015 0.00052 0.06629 0.00004 MINI INTERN> 4.41939 14.44194 0.00000 9.38226 2.69355 MINI EXTERN> -98.18064 -17.91051 0.00000 0.00000 0.00000 MINI CONSTR> 8.76386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9431 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -76.39100 0.00085 0.02147 0.00002 MINI INTERN> 4.41793 14.44309 0.00000 9.38222 2.69310 MINI EXTERN> -98.18159 -17.91094 0.00000 0.00000 0.00000 MINI CONSTR> 8.76519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -76.39145 0.00044 0.01595 0.00002 MINI INTERN> 4.41821 14.44307 0.00000 9.38163 2.69306 MINI EXTERN> -98.18370 -17.91002 0.00000 0.00000 0.00000 MINI CONSTR> 8.76631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9431 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -76.39198 0.00053 0.01583 0.00002 MINI INTERN> 4.41840 14.44315 0.00000 9.38099 2.69296 MINI EXTERN> -98.18610 -17.90907 0.00000 0.00000 0.00000 MINI CONSTR> 8.76769 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -76.39252 0.00054 0.01588 0.00002 MINI INTERN> 4.41860 14.44324 0.00000 9.38034 2.69286 MINI EXTERN> -98.18853 -17.90812 0.00000 0.00000 0.00000 MINI CONSTR> 8.76910 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9431 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -76.39305 0.00053 0.01632 0.00002 MINI INTERN> 4.41878 14.44332 0.00000 9.37970 2.69275 MINI EXTERN> -98.19094 -17.90719 0.00000 0.00000 0.00000 MINI CONSTR> 8.77051 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -76.39355 0.00050 0.03278 0.00002 MINI INTERN> 4.41894 14.44330 0.00000 9.37918 2.69259 MINI EXTERN> -98.19308 -17.90650 0.00000 0.00000 0.00000 MINI CONSTR> 8.77201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9431 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -76.39407 0.00052 0.02025 0.00002 MINI INTERN> 4.41915 14.44345 0.00000 9.37851 2.69255 MINI EXTERN> -98.19550 -17.90545 0.00000 0.00000 0.00000 MINI CONSTR> 8.77323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -76.39459 0.00052 0.02050 0.00002 MINI INTERN> 4.41937 14.44350 0.00000 9.37788 2.69246 MINI EXTERN> -98.19790 -17.90451 0.00000 0.00000 0.00000 MINI CONSTR> 8.77461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9431 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -76.39511 0.00052 0.02229 0.00002 MINI INTERN> 4.41959 14.44352 0.00000 9.37725 2.69237 MINI EXTERN> -98.20028 -17.90359 0.00000 0.00000 0.00000 MINI CONSTR> 8.77601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -76.39553 0.00042 0.03916 0.00002 MINI INTERN> 4.41993 14.44325 0.00000 9.37678 2.69227 MINI EXTERN> -98.20222 -17.90292 0.00000 0.00000 0.00000 MINI CONSTR> 8.77737 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9431 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -76.39603 0.00050 0.03927 0.00003 MINI INTERN> 4.42017 14.44326 0.00000 9.37618 2.69220 MINI EXTERN> -98.20451 -17.90201 0.00000 0.00000 0.00000 MINI CONSTR> 8.77869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -76.39653 0.00050 0.04026 0.00003 MINI INTERN> 4.42043 14.44324 0.00000 9.37556 2.69213 MINI EXTERN> -98.20686 -17.90108 0.00000 0.00000 0.00000 MINI CONSTR> 8.78006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9430 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -76.39703 0.00050 0.04245 0.00003 MINI INTERN> 4.42069 14.44320 0.00000 9.37495 2.69207 MINI EXTERN> -98.20923 -17.90015 0.00000 0.00000 0.00000 MINI CONSTR> 8.78144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -76.39751 0.00048 0.04652 0.00003 MINI INTERN> 4.42095 14.44316 0.00000 9.37436 2.69201 MINI EXTERN> -98.21154 -17.89926 0.00000 0.00000 0.00000 MINI CONSTR> 8.78281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9429 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -76.39797 0.00046 0.04485 0.00003 MINI INTERN> 4.42112 14.44329 0.00000 9.37380 2.69193 MINI EXTERN> -98.21366 -17.89844 0.00000 0.00000 0.00000 MINI CONSTR> 8.78400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -76.39844 0.00047 0.04724 0.00003 MINI INTERN> 4.42131 14.44334 0.00000 9.37322 2.69186 MINI EXTERN> -98.21592 -17.89757 0.00000 0.00000 0.00000 MINI CONSTR> 8.78532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9429 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -76.39892 0.00048 0.04896 0.00003 MINI INTERN> 4.42144 14.44349 0.00000 9.37261 2.69180 MINI EXTERN> -98.21827 -17.89666 0.00000 0.00000 0.00000 MINI CONSTR> 8.78667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -76.39941 0.00049 0.04976 0.00003 MINI INTERN> 4.42148 14.44377 0.00000 9.37200 2.69172 MINI EXTERN> -98.22068 -17.89572 0.00000 0.00000 0.00000 MINI CONSTR> 8.78802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9429 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -76.40006 0.00064 0.01561 0.00001 MINI INTERN> 4.42137 14.44518 0.00000 9.37103 2.69147 MINI EXTERN> -98.22385 -17.89448 0.00000 0.00000 0.00000 MINI CONSTR> 8.78923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -76.40030 0.00024 0.05428 0.00004 MINI INTERN> 4.42171 14.44411 0.00000 9.37087 2.69158 MINI EXTERN> -98.22504 -17.89407 0.00000 0.00000 0.00000 MINI CONSTR> 8.79053 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9429 ATOM PAIRS WERE FOUND FOR ATOM LIST 268 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -76.40077 0.00047 0.05535 0.00004 MINI INTERN> 4.42165 14.44454 0.00000 9.37027 2.69149 MINI EXTERN> -98.22739 -17.89317 0.00000 0.00000 0.00000 MINI CONSTR> 8.79184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -76.40146 0.00070 0.01711 0.00002 MINI INTERN> 4.42200 14.44555 0.00000 9.36925 2.69121 MINI EXTERN> -98.23062 -17.89193 0.00000 0.00000 0.00000 MINI CONSTR> 8.79307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9428 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -76.40163 0.00016 0.05937 0.00004 MINI INTERN> 4.42183 14.44498 0.00000 9.36916 2.69134 MINI EXTERN> -98.23170 -17.89154 0.00000 0.00000 0.00000 MINI CONSTR> 8.79431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -76.40209 0.00046 0.06278 0.00004 MINI INTERN> 4.42155 14.44570 0.00000 9.36853 2.69123 MINI EXTERN> -98.23417 -17.89059 0.00000 0.00000 0.00000 MINI CONSTR> 8.79567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9428 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -76.40286 0.00077 0.02096 0.00002 MINI INTERN> 4.42277 14.44582 0.00000 9.36746 2.69096 MINI EXTERN> -98.23740 -17.88938 0.00000 0.00000 0.00000 MINI CONSTR> 8.79692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -76.40325 0.00040 0.01468 0.00002 MINI INTERN> 4.42263 14.44602 0.00000 9.36705 2.69091 MINI EXTERN> -98.23908 -17.88875 0.00000 0.00000 0.00000 MINI CONSTR> 8.79796 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9429 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -76.40373 0.00048 0.01465 0.00002 MINI INTERN> 4.42283 14.44616 0.00000 9.36645 2.69083 MINI EXTERN> -98.24139 -17.88789 0.00000 0.00000 0.00000 MINI CONSTR> 8.79928 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -76.40422 0.00048 0.01487 0.00002 MINI INTERN> 4.42305 14.44628 0.00000 9.36584 2.69075 MINI EXTERN> -98.24373 -17.88702 0.00000 0.00000 0.00000 MINI CONSTR> 8.80061 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9429 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -76.40469 0.00047 0.02881 0.00002 MINI INTERN> 4.42406 14.44599 0.00000 9.36507 2.69063 MINI EXTERN> -98.24645 -17.88606 0.00000 0.00000 0.00000 MINI CONSTR> 8.80207 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 -76.40469 0.00047 0.02881 0.00002 STPD INTERN> 4.42406 14.44599 0.00000 9.36507 2.69063 STPD EXTERN> -98.24645 -17.88606 0.00000 0.00000 0.00000 STPD CONSTR> 8.80207 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 9429 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9429 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 -76.40469 0.00047 0.02881 0.00000 MINI INTERN> 4.42406 14.44599 0.00000 9.36507 2.69063 MINI EXTERN> -98.24645 -17.88606 0.00000 0.00000 0.00000 MINI CONSTR> 8.80207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -76.47410 0.06942 0.01998 0.00383 MINI INTERN> 4.48047 14.50854 0.00000 9.19871 2.66896 MINI EXTERN> -98.90031 -17.62550 0.00000 0.00000 0.00000 MINI CONSTR> 9.19503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -76.47588 0.00178 0.06133 0.00352 MINI INTERN> 4.47534 14.51006 0.00000 9.19833 2.66349 MINI EXTERN> -98.89578 -17.62510 0.00000 0.00000 0.00000 MINI CONSTR> 9.19778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -76.49118 0.01530 0.08963 0.04769 MINI INTERN> 4.42183 14.45472 0.00000 9.19231 2.65624 MINI EXTERN> -98.89416 -17.53962 0.00000 0.00000 0.00000 MINI CONSTR> 9.21751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -76.50586 0.01468 0.08019 0.02974 MINI INTERN> 4.48153 14.61317 0.00000 9.16613 2.68293 MINI EXTERN> -98.94382 -17.73869 0.00000 0.00000 0.00000 MINI CONSTR> 9.23289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -76.51483 0.00897 0.06423 0.02324 MINI INTERN> 4.48768 14.61971 0.00000 9.14999 2.68127 MINI EXTERN> -98.93836 -17.75457 0.00000 0.00000 0.00000 MINI CONSTR> 9.23946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -76.52166 0.00683 0.06035 0.01790 MINI INTERN> 4.49729 14.63600 0.00000 9.14988 2.66794 MINI EXTERN> -98.86926 -17.84323 0.00000 0.00000 0.00000 MINI CONSTR> 9.23972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -76.52826 0.00659 0.06960 0.01902 MINI INTERN> 4.48444 14.62833 0.00000 9.13884 2.66597 MINI EXTERN> -98.77468 -17.90798 0.00000 0.00000 0.00000 MINI CONSTR> 9.23683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -76.53277 0.00451 0.04458 0.00895 MINI INTERN> 4.46301 14.61315 0.00000 9.12652 2.65806 MINI EXTERN> -98.75239 -17.87566 0.00000 0.00000 0.00000 MINI CONSTR> 9.23455 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -76.53563 0.00286 0.04084 0.00570 MINI INTERN> 4.47396 14.60066 0.00000 9.12974 2.64608 MINI EXTERN> -98.75994 -17.85906 0.00000 0.00000 0.00000 MINI CONSTR> 9.23293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -76.53876 0.00313 0.03987 0.00732 MINI INTERN> 4.46032 14.60145 0.00000 9.12274 2.63995 MINI EXTERN> -98.74806 -17.84700 0.00000 0.00000 0.00000 MINI CONSTR> 9.23183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -76.54206 0.00330 0.05560 0.01295 MINI INTERN> 4.46225 14.58715 0.00000 9.11256 2.64445 MINI EXTERN> -98.76106 -17.81931 0.00000 0.00000 0.00000 MINI CONSTR> 9.23188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -76.54647 0.00441 0.05268 0.01375 MINI INTERN> 4.46159 14.59871 0.00000 9.11906 2.64358 MINI EXTERN> -98.79623 -17.80748 0.00000 0.00000 0.00000 MINI CONSTR> 9.23430 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -76.55051 0.00403 0.04607 0.01331 MINI INTERN> 4.46510 14.56991 0.00000 9.12767 2.65098 MINI EXTERN> -98.78603 -17.81599 0.00000 0.00000 0.00000 MINI CONSTR> 9.23785 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -76.55431 0.00380 0.04643 0.01077 MINI INTERN> 4.46822 14.55878 0.00000 9.14678 2.65257 MINI EXTERN> -98.84424 -17.77918 0.00000 0.00000 0.00000 MINI CONSTR> 9.24277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -76.55718 0.00287 0.04680 0.00851 MINI INTERN> 4.46334 14.58605 0.00000 9.16413 2.65823 MINI EXTERN> -98.88768 -17.78786 0.00000 0.00000 0.00000 MINI CONSTR> 9.24662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -76.55986 0.00268 0.03488 0.00961 MINI INTERN> 4.47316 14.58770 0.00000 9.17749 2.65533 MINI EXTERN> -98.90928 -17.79417 0.00000 0.00000 0.00000 MINI CONSTR> 9.24991 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -76.56165 0.00179 0.03307 0.00652 MINI INTERN> 4.46929 14.60175 0.00000 9.18137 2.65007 MINI EXTERN> -98.93569 -17.77984 0.00000 0.00000 0.00000 MINI CONSTR> 9.25140 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -76.56347 0.00182 0.02956 0.00658 MINI INTERN> 4.46453 14.58742 0.00000 9.19415 2.65816 MINI EXTERN> -98.91017 -17.80879 0.00000 0.00000 0.00000 MINI CONSTR> 9.25123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -76.56482 0.00136 0.02743 0.00534 MINI INTERN> 4.47088 14.56234 0.00000 9.20043 2.66176 MINI EXTERN> -98.89422 -17.81619 0.00000 0.00000 0.00000 MINI CONSTR> 9.25017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -76.56585 0.00102 0.02670 0.00417 MINI INTERN> 4.46985 14.56550 0.00000 9.19592 2.66528 MINI EXTERN> -98.90546 -17.80502 0.00000 0.00000 0.00000 MINI CONSTR> 9.24809 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 -76.56585 0.00102 0.02670 0.02000 CONJ INTERN> 4.46985 14.56550 0.00000 9.19592 2.66528 CONJ EXTERN> -98.90546 -17.80502 0.00000 0.00000 0.00000 CONJ CONSTR> 9.24809 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 ALA 1 HT1 ) 0.36249E-01 ( PROT ALA 1 HT2 ) 0.36249E-01 ( PROT ALA 1 N ) 0.45311E-01 ( PROT ALA 1 HT3 ) 0.36249E-01 ( PROT ALA 1 CA ) 0.45311E-01 ( PROT ALA 1 CB ) 0.36249E-01 ( PROT ALA 1 C ) 0.45311E-01 ( PROT ALA 1 O ) 0.45311E-01 ( PROT LEU 2 N ) 0.45311E-01 ( PROT LEU 2 H ) 0.36249E-01 ( PROT LEU 2 CA ) 0.45311E-01 ( PROT LEU 2 CB ) 0.36249E-01 ( PROT LEU 2 CG ) 0.36249E-01 ( PROT LEU 2 CD1 ) 0.36249E-01 ( PROT LEU 2 CD2 ) 0.36249E-01 ( PROT LEU 2 C ) 0.45311E-01 ( PROT LEU 2 O ) 0.45311E-01 ( PROT GLN 3 N ) 0.45311E-01 ( PROT GLN 3 H ) 0.36249E-01 ( PROT GLN 3 CA ) 0.45311E-01 ( PROT GLN 3 CB ) 0.36249E-01 ( PROT GLN 3 CG ) 0.36249E-01 ( PROT GLN 3 CD ) 0.36249E-01 ( PROT GLN 3 OE1 ) 0.36249E-01 ( PROT GLN 3 NE2 ) 0.36249E-01 ( PROT GLN 3 HE21 ) 0.36249E-01 ( PROT GLN 3 HE22 ) 0.36249E-01 ( PROT GLN 3 C ) 0.45311E-01 ( PROT GLN 3 O ) 0.45311E-01 ( PROT ALA 4 N ) 0.45311E-01 ( PROT ALA 4 H ) 0.36249E-01 ( PROT ALA 4 CA ) 0.45311E-01 ( PROT ALA 4 CB ) 0.36249E-01 ( PROT ALA 4 C ) 0.45311E-01 ( PROT ALA 4 O ) 0.45311E-01 ( PROT PHE 5 N ) 0.45311E-01 ( PROT PHE 5 H ) 0.36249E-01 ( PROT PHE 5 CA ) 0.45311E-01 ( PROT PHE 5 CB ) 0.36249E-01 ( PROT PHE 5 CG ) 0.36249E-01 ( PROT PHE 5 CD1 ) 0.36249E-01 ( PROT PHE 5 CD2 ) 0.36249E-01 ( PROT PHE 5 CE1 ) 0.36249E-01 ( PROT PHE 5 CE2 ) 0.36249E-01 ( PROT PHE 5 CZ ) 0.36249E-01 ( PROT PHE 5 C ) 0.45311E-01 ( PROT PHE 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 ILE 7 N ) 0.45311E-01 ( PROT ILE 7 H ) 0.36249E-01 ( PROT ILE 7 CA ) 0.45311E-01 ( PROT ILE 7 CB ) 0.36249E-01 ( PROT ILE 7 CG2 ) 0.36249E-01 ( PROT ILE 7 CG1 ) 0.36249E-01 ( PROT ILE 7 CD ) 0.36249E-01 ( PROT ILE 7 C ) 0.45311E-01 ( PROT ILE 7 O ) 0.45311E-01 ( PROT ALA 8 N ) 0.45311E-01 ( PROT ALA 8 H ) 0.36249E-01 ( PROT ALA 8 CA ) 0.45311E-01 ( PROT ALA 8 CB ) 0.36249E-01 ( PROT ALA 8 C ) 0.45311E-01 ( PROT ALA 8 O ) 0.45311E-01 ( PROT LEU 9 N ) 0.45311E-01 ( PROT LEU 9 H ) 0.36249E-01 ( PROT LEU 9 CA ) 0.45311E-01 ( PROT LEU 9 CB ) 0.36249E-01 ( PROT LEU 9 CG ) 0.36249E-01 ( PROT LEU 9 CD1 ) 0.36249E-01 ( PROT LEU 9 CD2 ) 0.36249E-01 ( PROT LEU 9 C ) 0.45311E-01 ( PROT LEU 9 O ) 0.45311E-01 ( PROT SER 10 N ) 0.45311E-01 ( PROT SER 10 H ) 0.36249E-01 ( PROT SER 10 CA ) 0.45311E-01 ( PROT SER 10 CB ) 0.36249E-01 ( PROT SER 10 OG ) 0.36249E-01 ( PROT SER 10 HG ) 0.36249E-01 ( PROT SER 10 C ) 0.45311E-01 ( PROT SER 10 O ) 0.45311E-01 ( PROT SER 11 N ) 0.45311E-01 ( PROT SER 11 H ) 0.36249E-01 ( PROT SER 11 CA ) 0.45311E-01 ( PROT SER 11 CB ) 0.36249E-01 ( PROT SER 11 OG ) 0.36249E-01 ( PROT SER 11 HG ) 0.36249E-01 ( PROT SER 11 C ) 0.45311E-01 ( PROT SER 11 O ) 0.45311E-01 ( PROT PHE 12 N ) 0.45311E-01 ( PROT PHE 12 H ) 0.36249E-01 ( PROT PHE 12 CA ) 0.45311E-01 ( PROT PHE 12 CB ) 0.36249E-01 ( PROT PHE 12 CG ) 0.36249E-01 ( PROT PHE 12 CD1 ) 0.36249E-01 ( PROT PHE 12 CD2 ) 0.36249E-01 ( PROT PHE 12 CE1 ) 0.36249E-01 ( PROT PHE 12 CE2 ) 0.36249E-01 ( PROT PHE 12 CZ ) 0.36249E-01 ( PROT PHE 12 C ) 0.45311E-01 ( PROT PHE 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 SER 14 N ) 0.45311E-01 ( PROT SER 14 H ) 0.36249E-01 ( PROT SER 14 CA ) 0.45311E-01 ( PROT SER 14 CB ) 0.36249E-01 ( PROT SER 14 OG ) 0.36249E-01 ( PROT SER 14 HG ) 0.36249E-01 ( PROT SER 14 C ) 0.45311E-01 ( PROT SER 14 O ) 0.45311E-01 ( PROT LYS 15 N ) 0.45311E-01 ( PROT LYS 15 H ) 0.36249E-01 ( PROT LYS 15 CA ) 0.45311E-01 ( PROT LYS 15 CB ) 0.36249E-01 ( PROT LYS 15 CG ) 0.36249E-01 ( PROT LYS 15 CD ) 0.36249E-01 ( PROT LYS 15 CE ) 0.36249E-01 ( PROT LYS 15 NZ ) 0.36249E-01 ( PROT LYS 15 HZ1 ) 0.36249E-01 ( PROT LYS 15 HZ2 ) 0.36249E-01 ( PROT LYS 15 HZ3 ) 0.36249E-01 ( PROT LYS 15 C ) 0.45311E-01 ( PROT LYS 15 O ) 0.45311E-01 ( PROT LEU 16 N ) 0.45311E-01 ( PROT LEU 16 H ) 0.36249E-01 ( PROT LEU 16 CA ) 0.45311E-01 ( PROT LEU 16 CB ) 0.36249E-01 ( PROT LEU 16 CG ) 0.36249E-01 ( PROT LEU 16 CD1 ) 0.36249E-01 ( PROT LEU 16 CD2 ) 0.36249E-01 ( PROT LEU 16 C ) 0.45311E-01 ( PROT LEU 16 O ) 0.45311E-01 ( PROT ALA 17 N ) 0.45311E-01 ( PROT ALA 17 H ) 0.36249E-01 ( PROT ALA 17 CA ) 0.45311E-01 ( PROT ALA 17 CB ) 0.36249E-01 ( PROT ALA 17 C ) 0.45311E-01 ( PROT ALA 17 O ) 0.45311E-01 ( PROT CYS 18 N ) 0.45311E-01 ( PROT CYS 18 H ) 0.36249E-01 ( PROT CYS 18 CA ) 0.45311E-01 ( PROT CYS 18 CB ) 0.36249E-01 ( PROT CYS 18 SG ) 0.36249E-01 ( PROT CYS 18 C ) 0.45311E-01 ( PROT CYS 18 O ) 0.45311E-01 ( PROT GLU 19 N ) 0.45311E-01 ( PROT GLU 19 H ) 0.36249E-01 ( PROT GLU 19 CA ) 0.45311E-01 ( PROT GLU 19 CB ) 0.36249E-01 ( PROT GLU 19 CG ) 0.36249E-01 ( PROT GLU 19 CD ) 0.36249E-01 ( PROT GLU 19 OE1 ) 0.36249E-01 ( PROT GLU 19 OE2 ) 0.36249E-01 ( PROT GLU 19 C ) 0.45311E-01 ( PROT GLU 19 OT1 ) 0.36249E-01 ( PROT GLU 19 OT2 ) 0.36249E-01 CHARMM> CHARMM> FORMAT (F7.4) CHARMM> ! protein structural changes. CHARMM> ! prot only CHARMM> coor orie rms sele ( prot ) end SELRPN> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.41916 4.56361 -7.51741 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.01554 0.01161 -0.01522 ROTATION MATRIX 0.999999 -0.001125 -0.001209 0.001128 0.999997 0.002243 0.001207 -0.002244 0.999997 AXIS OF ROTATION IS 0.805378 0.433542 -0.404238 ANGLE IS 0.16 TOTAL SQUARE DIFF IS 152.6787 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 0.953311 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.9533" Parameter: A <- "0.9533" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.98851 4.33284 -7.79658 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.05630 -0.05258 0.06432 ROTATION MATRIX 0.999957 0.007210 0.005866 -0.007137 0.999898 -0.012378 -0.005954 0.012336 0.999906 AXIS OF ROTATION IS -0.799161 -0.382216 0.463954 ANGLE IS 0.89 TOTAL SQUARE DIFF IS 10.7402 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.751848 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.9533" RDCMND substituted energy or value "?RMS" to " 0.7518" Parameter: A <- "0.9533 0.7518" 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 0.9533 0.7518 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 " 9.25" Parameter: H <- "9.25" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -85.81394 9.24809 0.07159 ENER INTERN> 4.46985 14.56550 0.00000 9.19592 2.66528 ENER EXTERN> -98.90546 -17.80502 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 " -85.81" Parameter: B <- "-85.81" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " -17.81" Parameter: C <- "-17.81" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -98.91" Parameter: C <- " -116.72" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -116.72" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.47" Parameter: D <- "4.47" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.57" Parameter: D <- " 19.04" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 9.20" Parameter: D <- " 28.24" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.67" Parameter: D <- " 30.91" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 30.91" 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= -85.81 GRMS= 0.07 ELEC= -17.81 VDW= -98.91 RDTITL> *EXTERNAL= -116.72 INTERNAL= 30.91 USER= 0.00 HARM= 9.25 RDTITL> *BOND= 4.47 ANGL= 14.57 DIHE= 9.20 IMPR= 2.67 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= -85.81 GRMS= 0.07 ELEC= -17.81 VDW= -98.91 RDTITL> *EXTERNAL= -116.72 INTERNAL= 30.91 USER= 0.00 HARM= 9.25 RDTITL> *BOND= 4.47 ANGL= 14.57 DIHE= 9.20 IMPR= 2.67 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= -85.81 GRMS= 0.07 ELEC= -17.81 VDW= -98.91 RDTITL> *EXTERNAL= -116.72 INTERNAL= 30.91 USER= 0.00 HARM= 9.25 RDTITL> *BOND= 4.47 ANGL= 14.57 DIHE= 9.20 IMPR= 2.67 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 12000 0.9533 0.7518 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 ALA 1 HT1 ) 0.0000 ( PROT ALA 1 HT2 ) 0.0000 ( PROT ALA 1 N ) 0.0000 ( PROT ALA 1 HT3 ) 0.0000 ( PROT ALA 1 CA ) 0.0000 ( PROT ALA 1 CB ) 0.0000 ( PROT ALA 1 C ) 0.0000 ( PROT ALA 1 O ) 0.0000 ( PROT LEU 2 N ) 0.0000 ( PROT LEU 2 H ) 0.0000 ( PROT LEU 2 CA ) 0.0000 ( PROT LEU 2 CB ) 0.0000 ( PROT LEU 2 CG ) 0.0000 ( PROT LEU 2 CD1 ) 0.0000 ( PROT LEU 2 CD2 ) 0.0000 ( PROT LEU 2 C ) 0.0000 ( PROT LEU 2 O ) 0.0000 ( PROT GLN 3 N ) 0.0000 ( PROT GLN 3 H ) 0.0000 ( PROT GLN 3 CA ) 0.0000 ( PROT GLN 3 CB ) 0.0000 ( PROT GLN 3 CG ) 0.0000 ( PROT GLN 3 CD ) 0.0000 ( PROT GLN 3 OE1 ) 0.0000 ( PROT GLN 3 NE2 ) 0.0000 ( PROT GLN 3 HE21 ) 0.0000 ( PROT GLN 3 HE22 ) 0.0000 ( PROT GLN 3 C ) 0.0000 ( PROT GLN 3 O ) 0.0000 ( PROT ALA 4 N ) 0.0000 ( PROT ALA 4 H ) 0.0000 ( PROT ALA 4 CA ) 0.0000 ( PROT ALA 4 CB ) 0.0000 ( PROT ALA 4 C ) 0.0000 ( PROT ALA 4 O ) 0.0000 ( PROT PHE 5 N ) 0.0000 ( PROT PHE 5 H ) 0.0000 ( PROT PHE 5 CA ) 0.0000 ( PROT PHE 5 CB ) 0.0000 ( PROT PHE 5 CG ) 0.0000 ( PROT PHE 5 CD1 ) 0.0000 ( PROT PHE 5 CD2 ) 0.0000 ( PROT PHE 5 CE1 ) 0.0000 ( PROT PHE 5 CE2 ) 0.0000 ( PROT PHE 5 CZ ) 0.0000 ( PROT PHE 5 C ) 0.0000 ( PROT PHE 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 ILE 7 N ) 0.0000 ( PROT ILE 7 H ) 0.0000 ( PROT ILE 7 CA ) 0.0000 ( PROT ILE 7 CB ) 0.0000 ( PROT ILE 7 CG2 ) 0.0000 ( PROT ILE 7 CG1 ) 0.0000 ( PROT ILE 7 CD ) 0.0000 ( PROT ILE 7 C ) 0.0000 ( PROT ILE 7 O ) 0.0000 ( PROT ALA 8 N ) 0.0000 ( PROT ALA 8 H ) 0.0000 ( PROT ALA 8 CA ) 0.0000 ( PROT ALA 8 CB ) 0.0000 ( PROT ALA 8 C ) 0.0000 ( PROT ALA 8 O ) 0.0000 ( PROT LEU 9 N ) 0.0000 ( PROT LEU 9 H ) 0.0000 ( PROT LEU 9 CA ) 0.0000 ( PROT LEU 9 CB ) 0.0000 ( PROT LEU 9 CG ) 0.0000 ( PROT LEU 9 CD1 ) 0.0000 ( PROT LEU 9 CD2 ) 0.0000 ( PROT LEU 9 C ) 0.0000 ( PROT LEU 9 O ) 0.0000 ( PROT SER 10 N ) 0.0000 ( PROT SER 10 H ) 0.0000 ( PROT SER 10 CA ) 0.0000 ( PROT SER 10 CB ) 0.0000 ( PROT SER 10 OG ) 0.0000 ( PROT SER 10 HG ) 0.0000 ( PROT SER 10 C ) 0.0000 ( PROT SER 10 O ) 0.0000 ( PROT SER 11 N ) 0.0000 ( PROT SER 11 H ) 0.0000 ( PROT SER 11 CA ) 0.0000 ( PROT SER 11 CB ) 0.0000 ( PROT SER 11 OG ) 0.0000 ( PROT SER 11 HG ) 0.0000 ( PROT SER 11 C ) 0.0000 ( PROT SER 11 O ) 0.0000 ( PROT PHE 12 N ) 0.0000 ( PROT PHE 12 H ) 0.0000 ( PROT PHE 12 CA ) 0.0000 ( PROT PHE 12 CB ) 0.0000 ( PROT PHE 12 CG ) 0.0000 ( PROT PHE 12 CD1 ) 0.0000 ( PROT PHE 12 CD2 ) 0.0000 ( PROT PHE 12 CE1 ) 0.0000 ( PROT PHE 12 CE2 ) 0.0000 ( PROT PHE 12 CZ ) 0.0000 ( PROT PHE 12 C ) 0.0000 ( PROT PHE 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 SER 14 N ) 0.0000 ( PROT SER 14 H ) 0.0000 ( PROT SER 14 CA ) 0.0000 ( PROT SER 14 CB ) 0.0000 ( PROT SER 14 OG ) 0.0000 ( PROT SER 14 HG ) 0.0000 ( PROT SER 14 C ) 0.0000 ( PROT SER 14 O ) 0.0000 ( PROT LYS 15 N ) 0.0000 ( PROT LYS 15 H ) 0.0000 ( PROT LYS 15 CA ) 0.0000 ( PROT LYS 15 CB ) 0.0000 ( PROT LYS 15 CG ) 0.0000 ( PROT LYS 15 CD ) 0.0000 ( PROT LYS 15 CE ) 0.0000 ( PROT LYS 15 NZ ) 0.0000 ( PROT LYS 15 HZ1 ) 0.0000 ( PROT LYS 15 HZ2 ) 0.0000 ( PROT LYS 15 HZ3 ) 0.0000 ( PROT LYS 15 C ) 0.0000 ( PROT LYS 15 O ) 0.0000 ( PROT LEU 16 N ) 0.0000 ( PROT LEU 16 H ) 0.0000 ( PROT LEU 16 CA ) 0.0000 ( PROT LEU 16 CB ) 0.0000 ( PROT LEU 16 CG ) 0.0000 ( PROT LEU 16 CD1 ) 0.0000 ( PROT LEU 16 CD2 ) 0.0000 ( PROT LEU 16 C ) 0.0000 ( PROT LEU 16 O ) 0.0000 ( PROT ALA 17 N ) 0.0000 ( PROT ALA 17 H ) 0.0000 ( PROT ALA 17 CA ) 0.0000 ( PROT ALA 17 CB ) 0.0000 ( PROT ALA 17 C ) 0.0000 ( PROT ALA 17 O ) 0.0000 ( PROT CYS 18 N ) 0.0000 ( PROT CYS 18 H ) 0.0000 ( PROT CYS 18 CA ) 0.0000 ( PROT CYS 18 CB ) 0.0000 ( PROT CYS 18 SG ) 0.0000 ( PROT CYS 18 C ) 0.0000 ( PROT CYS 18 O ) 0.0000 ( PROT GLU 19 N ) 0.0000 ( PROT GLU 19 H ) 0.0000 ( PROT GLU 19 CA ) 0.0000 ( PROT GLU 19 CB ) 0.0000 ( PROT GLU 19 CG ) 0.0000 ( PROT GLU 19 CD ) 0.0000 ( PROT GLU 19 OE1 ) 0.0000 ( PROT GLU 19 OE2 ) 0.0000 ( PROT GLU 19 C ) 0.0000 ( PROT GLU 19 OT1 ) 0.0000 ( PROT GLU 19 OT2 ) 0.0000 CHARMM> CHARMM> CHARMM> CHARMM> !write the structure after mini with constraints CHARMM> CHARMM> open unit 1 card write name ../coor/@output_intermediate.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" OPNLGU> Unit already open. The old file will be closed first. VCLOSE: Closing unit 1 with status "KEEP" VOPEN> Attempting to open::../coor/mini_helix_allh_intermediate.pdb:: OPNLGU> Unit 1 opened for WRITE access to ../coor/mini_helix_allh_intermediate.pdb CHARMM> write coor pdb unit 1 RDTITL> RDTITL> No title read. Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> ! 2000 conj grad. ! pour finir en beaute CHARMM> minimize conj nstep 2000 nprint 100 tolgrd 0.001 - CHARMM> inbfrq 10 NONBOND OPTION FLAGS: ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch BYGRoup NOEXtnd NOEWald CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000 WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000 NBXMOD = 5 There are 9429 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9424 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 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 -85.81394 9.24809 0.07159 0.00000 MINI INTERN> 4.46985 14.56550 0.00000 9.19592 2.66528 MINI EXTERN> -98.90546 -17.80502 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -86.80551 0.99157 0.07459 0.01379 MINI INTERN> 4.75838 15.08459 0.00000 8.90562 2.58690 MINI EXTERN> -101.97460 -16.16640 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9346 ATOM PAIRS WERE FOUND FOR ATOM LIST 267 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -86.80551 0.99157 0.07459 0.00000 MINI INTERN> 4.75838 15.08459 0.00000 8.90562 2.58690 MINI EXTERN> -101.97460 -16.16640 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -86.93137 0.12586 0.04254 0.01027 MINI INTERN> 4.73675 15.08651 0.00000 9.13686 2.59483 MINI EXTERN> -101.76599 -16.72033 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9363 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -86.93137 0.12586 0.04254 0.00000 MINI INTERN> 4.73675 15.08651 0.00000 9.13686 2.59483 MINI EXTERN> -101.76599 -16.72033 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -86.98330 0.05193 0.03961 0.00674 MINI INTERN> 4.78247 15.15374 0.00000 9.20515 2.60364 MINI EXTERN> -102.22064 -16.50765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9353 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -86.98330 0.05193 0.03961 0.00000 MINI INTERN> 4.78247 15.15374 0.00000 9.20515 2.60364 MINI EXTERN> -102.22064 -16.50765 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -87.00902 0.02572 0.02251 0.00536 MINI INTERN> 4.76208 15.08255 0.00000 9.32739 2.61222 MINI EXTERN> -102.06977 -16.72348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9363 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -87.00902 0.02572 0.02251 0.00000 MINI INTERN> 4.76208 15.08255 0.00000 9.32739 2.61222 MINI EXTERN> -102.06977 -16.72348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -87.02324 0.01422 0.03123 0.00484 MINI INTERN> 4.78786 15.12074 0.00000 9.36375 2.62085 MINI EXTERN> -102.32001 -16.59643 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9359 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -87.02324 0.01422 0.03123 0.00000 MINI INTERN> 4.78786 15.12074 0.00000 9.36375 2.62085 MINI EXTERN> -102.32001 -16.59643 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -87.03346 0.01021 0.01839 0.00463 MINI INTERN> 4.76940 15.08691 0.00000 9.43372 2.62685 MINI EXTERN> -102.21363 -16.73671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9365 ATOM PAIRS WERE FOUND FOR ATOM LIST 269 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -87.03346 0.01021 0.01839 0.00000 MINI INTERN> 4.76940 15.08691 0.00000 9.43372 2.62685 MINI EXTERN> -102.21363 -16.73671 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -87.04184 0.00838 0.02616 0.00451 MINI INTERN> 4.78862 15.12091 0.00000 9.46998 2.63474 MINI EXTERN> -102.40952 -16.64657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9361 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -87.04184 0.00838 0.02616 0.00000 MINI INTERN> 4.78862 15.12091 0.00000 9.46998 2.63474 MINI EXTERN> -102.40952 -16.64657 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -87.04970 0.00787 0.01918 0.00480 MINI INTERN> 4.76975 15.09390 0.00000 9.53326 2.64093 MINI EXTERN> -102.31080 -16.77673 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9368 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -87.04970 0.00787 0.01918 0.00000 MINI INTERN> 4.76975 15.09390 0.00000 9.53326 2.64093 MINI EXTERN> -102.31080 -16.77673 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -87.05857 0.00886 0.02859 0.00515 MINI INTERN> 4.78848 15.13530 0.00000 9.58157 2.64973 MINI EXTERN> -102.51372 -16.69994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9361 ATOM PAIRS WERE FOUND FOR ATOM LIST 270 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -87.05857 0.00886 0.02859 0.00000 MINI INTERN> 4.78848 15.13530 0.00000 9.58157 2.64973 MINI EXTERN> -102.51372 -16.69994 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -87.06765 0.00908 0.02054 0.00462 MINI INTERN> 4.76682 15.10247 0.00000 9.63606 2.65729 MINI EXTERN> -102.40551 -16.82477 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9372 ATOM PAIRS WERE FOUND FOR ATOM LIST 271 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -87.06765 0.00908 0.02054 0.00000 MINI INTERN> 4.76682 15.10247 0.00000 9.63606 2.65729 MINI EXTERN> -102.40551 -16.82477 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -87.07786 0.01021 0.03246 0.00613 MINI INTERN> 4.78705 15.13995 0.00000 9.68642 2.67003 MINI EXTERN> -102.61797 -16.74334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9364 ATOM PAIRS WERE FOUND FOR ATOM LIST 272 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -87.07786 0.01021 0.03246 0.00000 MINI INTERN> 4.78705 15.13995 0.00000 9.68642 2.67003 MINI EXTERN> -102.61797 -16.74334 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -87.09041 0.01255 0.02563 0.00580 MINI INTERN> 4.75951 15.09740 0.00000 9.74577 2.68036 MINI EXTERN> -102.48957 -16.88388 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9375 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -87.09041 0.01255 0.02563 0.00000 MINI INTERN> 4.75951 15.09740 0.00000 9.74577 2.68036 MINI EXTERN> -102.48957 -16.88388 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -87.10548 0.01507 0.03653 0.00670 MINI INTERN> 4.78452 15.14836 0.00000 9.80343 2.69572 MINI EXTERN> -102.75036 -16.78715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9368 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -87.10548 0.01507 0.03653 0.00000 MINI INTERN> 4.78452 15.14836 0.00000 9.80343 2.69572 MINI EXTERN> -102.75036 -16.78715 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -87.12254 0.01706 0.02594 0.00636 MINI INTERN> 4.75532 15.10582 0.00000 9.87200 2.70541 MINI EXTERN> -102.62562 -16.93547 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9379 ATOM PAIRS WERE FOUND FOR ATOM LIST 276 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -87.12254 0.01706 0.02594 0.00000 MINI INTERN> 4.75532 15.10582 0.00000 9.87200 2.70541 MINI EXTERN> -102.62562 -16.93547 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -87.14172 0.01918 0.07474 0.00819 MINI INTERN> 4.78336 15.16553 0.00000 9.94579 2.72043 MINI EXTERN> -102.92357 -16.83326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9368 ATOM PAIRS WERE FOUND FOR ATOM LIST 275 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -87.14172 0.01918 0.07474 0.00000 MINI INTERN> 4.78336 15.16553 0.00000 9.94579 2.72043 MINI EXTERN> -102.92357 -16.83326 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -87.16224 0.02052 0.02185 0.00712 MINI INTERN> 4.75013 15.12378 0.00000 10.01516 2.72688 MINI EXTERN> -102.82224 -16.95594 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9377 ATOM PAIRS WERE FOUND FOR ATOM LIST 275 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -87.16224 0.02052 0.02185 0.00000 MINI INTERN> 4.75013 15.12378 0.00000 10.01516 2.72688 MINI EXTERN> -102.82224 -16.95594 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -87.17952 0.01728 0.04972 0.00383 MINI INTERN> 4.77606 15.17359 0.00000 10.07096 2.73727 MINI EXTERN> -103.10581 -16.83159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9369 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -87.17952 0.01728 0.04972 0.00000 MINI INTERN> 4.77606 15.17359 0.00000 10.07096 2.73727 MINI EXTERN> -103.10581 -16.83159 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -87.18868 0.00916 0.00914 0.00231 MINI INTERN> 4.75588 15.14305 0.00000 10.10646 2.73898 MINI EXTERN> -103.06858 -16.86447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9376 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -87.18868 0.00916 0.00914 0.00000 MINI INTERN> 4.75588 15.14305 0.00000 10.10646 2.73898 MINI EXTERN> -103.06858 -16.86447 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -87.19199 0.00331 0.01860 0.00121 MINI INTERN> 4.76699 15.16343 0.00000 10.12453 2.74257 MINI EXTERN> -103.18795 -16.80156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9370 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -87.19199 0.00331 0.01860 0.00000 MINI INTERN> 4.76699 15.16343 0.00000 10.12453 2.74257 MINI EXTERN> -103.18795 -16.80156 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -87.19299 0.00100 0.00272 0.00065 MINI INTERN> 4.75976 15.15448 0.00000 10.13296 2.74194 MINI EXTERN> -103.17594 -16.80619 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 -87.19299 0.00100 0.00272 0.02000 CONJ INTERN> 4.75976 15.15448 0.00000 10.13296 2.74194 CONJ EXTERN> -103.17594 -16.80619 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 9370 atom pairs and 710 atom exclusions. There are 0 group pairs and 160 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9374 ATOM PAIRS WERE FOUND FOR ATOM LIST 274 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 -87.19299 0.00100 0.00272 0.00000 MINI INTERN> 4.75976 15.15448 0.00000 10.13296 2.74194 MINI EXTERN> -103.17594 -16.80619 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -87.19332 0.00033 0.00544 0.00049 MINI INTERN> 4.76333 15.16146 0.00000 10.13507 2.74248 MINI EXTERN> -103.20982 -16.78583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9372 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -87.19332 0.00033 0.00544 0.00000 MINI INTERN> 4.76333 15.16146 0.00000 10.13507 2.74248 MINI EXTERN> -103.20982 -16.78583 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -87.19346 0.00014 0.00126 0.00032 MINI INTERN> 4.76034 15.15815 0.00000 10.13546 2.74227 MINI EXTERN> -103.20077 -16.78891 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9374 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -87.19346 0.00014 0.00126 0.00000 MINI INTERN> 4.76034 15.15815 0.00000 10.13546 2.74227 MINI EXTERN> -103.20077 -16.78891 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -87.19352 0.00007 0.00257 0.00030 MINI INTERN> 4.76189 15.16158 0.00000 10.13412 2.74265 MINI EXTERN> -103.21287 -16.78089 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 13945 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 9374 ATOM PAIRS WERE FOUND FOR ATOM LIST 273 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -87.19352 0.00007 0.00257 0.00000 MINI INTERN> 4.76189 15.16158 0.00000 10.13412 2.74265 MINI EXTERN> -103.21287 -16.78089 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> 351 -87.19355 0.00002 0.00100 0.02000 CONJ INTERN> 4.76130 15.15927 0.00000 10.13523 2.74233 CONJ EXTERN> -103.21148 -16.78019 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> 168 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.37512 4.52189 -7.47458 CENTER OF REFERENCE COORDINATE SET 8.43470 4.57523 -7.53262 NET TRANSLATION OF ROTATED ATOMS 0.05958 0.05334 -0.05804 ROTATION MATRIX 0.999958 -0.006772 -0.006233 0.006846 0.999907 0.011824 0.006152 -0.011866 0.999911 AXIS OF ROTATION IS 0.789650 0.412817 -0.453911 ANGLE IS 0.86 TOTAL SQUARE DIFF IS 223.6057 DENOMINATOR IS 168.0000 THUS RMS DIFF IS 1.153684 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.1537" Parameter: A <- "1.1537" CHARMM> set a @a ?RMS Parameter: A -> "1.1537" RDCMND substituted energy or value "?RMS" to " 1.1537" Parameter: A <- "1.1537 1.1537" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 168 CENTER OF ATOMS BEFORE TRANSLATION 8.98262 4.32437 -7.83487 CENTER OF REFERENCE COORDINATE SET 8.93221 4.28026 -7.73226 NET TRANSLATION OF ROTATED ATOMS -0.05041 -0.04411 0.10260 ROTATION MATRIX 0.999996 -0.000610 0.002652 0.000620 0.999993 -0.003801 -0.002649 0.003803 0.999989 AXIS OF ROTATION IS -0.813242 -0.566875 -0.131495 ANGLE IS 0.27 TOTAL SQUARE DIFF IS 13.1755 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.832736 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.1537 1.1537" RDCMND substituted energy or value "?RMS" to " 0.8327" Parameter: A <- "1.1537 1.1537 0.8327" 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 1.1537 1.1537 0.8327 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" $$$$$$ New timer profile $$$$$ List time 0.00 Other: 0.00 Electrostatic & VDW 5.98 Other: 0.00 Nonbond force 6.00 Other: 0.02 Bond energy 0.06 Other: 0.00 Angle energy 0.50 Other: 0.00 Dihedral energy 0.30 Other: 0.00 Restraints energy 0.00 Other: 0.00 INTRNL energy 0.89 Other: 0.03 Energy time 6.95 Other: 0.06 Total time 7.62 Other: 0.66 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47522 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL 2 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 25100 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 7.62 SECONDS CPU TIME: 0.00 SECONDS