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 8/20/14 at 18: 9:54 by user: annesc Maximum number of ATOMS: 360720, and RESidues: 120240 Current HEAP size: 10240000, and STACK size: 10000000 RDTITL> * GENERATE PSF AND CHARMM COORDINATE SET FOR RDTITL> * HUMAN PHOSPHOLIPID SCRAMBLASE 1 RDTITL> * CHARMM> CHARMM> set name "helix_allh" Parameter: NAME <- ""helix_allh"" CHARMM> set output mini_@name ! this is the output : replace by any other complexe name ! Parameter: NAME -> ""helix_allh"" Parameter: OUTPUT <- "MINI_"helix_allh"" CHARMM> CHARMM> CHARMM> ! Read in Topology and Parameter files CHARMM> !_____________________________________ CHARMM> CHARMM> open unit 1 card read name "../lib/toph19_eef1.1.inp" VOPEN> Attempting to open::../lib/toph19_eef1.1.inp:: OPNLGU> Unit 1 opened for READONLY access to ../lib/toph19_eef1.1.inp CHARMM> read RTF card unit 1 MAINIO> Residue topology file being read from unit 1. TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 TITLE> * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL TITLE> * THIS DIFFERS FROM TOPH19_EEF1.INP IN: TITLE> * SCALED DOWN PARTIAL CHARGE DISTRIBUTIONS OF PSEUDO-IONIC AND TITLE> * POLAR SIDECHAINS, CTER, NTER TITLE> * INCLUDES (DE-)PROTONATED IONIC SIDECHAINS, PSEUDO-IONIC HIS AND AIB TITLE> * IN TYR CZ IS NOW TYPE CR TITLE> * THIS IS WORK IN PROGRESS. NO EXTENSIVE TESTS HAVE BEEN MADE. TITLE> * CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> open unit 1 card read name "../lib/param19_eef1.1.inp" VOPEN> Attempting to open::../lib/param19_eef1.1.inp:: OPNLGU> Unit 1 opened for READONLY access to ../lib/param19_eef1.1.inp CHARMM> read PARA card unit 1 PARAMETER FILE BEING READ FROM UNIT 1 TITLE> * - PARAMETER FILE PARAM19 * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 TITLE> * PARRDR> NOTE: atom type "CR " is removed from previous group PARRDR> NOTE: atom type "OC " is removed from previous group PARRDR> NOTE: atom type "OT " is removed from previous group PARRDR> NOTE: atom type "OH2 " is removed from previous group PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared. CHARMM> close unit 1 VCLOSE: Closing unit 1 with status "KEEP" CHARMM> CHARMM> CHARMM> CHARMM> ! Read in structure and psf file of the Bovine alpha lactalbumine 1f6r CHARMM> !_____________________________________________________________________ CHARMM> CHARMM> open read unit 9 card name ../lib/@name.psf Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../lib/helix_allh.psf:: OPNLGU> Unit 9 opened for READONLY access to ../lib/helix_allh.psf CHARMM> read psf card unit 9 MAINIO> Protein structure file being read from unit 9. TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 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 = 182 Number of groups = 68 Number of bonds = 185 Number of angles = 262 Number of dihedrals = 102 Number of impropers = 89 Number of cross-terms = 0 Number of HB acceptors = 24 Number of HB donors = 27 Number of NB exclusions = 12 Total charge = -0.00000 CHARMM> close unit 9 VCLOSE: Closing unit 9 with status "KEEP" CHARMM> CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 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 459 exclusions and 305 interactions(1-4) found 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11347 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 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 11347 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11347 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 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 140377.17883 0.00000 35281.15139 ENER INTERN> 185.61775 107.93003 0.00000 8.61972 2.65668 ENER EXTERN> 140114.98861 -42.63397 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> 182 atoms have been selected out of 182 CHARMM> define water sele ( segid solv) end SELRPN> 0 atoms have been selected out of 182 CHARMM> define nonh sele ( .not. hydrogen ) end SELRPN> 155 atoms have been selected out of 182 CHARMM> define trace sele ( type ca ) end SELRPN> 19 atoms have been selected out of 182 CHARMM> define back sele ( type n .or. type ca .or. type c ) end SELRPN> 57 atoms have been selected out of 182 CHARMM> define main sele ( type n .or. type ca .or. type c .or. type o) end SELRPN> 75 atoms have been selected out of 182 CHARMM> define side sele ( (.not. main) ) end SELRPN> 107 atoms have been selected out of 182 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: 182 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 182 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 182 CHARMM> CHARMM> ! { quite tight on sidechains of pcna } CHARMM> SCALar CONSTraint SET 200. SELEct ( prot .AND. side ) END SELRPN> 107 atoms have been selected out of 182 CHARMM> CHARMM> CHARMM> !SCALar CONSTraint SET 50. SELEct ( resname TIP3 ) END CHARMM> !SCALar CONSTraint SET 25. SELEct (side ) END CHARMM> CHARMM> ! to check CHARMM> SCAlar CONSTraint SHOW ( PROT LYS 1 HT1 ) 200.00 ( PROT LYS 1 HT2 ) 200.00 ( PROT LYS 1 N ) 250.00 ( PROT LYS 1 HT3 ) 200.00 ( PROT LYS 1 CA ) 250.00 ( PROT LYS 1 CB ) 200.00 ( PROT LYS 1 CG ) 200.00 ( PROT LYS 1 CD ) 200.00 ( PROT LYS 1 CE ) 200.00 ( PROT LYS 1 NZ ) 200.00 ( PROT LYS 1 HZ1 ) 200.00 ( PROT LYS 1 HZ2 ) 200.00 ( PROT LYS 1 HZ3 ) 200.00 ( PROT LYS 1 C ) 250.00 ( PROT LYS 1 O ) 250.00 ( PROT MET 2 N ) 250.00 ( PROT MET 2 H ) 200.00 ( PROT MET 2 CA ) 250.00 ( PROT MET 2 CB ) 200.00 ( PROT MET 2 CG ) 200.00 ( PROT MET 2 SD ) 200.00 ( PROT MET 2 CE ) 200.00 ( PROT MET 2 C ) 250.00 ( PROT MET 2 O ) 250.00 ( PROT LYS 3 N ) 250.00 ( PROT LYS 3 H ) 200.00 ( PROT LYS 3 CA ) 250.00 ( PROT LYS 3 CB ) 200.00 ( PROT LYS 3 CG ) 200.00 ( PROT LYS 3 CD ) 200.00 ( PROT LYS 3 CE ) 200.00 ( PROT LYS 3 NZ ) 200.00 ( PROT LYS 3 HZ1 ) 200.00 ( PROT LYS 3 HZ2 ) 200.00 ( PROT LYS 3 HZ3 ) 200.00 ( PROT LYS 3 C ) 250.00 ( PROT LYS 3 O ) 250.00 ( PROT ALA 4 N ) 250.00 ( PROT ALA 4 H ) 200.00 ( PROT ALA 4 CA ) 250.00 ( PROT ALA 4 CB ) 200.00 ( PROT ALA 4 C ) 250.00 ( PROT ALA 4 O ) 250.00 ( PROT VAL 5 N ) 250.00 ( PROT VAL 5 H ) 200.00 ( PROT VAL 5 CA ) 250.00 ( PROT VAL 5 CB ) 200.00 ( PROT VAL 5 CG1 ) 200.00 ( PROT VAL 5 CG2 ) 200.00 ( PROT VAL 5 C ) 250.00 ( PROT VAL 5 O ) 250.00 ( PROT MET 6 N ) 250.00 ( PROT MET 6 H ) 200.00 ( PROT MET 6 CA ) 250.00 ( PROT MET 6 CB ) 200.00 ( PROT MET 6 CG ) 200.00 ( PROT MET 6 SD ) 200.00 ( PROT MET 6 CE ) 200.00 ( PROT MET 6 C ) 250.00 ( PROT MET 6 O ) 250.00 ( PROT ILE 7 N ) 250.00 ( PROT ILE 7 H ) 200.00 ( PROT ILE 7 CA ) 250.00 ( PROT ILE 7 CB ) 200.00 ( PROT ILE 7 CG2 ) 200.00 ( PROT ILE 7 CG1 ) 200.00 ( PROT ILE 7 CD ) 200.00 ( PROT ILE 7 C ) 250.00 ( PROT ILE 7 O ) 250.00 ( PROT GLY 8 N ) 250.00 ( PROT GLY 8 H ) 200.00 ( PROT GLY 8 CA ) 250.00 ( PROT GLY 8 C ) 250.00 ( PROT GLY 8 O ) 250.00 ( PROT ALA 9 N ) 250.00 ( PROT ALA 9 H ) 200.00 ( PROT ALA 9 CA ) 250.00 ( PROT ALA 9 CB ) 200.00 ( PROT ALA 9 C ) 250.00 ( PROT ALA 9 O ) 250.00 ( PROT CYS 10 N ) 250.00 ( PROT CYS 10 H ) 200.00 ( PROT CYS 10 CA ) 250.00 ( PROT CYS 10 CB ) 200.00 ( PROT CYS 10 SG ) 200.00 ( PROT CYS 10 C ) 250.00 ( PROT CYS 10 O ) 250.00 ( PROT PHE 11 N ) 250.00 ( PROT PHE 11 H ) 200.00 ( PROT PHE 11 CA ) 250.00 ( PROT PHE 11 CB ) 200.00 ( PROT PHE 11 CG ) 200.00 ( PROT PHE 11 CD1 ) 200.00 ( PROT PHE 11 CD2 ) 200.00 ( PROT PHE 11 CE1 ) 200.00 ( PROT PHE 11 CE2 ) 200.00 ( PROT PHE 11 CZ ) 200.00 ( PROT PHE 11 C ) 250.00 ( PROT PHE 11 O ) 250.00 ( PROT LEU 12 N ) 250.00 ( PROT LEU 12 H ) 200.00 ( PROT LEU 12 CA ) 250.00 ( PROT LEU 12 CB ) 200.00 ( PROT LEU 12 CG ) 200.00 ( PROT LEU 12 CD1 ) 200.00 ( PROT LEU 12 CD2 ) 200.00 ( PROT LEU 12 C ) 250.00 ( PROT LEU 12 O ) 250.00 ( PROT ILE 13 N ) 250.00 ( PROT ILE 13 H ) 200.00 ( PROT ILE 13 CA ) 250.00 ( PROT ILE 13 CB ) 200.00 ( PROT ILE 13 CG2 ) 200.00 ( PROT ILE 13 CG1 ) 200.00 ( PROT ILE 13 CD ) 200.00 ( PROT ILE 13 C ) 250.00 ( PROT ILE 13 O ) 250.00 ( PROT ASP 14 N ) 250.00 ( PROT ASP 14 H ) 200.00 ( PROT ASP 14 CA ) 250.00 ( PROT ASP 14 CB ) 200.00 ( PROT ASP 14 CG ) 200.00 ( PROT ASP 14 OD1 ) 200.00 ( PROT ASP 14 OD2 ) 200.00 ( PROT ASP 14 C ) 250.00 ( PROT ASP 14 O ) 250.00 ( PROT PHE 15 N ) 250.00 ( PROT PHE 15 H ) 200.00 ( PROT PHE 15 CA ) 250.00 ( PROT PHE 15 CB ) 200.00 ( PROT PHE 15 CG ) 200.00 ( PROT PHE 15 CD1 ) 200.00 ( PROT PHE 15 CD2 ) 200.00 ( PROT PHE 15 CE1 ) 200.00 ( PROT PHE 15 CE2 ) 200.00 ( PROT PHE 15 CZ ) 200.00 ( PROT PHE 15 C ) 250.00 ( PROT PHE 15 O ) 250.00 ( PROT MET 16 N ) 250.00 ( PROT MET 16 H ) 200.00 ( PROT MET 16 CA ) 250.00 ( PROT MET 16 CB ) 200.00 ( PROT MET 16 CG ) 200.00 ( PROT MET 16 SD ) 200.00 ( PROT MET 16 CE ) 200.00 ( PROT MET 16 C ) 250.00 ( PROT MET 16 O ) 250.00 ( PROT PHE 17 N ) 250.00 ( PROT PHE 17 H ) 200.00 ( PROT PHE 17 CA ) 250.00 ( PROT PHE 17 CB ) 200.00 ( PROT PHE 17 CG ) 200.00 ( PROT PHE 17 CD1 ) 200.00 ( PROT PHE 17 CD2 ) 200.00 ( PROT PHE 17 CE1 ) 200.00 ( PROT PHE 17 CE2 ) 200.00 ( PROT PHE 17 CZ ) 200.00 ( PROT PHE 17 C ) 250.00 ( PROT PHE 17 O ) 250.00 ( PROT PHE 18 N ) 250.00 ( PROT PHE 18 H ) 200.00 ( PROT PHE 18 CA ) 250.00 ( PROT PHE 18 CB ) 200.00 ( PROT PHE 18 CG ) 200.00 ( PROT PHE 18 CD1 ) 200.00 ( PROT PHE 18 CD2 ) 200.00 ( PROT PHE 18 CE1 ) 200.00 ( PROT PHE 18 CE2 ) 200.00 ( PROT PHE 18 CZ ) 200.00 ( PROT PHE 18 C ) 250.00 ( PROT PHE 18 O ) 250.00 ( PROT GLU 19 N ) 250.00 ( PROT GLU 19 H ) 200.00 ( PROT GLU 19 CA ) 250.00 ( PROT GLU 19 CB ) 200.00 ( PROT GLU 19 CG ) 200.00 ( PROT GLU 19 CD ) 200.00 ( PROT GLU 19 OE1 ) 200.00 ( PROT GLU 19 OE2 ) 200.00 ( PROT GLU 19 C ) 250.00 ( PROT GLU 19 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: 3/17/14 17:11:11 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 11347 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11347 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 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 140377.17883 0.00000 35281.15139 0.02000 MINI INTERN> 185.61775 107.93003 0.00000 8.61972 2.65668 MINI EXTERN> 140114.98861 -42.63397 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 2254.39487 138122.78396 58.64952 0.02074 MINI INTERN> 324.96312 183.74436 0.00000 8.75631 102.66514 MINI EXTERN> 1115.34637 12.46599 0.00000 0.00000 0.00000 MINI CONSTR> 506.45358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11333 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1748.94827 505.44660 21.43271 0.00896 MINI INTERN> 57.09486 95.41346 0.00000 9.67735 30.13603 MINI EXTERN> 723.12297 12.14327 0.00000 0.00000 0.00000 MINI CONSTR> 821.36032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1720.69007 28.25820 7.19121 0.00387 MINI INTERN> 69.52472 92.36480 0.00000 10.20034 36.18535 MINI EXTERN> 635.40615 15.56475 0.00000 0.00000 0.00000 MINI CONSTR> 861.44397 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11333 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1717.40174 3.28832 3.60277 0.00167 MINI INTERN> 67.70113 91.48194 0.00000 9.97598 35.06748 MINI EXTERN> 632.23537 15.46100 0.00000 0.00000 0.00000 MINI CONSTR> 865.47884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1716.35613 1.04562 0.20538 0.00030 MINI INTERN> 67.16711 90.89751 0.00000 10.02790 34.73047 MINI EXTERN> 636.74189 15.71666 0.00000 0.00000 0.00000 MINI CONSTR> 861.07458 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11332 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1716.35291 0.00321 0.08575 0.00013 MINI INTERN> 67.04134 90.96679 0.00000 10.03222 34.76079 MINI EXTERN> 636.77234 15.73451 0.00000 0.00000 0.00000 MINI CONSTR> 861.04493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1716.35240 0.00051 0.04059 0.00006 MINI INTERN> 67.08637 90.92335 0.00000 10.03106 34.74980 MINI EXTERN> 636.71865 15.72814 0.00000 0.00000 0.00000 MINI CONSTR> 861.11503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11332 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1716.35227 0.00013 0.01418 0.00002 MINI INTERN> 67.06267 90.94164 0.00000 10.03146 34.75339 MINI EXTERN> 636.74866 15.73068 0.00000 0.00000 0.00000 MINI CONSTR> 861.08378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 1716.35226 0.00001 0.00945 0.00001 MINI INTERN> 67.07270 90.93187 0.00000 10.03136 34.75180 MINI EXTERN> 636.73636 15.72959 0.00000 0.00000 0.00000 MINI CONSTR> 861.09858 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> 45 1716.35226 0.00001 0.00945 0.00001 STPD INTERN> 67.07270 90.93187 0.00000 10.03136 34.75180 STPD EXTERN> 636.73636 15.72959 0.00000 0.00000 0.00000 STPD CONSTR> 861.09858 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 11332 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11332 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1716.35226 0.00001 0.00945 0.00000 MINI INTERN> 67.07270 90.93187 0.00000 10.03136 34.75180 MINI EXTERN> 636.73636 15.72959 0.00000 0.00000 0.00000 MINI CONSTR> 861.09858 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 1716.35225 0.00001 0.00046 0.02000 CONJ INTERN> 67.06807 90.93525 0.00000 10.03140 34.75192 CONJ EXTERN> 636.74553 15.72996 0.00000 0.00000 0.00000 CONJ CONSTR> 861.09013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 130.00 ( PROT LYS 1 HT2 ) 130.00 ( PROT LYS 1 N ) 162.50 ( PROT LYS 1 HT3 ) 130.00 ( PROT LYS 1 CA ) 162.50 ( PROT LYS 1 CB ) 130.00 ( PROT LYS 1 CG ) 130.00 ( PROT LYS 1 CD ) 130.00 ( PROT LYS 1 CE ) 130.00 ( PROT LYS 1 NZ ) 130.00 ( PROT LYS 1 HZ1 ) 130.00 ( PROT LYS 1 HZ2 ) 130.00 ( PROT LYS 1 HZ3 ) 130.00 ( PROT LYS 1 C ) 162.50 ( PROT LYS 1 O ) 162.50 ( PROT MET 2 N ) 162.50 ( PROT MET 2 H ) 130.00 ( PROT MET 2 CA ) 162.50 ( PROT MET 2 CB ) 130.00 ( PROT MET 2 CG ) 130.00 ( PROT MET 2 SD ) 130.00 ( PROT MET 2 CE ) 130.00 ( PROT MET 2 C ) 162.50 ( PROT MET 2 O ) 162.50 ( PROT LYS 3 N ) 162.50 ( PROT LYS 3 H ) 130.00 ( PROT LYS 3 CA ) 162.50 ( PROT LYS 3 CB ) 130.00 ( PROT LYS 3 CG ) 130.00 ( PROT LYS 3 CD ) 130.00 ( PROT LYS 3 CE ) 130.00 ( PROT LYS 3 NZ ) 130.00 ( PROT LYS 3 HZ1 ) 130.00 ( PROT LYS 3 HZ2 ) 130.00 ( PROT LYS 3 HZ3 ) 130.00 ( PROT LYS 3 C ) 162.50 ( PROT LYS 3 O ) 162.50 ( PROT ALA 4 N ) 162.50 ( PROT ALA 4 H ) 130.00 ( PROT ALA 4 CA ) 162.50 ( PROT ALA 4 CB ) 130.00 ( PROT ALA 4 C ) 162.50 ( PROT ALA 4 O ) 162.50 ( PROT VAL 5 N ) 162.50 ( PROT VAL 5 H ) 130.00 ( PROT VAL 5 CA ) 162.50 ( PROT VAL 5 CB ) 130.00 ( PROT VAL 5 CG1 ) 130.00 ( PROT VAL 5 CG2 ) 130.00 ( PROT VAL 5 C ) 162.50 ( PROT VAL 5 O ) 162.50 ( PROT MET 6 N ) 162.50 ( PROT MET 6 H ) 130.00 ( PROT MET 6 CA ) 162.50 ( PROT MET 6 CB ) 130.00 ( PROT MET 6 CG ) 130.00 ( PROT MET 6 SD ) 130.00 ( PROT MET 6 CE ) 130.00 ( PROT MET 6 C ) 162.50 ( PROT MET 6 O ) 162.50 ( PROT ILE 7 N ) 162.50 ( PROT ILE 7 H ) 130.00 ( PROT ILE 7 CA ) 162.50 ( PROT ILE 7 CB ) 130.00 ( PROT ILE 7 CG2 ) 130.00 ( PROT ILE 7 CG1 ) 130.00 ( PROT ILE 7 CD ) 130.00 ( PROT ILE 7 C ) 162.50 ( PROT ILE 7 O ) 162.50 ( PROT GLY 8 N ) 162.50 ( PROT GLY 8 H ) 130.00 ( PROT GLY 8 CA ) 162.50 ( PROT GLY 8 C ) 162.50 ( PROT GLY 8 O ) 162.50 ( PROT ALA 9 N ) 162.50 ( PROT ALA 9 H ) 130.00 ( PROT ALA 9 CA ) 162.50 ( PROT ALA 9 CB ) 130.00 ( PROT ALA 9 C ) 162.50 ( PROT ALA 9 O ) 162.50 ( PROT CYS 10 N ) 162.50 ( PROT CYS 10 H ) 130.00 ( PROT CYS 10 CA ) 162.50 ( PROT CYS 10 CB ) 130.00 ( PROT CYS 10 SG ) 130.00 ( PROT CYS 10 C ) 162.50 ( PROT CYS 10 O ) 162.50 ( PROT PHE 11 N ) 162.50 ( PROT PHE 11 H ) 130.00 ( PROT PHE 11 CA ) 162.50 ( PROT PHE 11 CB ) 130.00 ( PROT PHE 11 CG ) 130.00 ( PROT PHE 11 CD1 ) 130.00 ( PROT PHE 11 CD2 ) 130.00 ( PROT PHE 11 CE1 ) 130.00 ( PROT PHE 11 CE2 ) 130.00 ( PROT PHE 11 CZ ) 130.00 ( PROT PHE 11 C ) 162.50 ( PROT PHE 11 O ) 162.50 ( PROT LEU 12 N ) 162.50 ( PROT LEU 12 H ) 130.00 ( PROT LEU 12 CA ) 162.50 ( PROT LEU 12 CB ) 130.00 ( PROT LEU 12 CG ) 130.00 ( PROT LEU 12 CD1 ) 130.00 ( PROT LEU 12 CD2 ) 130.00 ( PROT LEU 12 C ) 162.50 ( PROT LEU 12 O ) 162.50 ( PROT ILE 13 N ) 162.50 ( PROT ILE 13 H ) 130.00 ( PROT ILE 13 CA ) 162.50 ( PROT ILE 13 CB ) 130.00 ( PROT ILE 13 CG2 ) 130.00 ( PROT ILE 13 CG1 ) 130.00 ( PROT ILE 13 CD ) 130.00 ( PROT ILE 13 C ) 162.50 ( PROT ILE 13 O ) 162.50 ( PROT ASP 14 N ) 162.50 ( PROT ASP 14 H ) 130.00 ( PROT ASP 14 CA ) 162.50 ( PROT ASP 14 CB ) 130.00 ( PROT ASP 14 CG ) 130.00 ( PROT ASP 14 OD1 ) 130.00 ( PROT ASP 14 OD2 ) 130.00 ( PROT ASP 14 C ) 162.50 ( PROT ASP 14 O ) 162.50 ( PROT PHE 15 N ) 162.50 ( PROT PHE 15 H ) 130.00 ( PROT PHE 15 CA ) 162.50 ( PROT PHE 15 CB ) 130.00 ( PROT PHE 15 CG ) 130.00 ( PROT PHE 15 CD1 ) 130.00 ( PROT PHE 15 CD2 ) 130.00 ( PROT PHE 15 CE1 ) 130.00 ( PROT PHE 15 CE2 ) 130.00 ( PROT PHE 15 CZ ) 130.00 ( PROT PHE 15 C ) 162.50 ( PROT PHE 15 O ) 162.50 ( PROT MET 16 N ) 162.50 ( PROT MET 16 H ) 130.00 ( PROT MET 16 CA ) 162.50 ( PROT MET 16 CB ) 130.00 ( PROT MET 16 CG ) 130.00 ( PROT MET 16 SD ) 130.00 ( PROT MET 16 CE ) 130.00 ( PROT MET 16 C ) 162.50 ( PROT MET 16 O ) 162.50 ( PROT PHE 17 N ) 162.50 ( PROT PHE 17 H ) 130.00 ( PROT PHE 17 CA ) 162.50 ( PROT PHE 17 CB ) 130.00 ( PROT PHE 17 CG ) 130.00 ( PROT PHE 17 CD1 ) 130.00 ( PROT PHE 17 CD2 ) 130.00 ( PROT PHE 17 CE1 ) 130.00 ( PROT PHE 17 CE2 ) 130.00 ( PROT PHE 17 CZ ) 130.00 ( PROT PHE 17 C ) 162.50 ( PROT PHE 17 O ) 162.50 ( PROT PHE 18 N ) 162.50 ( PROT PHE 18 H ) 130.00 ( PROT PHE 18 CA ) 162.50 ( PROT PHE 18 CB ) 130.00 ( PROT PHE 18 CG ) 130.00 ( PROT PHE 18 CD1 ) 130.00 ( PROT PHE 18 CD2 ) 130.00 ( PROT PHE 18 CE1 ) 130.00 ( PROT PHE 18 CE2 ) 130.00 ( PROT PHE 18 CZ ) 130.00 ( PROT PHE 18 C ) 162.50 ( PROT PHE 18 O ) 162.50 ( PROT GLU 19 N ) 162.50 ( PROT GLU 19 H ) 130.00 ( PROT GLU 19 CA ) 162.50 ( PROT GLU 19 CB ) 130.00 ( PROT GLU 19 CG ) 130.00 ( PROT GLU 19 CD ) 130.00 ( PROT GLU 19 OE1 ) 130.00 ( PROT GLU 19 OE2 ) 130.00 ( PROT GLU 19 C ) 162.50 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41256 5.26154 -8.67313 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS -0.00152 -0.00163 0.00143 ROTATION MATRIX 1.000000 -0.000026 -0.000031 0.000026 1.000000 0.000042 0.000030 -0.000042 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 4.0884 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.149879 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1499" Parameter: A <- "0.1499" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70621 5.25160 -8.78368 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00863 0.01283 -0.01069 ROTATION MATRIX 0.999952 0.007019 0.006810 -0.006969 0.999950 -0.007232 -0.006861 0.007184 0.999951 AXIS OF ROTATION IS -0.593304 -0.562646 0.575690 ANGLE IS 0.70 TOTAL SQUARE DIFF IS 0.0259 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.036916 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1499" RDCMND substituted energy or value "?RMS" to " 0.0369" Parameter: A <- "0.1499 0.0369" 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 0.1499 0.0369 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 " 861.09" Parameter: H <- "861.09" 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> 0 855.26213 861.09013 36.61589 ENER INTERN> 67.06807 90.93525 0.00000 10.03140 34.75192 ENER EXTERN> 636.74553 15.72996 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 " 855.26" Parameter: B <- "855.26" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 15.73" Parameter: C <- "15.73" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 636.75" Parameter: C <- " 652.48" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 652.48" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 67.07" Parameter: D <- "67.07" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 90.94" Parameter: D <- " 158.01" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.03" Parameter: D <- " 168.04" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 34.75" Parameter: D <- " 202.79" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 202.79" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 600 ENER= 855.26 GRMS= 36.62 ELEC= 15.73 VDW= 636.75 RDTITL> *EXTERNAL= 652.48 INTERNAL= 202.79 USER= 0.00 HARM= 861.09 RDTITL> *BOND= 67.07 ANGL= 90.94 DIHE= 10.03 IMPR= 34.75 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11332 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11332 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1478.44318 -623.18105 15.10525 0.02000 MINI INTERN> 67.06807 90.93525 0.00000 10.03140 34.75192 MINI EXTERN> 636.74553 15.72996 0.00000 0.00000 0.00000 MINI CONSTR> 623.18105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1412.40355 66.03963 17.53689 0.00864 MINI INTERN> 66.18264 89.32396 0.00000 11.18174 30.67674 MINI EXTERN> 516.75763 16.00758 0.00000 0.00000 0.00000 MINI CONSTR> 682.27327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11319 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1382.65582 29.74774 1.34444 0.00156 MINI INTERN> 56.20019 87.17063 0.00000 10.92378 28.24592 MINI EXTERN> 489.25697 17.02959 0.00000 0.00000 0.00000 MINI CONSTR> 693.82874 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1381.84678 0.80904 0.74103 0.00067 MINI INTERN> 55.70769 86.95853 0.00000 10.95263 28.43188 MINI EXTERN> 484.61494 17.07746 0.00000 0.00000 0.00000 MINI CONSTR> 698.10365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11320 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1381.80564 0.04114 0.48222 0.00029 MINI INTERN> 55.88563 86.85738 0.00000 10.92796 28.40625 MINI EXTERN> 485.58034 16.97021 0.00000 0.00000 0.00000 MINI CONSTR> 697.17788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1381.78017 0.02546 0.04088 0.00005 MINI INTERN> 55.93864 86.78931 0.00000 10.93798 28.42857 MINI EXTERN> 484.87437 17.01699 0.00000 0.00000 0.00000 MINI CONSTR> 697.79432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11320 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1381.77994 0.00023 0.03662 0.00002 MINI INTERN> 55.98573 86.80251 0.00000 10.94051 28.44360 MINI EXTERN> 484.56324 17.03633 0.00000 0.00000 0.00000 MINI CONSTR> 698.00802 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> 33 1381.77980 0.00014 0.00612 0.00001 STPD INTERN> 55.93639 86.78874 0.00000 10.93948 28.43376 STPD EXTERN> 484.73713 17.02489 0.00000 0.00000 0.00000 STPD CONSTR> 697.91941 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 11320 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11320 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1381.77980 0.00014 0.00612 0.00000 MINI INTERN> 55.93639 86.78874 0.00000 10.93948 28.43376 MINI EXTERN> 484.73713 17.02489 0.00000 0.00000 0.00000 MINI CONSTR> 697.91941 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 1381.77980 0.00000 0.00283 0.02000 CONJ INTERN> 55.94640 86.78905 0.00000 10.93965 28.43475 CONJ EXTERN> 484.70917 17.02711 0.00000 0.00000 0.00000 CONJ CONSTR> 697.93367 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "1200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 84.500 ( PROT LYS 1 HT2 ) 84.500 ( PROT LYS 1 N ) 105.63 ( PROT LYS 1 HT3 ) 84.500 ( PROT LYS 1 CA ) 105.63 ( PROT LYS 1 CB ) 84.500 ( PROT LYS 1 CG ) 84.500 ( PROT LYS 1 CD ) 84.500 ( PROT LYS 1 CE ) 84.500 ( PROT LYS 1 NZ ) 84.500 ( PROT LYS 1 HZ1 ) 84.500 ( PROT LYS 1 HZ2 ) 84.500 ( PROT LYS 1 HZ3 ) 84.500 ( PROT LYS 1 C ) 105.63 ( PROT LYS 1 O ) 105.63 ( PROT MET 2 N ) 105.63 ( PROT MET 2 H ) 84.500 ( PROT MET 2 CA ) 105.63 ( PROT MET 2 CB ) 84.500 ( PROT MET 2 CG ) 84.500 ( PROT MET 2 SD ) 84.500 ( PROT MET 2 CE ) 84.500 ( PROT MET 2 C ) 105.63 ( PROT MET 2 O ) 105.63 ( PROT LYS 3 N ) 105.63 ( PROT LYS 3 H ) 84.500 ( PROT LYS 3 CA ) 105.63 ( PROT LYS 3 CB ) 84.500 ( PROT LYS 3 CG ) 84.500 ( PROT LYS 3 CD ) 84.500 ( PROT LYS 3 CE ) 84.500 ( PROT LYS 3 NZ ) 84.500 ( PROT LYS 3 HZ1 ) 84.500 ( PROT LYS 3 HZ2 ) 84.500 ( PROT LYS 3 HZ3 ) 84.500 ( PROT LYS 3 C ) 105.63 ( PROT LYS 3 O ) 105.63 ( PROT ALA 4 N ) 105.63 ( PROT ALA 4 H ) 84.500 ( PROT ALA 4 CA ) 105.63 ( PROT ALA 4 CB ) 84.500 ( PROT ALA 4 C ) 105.63 ( PROT ALA 4 O ) 105.63 ( PROT VAL 5 N ) 105.63 ( PROT VAL 5 H ) 84.500 ( PROT VAL 5 CA ) 105.63 ( PROT VAL 5 CB ) 84.500 ( PROT VAL 5 CG1 ) 84.500 ( PROT VAL 5 CG2 ) 84.500 ( PROT VAL 5 C ) 105.63 ( PROT VAL 5 O ) 105.63 ( PROT MET 6 N ) 105.63 ( PROT MET 6 H ) 84.500 ( PROT MET 6 CA ) 105.63 ( PROT MET 6 CB ) 84.500 ( PROT MET 6 CG ) 84.500 ( PROT MET 6 SD ) 84.500 ( PROT MET 6 CE ) 84.500 ( PROT MET 6 C ) 105.63 ( PROT MET 6 O ) 105.63 ( PROT ILE 7 N ) 105.63 ( PROT ILE 7 H ) 84.500 ( PROT ILE 7 CA ) 105.63 ( PROT ILE 7 CB ) 84.500 ( PROT ILE 7 CG2 ) 84.500 ( PROT ILE 7 CG1 ) 84.500 ( PROT ILE 7 CD ) 84.500 ( PROT ILE 7 C ) 105.63 ( PROT ILE 7 O ) 105.63 ( PROT GLY 8 N ) 105.63 ( PROT GLY 8 H ) 84.500 ( PROT GLY 8 CA ) 105.63 ( PROT GLY 8 C ) 105.63 ( PROT GLY 8 O ) 105.63 ( PROT ALA 9 N ) 105.63 ( PROT ALA 9 H ) 84.500 ( PROT ALA 9 CA ) 105.63 ( PROT ALA 9 CB ) 84.500 ( PROT ALA 9 C ) 105.63 ( PROT ALA 9 O ) 105.63 ( PROT CYS 10 N ) 105.63 ( PROT CYS 10 H ) 84.500 ( PROT CYS 10 CA ) 105.63 ( PROT CYS 10 CB ) 84.500 ( PROT CYS 10 SG ) 84.500 ( PROT CYS 10 C ) 105.63 ( PROT CYS 10 O ) 105.63 ( PROT PHE 11 N ) 105.63 ( PROT PHE 11 H ) 84.500 ( PROT PHE 11 CA ) 105.63 ( PROT PHE 11 CB ) 84.500 ( PROT PHE 11 CG ) 84.500 ( PROT PHE 11 CD1 ) 84.500 ( PROT PHE 11 CD2 ) 84.500 ( PROT PHE 11 CE1 ) 84.500 ( PROT PHE 11 CE2 ) 84.500 ( PROT PHE 11 CZ ) 84.500 ( PROT PHE 11 C ) 105.63 ( PROT PHE 11 O ) 105.63 ( PROT LEU 12 N ) 105.63 ( PROT LEU 12 H ) 84.500 ( PROT LEU 12 CA ) 105.63 ( PROT LEU 12 CB ) 84.500 ( PROT LEU 12 CG ) 84.500 ( PROT LEU 12 CD1 ) 84.500 ( PROT LEU 12 CD2 ) 84.500 ( PROT LEU 12 C ) 105.63 ( PROT LEU 12 O ) 105.63 ( PROT ILE 13 N ) 105.63 ( PROT ILE 13 H ) 84.500 ( PROT ILE 13 CA ) 105.63 ( PROT ILE 13 CB ) 84.500 ( PROT ILE 13 CG2 ) 84.500 ( PROT ILE 13 CG1 ) 84.500 ( PROT ILE 13 CD ) 84.500 ( PROT ILE 13 C ) 105.63 ( PROT ILE 13 O ) 105.63 ( PROT ASP 14 N ) 105.63 ( PROT ASP 14 H ) 84.500 ( PROT ASP 14 CA ) 105.63 ( PROT ASP 14 CB ) 84.500 ( PROT ASP 14 CG ) 84.500 ( PROT ASP 14 OD1 ) 84.500 ( PROT ASP 14 OD2 ) 84.500 ( PROT ASP 14 C ) 105.63 ( PROT ASP 14 O ) 105.63 ( PROT PHE 15 N ) 105.63 ( PROT PHE 15 H ) 84.500 ( PROT PHE 15 CA ) 105.63 ( PROT PHE 15 CB ) 84.500 ( PROT PHE 15 CG ) 84.500 ( PROT PHE 15 CD1 ) 84.500 ( PROT PHE 15 CD2 ) 84.500 ( PROT PHE 15 CE1 ) 84.500 ( PROT PHE 15 CE2 ) 84.500 ( PROT PHE 15 CZ ) 84.500 ( PROT PHE 15 C ) 105.63 ( PROT PHE 15 O ) 105.63 ( PROT MET 16 N ) 105.63 ( PROT MET 16 H ) 84.500 ( PROT MET 16 CA ) 105.63 ( PROT MET 16 CB ) 84.500 ( PROT MET 16 CG ) 84.500 ( PROT MET 16 SD ) 84.500 ( PROT MET 16 CE ) 84.500 ( PROT MET 16 C ) 105.63 ( PROT MET 16 O ) 105.63 ( PROT PHE 17 N ) 105.63 ( PROT PHE 17 H ) 84.500 ( PROT PHE 17 CA ) 105.63 ( PROT PHE 17 CB ) 84.500 ( PROT PHE 17 CG ) 84.500 ( PROT PHE 17 CD1 ) 84.500 ( PROT PHE 17 CD2 ) 84.500 ( PROT PHE 17 CE1 ) 84.500 ( PROT PHE 17 CE2 ) 84.500 ( PROT PHE 17 CZ ) 84.500 ( PROT PHE 17 C ) 105.63 ( PROT PHE 17 O ) 105.63 ( PROT PHE 18 N ) 105.63 ( PROT PHE 18 H ) 84.500 ( PROT PHE 18 CA ) 105.63 ( PROT PHE 18 CB ) 84.500 ( PROT PHE 18 CG ) 84.500 ( PROT PHE 18 CD1 ) 84.500 ( PROT PHE 18 CD2 ) 84.500 ( PROT PHE 18 CE1 ) 84.500 ( PROT PHE 18 CE2 ) 84.500 ( PROT PHE 18 CZ ) 84.500 ( PROT PHE 18 C ) 105.63 ( PROT PHE 18 O ) 105.63 ( PROT GLU 19 N ) 105.63 ( PROT GLU 19 H ) 84.500 ( PROT GLU 19 CA ) 105.63 ( PROT GLU 19 CB ) 84.500 ( PROT GLU 19 CG ) 84.500 ( PROT GLU 19 CD ) 84.500 ( PROT GLU 19 OE1 ) 84.500 ( PROT GLU 19 OE2 ) 84.500 ( PROT GLU 19 C ) 105.63 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41256 5.26165 -8.67313 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS -0.00152 -0.00174 0.00144 ROTATION MATRIX 1.000000 -0.000028 -0.000031 0.000028 1.000000 0.000048 0.000031 -0.000048 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 5.0828 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.167115 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1671" Parameter: A <- "0.1671" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70632 5.24910 -8.78263 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00852 0.01532 -0.01174 ROTATION MATRIX 0.999930 0.008536 0.008211 -0.008464 0.999926 -0.008698 -0.008285 0.008628 0.999928 AXIS OF ROTATION IS -0.590366 -0.562089 0.579245 ANGLE IS 0.84 TOTAL SQUARE DIFF IS 0.0433 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.047764 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1671" RDCMND substituted energy or value "?RMS" to " 0.0478" Parameter: A <- "0.1671 0.0478" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *1200 0.1671 0.0478 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 697.93" Parameter: H <- "697.93" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 683.84612 697.93367 26.62208 ENER INTERN> 55.94640 86.78905 0.00000 10.93965 28.43475 ENER EXTERN> 484.70917 17.02711 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 " 683.85" Parameter: B <- "683.85" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 17.03" Parameter: C <- "17.03" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 484.71" Parameter: C <- " 501.74" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 501.74" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 55.95" Parameter: D <- "55.95" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 86.79" Parameter: D <- " 142.74" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.94" Parameter: D <- " 153.68" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 28.43" Parameter: D <- " 182.11" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 182.11" 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= 683.85 GRMS= 26.62 ELEC= 17.03 VDW= 484.71 RDTITL> *EXTERNAL= 501.74 INTERNAL= 182.11 USER= 0.00 HARM= 697.93 RDTITL> *BOND= 55.95 ANGL= 86.79 DIHE= 10.94 IMPR= 28.43 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= 683.85 GRMS= 26.62 ELEC= 17.03 VDW= 484.71 RDTITL> *EXTERNAL= 501.74 INTERNAL= 182.11 USER= 0.00 HARM= 697.93 RDTITL> *BOND= 55.95 ANGL= 86.79 DIHE= 10.94 IMPR= 28.43 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= 683.85 GRMS= 26.62 ELEC= 17.03 VDW= 484.71 RDTITL> *EXTERNAL= 501.74 INTERNAL= 182.11 USER= 0.00 HARM= 697.93 RDTITL> *BOND= 55.95 ANGL= 86.79 DIHE= 10.94 IMPR= 28.43 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 1200 0.1671 0.0478 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "1200" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11320 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11320 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 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 1197.06137 -513.21525 11.20367 0.02000 MINI INTERN> 55.94640 86.78905 0.00000 10.93965 28.43475 MINI EXTERN> 484.70917 17.02711 0.00000 0.00000 0.00000 MINI CONSTR> 513.21525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 1146.07152 50.98986 18.06439 0.00864 MINI INTERN> 97.65653 80.04419 0.00000 12.11168 22.17834 MINI EXTERN> 349.92297 21.64858 0.00000 0.00000 0.00000 MINI CONSTR> 562.50923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11309 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 1116.53522 29.53629 6.70630 0.00373 MINI INTERN> 41.11545 87.61411 0.00000 12.15276 22.22886 MINI EXTERN> 373.18390 16.33619 0.00000 0.00000 0.00000 MINI CONSTR> 563.90396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1111.67828 4.85695 2.81862 0.00161 MINI INTERN> 47.94309 83.86499 0.00000 12.25785 21.76410 MINI EXTERN> 365.38006 17.16420 0.00000 0.00000 0.00000 MINI CONSTR> 563.30400 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11308 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 1110.67941 0.99886 0.80359 0.00070 MINI INTERN> 47.20677 83.72486 0.00000 12.25770 22.32304 MINI EXTERN> 361.32472 17.15955 0.00000 0.00000 0.00000 MINI CONSTR> 566.68278 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 1110.56767 0.11174 0.38563 0.00030 MINI INTERN> 46.60532 83.24055 0.00000 12.25851 21.64984 MINI EXTERN> 364.56261 17.10160 0.00000 0.00000 0.00000 MINI CONSTR> 565.14924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11307 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 1110.54308 0.02459 0.05251 0.00005 MINI INTERN> 46.73664 83.30317 0.00000 12.26162 21.85583 MINI EXTERN> 363.32639 17.11697 0.00000 0.00000 0.00000 MINI CONSTR> 565.94247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 1110.54213 0.00095 0.08371 0.00006 MINI INTERN> 46.72819 83.26657 0.00000 12.26320 21.84899 MINI EXTERN> 363.31932 17.11362 0.00000 0.00000 0.00000 MINI CONSTR> 566.00225 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11307 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 1110.54123 0.00091 0.00986 0.00001 MINI INTERN> 46.74416 83.26727 0.00000 12.26352 21.86827 MINI EXTERN> 363.17110 17.12192 0.00000 0.00000 0.00000 MINI CONSTR> 566.10499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with gradient tolerance ( 0.0100000) satisfied. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 40 1110.54123 0.00091 0.00986 0.00001 STPD INTERN> 46.74416 83.26727 0.00000 12.26352 21.86827 STPD EXTERN> 363.17110 17.12192 0.00000 0.00000 0.00000 STPD CONSTR> 566.10499 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 11307 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11307 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 1110.54123 0.00091 0.00986 0.00000 MINI INTERN> 46.74416 83.26727 0.00000 12.26352 21.86827 MINI EXTERN> 363.17110 17.12192 0.00000 0.00000 0.00000 MINI CONSTR> 566.10499 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 1110.54121 0.00002 0.00889 0.02000 CONJ INTERN> 46.73472 83.27128 0.00000 12.26359 21.87328 CONJ EXTERN> 363.15705 17.11992 0.00000 0.00000 0.00000 CONJ CONSTR> 566.12138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "1800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 54.925 ( PROT LYS 1 HT2 ) 54.925 ( PROT LYS 1 N ) 68.656 ( PROT LYS 1 HT3 ) 54.925 ( PROT LYS 1 CA ) 68.656 ( PROT LYS 1 CB ) 54.925 ( PROT LYS 1 CG ) 54.925 ( PROT LYS 1 CD ) 54.925 ( PROT LYS 1 CE ) 54.925 ( PROT LYS 1 NZ ) 54.925 ( PROT LYS 1 HZ1 ) 54.925 ( PROT LYS 1 HZ2 ) 54.925 ( PROT LYS 1 HZ3 ) 54.925 ( PROT LYS 1 C ) 68.656 ( PROT LYS 1 O ) 68.656 ( PROT MET 2 N ) 68.656 ( PROT MET 2 H ) 54.925 ( PROT MET 2 CA ) 68.656 ( PROT MET 2 CB ) 54.925 ( PROT MET 2 CG ) 54.925 ( PROT MET 2 SD ) 54.925 ( PROT MET 2 CE ) 54.925 ( PROT MET 2 C ) 68.656 ( PROT MET 2 O ) 68.656 ( PROT LYS 3 N ) 68.656 ( PROT LYS 3 H ) 54.925 ( PROT LYS 3 CA ) 68.656 ( PROT LYS 3 CB ) 54.925 ( PROT LYS 3 CG ) 54.925 ( PROT LYS 3 CD ) 54.925 ( PROT LYS 3 CE ) 54.925 ( PROT LYS 3 NZ ) 54.925 ( PROT LYS 3 HZ1 ) 54.925 ( PROT LYS 3 HZ2 ) 54.925 ( PROT LYS 3 HZ3 ) 54.925 ( PROT LYS 3 C ) 68.656 ( PROT LYS 3 O ) 68.656 ( PROT ALA 4 N ) 68.656 ( PROT ALA 4 H ) 54.925 ( PROT ALA 4 CA ) 68.656 ( PROT ALA 4 CB ) 54.925 ( PROT ALA 4 C ) 68.656 ( PROT ALA 4 O ) 68.656 ( PROT VAL 5 N ) 68.656 ( PROT VAL 5 H ) 54.925 ( PROT VAL 5 CA ) 68.656 ( PROT VAL 5 CB ) 54.925 ( PROT VAL 5 CG1 ) 54.925 ( PROT VAL 5 CG2 ) 54.925 ( PROT VAL 5 C ) 68.656 ( PROT VAL 5 O ) 68.656 ( PROT MET 6 N ) 68.656 ( PROT MET 6 H ) 54.925 ( PROT MET 6 CA ) 68.656 ( PROT MET 6 CB ) 54.925 ( PROT MET 6 CG ) 54.925 ( PROT MET 6 SD ) 54.925 ( PROT MET 6 CE ) 54.925 ( PROT MET 6 C ) 68.656 ( PROT MET 6 O ) 68.656 ( PROT ILE 7 N ) 68.656 ( PROT ILE 7 H ) 54.925 ( PROT ILE 7 CA ) 68.656 ( PROT ILE 7 CB ) 54.925 ( PROT ILE 7 CG2 ) 54.925 ( PROT ILE 7 CG1 ) 54.925 ( PROT ILE 7 CD ) 54.925 ( PROT ILE 7 C ) 68.656 ( PROT ILE 7 O ) 68.656 ( PROT GLY 8 N ) 68.656 ( PROT GLY 8 H ) 54.925 ( PROT GLY 8 CA ) 68.656 ( PROT GLY 8 C ) 68.656 ( PROT GLY 8 O ) 68.656 ( PROT ALA 9 N ) 68.656 ( PROT ALA 9 H ) 54.925 ( PROT ALA 9 CA ) 68.656 ( PROT ALA 9 CB ) 54.925 ( PROT ALA 9 C ) 68.656 ( PROT ALA 9 O ) 68.656 ( PROT CYS 10 N ) 68.656 ( PROT CYS 10 H ) 54.925 ( PROT CYS 10 CA ) 68.656 ( PROT CYS 10 CB ) 54.925 ( PROT CYS 10 SG ) 54.925 ( PROT CYS 10 C ) 68.656 ( PROT CYS 10 O ) 68.656 ( PROT PHE 11 N ) 68.656 ( PROT PHE 11 H ) 54.925 ( PROT PHE 11 CA ) 68.656 ( PROT PHE 11 CB ) 54.925 ( PROT PHE 11 CG ) 54.925 ( PROT PHE 11 CD1 ) 54.925 ( PROT PHE 11 CD2 ) 54.925 ( PROT PHE 11 CE1 ) 54.925 ( PROT PHE 11 CE2 ) 54.925 ( PROT PHE 11 CZ ) 54.925 ( PROT PHE 11 C ) 68.656 ( PROT PHE 11 O ) 68.656 ( PROT LEU 12 N ) 68.656 ( PROT LEU 12 H ) 54.925 ( PROT LEU 12 CA ) 68.656 ( PROT LEU 12 CB ) 54.925 ( PROT LEU 12 CG ) 54.925 ( PROT LEU 12 CD1 ) 54.925 ( PROT LEU 12 CD2 ) 54.925 ( PROT LEU 12 C ) 68.656 ( PROT LEU 12 O ) 68.656 ( PROT ILE 13 N ) 68.656 ( PROT ILE 13 H ) 54.925 ( PROT ILE 13 CA ) 68.656 ( PROT ILE 13 CB ) 54.925 ( PROT ILE 13 CG2 ) 54.925 ( PROT ILE 13 CG1 ) 54.925 ( PROT ILE 13 CD ) 54.925 ( PROT ILE 13 C ) 68.656 ( PROT ILE 13 O ) 68.656 ( PROT ASP 14 N ) 68.656 ( PROT ASP 14 H ) 54.925 ( PROT ASP 14 CA ) 68.656 ( PROT ASP 14 CB ) 54.925 ( PROT ASP 14 CG ) 54.925 ( PROT ASP 14 OD1 ) 54.925 ( PROT ASP 14 OD2 ) 54.925 ( PROT ASP 14 C ) 68.656 ( PROT ASP 14 O ) 68.656 ( PROT PHE 15 N ) 68.656 ( PROT PHE 15 H ) 54.925 ( PROT PHE 15 CA ) 68.656 ( PROT PHE 15 CB ) 54.925 ( PROT PHE 15 CG ) 54.925 ( PROT PHE 15 CD1 ) 54.925 ( PROT PHE 15 CD2 ) 54.925 ( PROT PHE 15 CE1 ) 54.925 ( PROT PHE 15 CE2 ) 54.925 ( PROT PHE 15 CZ ) 54.925 ( PROT PHE 15 C ) 68.656 ( PROT PHE 15 O ) 68.656 ( PROT MET 16 N ) 68.656 ( PROT MET 16 H ) 54.925 ( PROT MET 16 CA ) 68.656 ( PROT MET 16 CB ) 54.925 ( PROT MET 16 CG ) 54.925 ( PROT MET 16 SD ) 54.925 ( PROT MET 16 CE ) 54.925 ( PROT MET 16 C ) 68.656 ( PROT MET 16 O ) 68.656 ( PROT PHE 17 N ) 68.656 ( PROT PHE 17 H ) 54.925 ( PROT PHE 17 CA ) 68.656 ( PROT PHE 17 CB ) 54.925 ( PROT PHE 17 CG ) 54.925 ( PROT PHE 17 CD1 ) 54.925 ( PROT PHE 17 CD2 ) 54.925 ( PROT PHE 17 CE1 ) 54.925 ( PROT PHE 17 CE2 ) 54.925 ( PROT PHE 17 CZ ) 54.925 ( PROT PHE 17 C ) 68.656 ( PROT PHE 17 O ) 68.656 ( PROT PHE 18 N ) 68.656 ( PROT PHE 18 H ) 54.925 ( PROT PHE 18 CA ) 68.656 ( PROT PHE 18 CB ) 54.925 ( PROT PHE 18 CG ) 54.925 ( PROT PHE 18 CD1 ) 54.925 ( PROT PHE 18 CD2 ) 54.925 ( PROT PHE 18 CE1 ) 54.925 ( PROT PHE 18 CE2 ) 54.925 ( PROT PHE 18 CZ ) 54.925 ( PROT PHE 18 C ) 68.656 ( PROT PHE 18 O ) 68.656 ( PROT GLU 19 N ) 68.656 ( PROT GLU 19 H ) 54.925 ( PROT GLU 19 CA ) 68.656 ( PROT GLU 19 CB ) 54.925 ( PROT GLU 19 CG ) 54.925 ( PROT GLU 19 CD ) 54.925 ( PROT GLU 19 OE1 ) 54.925 ( PROT GLU 19 OE2 ) 54.925 ( PROT GLU 19 C ) 68.656 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41247 5.26173 -8.67305 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS -0.00143 -0.00182 0.00136 ROTATION MATRIX 1.000000 -0.000040 -0.000036 0.000040 1.000000 0.000063 0.000036 -0.000063 1.000000 VERY LITTLE ROTATION: NO AXIS FOUND TOTAL SQUARE DIFF IS 6.3278 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.186462 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.1865" Parameter: A <- "0.1865" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70685 5.24615 -8.78175 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00800 0.01827 -0.01262 ROTATION MATRIX 0.999904 0.010050 0.009545 -0.009954 0.999899 -0.010114 -0.009646 0.010018 0.999903 AXIS OF ROTATION IS -0.587607 -0.560169 0.583892 ANGLE IS 0.98 TOTAL SQUARE DIFF IS 0.0692 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.060347 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.1865" RDCMND substituted energy or value "?RMS" to " 0.0603" Parameter: A <- "0.1865 0.0603" 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 0.1865 0.0603 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 " 566.12" Parameter: H <- "566.12" 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> 0 544.41983 566.12138 19.35670 ENER INTERN> 46.73472 83.27128 0.00000 12.26359 21.87328 ENER EXTERN> 363.15705 17.11992 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 " 544.42" Parameter: B <- "544.42" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 17.12" Parameter: C <- "17.12" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 363.16" Parameter: C <- " 380.28" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 380.28" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 46.73" Parameter: D <- "46.73" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 83.27" Parameter: D <- " 130.00" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 12.26" Parameter: D <- " 142.26" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 21.87" Parameter: D <- " 164.13" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 164.13" 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= 544.42 GRMS= 19.36 ELEC= 17.12 VDW= 363.16 RDTITL> *EXTERNAL= 380.28 INTERNAL= 164.13 USER= 0.00 HARM= 566.12 RDTITL> *BOND= 46.73 ANGL= 83.27 DIHE= 12.26 IMPR= 21.87 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11307 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11307 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 964.96717 -420.54734 8.24494 0.02000 MINI INTERN> 46.73472 83.27128 0.00000 12.26359 21.87328 MINI EXTERN> 363.15705 17.11992 0.00000 0.00000 0.00000 MINI CONSTR> 420.54734 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 927.96969 36.99748 16.98802 0.00864 MINI INTERN> 88.18994 76.81196 0.00000 13.43965 16.06092 MINI EXTERN> 252.54720 21.52194 0.00000 0.00000 0.00000 MINI CONSTR> 459.39809 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11294 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 899.23821 28.73148 6.66970 0.00373 MINI INTERN> 33.25311 84.13117 0.00000 14.12653 16.82191 MINI EXTERN> 279.15768 15.24491 0.00000 0.00000 0.00000 MINI CONSTR> 456.50290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 892.52936 6.70885 2.14431 0.00161 MINI INTERN> 40.56057 80.63841 0.00000 13.94870 16.37569 MINI EXTERN> 265.70538 16.50774 0.00000 0.00000 0.00000 MINI CONSTR> 458.79287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11292 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 890.96990 1.55946 0.69217 0.00070 MINI INTERN> 38.73033 79.55706 0.00000 14.08108 16.28782 MINI EXTERN> 266.97385 16.22040 0.00000 0.00000 0.00000 MINI CONSTR> 459.11935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 890.51395 0.45595 1.21674 0.00072 MINI INTERN> 38.09677 78.90448 0.00000 14.14316 16.16908 MINI EXTERN> 267.43093 16.07170 0.00000 0.00000 0.00000 MINI CONSTR> 459.69784 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11292 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 890.21904 0.29491 0.32306 0.00031 MINI INTERN> 38.59126 78.86540 0.00000 14.09514 16.16728 MINI EXTERN> 265.79950 16.10403 0.00000 0.00000 0.00000 MINI CONSTR> 460.59643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 890.14970 0.06934 0.37929 0.00032 MINI INTERN> 38.55428 78.70844 0.00000 14.09855 16.14831 MINI EXTERN> 265.51668 16.07930 0.00000 0.00000 0.00000 MINI CONSTR> 461.04414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11292 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 890.11855 0.03116 0.19358 0.00014 MINI INTERN> 38.21510 78.54711 0.00000 14.12820 16.13528 MINI EXTERN> 265.92557 16.03163 0.00000 0.00000 0.00000 MINI CONSTR> 461.13565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 890.10710 0.01145 0.05654 0.00006 MINI INTERN> 38.27854 78.50997 0.00000 14.12156 16.12537 MINI EXTERN> 265.72896 16.03628 0.00000 0.00000 0.00000 MINI CONSTR> 461.30643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11292 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 890.10403 0.00307 0.09483 0.00006 MINI INTERN> 38.26985 78.46494 0.00000 14.12182 16.11638 MINI EXTERN> 265.68768 16.03356 0.00000 0.00000 0.00000 MINI CONSTR> 461.40981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 890.10205 0.00198 0.02480 0.00003 MINI INTERN> 38.21857 78.45124 0.00000 14.12667 16.12311 MINI EXTERN> 265.68318 16.02456 0.00000 0.00000 0.00000 MINI CONSTR> 461.47471 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11292 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 890.10161 0.00045 0.02979 0.00003 MINI INTERN> 38.20394 78.43763 0.00000 14.12774 16.12267 MINI EXTERN> 265.66795 16.02195 0.00000 0.00000 0.00000 MINI CONSTR> 461.51973 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> 64 890.10141 0.00020 0.00832 0.00001 STPD INTERN> 38.20437 78.42632 0.00000 14.12776 16.11985 STPD EXTERN> 265.66950 16.02239 0.00000 0.00000 0.00000 STPD CONSTR> 461.53122 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 11292 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11292 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 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> 0 890.10141 0.00020 0.00832 0.00000 MINI INTERN> 38.20437 78.42632 0.00000 14.12776 16.11985 MINI EXTERN> 265.66950 16.02239 0.00000 0.00000 0.00000 MINI CONSTR> 461.53122 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> 1 890.10139 0.00002 0.00892 0.02000 CONJ INTERN> 38.20484 78.42204 0.00000 14.12774 16.11866 CONJ EXTERN> 265.67321 16.02279 0.00000 0.00000 0.00000 CONJ CONSTR> 461.53211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "2400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 35.701 ( PROT LYS 1 HT2 ) 35.701 ( PROT LYS 1 N ) 44.627 ( PROT LYS 1 HT3 ) 35.701 ( PROT LYS 1 CA ) 44.627 ( PROT LYS 1 CB ) 35.701 ( PROT LYS 1 CG ) 35.701 ( PROT LYS 1 CD ) 35.701 ( PROT LYS 1 CE ) 35.701 ( PROT LYS 1 NZ ) 35.701 ( PROT LYS 1 HZ1 ) 35.701 ( PROT LYS 1 HZ2 ) 35.701 ( PROT LYS 1 HZ3 ) 35.701 ( PROT LYS 1 C ) 44.627 ( PROT LYS 1 O ) 44.627 ( PROT MET 2 N ) 44.627 ( PROT MET 2 H ) 35.701 ( PROT MET 2 CA ) 44.627 ( PROT MET 2 CB ) 35.701 ( PROT MET 2 CG ) 35.701 ( PROT MET 2 SD ) 35.701 ( PROT MET 2 CE ) 35.701 ( PROT MET 2 C ) 44.627 ( PROT MET 2 O ) 44.627 ( PROT LYS 3 N ) 44.627 ( PROT LYS 3 H ) 35.701 ( PROT LYS 3 CA ) 44.627 ( PROT LYS 3 CB ) 35.701 ( PROT LYS 3 CG ) 35.701 ( PROT LYS 3 CD ) 35.701 ( PROT LYS 3 CE ) 35.701 ( PROT LYS 3 NZ ) 35.701 ( PROT LYS 3 HZ1 ) 35.701 ( PROT LYS 3 HZ2 ) 35.701 ( PROT LYS 3 HZ3 ) 35.701 ( PROT LYS 3 C ) 44.627 ( PROT LYS 3 O ) 44.627 ( PROT ALA 4 N ) 44.627 ( PROT ALA 4 H ) 35.701 ( PROT ALA 4 CA ) 44.627 ( PROT ALA 4 CB ) 35.701 ( PROT ALA 4 C ) 44.627 ( PROT ALA 4 O ) 44.627 ( PROT VAL 5 N ) 44.627 ( PROT VAL 5 H ) 35.701 ( PROT VAL 5 CA ) 44.627 ( PROT VAL 5 CB ) 35.701 ( PROT VAL 5 CG1 ) 35.701 ( PROT VAL 5 CG2 ) 35.701 ( PROT VAL 5 C ) 44.627 ( PROT VAL 5 O ) 44.627 ( PROT MET 6 N ) 44.627 ( PROT MET 6 H ) 35.701 ( PROT MET 6 CA ) 44.627 ( PROT MET 6 CB ) 35.701 ( PROT MET 6 CG ) 35.701 ( PROT MET 6 SD ) 35.701 ( PROT MET 6 CE ) 35.701 ( PROT MET 6 C ) 44.627 ( PROT MET 6 O ) 44.627 ( PROT ILE 7 N ) 44.627 ( PROT ILE 7 H ) 35.701 ( PROT ILE 7 CA ) 44.627 ( PROT ILE 7 CB ) 35.701 ( PROT ILE 7 CG2 ) 35.701 ( PROT ILE 7 CG1 ) 35.701 ( PROT ILE 7 CD ) 35.701 ( PROT ILE 7 C ) 44.627 ( PROT ILE 7 O ) 44.627 ( PROT GLY 8 N ) 44.627 ( PROT GLY 8 H ) 35.701 ( PROT GLY 8 CA ) 44.627 ( PROT GLY 8 C ) 44.627 ( PROT GLY 8 O ) 44.627 ( PROT ALA 9 N ) 44.627 ( PROT ALA 9 H ) 35.701 ( PROT ALA 9 CA ) 44.627 ( PROT ALA 9 CB ) 35.701 ( PROT ALA 9 C ) 44.627 ( PROT ALA 9 O ) 44.627 ( PROT CYS 10 N ) 44.627 ( PROT CYS 10 H ) 35.701 ( PROT CYS 10 CA ) 44.627 ( PROT CYS 10 CB ) 35.701 ( PROT CYS 10 SG ) 35.701 ( PROT CYS 10 C ) 44.627 ( PROT CYS 10 O ) 44.627 ( PROT PHE 11 N ) 44.627 ( PROT PHE 11 H ) 35.701 ( PROT PHE 11 CA ) 44.627 ( PROT PHE 11 CB ) 35.701 ( PROT PHE 11 CG ) 35.701 ( PROT PHE 11 CD1 ) 35.701 ( PROT PHE 11 CD2 ) 35.701 ( PROT PHE 11 CE1 ) 35.701 ( PROT PHE 11 CE2 ) 35.701 ( PROT PHE 11 CZ ) 35.701 ( PROT PHE 11 C ) 44.627 ( PROT PHE 11 O ) 44.627 ( PROT LEU 12 N ) 44.627 ( PROT LEU 12 H ) 35.701 ( PROT LEU 12 CA ) 44.627 ( PROT LEU 12 CB ) 35.701 ( PROT LEU 12 CG ) 35.701 ( PROT LEU 12 CD1 ) 35.701 ( PROT LEU 12 CD2 ) 35.701 ( PROT LEU 12 C ) 44.627 ( PROT LEU 12 O ) 44.627 ( PROT ILE 13 N ) 44.627 ( PROT ILE 13 H ) 35.701 ( PROT ILE 13 CA ) 44.627 ( PROT ILE 13 CB ) 35.701 ( PROT ILE 13 CG2 ) 35.701 ( PROT ILE 13 CG1 ) 35.701 ( PROT ILE 13 CD ) 35.701 ( PROT ILE 13 C ) 44.627 ( PROT ILE 13 O ) 44.627 ( PROT ASP 14 N ) 44.627 ( PROT ASP 14 H ) 35.701 ( PROT ASP 14 CA ) 44.627 ( PROT ASP 14 CB ) 35.701 ( PROT ASP 14 CG ) 35.701 ( PROT ASP 14 OD1 ) 35.701 ( PROT ASP 14 OD2 ) 35.701 ( PROT ASP 14 C ) 44.627 ( PROT ASP 14 O ) 44.627 ( PROT PHE 15 N ) 44.627 ( PROT PHE 15 H ) 35.701 ( PROT PHE 15 CA ) 44.627 ( PROT PHE 15 CB ) 35.701 ( PROT PHE 15 CG ) 35.701 ( PROT PHE 15 CD1 ) 35.701 ( PROT PHE 15 CD2 ) 35.701 ( PROT PHE 15 CE1 ) 35.701 ( PROT PHE 15 CE2 ) 35.701 ( PROT PHE 15 CZ ) 35.701 ( PROT PHE 15 C ) 44.627 ( PROT PHE 15 O ) 44.627 ( PROT MET 16 N ) 44.627 ( PROT MET 16 H ) 35.701 ( PROT MET 16 CA ) 44.627 ( PROT MET 16 CB ) 35.701 ( PROT MET 16 CG ) 35.701 ( PROT MET 16 SD ) 35.701 ( PROT MET 16 CE ) 35.701 ( PROT MET 16 C ) 44.627 ( PROT MET 16 O ) 44.627 ( PROT PHE 17 N ) 44.627 ( PROT PHE 17 H ) 35.701 ( PROT PHE 17 CA ) 44.627 ( PROT PHE 17 CB ) 35.701 ( PROT PHE 17 CG ) 35.701 ( PROT PHE 17 CD1 ) 35.701 ( PROT PHE 17 CD2 ) 35.701 ( PROT PHE 17 CE1 ) 35.701 ( PROT PHE 17 CE2 ) 35.701 ( PROT PHE 17 CZ ) 35.701 ( PROT PHE 17 C ) 44.627 ( PROT PHE 17 O ) 44.627 ( PROT PHE 18 N ) 44.627 ( PROT PHE 18 H ) 35.701 ( PROT PHE 18 CA ) 44.627 ( PROT PHE 18 CB ) 35.701 ( PROT PHE 18 CG ) 35.701 ( PROT PHE 18 CD1 ) 35.701 ( PROT PHE 18 CD2 ) 35.701 ( PROT PHE 18 CE1 ) 35.701 ( PROT PHE 18 CE2 ) 35.701 ( PROT PHE 18 CZ ) 35.701 ( PROT PHE 18 C ) 44.627 ( PROT PHE 18 O ) 44.627 ( PROT GLU 19 N ) 44.627 ( PROT GLU 19 H ) 35.701 ( PROT GLU 19 CA ) 44.627 ( PROT GLU 19 CB ) 35.701 ( PROT GLU 19 CG ) 35.701 ( PROT GLU 19 CD ) 35.701 ( PROT GLU 19 OE1 ) 35.701 ( PROT GLU 19 OE2 ) 35.701 ( PROT GLU 19 C ) 44.627 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41228 5.26175 -8.67284 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS -0.00124 -0.00184 0.00115 ROTATION MATRIX 1.000000 -0.000059 -0.000042 0.000059 1.000000 0.000084 0.000042 -0.000084 1.000000 AXIS OF ROTATION IS 0.755177 0.382698 -0.532212 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 7.9183 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.208584 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2086" Parameter: A <- "0.2086" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70759 5.24265 -8.78095 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00725 0.02177 -0.01341 ROTATION MATRIX 0.999875 0.011576 0.010815 -0.011451 0.999868 -0.011489 -0.010946 0.011363 0.999876 AXIS OF ROTATION IS -0.584985 -0.557060 0.589472 ANGLE IS 1.12 CENTER OF ROTATION 9.436730 5.070509 -9.233021 SHIFT IS -0.024276 TOTAL SQUARE DIFF IS 0.1048 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.074271 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2086" RDCMND substituted energy or value "?RMS" to " 0.0743" Parameter: A <- "0.2086 0.0743" 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 0.2086 0.0743 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 " 461.53" Parameter: H <- "461.53" 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> 0 428.56928 461.53211 14.11005 ENER INTERN> 38.20484 78.42204 0.00000 14.12774 16.11866 ENER EXTERN> 265.67321 16.02279 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 " 428.57" Parameter: B <- "428.57" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 16.02" Parameter: C <- "16.02" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 265.67" Parameter: C <- " 281.69" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 281.69" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 38.20" Parameter: D <- "38.20" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 78.42" Parameter: D <- " 116.62" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 14.13" Parameter: D <- " 130.75" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 16.12" Parameter: D <- " 146.87" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 146.87" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 2400 ENER= 428.57 GRMS= 14.11 ELEC= 16.02 VDW= 265.67 RDTITL> *EXTERNAL= 281.69 INTERNAL= 146.87 USER= 0.00 HARM= 461.53 RDTITL> *BOND= 38.20 ANGL= 78.42 DIHE= 14.13 IMPR= 16.12 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 428.57 GRMS= 14.11 ELEC= 16.02 VDW= 265.67 RDTITL> *EXTERNAL= 281.69 INTERNAL= 146.87 USER= 0.00 HARM= 461.53 RDTITL> *BOND= 38.20 ANGL= 78.42 DIHE= 14.13 IMPR= 16.12 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 428.57 GRMS= 14.11 ELEC= 16.02 VDW= 265.67 RDTITL> *EXTERNAL= 281.69 INTERNAL= 146.87 USER= 0.00 HARM= 461.53 RDTITL> *BOND= 38.20 ANGL= 78.42 DIHE= 14.13 IMPR= 16.12 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 2400 0.2086 0.0743 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "2400" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11292 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11292 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 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> 0 773.08953 -344.52025 6.04177 0.02000 MINI INTERN> 38.20484 78.42204 0.00000 14.12774 16.11866 MINI EXTERN> 265.67321 16.02279 0.00000 0.00000 0.00000 MINI CONSTR> 344.52025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 748.07437 25.01516 15.68598 0.00864 MINI INTERN> 68.04593 73.33935 0.00000 15.38485 11.71007 MINI EXTERN> 187.09766 18.57345 0.00000 0.00000 0.00000 MINI CONSTR> 373.92305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11281 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 720.21135 27.86302 5.34949 0.00373 MINI INTERN> 36.59117 74.96813 0.00000 16.56816 13.11305 MINI EXTERN> 187.38952 15.80296 0.00000 0.00000 0.00000 MINI CONSTR> 375.77835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 713.79042 6.42092 1.54306 0.00161 MINI INTERN> 31.99250 73.40480 0.00000 16.39910 11.98291 MINI EXTERN> 189.83135 14.81415 0.00000 0.00000 0.00000 MINI CONSTR> 375.36561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11278 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 712.17646 1.61396 2.85369 0.00167 MINI INTERN> 34.39986 71.17270 0.00000 16.48040 11.88903 MINI EXTERN> 186.61142 15.06500 0.00000 0.00000 0.00000 MINI CONSTR> 376.55805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 711.20397 0.97249 2.75400 0.00173 MINI INTERN> 33.89453 70.64608 0.00000 16.50721 11.86241 MINI EXTERN> 185.92472 14.90880 0.00000 0.00000 0.00000 MINI CONSTR> 377.46022 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11281 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 710.05106 1.15291 0.88334 0.00075 MINI INTERN> 29.43361 72.31994 0.00000 16.57458 12.09015 MINI EXTERN> 186.98711 14.14701 0.00000 0.00000 0.00000 MINI CONSTR> 378.49867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 709.74975 0.30131 0.31475 0.00032 MINI INTERN> 29.91193 71.58820 0.00000 16.57434 11.99808 MINI EXTERN> 186.57549 14.20685 0.00000 0.00000 0.00000 MINI CONSTR> 378.89485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11280 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 709.61831 0.13144 0.24366 0.00034 MINI INTERN> 29.81813 71.41147 0.00000 16.58333 11.98850 MINI EXTERN> 186.35480 14.16401 0.00000 0.00000 0.00000 MINI CONSTR> 379.29806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 709.55823 0.06008 0.51723 0.00035 MINI INTERN> 29.54827 71.30899 0.00000 16.58108 11.95986 MINI EXTERN> 186.44145 14.08239 0.00000 0.00000 0.00000 MINI CONSTR> 379.63619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11280 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 709.50133 0.05690 0.16269 0.00015 MINI INTERN> 29.59877 71.25562 0.00000 16.59976 11.99797 MINI EXTERN> 186.05178 14.08887 0.00000 0.00000 0.00000 MINI CONSTR> 379.90854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 709.48393 0.01740 0.19141 0.00016 MINI INTERN> 29.45744 71.24413 0.00000 16.60267 12.00199 MINI EXTERN> 186.04475 14.05293 0.00000 0.00000 0.00000 MINI CONSTR> 380.08002 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11279 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 709.47185 0.01208 0.06277 0.00007 MINI INTERN> 29.55997 71.12717 0.00000 16.59941 11.98337 MINI EXTERN> 185.97185 14.06149 0.00000 0.00000 0.00000 MINI CONSTR> 380.16859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 709.46649 0.00536 0.05157 0.00007 MINI INTERN> 29.54754 71.09871 0.00000 16.59969 11.98209 MINI EXTERN> 185.93231 14.05155 0.00000 0.00000 0.00000 MINI CONSTR> 380.25461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11279 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 709.46386 0.00263 0.11298 0.00007 MINI INTERN> 29.51214 71.07396 0.00000 16.59778 11.97731 MINI EXTERN> 185.93791 14.03613 0.00000 0.00000 0.00000 MINI CONSTR> 380.32863 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 709.46238 0.00148 0.12424 0.00007 MINI INTERN> 29.59993 71.03012 0.00000 16.59871 11.97502 MINI EXTERN> 185.83362 14.04509 0.00000 0.00000 0.00000 MINI CONSTR> 380.37988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11280 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 709.46000 0.00238 0.03173 0.00003 MINI INTERN> 29.49832 71.06645 0.00000 16.60062 11.98557 MINI EXTERN> 185.85506 14.02537 0.00000 0.00000 0.00000 MINI CONSTR> 380.42862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 709.45945 0.00054 0.04842 0.00003 MINI INTERN> 29.49054 71.06515 0.00000 16.60064 11.98619 MINI EXTERN> 185.83730 14.01802 0.00000 0.00000 0.00000 MINI CONSTR> 380.46162 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11280 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 709.45888 0.00058 0.01382 0.00001 MINI INTERN> 29.50463 71.04475 0.00000 16.59914 11.98266 MINI EXTERN> 185.83213 14.01783 0.00000 0.00000 0.00000 MINI CONSTR> 380.47773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 709.45861 0.00027 0.01194 0.00002 MINI INTERN> 29.50403 71.04076 0.00000 16.59876 11.98255 MINI EXTERN> 185.82261 14.01428 0.00000 0.00000 0.00000 MINI CONSTR> 380.49562 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> 98 709.45846 0.00014 0.00959 0.00001 STPD INTERN> 29.50228 71.03941 0.00000 16.59861 11.98280 STPD EXTERN> 185.81717 14.01209 0.00000 0.00000 0.00000 STPD CONSTR> 380.50611 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 11280 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11280 ATOM PAIRS WERE FOUND FOR ATOM LIST 332 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> 0 709.45846 0.00014 0.00959 0.00000 MINI INTERN> 29.50228 71.03941 0.00000 16.59861 11.98280 MINI EXTERN> 185.81717 14.01209 0.00000 0.00000 0.00000 MINI CONSTR> 380.50611 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> 3 709.45792 0.00055 0.00414 0.02000 CONJ INTERN> 29.49905 71.02252 0.00000 16.59648 11.98294 CONJ EXTERN> 185.77109 13.99375 0.00000 0.00000 0.00000 CONJ CONSTR> 380.59209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "3000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 23.206 ( PROT LYS 1 HT2 ) 23.206 ( PROT LYS 1 N ) 29.007 ( PROT LYS 1 HT3 ) 23.206 ( PROT LYS 1 CA ) 29.007 ( PROT LYS 1 CB ) 23.206 ( PROT LYS 1 CG ) 23.206 ( PROT LYS 1 CD ) 23.206 ( PROT LYS 1 CE ) 23.206 ( PROT LYS 1 NZ ) 23.206 ( PROT LYS 1 HZ1 ) 23.206 ( PROT LYS 1 HZ2 ) 23.206 ( PROT LYS 1 HZ3 ) 23.206 ( PROT LYS 1 C ) 29.007 ( PROT LYS 1 O ) 29.007 ( PROT MET 2 N ) 29.007 ( PROT MET 2 H ) 23.206 ( PROT MET 2 CA ) 29.007 ( PROT MET 2 CB ) 23.206 ( PROT MET 2 CG ) 23.206 ( PROT MET 2 SD ) 23.206 ( PROT MET 2 CE ) 23.206 ( PROT MET 2 C ) 29.007 ( PROT MET 2 O ) 29.007 ( PROT LYS 3 N ) 29.007 ( PROT LYS 3 H ) 23.206 ( PROT LYS 3 CA ) 29.007 ( PROT LYS 3 CB ) 23.206 ( PROT LYS 3 CG ) 23.206 ( PROT LYS 3 CD ) 23.206 ( PROT LYS 3 CE ) 23.206 ( PROT LYS 3 NZ ) 23.206 ( PROT LYS 3 HZ1 ) 23.206 ( PROT LYS 3 HZ2 ) 23.206 ( PROT LYS 3 HZ3 ) 23.206 ( PROT LYS 3 C ) 29.007 ( PROT LYS 3 O ) 29.007 ( PROT ALA 4 N ) 29.007 ( PROT ALA 4 H ) 23.206 ( PROT ALA 4 CA ) 29.007 ( PROT ALA 4 CB ) 23.206 ( PROT ALA 4 C ) 29.007 ( PROT ALA 4 O ) 29.007 ( PROT VAL 5 N ) 29.007 ( PROT VAL 5 H ) 23.206 ( PROT VAL 5 CA ) 29.007 ( PROT VAL 5 CB ) 23.206 ( PROT VAL 5 CG1 ) 23.206 ( PROT VAL 5 CG2 ) 23.206 ( PROT VAL 5 C ) 29.007 ( PROT VAL 5 O ) 29.007 ( PROT MET 6 N ) 29.007 ( PROT MET 6 H ) 23.206 ( PROT MET 6 CA ) 29.007 ( PROT MET 6 CB ) 23.206 ( PROT MET 6 CG ) 23.206 ( PROT MET 6 SD ) 23.206 ( PROT MET 6 CE ) 23.206 ( PROT MET 6 C ) 29.007 ( PROT MET 6 O ) 29.007 ( PROT ILE 7 N ) 29.007 ( PROT ILE 7 H ) 23.206 ( PROT ILE 7 CA ) 29.007 ( PROT ILE 7 CB ) 23.206 ( PROT ILE 7 CG2 ) 23.206 ( PROT ILE 7 CG1 ) 23.206 ( PROT ILE 7 CD ) 23.206 ( PROT ILE 7 C ) 29.007 ( PROT ILE 7 O ) 29.007 ( PROT GLY 8 N ) 29.007 ( PROT GLY 8 H ) 23.206 ( PROT GLY 8 CA ) 29.007 ( PROT GLY 8 C ) 29.007 ( PROT GLY 8 O ) 29.007 ( PROT ALA 9 N ) 29.007 ( PROT ALA 9 H ) 23.206 ( PROT ALA 9 CA ) 29.007 ( PROT ALA 9 CB ) 23.206 ( PROT ALA 9 C ) 29.007 ( PROT ALA 9 O ) 29.007 ( PROT CYS 10 N ) 29.007 ( PROT CYS 10 H ) 23.206 ( PROT CYS 10 CA ) 29.007 ( PROT CYS 10 CB ) 23.206 ( PROT CYS 10 SG ) 23.206 ( PROT CYS 10 C ) 29.007 ( PROT CYS 10 O ) 29.007 ( PROT PHE 11 N ) 29.007 ( PROT PHE 11 H ) 23.206 ( PROT PHE 11 CA ) 29.007 ( PROT PHE 11 CB ) 23.206 ( PROT PHE 11 CG ) 23.206 ( PROT PHE 11 CD1 ) 23.206 ( PROT PHE 11 CD2 ) 23.206 ( PROT PHE 11 CE1 ) 23.206 ( PROT PHE 11 CE2 ) 23.206 ( PROT PHE 11 CZ ) 23.206 ( PROT PHE 11 C ) 29.007 ( PROT PHE 11 O ) 29.007 ( PROT LEU 12 N ) 29.007 ( PROT LEU 12 H ) 23.206 ( PROT LEU 12 CA ) 29.007 ( PROT LEU 12 CB ) 23.206 ( PROT LEU 12 CG ) 23.206 ( PROT LEU 12 CD1 ) 23.206 ( PROT LEU 12 CD2 ) 23.206 ( PROT LEU 12 C ) 29.007 ( PROT LEU 12 O ) 29.007 ( PROT ILE 13 N ) 29.007 ( PROT ILE 13 H ) 23.206 ( PROT ILE 13 CA ) 29.007 ( PROT ILE 13 CB ) 23.206 ( PROT ILE 13 CG2 ) 23.206 ( PROT ILE 13 CG1 ) 23.206 ( PROT ILE 13 CD ) 23.206 ( PROT ILE 13 C ) 29.007 ( PROT ILE 13 O ) 29.007 ( PROT ASP 14 N ) 29.007 ( PROT ASP 14 H ) 23.206 ( PROT ASP 14 CA ) 29.007 ( PROT ASP 14 CB ) 23.206 ( PROT ASP 14 CG ) 23.206 ( PROT ASP 14 OD1 ) 23.206 ( PROT ASP 14 OD2 ) 23.206 ( PROT ASP 14 C ) 29.007 ( PROT ASP 14 O ) 29.007 ( PROT PHE 15 N ) 29.007 ( PROT PHE 15 H ) 23.206 ( PROT PHE 15 CA ) 29.007 ( PROT PHE 15 CB ) 23.206 ( PROT PHE 15 CG ) 23.206 ( PROT PHE 15 CD1 ) 23.206 ( PROT PHE 15 CD2 ) 23.206 ( PROT PHE 15 CE1 ) 23.206 ( PROT PHE 15 CE2 ) 23.206 ( PROT PHE 15 CZ ) 23.206 ( PROT PHE 15 C ) 29.007 ( PROT PHE 15 O ) 29.007 ( PROT MET 16 N ) 29.007 ( PROT MET 16 H ) 23.206 ( PROT MET 16 CA ) 29.007 ( PROT MET 16 CB ) 23.206 ( PROT MET 16 CG ) 23.206 ( PROT MET 16 SD ) 23.206 ( PROT MET 16 CE ) 23.206 ( PROT MET 16 C ) 29.007 ( PROT MET 16 O ) 29.007 ( PROT PHE 17 N ) 29.007 ( PROT PHE 17 H ) 23.206 ( PROT PHE 17 CA ) 29.007 ( PROT PHE 17 CB ) 23.206 ( PROT PHE 17 CG ) 23.206 ( PROT PHE 17 CD1 ) 23.206 ( PROT PHE 17 CD2 ) 23.206 ( PROT PHE 17 CE1 ) 23.206 ( PROT PHE 17 CE2 ) 23.206 ( PROT PHE 17 CZ ) 23.206 ( PROT PHE 17 C ) 29.007 ( PROT PHE 17 O ) 29.007 ( PROT PHE 18 N ) 29.007 ( PROT PHE 18 H ) 23.206 ( PROT PHE 18 CA ) 29.007 ( PROT PHE 18 CB ) 23.206 ( PROT PHE 18 CG ) 23.206 ( PROT PHE 18 CD1 ) 23.206 ( PROT PHE 18 CD2 ) 23.206 ( PROT PHE 18 CE1 ) 23.206 ( PROT PHE 18 CE2 ) 23.206 ( PROT PHE 18 CZ ) 23.206 ( PROT PHE 18 C ) 29.007 ( PROT PHE 18 O ) 29.007 ( PROT GLU 19 N ) 29.007 ( PROT GLU 19 H ) 23.206 ( PROT GLU 19 CA ) 29.007 ( PROT GLU 19 CB ) 23.206 ( PROT GLU 19 CG ) 23.206 ( PROT GLU 19 CD ) 23.206 ( PROT GLU 19 OE1 ) 23.206 ( PROT GLU 19 OE2 ) 23.206 ( PROT GLU 19 C ) 29.007 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41200 5.26169 -8.67249 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS -0.00097 -0.00178 0.00079 ROTATION MATRIX 1.000000 -0.000068 -0.000030 0.000068 1.000000 0.000096 0.000030 -0.000096 1.000000 AXIS OF ROTATION IS 0.789124 0.244097 -0.563649 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 10.0109 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.234531 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2345" Parameter: A <- "0.2345" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70820 5.23860 -8.78013 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00664 0.02582 -0.01424 ROTATION MATRIX 0.999844 0.013021 0.011948 -0.012869 0.999836 -0.012761 -0.012112 0.012605 0.999847 AXIS OF ROTATION IS -0.583073 -0.553047 0.595118 ANGLE IS 1.25 CENTER OF ROTATION 9.367186 5.051541 -9.310449 SHIFT IS -0.026626 TOTAL SQUARE DIFF IS 0.1517 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.089353 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2345" RDCMND substituted energy or value "?RMS" to " 0.0894" Parameter: A <- "0.2345 0.0894" 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 0.2345 0.0894 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 " 380.59" Parameter: H <- "380.59" 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> 0 328.86582 380.59209 10.34948 ENER INTERN> 29.49905 71.02252 0.00000 16.59648 11.98294 ENER EXTERN> 185.77109 13.99375 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 " 328.87" Parameter: B <- "328.87" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 13.99" Parameter: C <- "13.99" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 185.77" Parameter: C <- " 199.76" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 199.76" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 29.50" Parameter: D <- "29.50" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 71.02" Parameter: D <- " 100.52" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 16.60" Parameter: D <- " 117.12" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 11.98" Parameter: D <- " 129.10" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 129.10" 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= 3000 ENER= 328.87 GRMS= 10.35 ELEC= 13.99 VDW= 185.77 RDTITL> *EXTERNAL= 199.76 INTERNAL= 129.10 USER= 0.00 HARM= 380.59 RDTITL> *BOND= 29.50 ANGL= 71.02 DIHE= 16.60 IMPR= 11.98 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11280 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11280 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 612.44646 -283.58064 4.41639 0.02000 MINI INTERN> 29.49905 71.02252 0.00000 16.59648 11.98294 MINI EXTERN> 185.77109 13.99375 0.00000 0.00000 0.00000 MINI CONSTR> 283.58064 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 593.47807 18.96839 12.21966 0.00864 MINI INTERN> 32.78233 67.74742 0.00000 18.59445 9.09850 MINI EXTERN> 146.34987 13.18065 0.00000 0.00000 0.00000 MINI CONSTR> 305.72483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11276 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 574.93768 18.54039 6.86356 0.00373 MINI INTERN> 26.59462 67.97277 0.00000 19.08616 10.02983 MINI EXTERN> 128.47486 12.57881 0.00000 0.00000 0.00000 MINI CONSTR> 310.20063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 567.83276 7.10492 2.30634 0.00161 MINI INTERN> 23.39299 66.16417 0.00000 19.28668 9.82298 MINI EXTERN> 125.07765 13.02686 0.00000 0.00000 0.00000 MINI CONSTR> 311.06144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11268 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 565.73861 2.09415 2.95393 0.00167 MINI INTERN> 23.17998 65.27648 0.00000 19.39248 9.82139 MINI EXTERN> 123.29604 12.92961 0.00000 0.00000 0.00000 MINI CONSTR> 311.84263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 564.27256 1.46605 3.45902 0.00173 MINI INTERN> 23.05334 64.55273 0.00000 19.46782 9.81528 MINI EXTERN> 121.97445 12.84107 0.00000 0.00000 0.00000 MINI CONSTR> 312.56786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 563.14125 1.13131 3.14947 0.00180 MINI INTERN> 22.75432 64.04523 0.00000 19.50713 9.80700 MINI EXTERN> 121.27321 12.72910 0.00000 0.00000 0.00000 MINI CONSTR> 313.02527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 561.61634 1.52491 1.26378 0.00078 MINI INTERN> 21.85275 63.42690 0.00000 19.52738 9.82048 MINI EXTERN> 121.35081 12.25200 0.00000 0.00000 0.00000 MINI CONSTR> 313.38603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11266 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 561.02245 0.59389 0.89722 0.00080 MINI INTERN> 21.67698 63.13961 0.00000 19.54450 9.81260 MINI EXTERN> 120.82654 12.21919 0.00000 0.00000 0.00000 MINI CONSTR> 313.80303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 560.78081 0.24165 1.41704 0.00083 MINI INTERN> 21.66049 62.93413 0.00000 19.55169 9.80985 MINI EXTERN> 120.59813 12.11236 0.00000 0.00000 0.00000 MINI CONSTR> 314.11416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 560.37294 0.40787 0.42437 0.00036 MINI INTERN> 21.45682 62.81924 0.00000 19.55597 9.79893 MINI EXTERN> 120.06147 12.22094 0.00000 0.00000 0.00000 MINI CONSTR> 314.45957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 560.20754 0.16539 0.28718 0.00037 MINI INTERN> 21.41451 62.69877 0.00000 19.55553 9.79382 MINI EXTERN> 119.90015 12.17292 0.00000 0.00000 0.00000 MINI CONSTR> 314.67184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 560.08958 0.11797 0.66758 0.00039 MINI INTERN> 21.37013 62.61944 0.00000 19.55216 9.78771 MINI EXTERN> 119.63230 12.18029 0.00000 0.00000 0.00000 MINI CONSTR> 314.94754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 560.01204 0.07754 0.79170 0.00040 MINI INTERN> 21.32963 62.55962 0.00000 19.54702 9.78342 MINI EXTERN> 119.47863 12.16003 0.00000 0.00000 0.00000 MINI CONSTR> 315.15370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 559.94978 0.06226 0.71869 0.00042 MINI INTERN> 21.32336 62.49892 0.00000 19.54263 9.77892 MINI EXTERN> 119.38248 12.13663 0.00000 0.00000 0.00000 MINI CONSTR> 315.28683 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 559.86434 0.08544 0.27714 0.00018 MINI INTERN> 21.35658 62.37325 0.00000 19.53755 9.77263 MINI EXTERN> 119.38720 12.04035 0.00000 0.00000 0.00000 MINI CONSTR> 315.39678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 559.82896 0.03538 0.20240 0.00019 MINI INTERN> 21.33894 62.34216 0.00000 19.53181 9.76931 MINI EXTERN> 119.29785 12.02907 0.00000 0.00000 0.00000 MINI CONSTR> 315.51982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 559.81029 0.01867 0.31937 0.00019 MINI INTERN> 21.35476 62.29972 0.00000 19.52639 9.76574 MINI EXTERN> 119.23932 12.00401 0.00000 0.00000 0.00000 MINI CONSTR> 315.62035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 559.78443 0.02586 0.09809 0.00008 MINI INTERN> 21.29490 62.31181 0.00000 19.52050 9.76491 MINI EXTERN> 119.15199 12.01421 0.00000 0.00000 0.00000 MINI CONSTR> 315.72612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 559.77065 0.01378 0.08114 0.00009 MINI INTERN> 21.29562 62.29005 0.00000 19.51549 9.76268 MINI EXTERN> 119.10045 12.00084 0.00000 0.00000 0.00000 MINI CONSTR> 315.80552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 559.75821 0.01244 0.07291 0.00009 MINI INTERN> 21.29323 62.27150 0.00000 19.50992 9.76060 MINI EXTERN> 119.04540 11.98818 0.00000 0.00000 0.00000 MINI CONSTR> 315.88937 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 559.74893 0.00928 0.16157 0.00009 MINI INTERN> 21.26790 62.27086 0.00000 19.50361 9.75959 MINI EXTERN> 118.98409 11.98170 0.00000 0.00000 0.00000 MINI CONSTR> 315.98118 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 559.74145 0.00748 0.16917 0.00010 MINI INTERN> 21.26437 62.25980 0.00000 19.49860 9.75828 MINI EXTERN> 118.93944 11.97150 0.00000 0.00000 0.00000 MINI CONSTR> 316.04945 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 559.73559 0.00585 0.18925 0.00010 MINI INTERN> 21.25926 62.25202 0.00000 19.49378 9.75728 MINI EXTERN> 118.89719 11.96268 0.00000 0.00000 0.00000 MINI CONSTR> 316.11338 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 559.73052 0.00507 0.17727 0.00010 MINI INTERN> 21.26219 62.24198 0.00000 19.48994 9.75627 MINI EXTERN> 118.86336 11.95461 0.00000 0.00000 0.00000 MINI CONSTR> 316.16217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 559.72586 0.00466 0.18151 0.00011 MINI INTERN> 21.26065 62.23430 0.00000 19.48565 9.75545 MINI EXTERN> 118.82720 11.94622 0.00000 0.00000 0.00000 MINI CONSTR> 316.21637 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 559.71892 0.00694 0.05253 0.00005 MINI INTERN> 21.30553 62.19585 0.00000 19.48191 9.75269 MINI EXTERN> 118.79473 11.92875 0.00000 0.00000 0.00000 MINI CONSTR> 316.25947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 559.71566 0.00326 0.04190 0.00005 MINI INTERN> 21.30195 62.19232 0.00000 19.47860 9.75225 MINI EXTERN> 118.76670 11.92339 0.00000 0.00000 0.00000 MINI CONSTR> 316.30045 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 559.71231 0.00336 0.08089 0.00005 MINI INTERN> 21.31642 62.17704 0.00000 19.47452 9.75098 MINI EXTERN> 118.73138 11.91330 0.00000 0.00000 0.00000 MINI CONSTR> 316.34867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 559.70923 0.00307 0.05140 0.00005 MINI INTERN> 21.30892 62.17658 0.00000 19.47126 9.75083 MINI EXTERN> 118.70424 11.90901 0.00000 0.00000 0.00000 MINI CONSTR> 316.38839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 559.70695 0.00228 0.09251 0.00005 MINI INTERN> 21.32121 62.16455 0.00000 19.46786 9.74983 MINI EXTERN> 118.67507 11.90083 0.00000 0.00000 0.00000 MINI CONSTR> 316.42760 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 559.70459 0.00235 0.09812 0.00006 MINI INTERN> 21.32335 62.15910 0.00000 19.46469 9.74933 MINI EXTERN> 118.64833 11.89502 0.00000 0.00000 0.00000 MINI CONSTR> 316.46477 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 559.70255 0.00204 0.10727 0.00006 MINI INTERN> 21.32628 62.15357 0.00000 19.46170 9.74883 MINI EXTERN> 118.62321 11.88946 0.00000 0.00000 0.00000 MINI CONSTR> 316.49950 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 559.70068 0.00187 0.10088 0.00006 MINI INTERN> 21.32551 62.15050 0.00000 19.45925 9.74858 MINI EXTERN> 118.60278 11.88558 0.00000 0.00000 0.00000 MINI CONSTR> 316.52847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 559.69808 0.00260 0.02979 0.00003 MINI INTERN> 21.30230 62.16062 0.00000 19.45646 9.74945 MINI EXTERN> 118.58063 11.88563 0.00000 0.00000 0.00000 MINI CONSTR> 316.56298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 559.69727 0.00081 0.10934 0.00006 MINI INTERN> 21.32834 62.14276 0.00000 19.45390 9.74786 MINI EXTERN> 118.55819 11.87634 0.00000 0.00000 0.00000 MINI CONSTR> 316.58990 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 559.69476 0.00251 0.03261 0.00003 MINI INTERN> 21.30202 62.15453 0.00000 19.45126 9.74900 MINI EXTERN> 118.53730 11.87763 0.00000 0.00000 0.00000 MINI CONSTR> 316.62302 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 559.69348 0.00128 0.02626 0.00003 MINI INTERN> 21.30493 62.15064 0.00000 19.44920 9.74867 MINI EXTERN> 118.52004 11.87385 0.00000 0.00000 0.00000 MINI CONSTR> 316.64615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 559.69209 0.00138 0.02548 0.00003 MINI INTERN> 21.30561 62.14762 0.00000 19.44684 9.74843 MINI EXTERN> 118.50043 11.87020 0.00000 0.00000 0.00000 MINI CONSTR> 316.67296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 559.69080 0.00129 0.04894 0.00003 MINI INTERN> 21.30058 62.14729 0.00000 19.44428 9.74856 MINI EXTERN> 118.47920 11.86777 0.00000 0.00000 0.00000 MINI CONSTR> 316.70313 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11264 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 559.68961 0.00119 0.03163 0.00003 MINI INTERN> 21.30487 62.14294 0.00000 19.44230 9.74813 MINI EXTERN> 118.46278 11.86390 0.00000 0.00000 0.00000 MINI CONSTR> 316.72469 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 559.68851 0.00110 0.03559 0.00003 MINI INTERN> 21.30489 62.14052 0.00000 19.44015 9.74798 MINI EXTERN> 118.44498 11.86097 0.00000 0.00000 0.00000 MINI CONSTR> 316.74902 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 559.68771 0.00080 0.05623 0.00003 MINI INTERN> 21.30211 62.13987 0.00000 19.43823 9.74806 MINI EXTERN> 118.42901 11.85922 0.00000 0.00000 0.00000 MINI CONSTR> 316.77120 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 559.68679 0.00092 0.06061 0.00004 MINI INTERN> 21.30307 62.13693 0.00000 19.43627 9.74788 MINI EXTERN> 118.41267 11.85655 0.00000 0.00000 0.00000 MINI CONSTR> 316.79341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 559.68599 0.00080 0.06716 0.00004 MINI INTERN> 21.30355 62.13452 0.00000 19.43443 9.74774 MINI EXTERN> 118.39734 11.85420 0.00000 0.00000 0.00000 MINI CONSTR> 316.81422 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 559.68524 0.00075 0.06312 0.00004 MINI INTERN> 21.30442 62.13287 0.00000 19.43284 9.74757 MINI EXTERN> 118.38436 11.85193 0.00000 0.00000 0.00000 MINI CONSTR> 316.83125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 559.68420 0.00105 0.01870 0.00002 MINI INTERN> 21.31201 62.12879 0.00000 19.43106 9.74672 MINI EXTERN> 118.37098 11.84692 0.00000 0.00000 0.00000 MINI CONSTR> 316.84772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 559.68386 0.00034 0.06794 0.00004 MINI INTERN> 21.30662 62.12793 0.00000 19.42954 9.74719 MINI EXTERN> 118.35722 11.84749 0.00000 0.00000 0.00000 MINI CONSTR> 316.86786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 559.68323 0.00062 0.07085 0.00004 MINI INTERN> 21.30767 62.12554 0.00000 19.42796 9.74698 MINI EXTERN> 118.34429 11.84538 0.00000 0.00000 0.00000 MINI CONSTR> 316.88541 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 559.68223 0.00100 0.02312 0.00002 MINI INTERN> 21.31389 62.12402 0.00000 19.42611 9.74614 MINI EXTERN> 118.33116 11.84026 0.00000 0.00000 0.00000 MINI CONSTR> 316.90066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 559.68174 0.00049 0.01601 0.00002 MINI INTERN> 21.31331 62.12270 0.00000 19.42494 9.74607 MINI EXTERN> 118.32160 11.83914 0.00000 0.00000 0.00000 MINI CONSTR> 316.91398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 559.68118 0.00056 0.01584 0.00002 MINI INTERN> 21.31375 62.12126 0.00000 19.42340 9.74590 MINI EXTERN> 118.30930 11.83725 0.00000 0.00000 0.00000 MINI CONSTR> 316.93032 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 559.68069 0.00049 0.03257 0.00002 MINI INTERN> 21.31574 62.12014 0.00000 19.42166 9.74561 MINI EXTERN> 118.29550 11.83463 0.00000 0.00000 0.00000 MINI CONSTR> 316.94741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 559.68020 0.00049 0.01966 0.00002 MINI INTERN> 21.31502 62.11873 0.00000 19.42048 9.74554 MINI EXTERN> 118.28593 11.83362 0.00000 0.00000 0.00000 MINI CONSTR> 316.96087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 559.67975 0.00044 0.02355 0.00002 MINI INTERN> 21.31581 62.11755 0.00000 19.41904 9.74536 MINI EXTERN> 118.27442 11.83189 0.00000 0.00000 0.00000 MINI CONSTR> 316.97568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 559.67944 0.00031 0.03573 0.00002 MINI INTERN> 21.31708 62.11670 0.00000 19.41775 9.74516 MINI EXTERN> 118.26421 11.83016 0.00000 0.00000 0.00000 MINI CONSTR> 316.98837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 559.67906 0.00038 0.03921 0.00002 MINI INTERN> 21.31801 62.11559 0.00000 19.41641 9.74504 MINI EXTERN> 118.25309 11.82872 0.00000 0.00000 0.00000 MINI CONSTR> 317.00220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 559.67873 0.00034 0.03807 0.00002 MINI INTERN> 21.31820 62.11462 0.00000 19.41531 9.74490 MINI EXTERN> 118.24439 11.82757 0.00000 0.00000 0.00000 MINI CONSTR> 317.01373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 559.67840 0.00033 0.03888 0.00003 MINI INTERN> 21.31870 62.11368 0.00000 19.41414 9.74478 MINI EXTERN> 118.23482 11.82637 0.00000 0.00000 0.00000 MINI CONSTR> 317.02592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 559.67799 0.00041 0.01252 0.00001 MINI INTERN> 21.31489 62.11222 0.00000 19.41341 9.74462 MINI EXTERN> 118.23084 11.82610 0.00000 0.00000 0.00000 MINI CONSTR> 317.03590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 559.67787 0.00012 0.04322 0.00003 MINI INTERN> 21.31958 62.11207 0.00000 19.41204 9.74450 MINI EXTERN> 118.21821 11.82415 0.00000 0.00000 0.00000 MINI CONSTR> 317.04732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 559.67761 0.00026 0.04539 0.00003 MINI INTERN> 21.32029 62.11133 0.00000 19.41093 9.74440 MINI EXTERN> 118.20889 11.82312 0.00000 0.00000 0.00000 MINI CONSTR> 317.05865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 559.67719 0.00042 0.01532 0.00001 MINI INTERN> 21.31481 62.10962 0.00000 19.41032 9.74413 MINI EXTERN> 118.20738 11.82293 0.00000 0.00000 0.00000 MINI CONSTR> 317.06800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 559.67698 0.00020 0.01013 0.00001 MINI INTERN> 21.31588 62.10920 0.00000 19.40946 9.74405 MINI EXTERN> 118.20018 11.82204 0.00000 0.00000 0.00000 MINI CONSTR> 317.07617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 559.67675 0.00023 0.01013 0.00001 MINI INTERN> 21.31594 62.10843 0.00000 19.40848 9.74389 MINI EXTERN> 118.19271 11.82107 0.00000 0.00000 0.00000 MINI CONSTR> 317.08623 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 559.67655 0.00020 0.02157 0.00001 MINI INTERN> 21.31436 62.10728 0.00000 19.40758 9.74363 MINI EXTERN> 118.18725 11.82024 0.00000 0.00000 0.00000 MINI CONSTR> 317.09621 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> 329 559.67640 0.00015 0.00921 0.00001 STPD INTERN> 21.31698 62.10752 0.00000 19.40688 9.74369 STPD EXTERN> 118.17984 11.81954 0.00000 0.00000 0.00000 STPD CONSTR> 317.10196 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 11265 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 559.67640 0.00015 0.00921 0.00000 MINI INTERN> 21.31698 62.10752 0.00000 19.40688 9.74369 MINI EXTERN> 118.17984 11.81954 0.00000 0.00000 0.00000 MINI CONSTR> 317.10196 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> 3 559.67355 0.00285 0.00421 0.02000 CONJ INTERN> 21.31452 62.08745 0.00000 19.38102 9.74215 CONJ EXTERN> 117.96774 11.79969 0.00000 0.00000 0.00000 CONJ CONSTR> 317.38099 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "3600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 15.084 ( PROT LYS 1 HT2 ) 15.084 ( PROT LYS 1 N ) 18.855 ( PROT LYS 1 HT3 ) 15.084 ( PROT LYS 1 CA ) 18.855 ( PROT LYS 1 CB ) 15.084 ( PROT LYS 1 CG ) 15.084 ( PROT LYS 1 CD ) 15.084 ( PROT LYS 1 CE ) 15.084 ( PROT LYS 1 NZ ) 15.084 ( PROT LYS 1 HZ1 ) 15.084 ( PROT LYS 1 HZ2 ) 15.084 ( PROT LYS 1 HZ3 ) 15.084 ( PROT LYS 1 C ) 18.855 ( PROT LYS 1 O ) 18.855 ( PROT MET 2 N ) 18.855 ( PROT MET 2 H ) 15.084 ( PROT MET 2 CA ) 18.855 ( PROT MET 2 CB ) 15.084 ( PROT MET 2 CG ) 15.084 ( PROT MET 2 SD ) 15.084 ( PROT MET 2 CE ) 15.084 ( PROT MET 2 C ) 18.855 ( PROT MET 2 O ) 18.855 ( PROT LYS 3 N ) 18.855 ( PROT LYS 3 H ) 15.084 ( PROT LYS 3 CA ) 18.855 ( PROT LYS 3 CB ) 15.084 ( PROT LYS 3 CG ) 15.084 ( PROT LYS 3 CD ) 15.084 ( PROT LYS 3 CE ) 15.084 ( PROT LYS 3 NZ ) 15.084 ( PROT LYS 3 HZ1 ) 15.084 ( PROT LYS 3 HZ2 ) 15.084 ( PROT LYS 3 HZ3 ) 15.084 ( PROT LYS 3 C ) 18.855 ( PROT LYS 3 O ) 18.855 ( PROT ALA 4 N ) 18.855 ( PROT ALA 4 H ) 15.084 ( PROT ALA 4 CA ) 18.855 ( PROT ALA 4 CB ) 15.084 ( PROT ALA 4 C ) 18.855 ( PROT ALA 4 O ) 18.855 ( PROT VAL 5 N ) 18.855 ( PROT VAL 5 H ) 15.084 ( PROT VAL 5 CA ) 18.855 ( PROT VAL 5 CB ) 15.084 ( PROT VAL 5 CG1 ) 15.084 ( PROT VAL 5 CG2 ) 15.084 ( PROT VAL 5 C ) 18.855 ( PROT VAL 5 O ) 18.855 ( PROT MET 6 N ) 18.855 ( PROT MET 6 H ) 15.084 ( PROT MET 6 CA ) 18.855 ( PROT MET 6 CB ) 15.084 ( PROT MET 6 CG ) 15.084 ( PROT MET 6 SD ) 15.084 ( PROT MET 6 CE ) 15.084 ( PROT MET 6 C ) 18.855 ( PROT MET 6 O ) 18.855 ( PROT ILE 7 N ) 18.855 ( PROT ILE 7 H ) 15.084 ( PROT ILE 7 CA ) 18.855 ( PROT ILE 7 CB ) 15.084 ( PROT ILE 7 CG2 ) 15.084 ( PROT ILE 7 CG1 ) 15.084 ( PROT ILE 7 CD ) 15.084 ( PROT ILE 7 C ) 18.855 ( PROT ILE 7 O ) 18.855 ( PROT GLY 8 N ) 18.855 ( PROT GLY 8 H ) 15.084 ( PROT GLY 8 CA ) 18.855 ( PROT GLY 8 C ) 18.855 ( PROT GLY 8 O ) 18.855 ( PROT ALA 9 N ) 18.855 ( PROT ALA 9 H ) 15.084 ( PROT ALA 9 CA ) 18.855 ( PROT ALA 9 CB ) 15.084 ( PROT ALA 9 C ) 18.855 ( PROT ALA 9 O ) 18.855 ( PROT CYS 10 N ) 18.855 ( PROT CYS 10 H ) 15.084 ( PROT CYS 10 CA ) 18.855 ( PROT CYS 10 CB ) 15.084 ( PROT CYS 10 SG ) 15.084 ( PROT CYS 10 C ) 18.855 ( PROT CYS 10 O ) 18.855 ( PROT PHE 11 N ) 18.855 ( PROT PHE 11 H ) 15.084 ( PROT PHE 11 CA ) 18.855 ( PROT PHE 11 CB ) 15.084 ( PROT PHE 11 CG ) 15.084 ( PROT PHE 11 CD1 ) 15.084 ( PROT PHE 11 CD2 ) 15.084 ( PROT PHE 11 CE1 ) 15.084 ( PROT PHE 11 CE2 ) 15.084 ( PROT PHE 11 CZ ) 15.084 ( PROT PHE 11 C ) 18.855 ( PROT PHE 11 O ) 18.855 ( PROT LEU 12 N ) 18.855 ( PROT LEU 12 H ) 15.084 ( PROT LEU 12 CA ) 18.855 ( PROT LEU 12 CB ) 15.084 ( PROT LEU 12 CG ) 15.084 ( PROT LEU 12 CD1 ) 15.084 ( PROT LEU 12 CD2 ) 15.084 ( PROT LEU 12 C ) 18.855 ( PROT LEU 12 O ) 18.855 ( PROT ILE 13 N ) 18.855 ( PROT ILE 13 H ) 15.084 ( PROT ILE 13 CA ) 18.855 ( PROT ILE 13 CB ) 15.084 ( PROT ILE 13 CG2 ) 15.084 ( PROT ILE 13 CG1 ) 15.084 ( PROT ILE 13 CD ) 15.084 ( PROT ILE 13 C ) 18.855 ( PROT ILE 13 O ) 18.855 ( PROT ASP 14 N ) 18.855 ( PROT ASP 14 H ) 15.084 ( PROT ASP 14 CA ) 18.855 ( PROT ASP 14 CB ) 15.084 ( PROT ASP 14 CG ) 15.084 ( PROT ASP 14 OD1 ) 15.084 ( PROT ASP 14 OD2 ) 15.084 ( PROT ASP 14 C ) 18.855 ( PROT ASP 14 O ) 18.855 ( PROT PHE 15 N ) 18.855 ( PROT PHE 15 H ) 15.084 ( PROT PHE 15 CA ) 18.855 ( PROT PHE 15 CB ) 15.084 ( PROT PHE 15 CG ) 15.084 ( PROT PHE 15 CD1 ) 15.084 ( PROT PHE 15 CD2 ) 15.084 ( PROT PHE 15 CE1 ) 15.084 ( PROT PHE 15 CE2 ) 15.084 ( PROT PHE 15 CZ ) 15.084 ( PROT PHE 15 C ) 18.855 ( PROT PHE 15 O ) 18.855 ( PROT MET 16 N ) 18.855 ( PROT MET 16 H ) 15.084 ( PROT MET 16 CA ) 18.855 ( PROT MET 16 CB ) 15.084 ( PROT MET 16 CG ) 15.084 ( PROT MET 16 SD ) 15.084 ( PROT MET 16 CE ) 15.084 ( PROT MET 16 C ) 18.855 ( PROT MET 16 O ) 18.855 ( PROT PHE 17 N ) 18.855 ( PROT PHE 17 H ) 15.084 ( PROT PHE 17 CA ) 18.855 ( PROT PHE 17 CB ) 15.084 ( PROT PHE 17 CG ) 15.084 ( PROT PHE 17 CD1 ) 15.084 ( PROT PHE 17 CD2 ) 15.084 ( PROT PHE 17 CE1 ) 15.084 ( PROT PHE 17 CE2 ) 15.084 ( PROT PHE 17 CZ ) 15.084 ( PROT PHE 17 C ) 18.855 ( PROT PHE 17 O ) 18.855 ( PROT PHE 18 N ) 18.855 ( PROT PHE 18 H ) 15.084 ( PROT PHE 18 CA ) 18.855 ( PROT PHE 18 CB ) 15.084 ( PROT PHE 18 CG ) 15.084 ( PROT PHE 18 CD1 ) 15.084 ( PROT PHE 18 CD2 ) 15.084 ( PROT PHE 18 CE1 ) 15.084 ( PROT PHE 18 CE2 ) 15.084 ( PROT PHE 18 CZ ) 15.084 ( PROT PHE 18 C ) 18.855 ( PROT PHE 18 O ) 18.855 ( PROT GLU 19 N ) 18.855 ( PROT GLU 19 H ) 15.084 ( PROT GLU 19 CA ) 18.855 ( PROT GLU 19 CB ) 15.084 ( PROT GLU 19 CG ) 15.084 ( PROT GLU 19 CD ) 15.084 ( PROT GLU 19 OE1 ) 15.084 ( PROT GLU 19 OE2 ) 15.084 ( PROT GLU 19 C ) 18.855 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41163 5.26164 -8.67209 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS -0.00060 -0.00172 0.00040 ROTATION MATRIX 1.000000 -0.000111 -0.000029 0.000111 1.000000 0.000147 0.000029 -0.000147 1.000000 AXIS OF ROTATION IS 0.787853 0.156193 -0.595728 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 12.7509 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.264688 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2647" Parameter: A <- "0.2647" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70883 5.23446 -8.77913 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00601 0.02996 -0.01524 ROTATION MATRIX 0.999825 0.013931 0.012492 -0.013761 0.999813 -0.013604 -0.012680 0.013429 0.999829 AXIS OF ROTATION IS -0.585558 -0.545250 0.599853 ANGLE IS 1.32 CENTER OF ROTATION 9.293232 5.019085 -9.404761 SHIFT IS -0.029001 TOTAL SQUARE DIFF IS 0.2151 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.106393 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2647" RDCMND substituted energy or value "?RMS" to " 0.1064" Parameter: A <- "0.2647 0.1064" 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 0.2647 0.1064 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 " 317.38" Parameter: H <- "317.38" 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> 0 242.29256 317.38099 7.64906 ENER INTERN> 21.31452 62.08745 0.00000 19.38102 9.74215 ENER EXTERN> 117.96774 11.79969 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 " 242.29" Parameter: B <- "242.29" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 11.80" Parameter: C <- "11.80" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 117.97" Parameter: C <- " 129.77" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 129.77" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 21.31" Parameter: D <- "21.31" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 62.09" Parameter: D <- " 83.40" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 19.38" Parameter: D <- " 102.78" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 9.74" Parameter: D <- " 112.52" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 112.52" 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= 3600 ENER= 242.29 GRMS= 7.65 ELEC= 11.80 VDW= 117.97 RDTITL> *EXTERNAL= 129.77 INTERNAL= 112.52 USER= 0.00 HARM= 317.38 RDTITL> *BOND= 21.31 ANGL= 62.09 DIHE= 19.38 IMPR= 9.74 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "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= 242.29 GRMS= 7.65 ELEC= 11.80 VDW= 117.97 RDTITL> *EXTERNAL= 129.77 INTERNAL= 112.52 USER= 0.00 HARM= 317.38 RDTITL> *BOND= 21.31 ANGL= 62.09 DIHE= 19.38 IMPR= 9.74 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 -> "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= 242.29 GRMS= 7.65 ELEC= 11.80 VDW= 117.97 RDTITL> *EXTERNAL= 129.77 INTERNAL= 112.52 USER= 0.00 HARM= 317.38 RDTITL> *BOND= 21.31 ANGL= 62.09 DIHE= 19.38 IMPR= 9.74 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 3600 0.2647 0.1064 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "3600" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11265 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11265 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 475.60188 -233.30932 3.20328 0.02000 MINI INTERN> 21.31452 62.08745 0.00000 19.38102 9.74215 MINI EXTERN> 117.96774 11.79969 0.00000 0.00000 0.00000 MINI CONSTR> 233.30932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 454.05266 21.54922 2.61749 0.00360 MINI INTERN> 19.07279 62.74786 0.00000 22.03179 9.27127 MINI EXTERN> 72.83446 12.59042 0.00000 0.00000 0.00000 MINI CONSTR> 255.50408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11255 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 447.63307 6.41959 1.46826 0.00156 MINI INTERN> 16.06934 58.58767 0.00000 21.97954 8.84205 MINI EXTERN> 73.94236 11.55097 0.00000 0.00000 0.00000 MINI CONSTR> 256.66113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 444.18204 3.45103 1.88932 0.00161 MINI INTERN> 14.44099 58.25855 0.00000 22.25208 8.91437 MINI EXTERN> 71.02588 11.26465 0.00000 0.00000 0.00000 MINI CONSTR> 258.02553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11253 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 442.52256 1.65948 2.80625 0.00167 MINI INTERN> 13.25144 58.38384 0.00000 22.33057 8.98886 MINI EXTERN> 69.83227 11.02754 0.00000 0.00000 0.00000 MINI CONSTR> 258.70803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 440.95633 1.56623 2.86557 0.00173 MINI INTERN> 12.93450 57.86667 0.00000 22.39688 8.97528 MINI EXTERN> 68.67119 10.97020 0.00000 0.00000 0.00000 MINI CONSTR> 259.14161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11251 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 439.20316 1.75317 0.86821 0.00075 MINI INTERN> 15.80087 55.05019 0.00000 22.50425 8.81787 MINI EXTERN> 66.20031 11.59694 0.00000 0.00000 0.00000 MINI CONSTR> 259.23273 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 438.37813 0.82504 0.65035 0.00078 MINI INTERN> 15.33073 54.98544 0.00000 22.51846 8.81686 MINI EXTERN> 65.76611 11.51505 0.00000 0.00000 0.00000 MINI CONSTR> 259.44547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 437.68409 0.69404 1.38906 0.00080 MINI INTERN> 16.40099 53.99184 0.00000 22.55555 8.75348 MINI EXTERN> 64.68919 11.69043 0.00000 0.00000 0.00000 MINI CONSTR> 259.60261 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 437.14736 0.53672 1.47835 0.00083 MINI INTERN> 16.43919 53.72444 0.00000 22.55935 8.73109 MINI EXTERN> 64.24133 11.69510 0.00000 0.00000 0.00000 MINI CONSTR> 259.75685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 436.73673 0.41063 1.43413 0.00087 MINI INTERN> 16.34776 53.59727 0.00000 22.55193 8.71958 MINI EXTERN> 63.94609 11.68207 0.00000 0.00000 0.00000 MINI CONSTR> 259.89204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 436.25173 0.48500 0.43739 0.00037 MINI INTERN> 14.57176 54.48934 0.00000 22.50418 8.75995 MINI EXTERN> 64.43311 11.39231 0.00000 0.00000 0.00000 MINI CONSTR> 260.10108 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 436.00492 0.24680 0.35122 0.00039 MINI INTERN> 14.64774 54.31155 0.00000 22.49703 8.74112 MINI EXTERN> 64.19158 11.41354 0.00000 0.00000 0.00000 MINI CONSTR> 260.20237 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 435.77251 0.23241 0.62094 0.00040 MINI INTERN> 14.24230 54.45983 0.00000 22.46921 8.74129 MINI EXTERN> 64.14304 11.34788 0.00000 0.00000 0.00000 MINI CONSTR> 260.36896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 435.59352 0.17899 0.44197 0.00042 MINI INTERN> 14.38284 54.26127 0.00000 22.46047 8.72230 MINI EXTERN> 63.91434 11.38504 0.00000 0.00000 0.00000 MINI CONSTR> 260.46726 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 435.48783 0.10568 0.71015 0.00043 MINI INTERN> 14.08481 54.39019 0.00000 22.43962 8.72113 MINI EXTERN> 63.91961 11.34101 0.00000 0.00000 0.00000 MINI CONSTR> 260.59146 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 435.37915 0.10868 0.73713 0.00045 MINI INTERN> 14.05021 54.34239 0.00000 22.42355 8.71299 MINI EXTERN> 63.79932 11.34753 0.00000 0.00000 0.00000 MINI CONSTR> 260.70316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 435.25255 0.12660 0.22723 0.00019 MINI INTERN> 14.73443 53.80396 0.00000 22.42976 8.67875 MINI EXTERN> 63.37207 11.47999 0.00000 0.00000 0.00000 MINI CONSTR> 260.75359 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 435.18649 0.06607 0.18301 0.00020 MINI INTERN> 14.66884 53.79860 0.00000 22.41496 8.67571 MINI EXTERN> 63.30409 11.47948 0.00000 0.00000 0.00000 MINI CONSTR> 260.84481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 435.12348 0.06301 0.17069 0.00021 MINI INTERN> 14.66112 53.75185 0.00000 22.40064 8.66983 MINI EXTERN> 63.20650 11.49093 0.00000 0.00000 0.00000 MINI CONSTR> 260.94262 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 435.07621 0.04727 0.36890 0.00022 MINI INTERN> 14.87451 53.56545 0.00000 22.39158 8.65604 MINI EXTERN> 63.01901 11.53790 0.00000 0.00000 0.00000 MINI CONSTR> 261.03173 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 435.03507 0.04114 0.38189 0.00022 MINI INTERN> 14.86871 53.52802 0.00000 22.37849 8.65177 MINI EXTERN> 62.93844 11.54937 0.00000 0.00000 0.00000 MINI CONSTR> 261.12027 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 435.00242 0.03265 0.42893 0.00023 MINI INTERN> 14.88925 53.47757 0.00000 22.36643 8.64709 MINI EXTERN> 62.85234 11.56492 0.00000 0.00000 0.00000 MINI CONSTR> 261.20482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 434.97471 0.02771 0.40592 0.00024 MINI INTERN> 14.88195 53.45522 0.00000 22.35397 8.64673 MINI EXTERN> 62.78413 11.57531 0.00000 0.00000 0.00000 MINI CONSTR> 261.27739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 434.94901 0.02569 0.41270 0.00025 MINI INTERN> 14.86340 53.43465 0.00000 22.34220 8.64449 MINI EXTERN> 62.72402 11.58513 0.00000 0.00000 0.00000 MINI CONSTR> 261.35512 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 434.92642 0.02259 0.43162 0.00026 MINI INTERN> 14.83204 53.42158 0.00000 22.33090 8.64191 MINI EXTERN> 62.67374 11.59324 0.00000 0.00000 0.00000 MINI CONSTR> 261.43301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 434.89173 0.03469 0.15187 0.00011 MINI INTERN> 14.49373 53.61384 0.00000 22.30716 8.65777 MINI EXTERN> 62.71938 11.56486 0.00000 0.00000 0.00000 MINI CONSTR> 261.53498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 434.87468 0.01704 0.11542 0.00012 MINI INTERN> 14.50692 53.57875 0.00000 22.29883 8.65539 MINI EXTERN> 62.66002 11.58012 0.00000 0.00000 0.00000 MINI CONSTR> 261.59465 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 434.85843 0.01625 0.11285 0.00012 MINI INTERN> 14.50861 53.55305 0.00000 22.28817 8.65504 MINI EXTERN> 62.59692 11.59533 0.00000 0.00000 0.00000 MINI CONSTR> 261.66131 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 434.84383 0.01461 0.13113 0.00012 MINI INTERN> 14.50471 53.53323 0.00000 22.27682 8.65587 MINI EXTERN> 62.53453 11.61040 0.00000 0.00000 0.00000 MINI CONSTR> 261.72827 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 434.83377 0.01006 0.20530 0.00013 MINI INTERN> 14.48145 53.53155 0.00000 22.26581 8.65847 MINI EXTERN> 62.48514 11.62251 0.00000 0.00000 0.00000 MINI CONSTR> 261.78882 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 434.82222 0.01155 0.22772 0.00013 MINI INTERN> 14.50298 53.50004 0.00000 22.25475 8.65983 MINI EXTERN> 62.41451 11.64055 0.00000 0.00000 0.00000 MINI CONSTR> 261.84955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 434.81195 0.01027 0.22000 0.00014 MINI INTERN> 14.49657 53.48429 0.00000 22.24738 8.65949 MINI EXTERN> 62.37319 11.65321 0.00000 0.00000 0.00000 MINI CONSTR> 261.89782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 434.80168 0.01027 0.22126 0.00014 MINI INTERN> 14.51207 53.45731 0.00000 22.23796 8.66027 MINI EXTERN> 62.31432 11.66915 0.00000 0.00000 0.00000 MINI CONSTR> 261.95059 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11248 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 434.78905 0.01262 0.07081 0.00006 MINI INTERN> 14.46585 53.44990 0.00000 22.23908 8.65168 MINI EXTERN> 62.32534 11.67412 0.00000 0.00000 0.00000 MINI CONSTR> 261.98309 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 434.78552 0.00354 0.24683 0.00015 MINI INTERN> 14.50600 53.42874 0.00000 22.22238 8.66167 MINI EXTERN> 62.22892 11.69571 0.00000 0.00000 0.00000 MINI CONSTR> 262.04209 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 434.77744 0.00808 0.25972 0.00016 MINI INTERN> 14.53085 53.40153 0.00000 22.21224 8.66364 MINI EXTERN> 62.16643 11.71183 0.00000 0.00000 0.00000 MINI CONSTR> 262.09092 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 434.76419 0.01325 0.08609 0.00007 MINI INTERN> 14.42772 53.41967 0.00000 22.21740 8.65208 MINI EXTERN> 62.21793 11.71175 0.00000 0.00000 0.00000 MINI CONSTR> 262.11764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 434.75775 0.00643 0.05754 0.00007 MINI INTERN> 14.44260 53.40362 0.00000 22.20882 8.65491 MINI EXTERN> 62.16920 11.72423 0.00000 0.00000 0.00000 MINI CONSTR> 262.15438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 434.75034 0.00742 0.05792 0.00007 MINI INTERN> 14.43197 53.39381 0.00000 22.20163 8.65535 MINI EXTERN> 62.13406 11.73734 0.00000 0.00000 0.00000 MINI CONSTR> 262.19619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 434.74375 0.00659 0.11591 0.00008 MINI INTERN> 14.37898 53.39840 0.00000 22.19897 8.65180 MINI EXTERN> 62.13340 11.74797 0.00000 0.00000 0.00000 MINI CONSTR> 262.23423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 434.73704 0.00671 0.07230 0.00008 MINI INTERN> 14.39888 53.38029 0.00000 22.18943 8.65511 MINI EXTERN> 62.07921 11.76206 0.00000 0.00000 0.00000 MINI CONSTR> 262.27208 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 434.73079 0.00625 0.08209 0.00008 MINI INTERN> 14.38165 53.37417 0.00000 22.18349 8.65497 MINI EXTERN> 62.05307 11.77477 0.00000 0.00000 0.00000 MINI CONSTR> 262.30867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 434.72610 0.00469 0.12794 0.00009 MINI INTERN> 14.34043 53.37772 0.00000 22.18109 8.65251 MINI EXTERN> 62.05143 11.78468 0.00000 0.00000 0.00000 MINI CONSTR> 262.33825 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 434.72053 0.00557 0.13492 0.00009 MINI INTERN> 14.32764 53.37121 0.00000 22.17512 8.65267 MINI EXTERN> 62.02385 11.79778 0.00000 0.00000 0.00000 MINI CONSTR> 262.37228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 434.71549 0.00504 0.14910 0.00009 MINI INTERN> 14.31183 53.36659 0.00000 22.16970 8.65239 MINI EXTERN> 62.00061 11.81013 0.00000 0.00000 0.00000 MINI CONSTR> 262.40425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 434.71086 0.00463 0.14211 0.00010 MINI INTERN> 14.31154 53.35822 0.00000 22.16352 8.65330 MINI EXTERN> 61.97154 11.82080 0.00000 0.00000 0.00000 MINI CONSTR> 262.43193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 434.70609 0.00478 0.14604 0.00010 MINI INTERN> 14.30419 53.35168 0.00000 22.15748 8.65359 MINI EXTERN> 61.94404 11.83311 0.00000 0.00000 0.00000 MINI CONSTR> 262.46199 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 434.70001 0.00608 0.04569 0.00004 MINI INTERN> 14.40666 53.30840 0.00000 22.13899 8.66345 MINI EXTERN> 61.83422 11.84817 0.00000 0.00000 0.00000 MINI CONSTR> 262.50012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 434.69810 0.00191 0.15985 0.00011 MINI INTERN> 14.28571 53.34218 0.00000 22.14717 8.65353 MINI EXTERN> 61.90098 11.85471 0.00000 0.00000 0.00000 MINI CONSTR> 262.51381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 434.69415 0.00395 0.16690 0.00011 MINI INTERN> 14.27831 53.33731 0.00000 22.14168 8.65347 MINI EXTERN> 61.87745 11.86587 0.00000 0.00000 0.00000 MINI CONSTR> 262.54006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 434.68787 0.00628 0.05374 0.00005 MINI INTERN> 14.40344 53.28575 0.00000 22.12010 8.66543 MINI EXTERN> 61.75213 11.88155 0.00000 0.00000 0.00000 MINI CONSTR> 262.57947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 434.68474 0.00312 0.03897 0.00005 MINI INTERN> 14.38280 53.28702 0.00000 22.11763 8.66403 MINI EXTERN> 61.74665 11.88959 0.00000 0.00000 0.00000 MINI CONSTR> 262.59701 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 434.68117 0.00358 0.03869 0.00005 MINI INTERN> 14.37930 53.28106 0.00000 22.11190 8.66426 MINI EXTERN> 61.72350 11.90044 0.00000 0.00000 0.00000 MINI CONSTR> 262.62071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 434.67792 0.00324 0.07761 0.00005 MINI INTERN> 14.40894 53.26383 0.00000 22.10167 8.66742 MINI EXTERN> 61.67455 11.91224 0.00000 0.00000 0.00000 MINI CONSTR> 262.64928 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 434.67472 0.00320 0.04778 0.00006 MINI INTERN> 14.38225 53.26710 0.00000 22.09972 8.66534 MINI EXTERN> 61.67340 11.92107 0.00000 0.00000 0.00000 MINI CONSTR> 262.66584 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 434.67174 0.00298 0.05587 0.00006 MINI INTERN> 14.38449 53.26112 0.00000 22.09367 8.66571 MINI EXTERN> 61.64964 11.92977 0.00000 0.00000 0.00000 MINI CONSTR> 262.68733 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 434.66957 0.00217 0.08742 0.00006 MINI INTERN> 14.40322 53.24903 0.00000 22.08617 8.66766 MINI EXTERN> 61.61555 11.93979 0.00000 0.00000 0.00000 MINI CONSTR> 262.70815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11249 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 434.66695 0.00262 0.09322 0.00006 MINI INTERN> 14.39984 53.24372 0.00000 22.08096 8.66765 MINI EXTERN> 61.59654 11.95069 0.00000 0.00000 0.00000 MINI CONSTR> 262.72754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 434.66475 0.00220 0.10792 0.00006 MINI INTERN> 14.40347 53.24083 0.00000 22.07555 8.66759 MINI EXTERN> 61.57756 11.95451 0.00000 0.00000 0.00000 MINI CONSTR> 262.74524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 434.66259 0.00216 0.09888 0.00007 MINI INTERN> 14.39909 53.23683 0.00000 22.07173 8.66728 MINI EXTERN> 61.56373 11.96427 0.00000 0.00000 0.00000 MINI CONSTR> 262.75966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 434.65967 0.00292 0.03117 0.00003 MINI INTERN> 14.33637 53.25370 0.00000 22.07516 8.66136 MINI EXTERN> 61.59266 11.97281 0.00000 0.00000 0.00000 MINI CONSTR> 262.76761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 434.65863 0.00105 0.11057 0.00007 MINI INTERN> 14.39502 53.23176 0.00000 22.06296 8.66639 MINI EXTERN> 61.53510 11.97736 0.00000 0.00000 0.00000 MINI CONSTR> 262.79004 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 434.65691 0.00171 0.12143 0.00007 MINI INTERN> 14.38090 53.22623 0.00000 22.05985 8.66574 MINI EXTERN> 61.52451 11.99550 0.00000 0.00000 0.00000 MINI CONSTR> 262.80417 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 434.65398 0.00294 0.03494 0.00003 MINI INTERN> 14.32204 53.24764 0.00000 22.06362 8.65925 MINI EXTERN> 61.55660 11.99547 0.00000 0.00000 0.00000 MINI CONSTR> 262.80935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 434.65241 0.00156 0.02747 0.00003 MINI INTERN> 14.32724 53.24275 0.00000 22.05914 8.65946 MINI EXTERN> 61.54002 12.00196 0.00000 0.00000 0.00000 MINI CONSTR> 262.82184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 434.65066 0.00175 0.02673 0.00003 MINI INTERN> 14.32501 53.24028 0.00000 22.05497 8.65879 MINI EXTERN> 61.52698 12.00930 0.00000 0.00000 0.00000 MINI CONSTR> 262.83532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 434.64902 0.00164 0.02827 0.00004 MINI INTERN> 14.31928 53.23898 0.00000 22.05135 8.65775 MINI EXTERN> 61.51687 12.01692 0.00000 0.00000 0.00000 MINI CONSTR> 262.84787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 434.64758 0.00144 0.05348 0.00004 MINI INTERN> 14.29991 53.24299 0.00000 22.04950 8.65519 MINI EXTERN> 61.51689 12.02434 0.00000 0.00000 0.00000 MINI CONSTR> 262.85876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 434.64606 0.00151 0.03311 0.00004 MINI INTERN> 14.30993 53.23656 0.00000 22.04433 8.65568 MINI EXTERN> 61.49751 12.03097 0.00000 0.00000 0.00000 MINI CONSTR> 262.87108 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 434.64468 0.00138 0.04035 0.00004 MINI INTERN> 14.30458 53.23648 0.00000 22.04096 8.65434 MINI EXTERN> 61.48926 12.03688 0.00000 0.00000 0.00000 MINI CONSTR> 262.88218 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 434.64367 0.00101 0.06025 0.00004 MINI INTERN> 14.29067 53.23910 0.00000 22.03921 8.65232 MINI EXTERN> 61.48825 12.04342 0.00000 0.00000 0.00000 MINI CONSTR> 262.89071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 434.64246 0.00120 0.06661 0.00004 MINI INTERN> 14.28641 53.23690 0.00000 22.03578 8.65128 MINI EXTERN> 61.47845 12.05232 0.00000 0.00000 0.00000 MINI CONSTR> 262.90133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 434.64144 0.00102 0.07226 0.00004 MINI INTERN> 14.28298 53.23823 0.00000 22.03291 8.64988 MINI EXTERN> 61.47258 12.05489 0.00000 0.00000 0.00000 MINI CONSTR> 262.90998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 434.64041 0.00103 0.06784 0.00005 MINI INTERN> 14.28094 53.23625 0.00000 22.02989 8.64916 MINI EXTERN> 61.46403 12.06167 0.00000 0.00000 0.00000 MINI CONSTR> 262.91847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 434.63934 0.00107 0.06986 0.00005 MINI INTERN> 14.28087 53.23528 0.00000 22.02636 8.64805 MINI EXTERN> 61.45460 12.06632 0.00000 0.00000 0.00000 MINI CONSTR> 262.92786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 434.63801 0.00133 0.02252 0.00002 MINI INTERN> 14.31252 53.22141 0.00000 22.01865 8.65077 MINI EXTERN> 61.42248 12.07190 0.00000 0.00000 0.00000 MINI CONSTR> 262.94030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 434.63762 0.00039 0.07604 0.00005 MINI INTERN> 14.27293 53.23380 0.00000 22.02096 8.64579 MINI EXTERN> 61.44167 12.07897 0.00000 0.00000 0.00000 MINI CONSTR> 262.94350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 434.63681 0.00081 0.08531 0.00005 MINI INTERN> 14.27906 53.23338 0.00000 22.01709 8.64485 MINI EXTERN> 61.43139 12.07916 0.00000 0.00000 0.00000 MINI CONSTR> 262.95187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 434.63541 0.00139 0.02628 0.00002 MINI INTERN> 14.31104 53.21768 0.00000 22.00923 8.64790 MINI EXTERN> 61.39819 12.08727 0.00000 0.00000 0.00000 MINI CONSTR> 262.96411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 434.63471 0.00070 0.01845 0.00002 MINI INTERN> 14.30405 53.21922 0.00000 22.00766 8.64632 MINI EXTERN> 61.39666 12.09142 0.00000 0.00000 0.00000 MINI CONSTR> 262.96938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 434.63391 0.00080 0.01880 0.00002 MINI INTERN> 14.30323 53.21821 0.00000 22.00457 8.64520 MINI EXTERN> 61.38912 12.09667 0.00000 0.00000 0.00000 MINI CONSTR> 262.97691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 434.63322 0.00069 0.03736 0.00003 MINI INTERN> 14.31233 53.21383 0.00000 21.99996 8.64510 MINI EXTERN> 61.37464 12.10155 0.00000 0.00000 0.00000 MINI CONSTR> 262.98581 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 434.63249 0.00072 0.02374 0.00003 MINI INTERN> 14.30452 53.21619 0.00000 21.99845 8.64320 MINI EXTERN> 61.37406 12.10527 0.00000 0.00000 0.00000 MINI CONSTR> 262.99082 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 434.63188 0.00062 0.03180 0.00003 MINI INTERN> 14.30738 53.21392 0.00000 21.99513 8.64250 MINI EXTERN> 61.36493 12.11024 0.00000 0.00000 0.00000 MINI CONSTR> 262.99778 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 434.63136 0.00051 0.04191 0.00003 MINI INTERN> 14.31121 53.21203 0.00000 21.99199 8.64187 MINI EXTERN> 61.35639 12.11384 0.00000 0.00000 0.00000 MINI CONSTR> 263.00404 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 434.63076 0.00060 0.04447 0.00003 MINI INTERN> 14.30987 53.21142 0.00000 21.98928 8.64069 MINI EXTERN> 61.35044 12.11885 0.00000 0.00000 0.00000 MINI CONSTR> 263.01021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 434.63025 0.00051 0.05119 0.00003 MINI INTERN> 14.31149 53.21169 0.00000 21.98650 8.63952 MINI EXTERN> 61.34459 12.12062 0.00000 0.00000 0.00000 MINI CONSTR> 263.01583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 434.62975 0.00050 0.04691 0.00003 MINI INTERN> 14.30991 53.21095 0.00000 21.98445 8.63847 MINI EXTERN> 61.34015 12.12532 0.00000 0.00000 0.00000 MINI CONSTR> 263.02049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 434.62923 0.00051 0.04942 0.00003 MINI INTERN> 14.30593 53.21059 0.00000 21.98228 8.63713 MINI EXTERN> 61.33606 12.13151 0.00000 0.00000 0.00000 MINI CONSTR> 263.02574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 434.62860 0.00063 0.01548 0.00001 MINI INTERN> 14.28814 53.21754 0.00000 21.98302 8.63387 MINI EXTERN> 61.34512 12.13372 0.00000 0.00000 0.00000 MINI CONSTR> 263.02719 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 434.62839 0.00021 0.05236 0.00004 MINI INTERN> 14.30895 53.20977 0.00000 21.97748 8.63515 MINI EXTERN> 61.32546 12.13658 0.00000 0.00000 0.00000 MINI CONSTR> 263.03500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 434.62794 0.00045 0.05451 0.00004 MINI INTERN> 14.30853 53.21022 0.00000 21.97509 8.63386 MINI EXTERN> 61.32107 12.13941 0.00000 0.00000 0.00000 MINI CONSTR> 263.03977 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 434.62725 0.00069 0.01733 0.00002 MINI INTERN> 14.28429 53.21793 0.00000 21.97652 8.62989 MINI EXTERN> 61.33314 12.14470 0.00000 0.00000 0.00000 MINI CONSTR> 263.04078 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 434.62689 0.00035 0.01333 0.00002 MINI INTERN> 14.28616 53.21728 0.00000 21.97436 8.62914 MINI EXTERN> 61.32813 12.14718 0.00000 0.00000 0.00000 MINI CONSTR> 263.04466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 434.62651 0.00038 0.01403 0.00002 MINI INTERN> 14.28453 53.21765 0.00000 21.97247 8.62781 MINI EXTERN> 61.32502 12.15054 0.00000 0.00000 0.00000 MINI CONSTR> 263.04850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 434.62615 0.00036 0.02450 0.00002 MINI INTERN> 14.27911 53.21939 0.00000 21.97109 8.62586 MINI EXTERN> 61.32454 12.15426 0.00000 0.00000 0.00000 MINI CONSTR> 263.05191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 434.62579 0.00036 0.01602 0.00002 MINI INTERN> 14.28204 53.21838 0.00000 21.96869 8.62514 MINI EXTERN> 61.31878 12.15684 0.00000 0.00000 0.00000 MINI CONSTR> 263.05590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 434.62544 0.00035 0.01694 0.00002 MINI INTERN> 14.28099 53.21849 0.00000 21.96673 8.62380 MINI EXTERN> 61.31540 12.16039 0.00000 0.00000 0.00000 MINI CONSTR> 263.05964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 434.62516 0.00027 0.02970 0.00002 MINI INTERN> 14.27680 53.22044 0.00000 21.96551 8.62192 MINI EXTERN> 61.31532 12.16278 0.00000 0.00000 0.00000 MINI CONSTR> 263.06238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 434.62488 0.00028 0.03282 0.00002 MINI INTERN> 14.27475 53.22014 0.00000 21.96387 8.62073 MINI EXTERN> 61.31245 12.16732 0.00000 0.00000 0.00000 MINI CONSTR> 263.06563 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> 500 434.62488 0.00028 0.03282 0.00002 STPD INTERN> 14.27475 53.22014 0.00000 21.96387 8.62073 STPD EXTERN> 61.31245 12.16732 0.00000 0.00000 0.00000 STPD CONSTR> 263.06563 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 11250 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 434.62488 0.00028 0.03282 0.00000 MINI INTERN> 14.27475 53.22014 0.00000 21.96387 8.62073 MINI EXTERN> 61.31245 12.16732 0.00000 0.00000 0.00000 MINI CONSTR> 263.06563 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 434.61802 0.00686 0.01550 0.00090 MINI INTERN> 14.24262 53.21622 0.00000 21.88675 8.56889 MINI EXTERN> 61.17367 12.29728 0.00000 0.00000 0.00000 MINI CONSTR> 263.23259 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 434.61740 0.00062 0.02163 0.00184 MINI INTERN> 14.26466 53.26940 0.00000 21.87122 8.54650 MINI EXTERN> 61.22441 12.29132 0.00000 0.00000 0.00000 MINI CONSTR> 263.14989 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 434.61675 0.00064 0.01462 0.00178 MINI INTERN> 14.27648 53.27325 0.00000 21.86875 8.53179 MINI EXTERN> 61.22268 12.29628 0.00000 0.00000 0.00000 MINI CONSTR> 263.14752 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> 18 434.61662 0.00013 0.00974 0.02000 CONJ INTERN> 14.27537 53.27312 0.00000 21.86839 8.52448 CONJ EXTERN> 61.20283 12.30095 0.00000 0.00000 0.00000 CONJ CONSTR> 263.17147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "4200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 9.8045 ( PROT LYS 1 HT2 ) 9.8045 ( PROT LYS 1 N ) 12.256 ( PROT LYS 1 HT3 ) 9.8045 ( PROT LYS 1 CA ) 12.256 ( PROT LYS 1 CB ) 9.8045 ( PROT LYS 1 CG ) 9.8045 ( PROT LYS 1 CD ) 9.8045 ( PROT LYS 1 CE ) 9.8045 ( PROT LYS 1 NZ ) 9.8045 ( PROT LYS 1 HZ1 ) 9.8045 ( PROT LYS 1 HZ2 ) 9.8045 ( PROT LYS 1 HZ3 ) 9.8045 ( PROT LYS 1 C ) 12.256 ( PROT LYS 1 O ) 12.256 ( PROT MET 2 N ) 12.256 ( PROT MET 2 H ) 9.8045 ( PROT MET 2 CA ) 12.256 ( PROT MET 2 CB ) 9.8045 ( PROT MET 2 CG ) 9.8045 ( PROT MET 2 SD ) 9.8045 ( PROT MET 2 CE ) 9.8045 ( PROT MET 2 C ) 12.256 ( PROT MET 2 O ) 12.256 ( PROT LYS 3 N ) 12.256 ( PROT LYS 3 H ) 9.8045 ( PROT LYS 3 CA ) 12.256 ( PROT LYS 3 CB ) 9.8045 ( PROT LYS 3 CG ) 9.8045 ( PROT LYS 3 CD ) 9.8045 ( PROT LYS 3 CE ) 9.8045 ( PROT LYS 3 NZ ) 9.8045 ( PROT LYS 3 HZ1 ) 9.8045 ( PROT LYS 3 HZ2 ) 9.8045 ( PROT LYS 3 HZ3 ) 9.8045 ( PROT LYS 3 C ) 12.256 ( PROT LYS 3 O ) 12.256 ( PROT ALA 4 N ) 12.256 ( PROT ALA 4 H ) 9.8045 ( PROT ALA 4 CA ) 12.256 ( PROT ALA 4 CB ) 9.8045 ( PROT ALA 4 C ) 12.256 ( PROT ALA 4 O ) 12.256 ( PROT VAL 5 N ) 12.256 ( PROT VAL 5 H ) 9.8045 ( PROT VAL 5 CA ) 12.256 ( PROT VAL 5 CB ) 9.8045 ( PROT VAL 5 CG1 ) 9.8045 ( PROT VAL 5 CG2 ) 9.8045 ( PROT VAL 5 C ) 12.256 ( PROT VAL 5 O ) 12.256 ( PROT MET 6 N ) 12.256 ( PROT MET 6 H ) 9.8045 ( PROT MET 6 CA ) 12.256 ( PROT MET 6 CB ) 9.8045 ( PROT MET 6 CG ) 9.8045 ( PROT MET 6 SD ) 9.8045 ( PROT MET 6 CE ) 9.8045 ( PROT MET 6 C ) 12.256 ( PROT MET 6 O ) 12.256 ( PROT ILE 7 N ) 12.256 ( PROT ILE 7 H ) 9.8045 ( PROT ILE 7 CA ) 12.256 ( PROT ILE 7 CB ) 9.8045 ( PROT ILE 7 CG2 ) 9.8045 ( PROT ILE 7 CG1 ) 9.8045 ( PROT ILE 7 CD ) 9.8045 ( PROT ILE 7 C ) 12.256 ( PROT ILE 7 O ) 12.256 ( PROT GLY 8 N ) 12.256 ( PROT GLY 8 H ) 9.8045 ( PROT GLY 8 CA ) 12.256 ( PROT GLY 8 C ) 12.256 ( PROT GLY 8 O ) 12.256 ( PROT ALA 9 N ) 12.256 ( PROT ALA 9 H ) 9.8045 ( PROT ALA 9 CA ) 12.256 ( PROT ALA 9 CB ) 9.8045 ( PROT ALA 9 C ) 12.256 ( PROT ALA 9 O ) 12.256 ( PROT CYS 10 N ) 12.256 ( PROT CYS 10 H ) 9.8045 ( PROT CYS 10 CA ) 12.256 ( PROT CYS 10 CB ) 9.8045 ( PROT CYS 10 SG ) 9.8045 ( PROT CYS 10 C ) 12.256 ( PROT CYS 10 O ) 12.256 ( PROT PHE 11 N ) 12.256 ( PROT PHE 11 H ) 9.8045 ( PROT PHE 11 CA ) 12.256 ( PROT PHE 11 CB ) 9.8045 ( PROT PHE 11 CG ) 9.8045 ( PROT PHE 11 CD1 ) 9.8045 ( PROT PHE 11 CD2 ) 9.8045 ( PROT PHE 11 CE1 ) 9.8045 ( PROT PHE 11 CE2 ) 9.8045 ( PROT PHE 11 CZ ) 9.8045 ( PROT PHE 11 C ) 12.256 ( PROT PHE 11 O ) 12.256 ( PROT LEU 12 N ) 12.256 ( PROT LEU 12 H ) 9.8045 ( PROT LEU 12 CA ) 12.256 ( PROT LEU 12 CB ) 9.8045 ( PROT LEU 12 CG ) 9.8045 ( PROT LEU 12 CD1 ) 9.8045 ( PROT LEU 12 CD2 ) 9.8045 ( PROT LEU 12 C ) 12.256 ( PROT LEU 12 O ) 12.256 ( PROT ILE 13 N ) 12.256 ( PROT ILE 13 H ) 9.8045 ( PROT ILE 13 CA ) 12.256 ( PROT ILE 13 CB ) 9.8045 ( PROT ILE 13 CG2 ) 9.8045 ( PROT ILE 13 CG1 ) 9.8045 ( PROT ILE 13 CD ) 9.8045 ( PROT ILE 13 C ) 12.256 ( PROT ILE 13 O ) 12.256 ( PROT ASP 14 N ) 12.256 ( PROT ASP 14 H ) 9.8045 ( PROT ASP 14 CA ) 12.256 ( PROT ASP 14 CB ) 9.8045 ( PROT ASP 14 CG ) 9.8045 ( PROT ASP 14 OD1 ) 9.8045 ( PROT ASP 14 OD2 ) 9.8045 ( PROT ASP 14 C ) 12.256 ( PROT ASP 14 O ) 12.256 ( PROT PHE 15 N ) 12.256 ( PROT PHE 15 H ) 9.8045 ( PROT PHE 15 CA ) 12.256 ( PROT PHE 15 CB ) 9.8045 ( PROT PHE 15 CG ) 9.8045 ( PROT PHE 15 CD1 ) 9.8045 ( PROT PHE 15 CD2 ) 9.8045 ( PROT PHE 15 CE1 ) 9.8045 ( PROT PHE 15 CE2 ) 9.8045 ( PROT PHE 15 CZ ) 9.8045 ( PROT PHE 15 C ) 12.256 ( PROT PHE 15 O ) 12.256 ( PROT MET 16 N ) 12.256 ( PROT MET 16 H ) 9.8045 ( PROT MET 16 CA ) 12.256 ( PROT MET 16 CB ) 9.8045 ( PROT MET 16 CG ) 9.8045 ( PROT MET 16 SD ) 9.8045 ( PROT MET 16 CE ) 9.8045 ( PROT MET 16 C ) 12.256 ( PROT MET 16 O ) 12.256 ( PROT PHE 17 N ) 12.256 ( PROT PHE 17 H ) 9.8045 ( PROT PHE 17 CA ) 12.256 ( PROT PHE 17 CB ) 9.8045 ( PROT PHE 17 CG ) 9.8045 ( PROT PHE 17 CD1 ) 9.8045 ( PROT PHE 17 CD2 ) 9.8045 ( PROT PHE 17 CE1 ) 9.8045 ( PROT PHE 17 CE2 ) 9.8045 ( PROT PHE 17 CZ ) 9.8045 ( PROT PHE 17 C ) 12.256 ( PROT PHE 17 O ) 12.256 ( PROT PHE 18 N ) 12.256 ( PROT PHE 18 H ) 9.8045 ( PROT PHE 18 CA ) 12.256 ( PROT PHE 18 CB ) 9.8045 ( PROT PHE 18 CG ) 9.8045 ( PROT PHE 18 CD1 ) 9.8045 ( PROT PHE 18 CD2 ) 9.8045 ( PROT PHE 18 CE1 ) 9.8045 ( PROT PHE 18 CE2 ) 9.8045 ( PROT PHE 18 CZ ) 9.8045 ( PROT PHE 18 C ) 12.256 ( PROT PHE 18 O ) 12.256 ( PROT GLU 19 N ) 12.256 ( PROT GLU 19 H ) 9.8045 ( PROT GLU 19 CA ) 12.256 ( PROT GLU 19 CB ) 9.8045 ( PROT GLU 19 CG ) 9.8045 ( PROT GLU 19 CD ) 9.8045 ( PROT GLU 19 OE1 ) 9.8045 ( PROT GLU 19 OE2 ) 9.8045 ( PROT GLU 19 C ) 12.256 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41123 5.26174 -8.67156 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS -0.00020 -0.00182 -0.00014 ROTATION MATRIX 1.000000 -0.000137 -0.000008 0.000137 1.000000 0.000179 0.000008 -0.000179 1.000000 AXIS OF ROTATION IS 0.793954 0.037497 -0.606820 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 16.1345 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.297743 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.2977" Parameter: A <- "0.2977" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70969 5.22906 -8.77859 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00515 0.03536 -0.01578 ROTATION MATRIX 0.999822 0.014288 0.012289 -0.014117 0.999804 -0.013878 -0.012485 0.013702 0.999828 AXIS OF ROTATION IS -0.590537 -0.530434 0.608199 ANGLE IS 1.34 CENTER OF ROTATION 9.149848 4.981792 -9.563635 SHIFT IS -0.031398 TOTAL SQUARE DIFF IS 0.3039 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.126472 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.2977" RDCMND substituted energy or value "?RMS" to " 0.1265" Parameter: A <- "0.2977 0.1265" 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 0.2977 0.1265 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 " 263.17" Parameter: H <- "263.17" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 171.44515 263.17147 5.64015 ENER INTERN> 14.27537 53.27312 0.00000 21.86839 8.52448 ENER EXTERN> 61.20283 12.30095 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 " 171.45" Parameter: B <- "171.45" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 12.30" Parameter: C <- "12.30" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 61.20" Parameter: C <- " 73.50" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 73.50" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 14.28" Parameter: D <- "14.28" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 53.27" Parameter: D <- " 67.55" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 21.87" Parameter: D <- " 89.42" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 8.52" Parameter: D <- " 97.94" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 97.94" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 4200 ENER= 171.45 GRMS= 5.64 ELEC= 12.30 VDW= 61.20 RDTITL> *EXTERNAL= 73.50 INTERNAL= 97.94 USER= 0.00 HARM= 263.17 RDTITL> *BOND= 14.28 ANGL= 53.27 DIHE= 21.87 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: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11250 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11250 ATOM PAIRS WERE FOUND FOR ATOM LIST 340 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> 0 361.21987 -189.77473 2.30107 0.02000 MINI INTERN> 14.27537 53.27312 0.00000 21.86839 8.52448 MINI EXTERN> 61.20283 12.30095 0.00000 0.00000 0.00000 MINI CONSTR> 189.77473 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 347.46353 13.75634 1.91817 0.00360 MINI INTERN> 13.33207 52.19698 0.00000 24.14250 8.41354 MINI EXTERN> 28.90807 13.62835 0.00000 0.00000 0.00000 MINI CONSTR> 206.84203 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11227 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 343.70555 3.75798 1.33603 0.00156 MINI INTERN> 10.51023 50.81674 0.00000 24.37717 8.04561 MINI EXTERN> 28.14770 13.24197 0.00000 0.00000 0.00000 MINI CONSTR> 208.56612 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 342.13479 1.57076 2.90743 0.00161 MINI INTERN> 8.55573 51.51670 0.00000 24.60397 8.03437 MINI EXTERN> 26.91323 12.94568 0.00000 0.00000 0.00000 MINI CONSTR> 209.56511 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11224 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 340.77587 1.35892 2.80846 0.00167 MINI INTERN> 8.56021 50.96622 0.00000 24.68556 8.02085 MINI EXTERN> 25.53748 13.00735 0.00000 0.00000 0.00000 MINI CONSTR> 209.99820 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 338.97577 1.80010 0.83172 0.00072 MINI INTERN> 11.11377 48.36584 0.00000 24.75469 7.94409 MINI EXTERN> 23.02438 13.58173 0.00000 0.00000 0.00000 MINI CONSTR> 210.19127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11222 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 338.06959 0.90619 0.67916 0.00075 MINI INTERN> 10.73565 48.22399 0.00000 24.80273 7.90777 MINI EXTERN> 22.49665 13.54980 0.00000 0.00000 0.00000 MINI CONSTR> 210.35300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 337.19628 0.87331 0.63904 0.00078 MINI INTERN> 10.67354 47.90962 0.00000 24.83518 7.86876 MINI EXTERN> 21.87842 13.56583 0.00000 0.00000 0.00000 MINI CONSTR> 210.46493 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11223 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 336.52848 0.66780 1.37072 0.00080 MINI INTERN> 11.72341 46.99275 0.00000 24.85183 7.82111 MINI EXTERN> 20.88200 13.75213 0.00000 0.00000 0.00000 MINI CONSTR> 210.50526 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 335.93944 0.58904 1.40473 0.00083 MINI INTERN> 11.72657 46.76343 0.00000 24.85643 7.79025 MINI EXTERN> 20.49714 13.76945 0.00000 0.00000 0.00000 MINI CONSTR> 210.53617 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11222 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 335.46812 0.47132 1.58047 0.00087 MINI INTERN> 11.92172 46.46830 0.00000 24.85198 7.76122 MINI EXTERN> 20.10187 13.81207 0.00000 0.00000 0.00000 MINI CONSTR> 210.55097 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 335.07856 0.38956 1.51059 0.00090 MINI INTERN> 11.76192 46.39660 0.00000 24.85337 7.73543 MINI EXTERN> 19.96620 13.80608 0.00000 0.00000 0.00000 MINI CONSTR> 210.55896 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11223 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 334.54490 0.53367 0.43892 0.00039 MINI INTERN> 9.94114 47.32384 0.00000 24.84297 7.73201 MINI EXTERN> 20.55979 13.52706 0.00000 0.00000 0.00000 MINI CONSTR> 210.61809 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 334.26848 0.27642 0.37158 0.00040 MINI INTERN> 10.02848 47.15717 0.00000 24.82906 7.71522 MINI EXTERN> 20.35823 13.55318 0.00000 0.00000 0.00000 MINI CONSTR> 210.62713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11222 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 334.00213 0.26635 0.34554 0.00042 MINI INTERN> 10.00750 47.05859 0.00000 24.81394 7.69797 MINI EXTERN> 20.21899 13.56212 0.00000 0.00000 0.00000 MINI CONSTR> 210.64302 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 333.78386 0.21827 0.71923 0.00043 MINI INTERN> 9.48128 47.30235 0.00000 24.80084 7.68290 MINI EXTERN> 20.35636 13.48152 0.00000 0.00000 0.00000 MINI CONSTR> 210.67861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11222 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 333.57911 0.20474 0.42931 0.00045 MINI INTERN> 9.77354 47.01849 0.00000 24.78185 7.66882 MINI EXTERN> 20.09813 13.54579 0.00000 0.00000 0.00000 MINI CONSTR> 210.69250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 333.45579 0.12332 0.75437 0.00046 MINI INTERN> 9.43156 47.18902 0.00000 24.76565 7.66101 MINI EXTERN> 20.18613 13.49207 0.00000 0.00000 0.00000 MINI CONSTR> 210.73036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11221 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 333.32666 0.12913 0.79262 0.00048 MINI INTERN> 9.38375 47.15357 0.00000 24.75005 7.65023 MINI EXTERN> 20.13361 13.49466 0.00000 0.00000 0.00000 MINI CONSTR> 210.76080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 333.16934 0.15732 0.23838 0.00021 MINI INTERN> 10.18909 46.56063 0.00000 24.72488 7.63860 MINI EXTERN> 19.64020 13.64551 0.00000 0.00000 0.00000 MINI CONSTR> 210.77044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 333.13347 0.03587 0.86218 0.00052 MINI INTERN> 9.32362 47.09424 0.00000 24.71683 7.63573 MINI EXTERN> 20.03404 13.50131 0.00000 0.00000 0.00000 MINI CONSTR> 210.82770 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 332.98945 0.14402 0.28508 0.00022 MINI INTERN> 10.29495 46.39650 0.00000 24.68987 7.62391 MINI EXTERN> 19.46425 13.68103 0.00000 0.00000 0.00000 MINI CONSTR> 210.83894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11221 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 332.92039 0.06906 0.22645 0.00023 MINI INTERN> 10.21774 46.39961 0.00000 24.67741 7.61752 MINI EXTERN> 19.45604 13.67804 0.00000 0.00000 0.00000 MINI CONSTR> 210.87402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 332.85705 0.06334 0.22189 0.00024 MINI INTERN> 10.21778 46.36191 0.00000 24.66045 7.61299 MINI EXTERN> 19.40371 13.68632 0.00000 0.00000 0.00000 MINI CONSTR> 210.91390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11221 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 332.80443 0.05263 0.27748 0.00025 MINI INTERN> 10.28789 46.29034 0.00000 24.64074 7.61044 MINI EXTERN> 19.31534 13.70424 0.00000 0.00000 0.00000 MINI CONSTR> 210.95545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 332.77059 0.03384 0.39891 0.00026 MINI INTERN> 10.42385 46.18726 0.00000 24.62342 7.60833 MINI EXTERN> 19.20640 13.73117 0.00000 0.00000 0.00000 MINI CONSTR> 210.99016 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11221 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 332.73311 0.03748 0.40491 0.00027 MINI INTERN> 10.39916 46.18672 0.00000 24.60492 7.60910 MINI EXTERN> 19.16859 13.73172 0.00000 0.00000 0.00000 MINI CONSTR> 211.03291 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 332.68853 0.04458 0.12466 0.00012 MINI INTERN> 10.00896 46.33313 0.00000 24.62124 7.58910 MINI EXTERN> 19.38262 13.69471 0.00000 0.00000 0.00000 MINI CONSTR> 211.05876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11221 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 332.67698 0.01155 0.43600 0.00029 MINI INTERN> 10.34673 46.18795 0.00000 24.57401 7.60951 MINI EXTERN> 19.11243 13.73428 0.00000 0.00000 0.00000 MINI CONSTR> 211.11207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 332.63497 0.04201 0.13978 0.00012 MINI INTERN> 9.97588 46.28918 0.00000 24.60210 7.58022 MINI EXTERN> 19.34724 13.70922 0.00000 0.00000 0.00000 MINI CONSTR> 211.13113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 332.61656 0.01841 0.09285 0.00013 MINI INTERN> 10.02176 46.25386 0.00000 24.58709 7.58241 MINI EXTERN> 19.28803 13.72014 0.00000 0.00000 0.00000 MINI CONSTR> 211.16326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 332.59829 0.01827 0.20387 0.00013 MINI INTERN> 9.91219 46.26685 0.00000 24.58887 7.57086 MINI EXTERN> 19.34276 13.71939 0.00000 0.00000 0.00000 MINI CONSTR> 211.19736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 332.58305 0.01524 0.20505 0.00014 MINI INTERN> 9.90728 46.24757 0.00000 24.58003 7.56864 MINI EXTERN> 19.32245 13.72706 0.00000 0.00000 0.00000 MINI CONSTR> 211.23003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 332.57025 0.01280 0.22654 0.00014 MINI INTERN> 9.88421 46.23686 0.00000 24.57322 7.56541 MINI EXTERN> 19.31545 13.73291 0.00000 0.00000 0.00000 MINI CONSTR> 211.26220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 332.55975 0.01051 0.22032 0.00015 MINI INTERN> 9.88694 46.21898 0.00000 24.56502 7.56460 MINI EXTERN> 19.29392 13.74019 0.00000 0.00000 0.00000 MINI CONSTR> 211.29009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 332.54629 0.01346 0.06710 0.00006 MINI INTERN> 10.06031 46.13851 0.00000 24.53516 7.57825 MINI EXTERN> 19.14259 13.76353 0.00000 0.00000 0.00000 MINI CONSTR> 211.32795 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 332.54317 0.00312 0.23904 0.00016 MINI INTERN> 9.86820 46.19463 0.00000 24.55225 7.56146 MINI EXTERN> 19.27064 13.75245 0.00000 0.00000 0.00000 MINI CONSTR> 211.34353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 332.53046 0.01272 0.07797 0.00007 MINI INTERN> 10.08041 46.09914 0.00000 24.51747 7.57856 MINI EXTERN> 19.09078 13.77985 0.00000 0.00000 0.00000 MINI CONSTR> 211.38426 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 332.52487 0.00559 0.05117 0.00007 MINI INTERN> 10.04685 46.09967 0.00000 24.51604 7.57547 MINI EXTERN> 19.10144 13.78246 0.00000 0.00000 0.00000 MINI CONSTR> 211.40293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 332.51909 0.00578 0.11211 0.00007 MINI INTERN> 10.11443 46.05833 0.00000 24.49982 7.58057 MINI EXTERN> 19.03337 13.79658 0.00000 0.00000 0.00000 MINI CONSTR> 211.43598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 332.51360 0.00549 0.06523 0.00008 MINI INTERN> 10.07240 46.06143 0.00000 24.49917 7.57705 MINI EXTERN> 19.04913 13.79905 0.00000 0.00000 0.00000 MINI CONSTR> 211.45537 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 332.51011 0.00348 0.11683 0.00008 MINI INTERN> 10.11961 46.03155 0.00000 24.48740 7.58077 MINI EXTERN> 19.00062 13.80973 0.00000 0.00000 0.00000 MINI CONSTR> 211.48044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11220 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 332.50638 0.00373 0.13399 0.00008 MINI INTERN> 10.13496 46.01294 0.00000 24.47954 7.58201 MINI EXTERN> 18.97520 13.81777 0.00000 0.00000 0.00000 MINI CONSTR> 211.50396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 332.50321 0.00318 0.12893 0.00009 MINI INTERN> 10.13070 46.00473 0.00000 24.47542 7.58176 MINI EXTERN> 18.96627 13.82289 0.00000 0.00000 0.00000 MINI CONSTR> 211.52144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 332.49869 0.00451 0.03762 0.00004 MINI INTERN> 10.01901 46.03667 0.00000 24.48451 7.57293 MINI EXTERN> 19.03317 13.81900 0.00000 0.00000 0.00000 MINI CONSTR> 211.53341 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 332.49764 0.00105 0.13747 0.00009 MINI INTERN> 10.13800 45.98145 0.00000 24.46487 7.58277 MINI EXTERN> 18.93683 13.83506 0.00000 0.00000 0.00000 MINI CONSTR> 211.55866 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 332.49333 0.00431 0.04368 0.00004 MINI INTERN> 10.00654 46.02150 0.00000 24.47665 7.57246 MINI EXTERN> 19.01730 13.82982 0.00000 0.00000 0.00000 MINI CONSTR> 211.56906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 332.49134 0.00199 0.03082 0.00004 MINI INTERN> 10.02342 46.00722 0.00000 24.47093 7.57413 MINI EXTERN> 18.99590 13.83588 0.00000 0.00000 0.00000 MINI CONSTR> 211.58385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 332.48911 0.00223 0.06061 0.00004 MINI INTERN> 9.98810 46.01068 0.00000 24.47056 7.57166 MINI EXTERN> 19.00774 13.83956 0.00000 0.00000 0.00000 MINI CONSTR> 211.60081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 332.48713 0.00198 0.03961 0.00004 MINI INTERN> 10.00701 45.99530 0.00000 24.46448 7.57363 MINI EXTERN> 18.98447 13.84612 0.00000 0.00000 0.00000 MINI CONSTR> 211.61611 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 332.48564 0.00149 0.06994 0.00005 MINI INTERN> 9.97864 45.99827 0.00000 24.46427 7.57173 MINI EXTERN> 18.99390 13.84930 0.00000 0.00000 0.00000 MINI CONSTR> 211.62953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 332.48405 0.00159 0.07355 0.00005 MINI INTERN> 9.97510 45.99183 0.00000 24.46111 7.57191 MINI EXTERN> 18.98631 13.85429 0.00000 0.00000 0.00000 MINI CONSTR> 211.64350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 332.48265 0.00140 0.08079 0.00005 MINI INTERN> 9.96863 45.98686 0.00000 24.45849 7.57187 MINI EXTERN> 18.98111 13.85899 0.00000 0.00000 0.00000 MINI CONSTR> 211.65670 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 332.48137 0.00128 0.07631 0.00005 MINI INTERN> 9.97173 45.97930 0.00000 24.45520 7.57259 MINI EXTERN> 18.97096 13.86345 0.00000 0.00000 0.00000 MINI CONSTR> 211.66813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 332.48005 0.00133 0.07758 0.00005 MINI INTERN> 9.97029 45.97267 0.00000 24.45212 7.57301 MINI EXTERN> 18.96252 13.86851 0.00000 0.00000 0.00000 MINI CONSTR> 211.68093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 332.47839 0.00165 0.02446 0.00002 MINI INTERN> 10.03741 45.93927 0.00000 24.44056 7.57911 MINI EXTERN> 18.90807 13.87793 0.00000 0.00000 0.00000 MINI CONSTR> 211.69603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 332.47795 0.00044 0.08497 0.00006 MINI INTERN> 9.96349 45.96298 0.00000 24.44737 7.57347 MINI EXTERN> 18.95117 13.87684 0.00000 0.00000 0.00000 MINI CONSTR> 211.70264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 332.47692 0.00103 0.09006 0.00006 MINI INTERN> 9.95936 45.95813 0.00000 24.44499 7.57367 MINI EXTERN> 18.94533 13.88146 0.00000 0.00000 0.00000 MINI CONSTR> 211.71398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 332.47524 0.00168 0.03131 0.00003 MINI INTERN> 10.04623 45.91676 0.00000 24.43094 7.58152 MINI EXTERN> 18.87798 13.89209 0.00000 0.00000 0.00000 MINI CONSTR> 211.72972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 332.47444 0.00080 0.01965 0.00003 MINI INTERN> 10.03119 45.91812 0.00000 24.43083 7.58069 MINI EXTERN> 18.88217 13.89451 0.00000 0.00000 0.00000 MINI CONSTR> 211.73692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 332.47346 0.00098 0.03695 0.00003 MINI INTERN> 10.05123 45.90309 0.00000 24.42512 7.58308 MINI EXTERN> 18.85978 13.90097 0.00000 0.00000 0.00000 MINI CONSTR> 211.75020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 332.47263 0.00083 0.02626 0.00003 MINI INTERN> 10.04108 45.90208 0.00000 24.42420 7.58274 MINI EXTERN> 18.86007 13.90413 0.00000 0.00000 0.00000 MINI CONSTR> 211.75833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 332.47185 0.00078 0.02940 0.00003 MINI INTERN> 10.04412 45.89541 0.00000 24.42140 7.58356 MINI EXTERN> 18.85105 13.90844 0.00000 0.00000 0.00000 MINI CONSTR> 211.76787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 332.47126 0.00058 0.04519 0.00003 MINI INTERN> 10.05776 45.88497 0.00000 24.41745 7.58524 MINI EXTERN> 18.83563 13.91310 0.00000 0.00000 0.00000 MINI CONSTR> 211.77711 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 332.47056 0.00070 0.04782 0.00003 MINI INTERN> 10.05942 45.87912 0.00000 24.41494 7.58596 MINI EXTERN> 18.82791 13.91712 0.00000 0.00000 0.00000 MINI CONSTR> 211.78608 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 332.46993 0.00063 0.05318 0.00003 MINI INTERN> 10.06309 45.87257 0.00000 24.41224 7.58686 MINI EXTERN> 18.81902 13.92132 0.00000 0.00000 0.00000 MINI CONSTR> 211.79483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 332.46936 0.00058 0.05059 0.00003 MINI INTERN> 10.06118 45.86928 0.00000 24.41071 7.58712 MINI EXTERN> 18.81504 13.92437 0.00000 0.00000 0.00000 MINI CONSTR> 211.80166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 332.46876 0.00060 0.05179 0.00004 MINI INTERN> 10.06125 45.86441 0.00000 24.40861 7.58772 MINI EXTERN> 18.80884 13.92828 0.00000 0.00000 0.00000 MINI CONSTR> 211.80964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 332.46800 0.00076 0.01632 0.00002 MINI INTERN> 10.01916 45.87760 0.00000 24.41247 7.58449 MINI EXTERN> 18.83138 13.92912 0.00000 0.00000 0.00000 MINI CONSTR> 211.81378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 332.46777 0.00023 0.05667 0.00004 MINI INTERN> 10.06453 45.85479 0.00000 24.40456 7.58896 MINI EXTERN> 18.79604 13.93516 0.00000 0.00000 0.00000 MINI CONSTR> 211.82374 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 332.46728 0.00049 0.05980 0.00004 MINI INTERN> 10.06612 45.85057 0.00000 24.40250 7.58953 MINI EXTERN> 18.79015 13.93746 0.00000 0.00000 0.00000 MINI CONSTR> 211.83095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 332.46650 0.00078 0.02026 0.00002 MINI INTERN> 10.01309 45.86776 0.00000 24.40790 7.58539 MINI EXTERN> 18.81918 13.93908 0.00000 0.00000 0.00000 MINI CONSTR> 211.83411 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 332.46611 0.00039 0.01373 0.00002 MINI INTERN> 10.02076 45.86146 0.00000 24.40547 7.58647 MINI EXTERN> 18.80997 13.94211 0.00000 0.00000 0.00000 MINI CONSTR> 211.83987 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 332.46566 0.00045 0.01377 0.00002 MINI INTERN> 10.01994 45.85794 0.00000 24.40386 7.58686 MINI EXTERN> 18.80539 13.94531 0.00000 0.00000 0.00000 MINI CONSTR> 211.84637 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 332.46526 0.00040 0.02784 0.00002 MINI INTERN> 10.00602 45.85960 0.00000 24.40399 7.58607 MINI EXTERN> 18.80911 13.94825 0.00000 0.00000 0.00000 MINI CONSTR> 211.85222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 332.46486 0.00041 0.01709 0.00002 MINI INTERN> 10.01468 45.85260 0.00000 24.40135 7.58729 MINI EXTERN> 18.79897 13.95172 0.00000 0.00000 0.00000 MINI CONSTR> 211.85825 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 332.46449 0.00036 0.02199 0.00002 MINI INTERN> 10.01111 45.85093 0.00000 24.40031 7.58733 MINI EXTERN> 18.79693 13.95404 0.00000 0.00000 0.00000 MINI CONSTR> 211.86385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 332.46422 0.00028 0.03111 0.00002 MINI INTERN> 10.00301 45.85110 0.00000 24.40005 7.58700 MINI EXTERN> 18.79795 13.95667 0.00000 0.00000 0.00000 MINI CONSTR> 211.86844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 332.46389 0.00033 0.03425 0.00002 MINI INTERN> 10.00141 45.84771 0.00000 24.39874 7.58734 MINI EXTERN> 18.79390 13.96081 0.00000 0.00000 0.00000 MINI CONSTR> 211.87397 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 332.46361 0.00028 0.03715 0.00002 MINI INTERN> 9.99928 45.84662 0.00000 24.39779 7.58738 MINI EXTERN> 18.79211 13.96181 0.00000 0.00000 0.00000 MINI CONSTR> 211.87862 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 332.46333 0.00028 0.03488 0.00002 MINI INTERN> 9.99924 45.84351 0.00000 24.39654 7.58781 MINI EXTERN> 18.78810 13.96498 0.00000 0.00000 0.00000 MINI CONSTR> 211.88315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 332.46303 0.00029 0.03628 0.00002 MINI INTERN> 9.99969 45.84072 0.00000 24.39515 7.58812 MINI EXTERN> 18.78408 13.96708 0.00000 0.00000 0.00000 MINI CONSTR> 211.88818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 332.46267 0.00037 0.01170 0.00001 MINI INTERN> 10.02484 45.82728 0.00000 24.39042 7.59084 MINI EXTERN> 18.76415 13.97087 0.00000 0.00000 0.00000 MINI CONSTR> 211.89427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 332.46255 0.00012 0.03928 0.00003 MINI INTERN> 9.99598 45.83628 0.00000 24.39319 7.58856 MINI EXTERN> 18.77862 13.97306 0.00000 0.00000 0.00000 MINI CONSTR> 211.89686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 332.46232 0.00023 0.04373 0.00003 MINI INTERN> 10.00057 45.83317 0.00000 24.39146 7.58906 MINI EXTERN> 18.77332 13.97326 0.00000 0.00000 0.00000 MINI CONSTR> 211.90147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 332.46194 0.00038 0.01351 0.00001 MINI INTERN> 10.02673 45.81854 0.00000 24.38654 7.59199 MINI EXTERN> 18.75232 13.97831 0.00000 0.00000 0.00000 MINI CONSTR> 211.90751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 332.46174 0.00020 0.00978 0.00001 MINI INTERN> 10.02230 45.81827 0.00000 24.38619 7.59182 MINI EXTERN> 18.75228 13.98016 0.00000 0.00000 0.00000 MINI CONSTR> 211.91071 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> 430 332.46174 0.00020 0.00978 0.00001 STPD INTERN> 10.02230 45.81827 0.00000 24.38619 7.59182 STPD EXTERN> 18.75228 13.98016 0.00000 0.00000 0.00000 STPD CONSTR> 211.91071 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 11219 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 332.46174 0.00020 0.00978 0.00000 MINI INTERN> 10.02230 45.81827 0.00000 24.38619 7.59182 MINI EXTERN> 18.75228 13.98016 0.00000 0.00000 0.00000 MINI CONSTR> 211.91071 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> 3 332.45722 0.00452 0.00494 0.02000 CONJ INTERN> 10.00838 45.71804 0.00000 24.34140 7.60540 CONJ EXTERN> 18.60499 14.08438 0.00000 0.00000 0.00000 CONJ CONSTR> 212.09464 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "4800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 6.3729 ( PROT LYS 1 HT2 ) 6.3729 ( PROT LYS 1 N ) 7.9661 ( PROT LYS 1 HT3 ) 6.3729 ( PROT LYS 1 CA ) 7.9661 ( PROT LYS 1 CB ) 6.3729 ( PROT LYS 1 CG ) 6.3729 ( PROT LYS 1 CD ) 6.3729 ( PROT LYS 1 CE ) 6.3729 ( PROT LYS 1 NZ ) 6.3729 ( PROT LYS 1 HZ1 ) 6.3729 ( PROT LYS 1 HZ2 ) 6.3729 ( PROT LYS 1 HZ3 ) 6.3729 ( PROT LYS 1 C ) 7.9661 ( PROT LYS 1 O ) 7.9661 ( PROT MET 2 N ) 7.9661 ( PROT MET 2 H ) 6.3729 ( PROT MET 2 CA ) 7.9661 ( PROT MET 2 CB ) 6.3729 ( PROT MET 2 CG ) 6.3729 ( PROT MET 2 SD ) 6.3729 ( PROT MET 2 CE ) 6.3729 ( PROT MET 2 C ) 7.9661 ( PROT MET 2 O ) 7.9661 ( PROT LYS 3 N ) 7.9661 ( PROT LYS 3 H ) 6.3729 ( PROT LYS 3 CA ) 7.9661 ( PROT LYS 3 CB ) 6.3729 ( PROT LYS 3 CG ) 6.3729 ( PROT LYS 3 CD ) 6.3729 ( PROT LYS 3 CE ) 6.3729 ( PROT LYS 3 NZ ) 6.3729 ( PROT LYS 3 HZ1 ) 6.3729 ( PROT LYS 3 HZ2 ) 6.3729 ( PROT LYS 3 HZ3 ) 6.3729 ( PROT LYS 3 C ) 7.9661 ( PROT LYS 3 O ) 7.9661 ( PROT ALA 4 N ) 7.9661 ( PROT ALA 4 H ) 6.3729 ( PROT ALA 4 CA ) 7.9661 ( PROT ALA 4 CB ) 6.3729 ( PROT ALA 4 C ) 7.9661 ( PROT ALA 4 O ) 7.9661 ( PROT VAL 5 N ) 7.9661 ( PROT VAL 5 H ) 6.3729 ( PROT VAL 5 CA ) 7.9661 ( PROT VAL 5 CB ) 6.3729 ( PROT VAL 5 CG1 ) 6.3729 ( PROT VAL 5 CG2 ) 6.3729 ( PROT VAL 5 C ) 7.9661 ( PROT VAL 5 O ) 7.9661 ( PROT MET 6 N ) 7.9661 ( PROT MET 6 H ) 6.3729 ( PROT MET 6 CA ) 7.9661 ( PROT MET 6 CB ) 6.3729 ( PROT MET 6 CG ) 6.3729 ( PROT MET 6 SD ) 6.3729 ( PROT MET 6 CE ) 6.3729 ( PROT MET 6 C ) 7.9661 ( PROT MET 6 O ) 7.9661 ( PROT ILE 7 N ) 7.9661 ( PROT ILE 7 H ) 6.3729 ( PROT ILE 7 CA ) 7.9661 ( PROT ILE 7 CB ) 6.3729 ( PROT ILE 7 CG2 ) 6.3729 ( PROT ILE 7 CG1 ) 6.3729 ( PROT ILE 7 CD ) 6.3729 ( PROT ILE 7 C ) 7.9661 ( PROT ILE 7 O ) 7.9661 ( PROT GLY 8 N ) 7.9661 ( PROT GLY 8 H ) 6.3729 ( PROT GLY 8 CA ) 7.9661 ( PROT GLY 8 C ) 7.9661 ( PROT GLY 8 O ) 7.9661 ( PROT ALA 9 N ) 7.9661 ( PROT ALA 9 H ) 6.3729 ( PROT ALA 9 CA ) 7.9661 ( PROT ALA 9 CB ) 6.3729 ( PROT ALA 9 C ) 7.9661 ( PROT ALA 9 O ) 7.9661 ( PROT CYS 10 N ) 7.9661 ( PROT CYS 10 H ) 6.3729 ( PROT CYS 10 CA ) 7.9661 ( PROT CYS 10 CB ) 6.3729 ( PROT CYS 10 SG ) 6.3729 ( PROT CYS 10 C ) 7.9661 ( PROT CYS 10 O ) 7.9661 ( PROT PHE 11 N ) 7.9661 ( PROT PHE 11 H ) 6.3729 ( PROT PHE 11 CA ) 7.9661 ( PROT PHE 11 CB ) 6.3729 ( PROT PHE 11 CG ) 6.3729 ( PROT PHE 11 CD1 ) 6.3729 ( PROT PHE 11 CD2 ) 6.3729 ( PROT PHE 11 CE1 ) 6.3729 ( PROT PHE 11 CE2 ) 6.3729 ( PROT PHE 11 CZ ) 6.3729 ( PROT PHE 11 C ) 7.9661 ( PROT PHE 11 O ) 7.9661 ( PROT LEU 12 N ) 7.9661 ( PROT LEU 12 H ) 6.3729 ( PROT LEU 12 CA ) 7.9661 ( PROT LEU 12 CB ) 6.3729 ( PROT LEU 12 CG ) 6.3729 ( PROT LEU 12 CD1 ) 6.3729 ( PROT LEU 12 CD2 ) 6.3729 ( PROT LEU 12 C ) 7.9661 ( PROT LEU 12 O ) 7.9661 ( PROT ILE 13 N ) 7.9661 ( PROT ILE 13 H ) 6.3729 ( PROT ILE 13 CA ) 7.9661 ( PROT ILE 13 CB ) 6.3729 ( PROT ILE 13 CG2 ) 6.3729 ( PROT ILE 13 CG1 ) 6.3729 ( PROT ILE 13 CD ) 6.3729 ( PROT ILE 13 C ) 7.9661 ( PROT ILE 13 O ) 7.9661 ( PROT ASP 14 N ) 7.9661 ( PROT ASP 14 H ) 6.3729 ( PROT ASP 14 CA ) 7.9661 ( PROT ASP 14 CB ) 6.3729 ( PROT ASP 14 CG ) 6.3729 ( PROT ASP 14 OD1 ) 6.3729 ( PROT ASP 14 OD2 ) 6.3729 ( PROT ASP 14 C ) 7.9661 ( PROT ASP 14 O ) 7.9661 ( PROT PHE 15 N ) 7.9661 ( PROT PHE 15 H ) 6.3729 ( PROT PHE 15 CA ) 7.9661 ( PROT PHE 15 CB ) 6.3729 ( PROT PHE 15 CG ) 6.3729 ( PROT PHE 15 CD1 ) 6.3729 ( PROT PHE 15 CD2 ) 6.3729 ( PROT PHE 15 CE1 ) 6.3729 ( PROT PHE 15 CE2 ) 6.3729 ( PROT PHE 15 CZ ) 6.3729 ( PROT PHE 15 C ) 7.9661 ( PROT PHE 15 O ) 7.9661 ( PROT MET 16 N ) 7.9661 ( PROT MET 16 H ) 6.3729 ( PROT MET 16 CA ) 7.9661 ( PROT MET 16 CB ) 6.3729 ( PROT MET 16 CG ) 6.3729 ( PROT MET 16 SD ) 6.3729 ( PROT MET 16 CE ) 6.3729 ( PROT MET 16 C ) 7.9661 ( PROT MET 16 O ) 7.9661 ( PROT PHE 17 N ) 7.9661 ( PROT PHE 17 H ) 6.3729 ( PROT PHE 17 CA ) 7.9661 ( PROT PHE 17 CB ) 6.3729 ( PROT PHE 17 CG ) 6.3729 ( PROT PHE 17 CD1 ) 6.3729 ( PROT PHE 17 CD2 ) 6.3729 ( PROT PHE 17 CE1 ) 6.3729 ( PROT PHE 17 CE2 ) 6.3729 ( PROT PHE 17 CZ ) 6.3729 ( PROT PHE 17 C ) 7.9661 ( PROT PHE 17 O ) 7.9661 ( PROT PHE 18 N ) 7.9661 ( PROT PHE 18 H ) 6.3729 ( PROT PHE 18 CA ) 7.9661 ( PROT PHE 18 CB ) 6.3729 ( PROT PHE 18 CG ) 6.3729 ( PROT PHE 18 CD1 ) 6.3729 ( PROT PHE 18 CD2 ) 6.3729 ( PROT PHE 18 CE1 ) 6.3729 ( PROT PHE 18 CE2 ) 6.3729 ( PROT PHE 18 CZ ) 6.3729 ( PROT PHE 18 C ) 7.9661 ( PROT PHE 18 O ) 7.9661 ( PROT GLU 19 N ) 7.9661 ( PROT GLU 19 H ) 6.3729 ( PROT GLU 19 CA ) 7.9661 ( PROT GLU 19 CB ) 6.3729 ( PROT GLU 19 CG ) 6.3729 ( PROT GLU 19 CD ) 6.3729 ( PROT GLU 19 OE1 ) 6.3729 ( PROT GLU 19 OE2 ) 6.3729 ( PROT GLU 19 C ) 7.9661 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41097 5.26167 -8.67118 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00007 -0.00175 -0.00051 ROTATION MATRIX 1.000000 -0.000144 0.000003 0.000144 1.000000 0.000181 -0.000003 -0.000181 1.000000 AXIS OF ROTATION IS 0.782784 -0.012708 -0.622164 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 19.9036 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.330697 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3307" Parameter: A <- "0.3307" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70908 5.22506 -8.77857 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00576 0.03936 -0.01580 ROTATION MATRIX 0.999812 0.014981 0.012331 -0.014806 0.999789 -0.014206 -0.012542 0.014021 0.999823 AXIS OF ROTATION IS -0.588221 -0.518337 0.620744 ANGLE IS 1.37 CENTER OF ROTATION 9.035180 5.006417 -9.626796 SHIFT IS -0.033601 TOTAL SQUARE DIFF IS 0.4334 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.151033 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3307" RDCMND substituted energy or value "?RMS" to " 0.1510" Parameter: A <- "0.3307 0.1510" 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 0.3307 0.1510 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 " 212.09" Parameter: H <- "212.09" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 120.36258 212.09464 4.09250 ENER INTERN> 10.00838 45.71804 0.00000 24.34140 7.60540 ENER EXTERN> 18.60499 14.08438 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 120.36" Parameter: B <- "120.36" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 14.08" Parameter: C <- "14.08" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " 18.60" Parameter: C <- " 32.68" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 32.68" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 10.01" Parameter: D <- "10.01" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 45.72" Parameter: D <- " 55.73" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 24.34" Parameter: D <- " 80.07" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 7.61" Parameter: D <- " 87.68" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 87.68" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 4800 ENER= 120.36 GRMS= 4.09 ELEC= 14.08 VDW= 18.60 RDTITL> *EXTERNAL= 32.68 INTERNAL= 87.68 USER= 0.00 HARM= 212.09 RDTITL> *BOND= 10.01 ANGL= 45.72 DIHE= 24.34 IMPR= 7.61 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= 120.36 GRMS= 4.09 ELEC= 14.08 VDW= 18.60 RDTITL> *EXTERNAL= 32.68 INTERNAL= 87.68 USER= 0.00 HARM= 212.09 RDTITL> *BOND= 10.01 ANGL= 45.72 DIHE= 24.34 IMPR= 7.61 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= 120.36 GRMS= 4.09 ELEC= 14.08 VDW= 18.60 RDTITL> *EXTERNAL= 32.68 INTERNAL= 87.68 USER= 0.00 HARM= 212.09 RDTITL> *BOND= 10.01 ANGL= 45.72 DIHE= 24.34 IMPR= 7.61 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 4800 0.3307 0.1510 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "4800" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11219 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11219 ATOM PAIRS WERE FOUND FOR ATOM LIST 339 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> 0 271.42860 -151.06602 1.64100 0.02000 MINI INTERN> 10.00838 45.71804 0.00000 24.34140 7.60540 MINI EXTERN> 18.60499 14.08438 0.00000 0.00000 0.00000 MINI CONSTR> 151.06602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 262.78994 8.63866 1.82583 0.00360 MINI INTERN> 9.26139 43.76664 0.00000 26.26010 7.54898 MINI EXTERN> -2.36453 15.24509 0.00000 0.00000 0.00000 MINI CONSTR> 163.07228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11202 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 260.75437 2.03557 1.47793 0.00156 MINI INTERN> 8.22084 43.72745 0.00000 26.65475 7.28598 MINI EXTERN> -5.20431 15.56236 0.00000 0.00000 0.00000 MINI CONSTR> 164.50730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 259.76263 0.99174 2.62569 0.00161 MINI INTERN> 10.84202 41.78114 0.00000 26.76017 7.30532 MINI EXTERN> -8.18046 16.04140 0.00000 0.00000 0.00000 MINI CONSTR> 165.21305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11201 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 258.81244 0.95019 2.69536 0.00167 MINI INTERN> 11.10075 41.30115 0.00000 26.81468 7.30851 MINI EXTERN> -9.43902 16.10448 0.00000 0.00000 0.00000 MINI CONSTR> 165.62189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 257.35407 1.45837 0.77492 0.00072 MINI INTERN> 7.69982 42.78407 0.00000 26.99735 7.21587 MINI EXTERN> -8.96496 15.70532 0.00000 0.00000 0.00000 MINI CONSTR> 165.91659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11199 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 256.67675 0.67732 0.57198 0.00075 MINI INTERN> 7.87617 42.38183 0.00000 27.01230 7.19569 MINI EXTERN> -9.60333 15.75067 0.00000 0.00000 0.00000 MINI CONSTR> 166.06343 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 255.99091 0.68585 1.07987 0.00078 MINI INTERN> 7.35091 42.40683 0.00000 27.11589 7.10444 MINI EXTERN> -9.88955 15.72640 0.00000 0.00000 0.00000 MINI CONSTR> 166.17599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11198 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 255.37028 0.62063 0.70185 0.00080 MINI INTERN> 7.53052 42.06405 0.00000 27.08119 7.10416 MINI EXTERN> -10.40842 15.75065 0.00000 0.00000 0.00000 MINI CONSTR> 166.24812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 254.94155 0.42873 1.22165 0.00083 MINI INTERN> 7.12728 42.12855 0.00000 27.14561 7.03519 MINI EXTERN> -10.50054 15.73188 0.00000 0.00000 0.00000 MINI CONSTR> 166.27358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11197 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 254.50696 0.43459 1.35745 0.00087 MINI INTERN> 7.03430 42.03084 0.00000 27.15118 7.00094 MINI EXTERN> -10.72912 15.72534 0.00000 0.00000 0.00000 MINI CONSTR> 166.29349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 254.13649 0.37047 1.30755 0.00090 MINI INTERN> 7.01388 41.87418 0.00000 27.13733 6.98239 MINI EXTERN> -10.92512 15.74908 0.00000 0.00000 0.00000 MINI CONSTR> 166.30474 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11196 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 253.65030 0.48618 0.39858 0.00039 MINI INTERN> 7.92391 41.17292 0.00000 26.97274 7.04822 MINI EXTERN> -11.62811 15.81523 0.00000 0.00000 0.00000 MINI CONSTR> 166.34539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 253.52992 0.12038 1.43037 0.00096 MINI INTERN> 6.91547 41.68085 0.00000 27.11439 6.93978 MINI EXTERN> -11.21347 15.77485 0.00000 0.00000 0.00000 MINI CONSTR> 166.31805 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11195 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 253.08196 0.44797 0.49293 0.00042 MINI INTERN> 8.04634 40.88090 0.00000 26.91256 7.02315 MINI EXTERN> -11.98316 15.83771 0.00000 0.00000 0.00000 MINI CONSTR> 166.36446 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 252.87134 0.21062 0.31622 0.00043 MINI INTERN> 7.82403 40.92075 0.00000 26.92293 6.99547 MINI EXTERN> -11.98174 15.82459 0.00000 0.00000 0.00000 MINI CONSTR> 166.36530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11195 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 252.65633 0.21501 0.64735 0.00045 MINI INTERN> 8.19070 40.63248 0.00000 26.84881 7.00484 MINI EXTERN> -12.26472 15.85527 0.00000 0.00000 0.00000 MINI CONSTR> 166.38895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 252.45097 0.20536 0.39034 0.00046 MINI INTERN> 7.93880 40.67636 0.00000 26.85854 6.97628 MINI EXTERN> -12.24157 15.84757 0.00000 0.00000 0.00000 MINI CONSTR> 166.39499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11195 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 252.31058 0.14039 0.70251 0.00048 MINI INTERN> 8.22832 40.46080 0.00000 26.79897 6.98215 MINI EXTERN> -12.44427 15.86514 0.00000 0.00000 0.00000 MINI CONSTR> 166.41947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 252.17366 0.13691 0.80980 0.00050 MINI INTERN> 8.25458 40.36426 0.00000 26.77356 6.97234 MINI EXTERN> -12.52807 15.89625 0.00000 0.00000 0.00000 MINI CONSTR> 166.44074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11195 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 252.05193 0.12173 0.75538 0.00052 MINI INTERN> 8.26085 40.32862 0.00000 26.75258 6.96599 MINI EXTERN> -12.59004 15.87531 0.00000 0.00000 0.00000 MINI CONSTR> 166.45861 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 251.88878 0.16315 0.22857 0.00022 MINI INTERN> 7.62576 40.59765 0.00000 26.81412 6.91903 MINI EXTERN> -12.37943 15.84885 0.00000 0.00000 0.00000 MINI CONSTR> 166.46280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 251.84858 0.04020 0.83250 0.00056 MINI INTERN> 8.28481 40.22512 0.00000 26.71132 6.94919 MINI EXTERN> -12.69424 15.86892 0.00000 0.00000 0.00000 MINI CONSTR> 166.50346 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 251.70162 0.14697 0.28939 0.00024 MINI INTERN> 7.53699 40.55450 0.00000 26.78835 6.89923 MINI EXTERN> -12.43676 15.85100 0.00000 0.00000 0.00000 MINI CONSTR> 166.50830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11194 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 251.63123 0.07039 0.19036 0.00025 MINI INTERN> 7.63129 40.45380 0.00000 26.76057 6.89918 MINI EXTERN> -12.51239 15.86697 0.00000 0.00000 0.00000 MINI CONSTR> 166.53181 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 251.56283 0.06840 0.37468 0.00026 MINI INTERN> 7.45810 40.51196 0.00000 26.76664 6.88170 MINI EXTERN> -12.47629 15.86482 0.00000 0.00000 0.00000 MINI CONSTR> 166.55590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11194 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 251.49723 0.06560 0.28203 0.00027 MINI INTERN> 7.54494 40.42920 0.00000 26.73954 6.88105 MINI EXTERN> -12.54341 15.86323 0.00000 0.00000 0.00000 MINI CONSTR> 166.58269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 251.45226 0.04497 0.40308 0.00028 MINI INTERN> 7.44946 40.44916 0.00000 26.73993 6.86846 MINI EXTERN> -12.52402 15.86450 0.00000 0.00000 0.00000 MINI CONSTR> 166.60478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11194 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 251.40744 0.04482 0.48824 0.00029 MINI INTERN> 7.41642 40.42154 0.00000 26.72881 6.86319 MINI EXTERN> -12.54865 15.89249 0.00000 0.00000 0.00000 MINI CONSTR> 166.63363 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 251.36470 0.04274 0.44496 0.00030 MINI INTERN> 7.41727 40.39170 0.00000 26.71732 6.85738 MINI EXTERN> -12.56575 15.89030 0.00000 0.00000 0.00000 MINI CONSTR> 166.65647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11194 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 251.31068 0.05402 0.14233 0.00013 MINI INTERN> 7.71262 40.20412 0.00000 26.66055 6.87579 MINI EXTERN> -12.73304 15.89938 0.00000 0.00000 0.00000 MINI CONSTR> 166.69127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 251.29550 0.01518 0.48284 0.00032 MINI INTERN> 7.42782 40.34458 0.00000 26.69374 6.84737 MINI EXTERN> -12.60131 15.87754 0.00000 0.00000 0.00000 MINI CONSTR> 166.70577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11194 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 251.24378 0.05172 0.16155 0.00014 MINI INTERN> 7.73929 40.13948 0.00000 26.63210 6.87100 MINI EXTERN> -12.79173 15.90821 0.00000 0.00000 0.00000 MINI CONSTR> 166.74543 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 251.21803 0.02575 0.11238 0.00014 MINI INTERN> 7.68478 40.14667 0.00000 26.63007 6.86479 MINI EXTERN> -12.78538 15.91120 0.00000 0.00000 0.00000 MINI CONSTR> 166.76591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 251.19143 0.02660 0.20882 0.00015 MINI INTERN> 7.77526 40.07513 0.00000 26.60451 6.86810 MINI EXTERN> -12.85008 15.91946 0.00000 0.00000 0.00000 MINI CONSTR> 166.79904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 251.16671 0.02472 0.13333 0.00015 MINI INTERN> 7.71786 40.08393 0.00000 26.60288 6.86121 MINI EXTERN> -12.84017 15.91972 0.00000 0.00000 0.00000 MINI CONSTR> 166.82128 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 251.14580 0.02091 0.17444 0.00016 MINI INTERN> 7.74034 40.04821 0.00000 26.58879 6.86058 MINI EXTERN> -12.87124 15.92965 0.00000 0.00000 0.00000 MINI CONSTR> 166.84948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 251.13118 0.01462 0.23825 0.00017 MINI INTERN> 7.78867 40.00906 0.00000 26.57299 6.86239 MINI EXTERN> -12.90953 15.93325 0.00000 0.00000 0.00000 MINI CONSTR> 166.87434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 251.11572 0.01546 0.28754 0.00017 MINI INTERN> 7.81083 39.98417 0.00000 26.56131 6.86027 MINI EXTERN> -12.92908 15.92839 0.00000 0.00000 0.00000 MINI CONSTR> 166.89982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 251.10159 0.01412 0.26305 0.00018 MINI INTERN> 7.80415 39.97038 0.00000 26.55397 6.85949 MINI EXTERN> -12.94447 15.93707 0.00000 0.00000 0.00000 MINI CONSTR> 166.92101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 251.08256 0.01903 0.08197 0.00008 MINI INTERN> 7.63352 40.03809 0.00000 26.57127 6.84510 MINI EXTERN> -12.87919 15.93753 0.00000 0.00000 0.00000 MINI CONSTR> 166.93624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 251.07797 0.00459 0.28183 0.00019 MINI INTERN> 7.80102 39.93845 0.00000 26.53869 6.85680 MINI EXTERN> -12.97289 15.95059 0.00000 0.00000 0.00000 MINI CONSTR> 166.96531 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 251.06001 0.01796 0.09640 0.00008 MINI INTERN> 7.61691 40.01654 0.00000 26.55904 6.84074 MINI EXTERN> -12.89739 15.94496 0.00000 0.00000 0.00000 MINI CONSTR> 166.97922 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 251.05146 0.00855 0.06311 0.00009 MINI INTERN> 7.64529 39.98914 0.00000 26.54916 6.84148 MINI EXTERN> -12.92009 15.94904 0.00000 0.00000 0.00000 MINI CONSTR> 166.99742 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 251.04198 0.00948 0.12327 0.00009 MINI INTERN> 7.59947 39.99822 0.00000 26.54814 6.83706 MINI EXTERN> -12.91424 15.95292 0.00000 0.00000 0.00000 MINI CONSTR> 167.02040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 251.03420 0.00778 0.09737 0.00009 MINI INTERN> 7.62044 39.97593 0.00000 26.53964 6.83695 MINI EXTERN> -12.93176 15.95421 0.00000 0.00000 0.00000 MINI CONSTR> 167.03880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 251.02866 0.00554 0.13805 0.00010 MINI INTERN> 7.59488 39.97752 0.00000 26.53837 6.83382 MINI EXTERN> -12.92901 15.95784 0.00000 0.00000 0.00000 MINI CONSTR> 167.05524 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 251.02279 0.00587 0.16200 0.00010 MINI INTERN> 7.58654 39.96769 0.00000 26.53361 6.83284 MINI EXTERN> -12.93865 15.96642 0.00000 0.00000 0.00000 MINI CONSTR> 167.07434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 251.01746 0.00533 0.14866 0.00010 MINI INTERN> 7.59028 39.95752 0.00000 26.52909 6.83139 MINI EXTERN> -12.94498 15.96497 0.00000 0.00000 0.00000 MINI CONSTR> 167.08920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 251.01224 0.00522 0.15373 0.00011 MINI INTERN> 7.58919 39.94550 0.00000 26.52382 6.83104 MINI EXTERN> -12.95648 15.97194 0.00000 0.00000 0.00000 MINI CONSTR> 167.10722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 251.00606 0.00618 0.04868 0.00005 MINI INTERN> 7.66366 39.89598 0.00000 26.50838 6.83509 MINI EXTERN> -12.99602 15.97466 0.00000 0.00000 0.00000 MINI CONSTR> 167.12431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 251.00456 0.00150 0.16710 0.00011 MINI INTERN> 7.58840 39.92925 0.00000 26.51646 6.82844 MINI EXTERN> -12.96750 15.97352 0.00000 0.00000 0.00000 MINI CONSTR> 167.13599 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 250.99823 0.00634 0.05745 0.00005 MINI INTERN> 7.67014 39.87288 0.00000 26.49901 6.83393 MINI EXTERN> -13.01439 15.98138 0.00000 0.00000 0.00000 MINI CONSTR> 167.15527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 250.99523 0.00299 0.03722 0.00005 MINI INTERN> 7.65623 39.87343 0.00000 26.49790 6.83264 MINI EXTERN> -13.01484 15.98323 0.00000 0.00000 0.00000 MINI CONSTR> 167.16664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 250.99184 0.00339 0.07232 0.00005 MINI INTERN> 7.67598 39.85027 0.00000 26.49058 6.83271 MINI EXTERN> -13.03102 15.98879 0.00000 0.00000 0.00000 MINI CONSTR> 167.18453 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 250.98905 0.00279 0.05655 0.00006 MINI INTERN> 7.66866 39.84831 0.00000 26.48856 6.83179 MINI EXTERN> -13.03398 15.98908 0.00000 0.00000 0.00000 MINI CONSTR> 167.19664 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 250.98707 0.00198 0.08204 0.00006 MINI INTERN> 7.67976 39.83440 0.00000 26.48378 6.83207 MINI EXTERN> -13.04498 15.99281 0.00000 0.00000 0.00000 MINI CONSTR> 167.20923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 250.98498 0.00209 0.09764 0.00006 MINI INTERN> 7.67588 39.82519 0.00000 26.48106 6.83146 MINI EXTERN> -13.05090 16.00028 0.00000 0.00000 0.00000 MINI CONSTR> 167.22201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 250.98304 0.00195 0.08822 0.00006 MINI INTERN> 7.67991 39.81948 0.00000 26.47800 6.83139 MINI EXTERN> -13.05726 15.99900 0.00000 0.00000 0.00000 MINI CONSTR> 167.23251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 250.98111 0.00192 0.09131 0.00006 MINI INTERN> 7.68025 39.81154 0.00000 26.47530 6.83060 MINI EXTERN> -13.06234 16.00133 0.00000 0.00000 0.00000 MINI CONSTR> 167.24442 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 250.97874 0.00238 0.02887 0.00003 MINI INTERN> 7.64621 39.82536 0.00000 26.47777 6.82916 MINI EXTERN> -13.05598 16.00261 0.00000 0.00000 0.00000 MINI CONSTR> 167.25361 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 250.97811 0.00062 0.09929 0.00007 MINI INTERN> 7.68092 39.79850 0.00000 26.47046 6.82996 MINI EXTERN> -13.07292 16.00590 0.00000 0.00000 0.00000 MINI CONSTR> 167.26528 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 250.97578 0.00233 0.03288 0.00003 MINI INTERN> 7.64327 39.81437 0.00000 26.47351 6.82863 MINI EXTERN> -13.06589 16.00757 0.00000 0.00000 0.00000 MINI CONSTR> 167.27433 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 250.97464 0.00113 0.02384 0.00003 MINI INTERN> 7.64843 39.80585 0.00000 26.47111 6.82839 MINI EXTERN> -13.07132 16.00964 0.00000 0.00000 0.00000 MINI CONSTR> 167.28253 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 250.97349 0.00115 0.04448 0.00003 MINI INTERN> 7.64001 39.80550 0.00000 26.47014 6.82811 MINI EXTERN> -13.07406 16.01130 0.00000 0.00000 0.00000 MINI CONSTR> 167.29250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 250.97240 0.00109 0.03383 0.00003 MINI INTERN> 7.64340 39.79661 0.00000 26.46790 6.82797 MINI EXTERN> -13.07968 16.01525 0.00000 0.00000 0.00000 MINI CONSTR> 167.30095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11192 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 250.97159 0.00082 0.04925 0.00003 MINI INTERN> 7.63873 39.79482 0.00000 26.46701 6.82765 MINI EXTERN> -13.08215 16.01658 0.00000 0.00000 0.00000 MINI CONSTR> 167.30894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 250.97072 0.00087 0.05601 0.00004 MINI INTERN> 7.64127 39.79005 0.00000 26.46513 6.82756 MINI EXTERN> -13.08678 16.01619 0.00000 0.00000 0.00000 MINI CONSTR> 167.31730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11192 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 250.96997 0.00075 0.05797 0.00004 MINI INTERN> 7.63941 39.78541 0.00000 26.46406 6.82725 MINI EXTERN> -13.08989 16.01912 0.00000 0.00000 0.00000 MINI CONSTR> 167.32460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 250.96923 0.00074 0.05539 0.00004 MINI INTERN> 7.63867 39.77922 0.00000 26.46277 6.82713 MINI EXTERN> -13.09380 16.02359 0.00000 0.00000 0.00000 MINI CONSTR> 167.33166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11192 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 250.96832 0.00091 0.01850 0.00002 MINI INTERN> 7.65247 39.76659 0.00000 26.45953 6.82731 MINI EXTERN> -13.10142 16.02515 0.00000 0.00000 0.00000 MINI CONSTR> 167.33868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 250.96798 0.00035 0.05959 0.00004 MINI INTERN> 7.63979 39.77069 0.00000 26.46041 6.82677 MINI EXTERN> -13.10046 16.02561 0.00000 0.00000 0.00000 MINI CONSTR> 167.34516 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11192 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 250.96740 0.00057 0.06721 0.00004 MINI INTERN> 7.63904 39.76393 0.00000 26.45898 6.82703 MINI EXTERN> -13.10547 16.03137 0.00000 0.00000 0.00000 MINI CONSTR> 167.35252 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 250.96649 0.00091 0.02047 0.00002 MINI INTERN> 7.65339 39.75257 0.00000 26.45591 6.82713 MINI EXTERN> -13.11240 16.03082 0.00000 0.00000 0.00000 MINI CONSTR> 167.35906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 250.96601 0.00047 0.01529 0.00002 MINI INTERN> 7.65122 39.75026 0.00000 26.45534 6.82711 MINI EXTERN> -13.11475 16.03242 0.00000 0.00000 0.00000 MINI CONSTR> 167.36440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 250.96550 0.00051 0.02615 0.00002 MINI INTERN> 7.65456 39.74352 0.00000 26.45379 6.82710 MINI EXTERN> -13.11930 16.03446 0.00000 0.00000 0.00000 MINI CONSTR> 167.37138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 250.96503 0.00047 0.01792 0.00002 MINI INTERN> 7.65219 39.74105 0.00000 26.45330 6.82706 MINI EXTERN> -13.12167 16.03624 0.00000 0.00000 0.00000 MINI CONSTR> 167.37687 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 250.96461 0.00042 0.02281 0.00002 MINI INTERN> 7.65369 39.73664 0.00000 26.45227 6.82706 MINI EXTERN> -13.12506 16.03726 0.00000 0.00000 0.00000 MINI CONSTR> 167.38275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 250.96427 0.00033 0.03159 0.00002 MINI INTERN> 7.65478 39.73186 0.00000 26.45130 6.82713 MINI EXTERN> -13.12847 16.03955 0.00000 0.00000 0.00000 MINI CONSTR> 167.38812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 250.96388 0.00039 0.03239 0.00002 MINI INTERN> 7.65535 39.72792 0.00000 26.45056 6.82706 MINI EXTERN> -13.13131 16.04066 0.00000 0.00000 0.00000 MINI CONSTR> 167.39366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 250.96358 0.00030 0.04045 0.00002 MINI INTERN> 7.65324 39.72391 0.00000 26.45007 6.82712 MINI EXTERN> -13.13412 16.04449 0.00000 0.00000 0.00000 MINI CONSTR> 167.39886 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 250.96327 0.00031 0.03681 0.00002 MINI INTERN> 7.65316 39.72157 0.00000 26.44952 6.82725 MINI EXTERN> -13.13652 16.04514 0.00000 0.00000 0.00000 MINI CONSTR> 167.40315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 250.96288 0.00039 0.01191 0.00001 MINI INTERN> 7.64931 39.72242 0.00000 26.44976 6.82728 MINI EXTERN> -13.13744 16.04461 0.00000 0.00000 0.00000 MINI CONSTR> 167.40694 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 250.96272 0.00016 0.03962 0.00003 MINI INTERN> 7.65296 39.71570 0.00000 26.44848 6.82744 MINI EXTERN> -13.14152 16.04766 0.00000 0.00000 0.00000 MINI CONSTR> 167.41199 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 250.96250 0.00023 0.04631 0.00003 MINI INTERN> 7.65500 39.71436 0.00000 26.44803 6.82741 MINI EXTERN> -13.14337 16.04505 0.00000 0.00000 0.00000 MINI CONSTR> 167.41600 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 250.96209 0.00041 0.01277 0.00001 MINI INTERN> 7.64908 39.71341 0.00000 26.44847 6.82746 MINI EXTERN> -13.14451 16.04844 0.00000 0.00000 0.00000 MINI CONSTR> 167.41975 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 250.96187 0.00022 0.01062 0.00001 MINI INTERN> 7.64937 39.71042 0.00000 26.44806 6.82753 MINI EXTERN> -13.14666 16.04977 0.00000 0.00000 0.00000 MINI CONSTR> 167.42337 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 250.96165 0.00022 0.01080 0.00001 MINI INTERN> 7.64932 39.70768 0.00000 26.44775 6.82760 MINI EXTERN> -13.14878 16.05090 0.00000 0.00000 0.00000 MINI CONSTR> 167.42718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 250.96142 0.00022 0.01700 0.00001 MINI INTERN> 7.64876 39.70514 0.00000 26.44755 6.82768 MINI EXTERN> -13.15091 16.05188 0.00000 0.00000 0.00000 MINI CONSTR> 167.43132 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> 444 250.96127 0.00015 0.00984 0.00001 STPD INTERN> 7.65017 39.70236 0.00000 26.44705 6.82779 STPD EXTERN> -13.15278 16.05285 0.00000 0.00000 0.00000 STPD CONSTR> 167.43383 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 11193 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 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> 0 250.96127 0.00015 0.00984 0.00000 MINI INTERN> 7.65017 39.70236 0.00000 26.44705 6.82779 MINI EXTERN> -13.15278 16.05285 0.00000 0.00000 0.00000 MINI CONSTR> 167.43383 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> 3 250.95751 0.00376 0.00679 0.02000 CONJ INTERN> 7.64471 39.60302 0.00000 26.43793 6.83265 CONJ EXTERN> -13.23716 16.09880 0.00000 0.00000 0.00000 CONJ CONSTR> 167.57756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "5400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 4.1424 ( PROT LYS 1 HT2 ) 4.1424 ( PROT LYS 1 N ) 5.1780 ( PROT LYS 1 HT3 ) 4.1424 ( PROT LYS 1 CA ) 5.1780 ( PROT LYS 1 CB ) 4.1424 ( PROT LYS 1 CG ) 4.1424 ( PROT LYS 1 CD ) 4.1424 ( PROT LYS 1 CE ) 4.1424 ( PROT LYS 1 NZ ) 4.1424 ( PROT LYS 1 HZ1 ) 4.1424 ( PROT LYS 1 HZ2 ) 4.1424 ( PROT LYS 1 HZ3 ) 4.1424 ( PROT LYS 1 C ) 5.1780 ( PROT LYS 1 O ) 5.1780 ( PROT MET 2 N ) 5.1780 ( PROT MET 2 H ) 4.1424 ( PROT MET 2 CA ) 5.1780 ( PROT MET 2 CB ) 4.1424 ( PROT MET 2 CG ) 4.1424 ( PROT MET 2 SD ) 4.1424 ( PROT MET 2 CE ) 4.1424 ( PROT MET 2 C ) 5.1780 ( PROT MET 2 O ) 5.1780 ( PROT LYS 3 N ) 5.1780 ( PROT LYS 3 H ) 4.1424 ( PROT LYS 3 CA ) 5.1780 ( PROT LYS 3 CB ) 4.1424 ( PROT LYS 3 CG ) 4.1424 ( PROT LYS 3 CD ) 4.1424 ( PROT LYS 3 CE ) 4.1424 ( PROT LYS 3 NZ ) 4.1424 ( PROT LYS 3 HZ1 ) 4.1424 ( PROT LYS 3 HZ2 ) 4.1424 ( PROT LYS 3 HZ3 ) 4.1424 ( PROT LYS 3 C ) 5.1780 ( PROT LYS 3 O ) 5.1780 ( PROT ALA 4 N ) 5.1780 ( PROT ALA 4 H ) 4.1424 ( PROT ALA 4 CA ) 5.1780 ( PROT ALA 4 CB ) 4.1424 ( PROT ALA 4 C ) 5.1780 ( PROT ALA 4 O ) 5.1780 ( PROT VAL 5 N ) 5.1780 ( PROT VAL 5 H ) 4.1424 ( PROT VAL 5 CA ) 5.1780 ( PROT VAL 5 CB ) 4.1424 ( PROT VAL 5 CG1 ) 4.1424 ( PROT VAL 5 CG2 ) 4.1424 ( PROT VAL 5 C ) 5.1780 ( PROT VAL 5 O ) 5.1780 ( PROT MET 6 N ) 5.1780 ( PROT MET 6 H ) 4.1424 ( PROT MET 6 CA ) 5.1780 ( PROT MET 6 CB ) 4.1424 ( PROT MET 6 CG ) 4.1424 ( PROT MET 6 SD ) 4.1424 ( PROT MET 6 CE ) 4.1424 ( PROT MET 6 C ) 5.1780 ( PROT MET 6 O ) 5.1780 ( PROT ILE 7 N ) 5.1780 ( PROT ILE 7 H ) 4.1424 ( PROT ILE 7 CA ) 5.1780 ( PROT ILE 7 CB ) 4.1424 ( PROT ILE 7 CG2 ) 4.1424 ( PROT ILE 7 CG1 ) 4.1424 ( PROT ILE 7 CD ) 4.1424 ( PROT ILE 7 C ) 5.1780 ( PROT ILE 7 O ) 5.1780 ( PROT GLY 8 N ) 5.1780 ( PROT GLY 8 H ) 4.1424 ( PROT GLY 8 CA ) 5.1780 ( PROT GLY 8 C ) 5.1780 ( PROT GLY 8 O ) 5.1780 ( PROT ALA 9 N ) 5.1780 ( PROT ALA 9 H ) 4.1424 ( PROT ALA 9 CA ) 5.1780 ( PROT ALA 9 CB ) 4.1424 ( PROT ALA 9 C ) 5.1780 ( PROT ALA 9 O ) 5.1780 ( PROT CYS 10 N ) 5.1780 ( PROT CYS 10 H ) 4.1424 ( PROT CYS 10 CA ) 5.1780 ( PROT CYS 10 CB ) 4.1424 ( PROT CYS 10 SG ) 4.1424 ( PROT CYS 10 C ) 5.1780 ( PROT CYS 10 O ) 5.1780 ( PROT PHE 11 N ) 5.1780 ( PROT PHE 11 H ) 4.1424 ( PROT PHE 11 CA ) 5.1780 ( PROT PHE 11 CB ) 4.1424 ( PROT PHE 11 CG ) 4.1424 ( PROT PHE 11 CD1 ) 4.1424 ( PROT PHE 11 CD2 ) 4.1424 ( PROT PHE 11 CE1 ) 4.1424 ( PROT PHE 11 CE2 ) 4.1424 ( PROT PHE 11 CZ ) 4.1424 ( PROT PHE 11 C ) 5.1780 ( PROT PHE 11 O ) 5.1780 ( PROT LEU 12 N ) 5.1780 ( PROT LEU 12 H ) 4.1424 ( PROT LEU 12 CA ) 5.1780 ( PROT LEU 12 CB ) 4.1424 ( PROT LEU 12 CG ) 4.1424 ( PROT LEU 12 CD1 ) 4.1424 ( PROT LEU 12 CD2 ) 4.1424 ( PROT LEU 12 C ) 5.1780 ( PROT LEU 12 O ) 5.1780 ( PROT ILE 13 N ) 5.1780 ( PROT ILE 13 H ) 4.1424 ( PROT ILE 13 CA ) 5.1780 ( PROT ILE 13 CB ) 4.1424 ( PROT ILE 13 CG2 ) 4.1424 ( PROT ILE 13 CG1 ) 4.1424 ( PROT ILE 13 CD ) 4.1424 ( PROT ILE 13 C ) 5.1780 ( PROT ILE 13 O ) 5.1780 ( PROT ASP 14 N ) 5.1780 ( PROT ASP 14 H ) 4.1424 ( PROT ASP 14 CA ) 5.1780 ( PROT ASP 14 CB ) 4.1424 ( PROT ASP 14 CG ) 4.1424 ( PROT ASP 14 OD1 ) 4.1424 ( PROT ASP 14 OD2 ) 4.1424 ( PROT ASP 14 C ) 5.1780 ( PROT ASP 14 O ) 5.1780 ( PROT PHE 15 N ) 5.1780 ( PROT PHE 15 H ) 4.1424 ( PROT PHE 15 CA ) 5.1780 ( PROT PHE 15 CB ) 4.1424 ( PROT PHE 15 CG ) 4.1424 ( PROT PHE 15 CD1 ) 4.1424 ( PROT PHE 15 CD2 ) 4.1424 ( PROT PHE 15 CE1 ) 4.1424 ( PROT PHE 15 CE2 ) 4.1424 ( PROT PHE 15 CZ ) 4.1424 ( PROT PHE 15 C ) 5.1780 ( PROT PHE 15 O ) 5.1780 ( PROT MET 16 N ) 5.1780 ( PROT MET 16 H ) 4.1424 ( PROT MET 16 CA ) 5.1780 ( PROT MET 16 CB ) 4.1424 ( PROT MET 16 CG ) 4.1424 ( PROT MET 16 SD ) 4.1424 ( PROT MET 16 CE ) 4.1424 ( PROT MET 16 C ) 5.1780 ( PROT MET 16 O ) 5.1780 ( PROT PHE 17 N ) 5.1780 ( PROT PHE 17 H ) 4.1424 ( PROT PHE 17 CA ) 5.1780 ( PROT PHE 17 CB ) 4.1424 ( PROT PHE 17 CG ) 4.1424 ( PROT PHE 17 CD1 ) 4.1424 ( PROT PHE 17 CD2 ) 4.1424 ( PROT PHE 17 CE1 ) 4.1424 ( PROT PHE 17 CE2 ) 4.1424 ( PROT PHE 17 CZ ) 4.1424 ( PROT PHE 17 C ) 5.1780 ( PROT PHE 17 O ) 5.1780 ( PROT PHE 18 N ) 5.1780 ( PROT PHE 18 H ) 4.1424 ( PROT PHE 18 CA ) 5.1780 ( PROT PHE 18 CB ) 4.1424 ( PROT PHE 18 CG ) 4.1424 ( PROT PHE 18 CD1 ) 4.1424 ( PROT PHE 18 CD2 ) 4.1424 ( PROT PHE 18 CE1 ) 4.1424 ( PROT PHE 18 CE2 ) 4.1424 ( PROT PHE 18 CZ ) 4.1424 ( PROT PHE 18 C ) 5.1780 ( PROT PHE 18 O ) 5.1780 ( PROT GLU 19 N ) 5.1780 ( PROT GLU 19 H ) 4.1424 ( PROT GLU 19 CA ) 5.1780 ( PROT GLU 19 CB ) 4.1424 ( PROT GLU 19 CG ) 4.1424 ( PROT GLU 19 CD ) 4.1424 ( PROT GLU 19 OE1 ) 4.1424 ( PROT GLU 19 OE2 ) 4.1424 ( PROT GLU 19 C ) 5.1780 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41079 5.26148 -8.67084 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00024 -0.00157 -0.00085 ROTATION MATRIX 1.000000 -0.000097 0.000057 0.000097 1.000000 0.000143 -0.000057 -0.000143 1.000000 AXIS OF ROTATION IS 0.785930 -0.313621 -0.532875 ANGLE IS 0.01 TOTAL SQUARE DIFF IS 24.1276 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.364101 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3641" Parameter: A <- "0.3641" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70775 5.22214 -8.77840 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00709 0.04228 -0.01597 ROTATION MATRIX 0.999793 0.015921 0.012629 -0.015734 0.999767 -0.014779 -0.012862 0.014577 0.999811 AXIS OF ROTATION IS -0.585523 -0.508446 0.631384 ANGLE IS 1.44 CENTER OF ROTATION 8.970373 5.048882 -9.630041 SHIFT IS -0.035727 TOTAL SQUARE DIFF IS 0.6237 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.181183 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3641" RDCMND substituted energy or value "?RMS" to " 0.1812" Parameter: A <- "0.3641 0.1812" 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 0.3641 0.1812 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 " 167.58" Parameter: H <- "167.58" 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 83.37995 167.57756 2.93709 ENER INTERN> 7.64471 39.60302 0.00000 26.43793 6.83265 ENER EXTERN> -13.23716 16.09880 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 " 83.38" Parameter: B <- "83.38" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 16.10" Parameter: C <- "16.10" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -13.24" Parameter: C <- " 2.86" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " 2.86" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 7.64" Parameter: D <- "7.64" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 39.60" Parameter: D <- " 47.24" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 26.44" Parameter: D <- " 73.68" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.83" Parameter: D <- " 80.51" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 80.51" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 5400 ENER= 83.38 GRMS= 2.94 ELEC= 16.10 VDW= -13.24 RDTITL> *EXTERNAL= 2.86 INTERNAL= 80.51 USER= 0.00 HARM= 167.58 RDTITL> *BOND= 7.64 ANGL= 39.60 DIHE= 26.44 IMPR= 6.83 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11193 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11193 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 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> 0 201.81710 -118.43715 1.16505 0.02000 MINI INTERN> 7.64471 39.60302 0.00000 26.43793 6.83265 MINI EXTERN> -13.23716 16.09880 0.00000 0.00000 0.00000 MINI CONSTR> 118.43715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 196.35575 5.46135 1.42474 0.00360 MINI INTERN> 7.35780 37.26566 0.00000 28.09726 6.78568 MINI EXTERN> -27.03350 17.17235 0.00000 0.00000 0.00000 MINI CONSTR> 126.71051 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11184 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 195.19805 1.15769 1.78610 0.00156 MINI INTERN> 6.90477 38.21850 0.00000 28.50873 6.61530 MINI EXTERN> -30.54053 17.67590 0.00000 0.00000 0.00000 MINI CONSTR> 127.81537 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 194.11515 1.08291 0.55257 0.00067 MINI INTERN> 6.88854 37.98991 0.00000 28.54263 6.72923 MINI EXTERN> -32.07305 17.77821 0.00000 0.00000 0.00000 MINI CONSTR> 128.25968 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11183 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 193.41949 0.69565 0.66343 0.00070 MINI INTERN> 6.80059 37.68891 0.00000 28.62605 6.66299 MINI EXTERN> -32.76723 17.81205 0.00000 0.00000 0.00000 MINI CONSTR> 128.59614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 192.91687 0.50263 0.51386 0.00072 MINI INTERN> 6.73980 37.52261 0.00000 28.65132 6.62698 MINI EXTERN> -33.20207 17.79310 0.00000 0.00000 0.00000 MINI CONSTR> 128.78514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11182 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 192.46866 0.44821 1.07417 0.00075 MINI INTERN> 6.66620 37.27752 0.00000 28.71562 6.54193 MINI EXTERN> -33.51419 17.82889 0.00000 0.00000 0.00000 MINI CONSTR> 128.95268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 192.03683 0.43182 1.17139 0.00078 MINI INTERN> 6.68055 37.06216 0.00000 28.71654 6.51879 MINI EXTERN> -33.90115 17.87919 0.00000 0.00000 0.00000 MINI CONSTR> 129.08076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11180 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 191.67555 0.36129 1.22547 0.00080 MINI INTERN> 6.59672 36.96372 0.00000 28.73165 6.47933 MINI EXTERN> -34.11482 17.85364 0.00000 0.00000 0.00000 MINI CONSTR> 129.16530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 191.31666 0.35888 1.17120 0.00083 MINI INTERN> 6.56855 36.85037 0.00000 28.71878 6.46273 MINI EXTERN> -34.36291 17.84154 0.00000 0.00000 0.00000 MINI CONSTR> 129.23760 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11178 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 190.97844 0.33822 1.24856 0.00087 MINI INTERN> 6.61451 36.66424 0.00000 28.69336 6.44881 MINI EXTERN> -34.63459 17.88604 0.00000 0.00000 0.00000 MINI CONSTR> 129.30607 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 190.57272 0.40572 0.37992 0.00037 MINI INTERN> 6.57078 36.71619 0.00000 28.61973 6.51121 MINI EXTERN> -35.01042 17.79407 0.00000 0.00000 0.00000 MINI CONSTR> 129.37116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11178 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 190.46233 0.11040 1.42864 0.00093 MINI INTERN> 6.50504 36.52159 0.00000 28.67043 6.40724 MINI EXTERN> -34.92965 17.89418 0.00000 0.00000 0.00000 MINI CONSTR> 129.39349 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 190.04318 0.41914 0.45415 0.00040 MINI INTERN> 6.55820 36.53319 0.00000 28.56773 6.48863 MINI EXTERN> -35.34593 17.78732 0.00000 0.00000 0.00000 MINI CONSTR> 129.45405 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11177 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 189.82586 0.21732 0.31732 0.00042 MINI INTERN> 6.52625 36.42186 0.00000 28.55655 6.46007 MINI EXTERN> -35.41724 17.80019 0.00000 0.00000 0.00000 MINI CONSTR> 129.47818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 189.58719 0.23867 0.32669 0.00043 MINI INTERN> 6.51154 36.34287 0.00000 28.52764 6.44735 MINI EXTERN> -35.54712 17.79265 0.00000 0.00000 0.00000 MINI CONSTR> 129.51226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11176 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 189.39269 0.19450 0.62102 0.00045 MINI INTERN> 6.51072 36.33465 0.00000 28.48497 6.45892 MINI EXTERN> -35.71806 17.76951 0.00000 0.00000 0.00000 MINI CONSTR> 129.55198 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 189.19071 0.20198 0.43855 0.00046 MINI INTERN> 6.45556 36.22817 0.00000 28.47131 6.43026 MINI EXTERN> -35.76460 17.79565 0.00000 0.00000 0.00000 MINI CONSTR> 129.57435 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11172 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 189.04755 0.14316 0.66982 0.00048 MINI INTERN> 6.47268 36.21616 0.00000 28.43343 6.43875 MINI EXTERN> -35.89127 17.77119 0.00000 0.00000 0.00000 MINI CONSTR> 129.60662 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 188.89103 0.15652 0.77274 0.00050 MINI INTERN> 6.43177 36.20062 0.00000 28.41255 6.42405 MINI EXTERN> -35.94731 17.73638 0.00000 0.00000 0.00000 MINI CONSTR> 129.63296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11171 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 188.75733 0.13370 0.79645 0.00052 MINI INTERN> 6.39356 36.10573 0.00000 28.39253 6.41094 MINI EXTERN> -36.00662 17.80277 0.00000 0.00000 0.00000 MINI CONSTR> 129.65842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 188.62357 0.13376 0.73373 0.00054 MINI INTERN> 6.43062 36.05562 0.00000 28.35826 6.41120 MINI EXTERN> -36.09352 17.77598 0.00000 0.00000 0.00000 MINI CONSTR> 129.68541 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11171 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 188.46258 0.16099 0.24829 0.00023 MINI INTERN> 6.49091 35.82308 0.00000 28.35150 6.35669 MINI EXTERN> -36.06458 17.81058 0.00000 0.00000 0.00000 MINI CONSTR> 129.69441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 188.40846 0.05412 0.84046 0.00058 MINI INTERN> 6.44839 35.95039 0.00000 28.30617 6.39956 MINI EXTERN> -36.21593 17.78176 0.00000 0.00000 0.00000 MINI CONSTR> 129.73813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11171 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 188.24333 0.16513 0.28082 0.00025 MINI INTERN> 6.49711 35.70486 0.00000 28.30419 6.33651 MINI EXTERN> -36.16260 17.81711 0.00000 0.00000 0.00000 MINI CONSTR> 129.74615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 188.15405 0.08928 0.21381 0.00026 MINI INTERN> 6.46695 35.70198 0.00000 28.28304 6.33633 MINI EXTERN> -36.21047 17.80514 0.00000 0.00000 0.00000 MINI CONSTR> 129.77108 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11170 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 188.06142 0.09263 0.34004 0.00027 MINI INTERN> 6.50683 35.60094 0.00000 28.26076 6.31754 MINI EXTERN> -36.24202 17.81997 0.00000 0.00000 0.00000 MINI CONSTR> 129.79739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 187.98205 0.07938 0.19199 0.00028 MINI INTERN> 6.45346 35.62622 0.00000 28.23996 6.32432 MINI EXTERN> -36.29319 17.80741 0.00000 0.00000 0.00000 MINI CONSTR> 129.82385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11170 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 187.90008 0.08197 0.39764 0.00029 MINI INTERN> 6.54603 35.48610 0.00000 28.21398 6.30168 MINI EXTERN> -36.32500 17.82489 0.00000 0.00000 0.00000 MINI CONSTR> 129.85240 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 187.82048 0.07959 0.29015 0.00030 MINI INTERN> 6.49156 35.49471 0.00000 28.19274 6.30487 MINI EXTERN> -36.37041 17.82415 0.00000 0.00000 0.00000 MINI CONSTR> 129.88285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11170 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 187.76698 0.05350 0.43989 0.00031 MINI INTERN> 6.53928 35.41110 0.00000 28.17384 6.29084 MINI EXTERN> -36.39344 17.83814 0.00000 0.00000 0.00000 MINI CONSTR> 129.90722 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 187.71155 0.05543 0.49188 0.00032 MINI INTERN> 6.57210 35.36978 0.00000 28.15462 6.28217 MINI EXTERN> -36.41885 17.81955 0.00000 0.00000 0.00000 MINI CONSTR> 129.93218 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11170 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 187.65756 0.05398 0.49852 0.00033 MINI INTERN> 6.51586 35.36263 0.00000 28.14064 6.28094 MINI EXTERN> -36.44689 17.84439 0.00000 0.00000 0.00000 MINI CONSTR> 129.95998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 187.60477 0.05279 0.46929 0.00034 MINI INTERN> 6.53689 35.33403 0.00000 28.12349 6.27320 MINI EXTERN> -36.46651 17.81939 0.00000 0.00000 0.00000 MINI CONSTR> 129.98428 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11169 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 187.54036 0.06441 0.15719 0.00015 MINI INTERN> 6.38690 35.45253 0.00000 28.10752 6.29463 MINI EXTERN> -36.51351 17.79570 0.00000 0.00000 0.00000 MINI CONSTR> 130.01661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 187.51998 0.02038 0.54175 0.00037 MINI INTERN> 6.53764 35.28541 0.00000 28.09261 6.26272 MINI EXTERN> -36.50868 17.81452 0.00000 0.00000 0.00000 MINI CONSTR> 130.03575 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11169 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 187.45354 0.06644 0.18428 0.00016 MINI INTERN> 6.36958 35.41988 0.00000 28.07540 6.28910 MINI EXTERN> -36.56141 17.79013 0.00000 0.00000 0.00000 MINI CONSTR> 130.07086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 187.41864 0.03490 0.13859 0.00017 MINI INTERN> 6.38793 35.37424 0.00000 28.06190 6.28258 MINI EXTERN> -36.57834 17.79791 0.00000 0.00000 0.00000 MINI CONSTR> 130.09241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 187.38148 0.03716 0.22219 0.00017 MINI INTERN> 6.36226 35.38563 0.00000 28.04550 6.28427 MINI EXTERN> -36.60477 17.78573 0.00000 0.00000 0.00000 MINI CONSTR> 130.12285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 187.34879 0.03269 0.18955 0.00018 MINI INTERN> 6.36837 35.35046 0.00000 28.03209 6.27961 MINI EXTERN> -36.62275 17.79438 0.00000 0.00000 0.00000 MINI CONSTR> 130.14663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 187.31843 0.03036 0.20779 0.00019 MINI INTERN> 6.37294 35.33296 0.00000 28.01765 6.27728 MINI EXTERN> -36.64253 17.78813 0.00000 0.00000 0.00000 MINI CONSTR> 130.17201 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 187.29322 0.02521 0.27911 0.00019 MINI INTERN> 6.35573 35.32657 0.00000 28.00458 6.27764 MINI EXTERN> -36.66375 17.79417 0.00000 0.00000 0.00000 MINI CONSTR> 130.19829 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 187.26850 0.02472 0.30997 0.00020 MINI INTERN> 6.37356 35.30945 0.00000 27.99025 6.27550 MINI EXTERN> -36.68232 17.77973 0.00000 0.00000 0.00000 MINI CONSTR> 130.22233 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 187.24459 0.02391 0.30450 0.00021 MINI INTERN> 6.36396 35.28073 0.00000 27.97981 6.27203 MINI EXTERN> -36.69699 17.79954 0.00000 0.00000 0.00000 MINI CONSTR> 130.24551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 187.22233 0.02226 0.30878 0.00021 MINI INTERN> 6.38970 35.26142 0.00000 27.96615 6.26944 MINI EXTERN> -36.71346 17.78106 0.00000 0.00000 0.00000 MINI CONSTR> 130.26803 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 187.19499 0.02734 0.09941 0.00009 MINI INTERN> 6.40273 35.19519 0.00000 27.96131 6.25442 MINI EXTERN> -36.70764 17.80421 0.00000 0.00000 0.00000 MINI CONSTR> 130.28478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 187.18485 0.01014 0.35514 0.00023 MINI INTERN> 6.40550 35.22326 0.00000 27.94308 6.26517 MINI EXTERN> -36.74382 17.77861 0.00000 0.00000 0.00000 MINI CONSTR> 130.31306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 187.16892 0.01593 0.39669 0.00024 MINI INTERN> 6.38174 35.19692 0.00000 27.93545 6.26193 MINI EXTERN> -36.75518 17.81210 0.00000 0.00000 0.00000 MINI CONSTR> 130.33597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 187.13938 0.02954 0.10734 0.00010 MINI INTERN> 6.40028 35.14762 0.00000 27.93135 6.24645 MINI EXTERN> -36.74381 17.80594 0.00000 0.00000 0.00000 MINI CONSTR> 130.35155 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 187.12446 0.01492 0.08675 0.00011 MINI INTERN> 6.39669 35.14127 0.00000 27.92223 6.24614 MINI EXTERN> -36.75653 17.80325 0.00000 0.00000 0.00000 MINI CONSTR> 130.37142 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 187.10893 0.01553 0.14632 0.00011 MINI INTERN> 6.40230 35.11413 0.00000 27.91355 6.24023 MINI EXTERN> -36.76351 17.80805 0.00000 0.00000 0.00000 MINI CONSTR> 130.39418 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 187.09569 0.01324 0.07842 0.00011 MINI INTERN> 6.39458 35.11619 0.00000 27.90447 6.24269 MINI EXTERN> -36.77888 17.80384 0.00000 0.00000 0.00000 MINI CONSTR> 130.41281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 187.08192 0.01378 0.17091 0.00012 MINI INTERN> 6.40753 35.08181 0.00000 27.89569 6.23550 MINI EXTERN> -36.78509 17.81000 0.00000 0.00000 0.00000 MINI CONSTR> 130.43647 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 187.06793 0.01398 0.10444 0.00012 MINI INTERN> 6.40373 35.07867 0.00000 27.88592 6.23686 MINI EXTERN> -36.80023 17.80554 0.00000 0.00000 0.00000 MINI CONSTR> 130.45745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 187.05832 0.00962 0.18304 0.00013 MINI INTERN> 6.41169 35.05175 0.00000 27.87871 6.23201 MINI EXTERN> -36.80692 17.81375 0.00000 0.00000 0.00000 MINI CONSTR> 130.47732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 187.04911 0.00920 0.22271 0.00013 MINI INTERN> 6.42366 35.04184 0.00000 27.87035 6.23021 MINI EXTERN> -36.81612 17.80295 0.00000 0.00000 0.00000 MINI CONSTR> 130.49622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 187.03962 0.00949 0.19963 0.00014 MINI INTERN> 6.41151 35.03650 0.00000 27.86510 6.22883 MINI EXTERN> -36.82228 17.80688 0.00000 0.00000 0.00000 MINI CONSTR> 130.51307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 187.02782 0.01180 0.06678 0.00006 MINI INTERN> 6.38291 35.05617 0.00000 27.85705 6.23486 MINI EXTERN> -36.83869 17.80329 0.00000 0.00000 0.00000 MINI CONSTR> 130.53223 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11169 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 187.02339 0.00443 0.21669 0.00015 MINI INTERN> 6.39909 35.01850 0.00000 27.85333 6.22606 MINI EXTERN> -36.83708 17.81546 0.00000 0.00000 0.00000 MINI CONSTR> 130.54802 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 187.01677 0.00662 0.26033 0.00015 MINI INTERN> 6.41590 35.01671 0.00000 27.84451 6.22663 MINI EXTERN> -36.84854 17.79605 0.00000 0.00000 0.00000 MINI CONSTR> 130.56551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11169 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 187.00442 0.01235 0.07288 0.00007 MINI INTERN> 6.38172 35.02871 0.00000 27.83795 6.23150 MINI EXTERN> -36.86277 17.80348 0.00000 0.00000 0.00000 MINI CONSTR> 130.58383 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 186.99817 0.00625 0.05602 0.00007 MINI INTERN> 6.38403 35.01611 0.00000 27.83312 6.22950 MINI EXTERN> -36.86819 17.80568 0.00000 0.00000 0.00000 MINI CONSTR> 130.59792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 186.99148 0.00669 0.09290 0.00007 MINI INTERN> 6.37944 35.01378 0.00000 27.82625 6.22998 MINI EXTERN> -36.87810 17.80344 0.00000 0.00000 0.00000 MINI CONSTR> 130.61669 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 186.98587 0.00561 0.05125 0.00007 MINI INTERN> 6.38407 34.99866 0.00000 27.82239 6.22719 MINI EXTERN> -36.88159 17.80615 0.00000 0.00000 0.00000 MINI CONSTR> 130.62901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 186.97996 0.00591 0.10954 0.00008 MINI INTERN> 6.37595 34.99994 0.00000 27.81555 6.22830 MINI EXTERN> -36.89187 17.80344 0.00000 0.00000 0.00000 MINI CONSTR> 130.64865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 186.97398 0.00598 0.06547 0.00008 MINI INTERN> 6.37827 34.98610 0.00000 27.81125 6.22582 MINI EXTERN> -36.89630 17.80593 0.00000 0.00000 0.00000 MINI CONSTR> 130.66290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 186.96965 0.00433 0.12222 0.00008 MINI INTERN> 6.37251 34.98829 0.00000 27.80586 6.22637 MINI EXTERN> -36.90375 17.80088 0.00000 0.00000 0.00000 MINI CONSTR> 130.67947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 186.96551 0.00414 0.13416 0.00009 MINI INTERN> 6.36780 34.98012 0.00000 27.80159 6.22583 MINI EXTERN> -36.91018 17.80667 0.00000 0.00000 0.00000 MINI CONSTR> 130.69368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 186.96140 0.00411 0.12772 0.00009 MINI INTERN> 6.37597 34.97127 0.00000 27.79703 6.22466 MINI EXTERN> -36.91562 17.80194 0.00000 0.00000 0.00000 MINI CONSTR> 130.70614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 186.95638 0.00502 0.04330 0.00004 MINI INTERN> 6.38888 34.94564 0.00000 27.79387 6.22054 MINI EXTERN> -36.91838 17.80894 0.00000 0.00000 0.00000 MINI CONSTR> 130.71688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 186.95422 0.00215 0.13717 0.00010 MINI INTERN> 6.37583 34.95690 0.00000 27.78901 6.22337 MINI EXTERN> -36.92687 17.80410 0.00000 0.00000 0.00000 MINI CONSTR> 130.73189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 186.94899 0.00523 0.04310 0.00004 MINI INTERN> 6.38965 34.93102 0.00000 27.78595 6.21891 MINI EXTERN> -36.92925 17.80964 0.00000 0.00000 0.00000 MINI CONSTR> 130.74307 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 186.94763 0.00136 0.14610 0.00010 MINI INTERN> 6.37261 34.94493 0.00000 27.78178 6.22201 MINI EXTERN> -36.93690 17.80585 0.00000 0.00000 0.00000 MINI CONSTR> 130.75735 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 186.94448 0.00315 0.15633 0.00011 MINI INTERN> 6.36886 34.94345 0.00000 27.77840 6.22138 MINI EXTERN> -36.94110 17.80272 0.00000 0.00000 0.00000 MINI CONSTR> 130.77077 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 186.93941 0.00507 0.05518 0.00005 MINI INTERN> 6.39483 34.90639 0.00000 27.77484 6.21628 MINI EXTERN> -36.94503 17.81127 0.00000 0.00000 0.00000 MINI CONSTR> 130.78083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 186.93693 0.00248 0.03406 0.00005 MINI INTERN> 6.38740 34.90802 0.00000 27.77243 6.21665 MINI EXTERN> -36.94887 17.81049 0.00000 0.00000 0.00000 MINI CONSTR> 130.79080 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 186.93412 0.00281 0.06794 0.00005 MINI INTERN> 6.40045 34.89017 0.00000 27.76810 6.21468 MINI EXTERN> -36.95499 17.81159 0.00000 0.00000 0.00000 MINI CONSTR> 130.80412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 186.93173 0.00239 0.05567 0.00005 MINI INTERN> 6.39377 34.88875 0.00000 27.76582 6.21466 MINI EXTERN> -36.95887 17.81315 0.00000 0.00000 0.00000 MINI CONSTR> 130.81446 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 186.92982 0.00191 0.07576 0.00005 MINI INTERN> 6.39969 34.87988 0.00000 27.76295 6.21362 MINI EXTERN> -36.96304 17.81230 0.00000 0.00000 0.00000 MINI CONSTR> 130.82441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 186.92780 0.00202 0.08772 0.00005 MINI INTERN> 6.39652 34.87360 0.00000 27.76046 6.21323 MINI EXTERN> -36.96757 17.81642 0.00000 0.00000 0.00000 MINI CONSTR> 130.83514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 186.92600 0.00180 0.09106 0.00006 MINI INTERN> 6.39616 34.86943 0.00000 27.75829 6.21275 MINI EXTERN> -36.97109 17.81606 0.00000 0.00000 0.00000 MINI CONSTR> 130.84440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 186.92417 0.00183 0.08440 0.00006 MINI INTERN> 6.39822 34.86662 0.00000 27.75600 6.21237 MINI EXTERN> -36.97446 17.81224 0.00000 0.00000 0.00000 MINI CONSTR> 130.85317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 186.92189 0.00228 0.02866 0.00003 MINI INTERN> 6.38225 34.87520 0.00000 27.75442 6.21377 MINI EXTERN> -36.97774 17.81135 0.00000 0.00000 0.00000 MINI CONSTR> 130.86265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 186.92092 0.00097 0.09339 0.00006 MINI INTERN> 6.39914 34.85711 0.00000 27.75170 6.21156 MINI EXTERN> -36.98191 17.81196 0.00000 0.00000 0.00000 MINI CONSTR> 130.87136 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 186.91868 0.00224 0.03002 0.00003 MINI INTERN> 6.38192 34.86641 0.00000 27.75034 6.21310 MINI EXTERN> -36.98498 17.81147 0.00000 0.00000 0.00000 MINI CONSTR> 130.88042 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 186.91818 0.00049 0.10821 0.00007 MINI INTERN> 6.38912 34.85069 0.00000 27.74862 6.21136 MINI EXTERN> -36.98864 17.81855 0.00000 0.00000 0.00000 MINI CONSTR> 130.88848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 186.91583 0.00236 0.03238 0.00003 MINI INTERN> 6.38169 34.85781 0.00000 27.74667 6.21251 MINI EXTERN> -36.99187 17.81189 0.00000 0.00000 0.00000 MINI CONSTR> 130.89713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 186.91459 0.00124 0.02493 0.00003 MINI INTERN> 6.38327 34.85207 0.00000 27.74513 6.21201 MINI EXTERN> -36.99490 17.81276 0.00000 0.00000 0.00000 MINI CONSTR> 130.90424 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11168 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 186.91323 0.00136 0.04085 0.00003 MINI INTERN> 6.38044 34.85037 0.00000 27.74332 6.21208 MINI EXTERN> -36.99857 17.81207 0.00000 0.00000 0.00000 MINI CONSTR> 130.91352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 186.91209 0.00114 0.02367 0.00003 MINI INTERN> 6.38342 34.84362 0.00000 27.74198 6.21145 MINI EXTERN> -37.00136 17.81317 0.00000 0.00000 0.00000 MINI CONSTR> 130.91982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11167 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 186.91092 0.00118 0.04908 0.00003 MINI INTERN> 6.37896 34.84262 0.00000 27.74038 6.21167 MINI EXTERN> -37.00495 17.81326 0.00000 0.00000 0.00000 MINI CONSTR> 130.92897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 186.90977 0.00115 0.03808 0.00004 MINI INTERN> 6.38233 34.83725 0.00000 27.73891 6.21121 MINI EXTERN> -37.00794 17.81223 0.00000 0.00000 0.00000 MINI CONSTR> 130.93579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11165 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 186.90886 0.00091 0.05229 0.00004 MINI INTERN> 6.38020 34.83466 0.00000 27.73766 6.21123 MINI EXTERN> -37.01097 17.81305 0.00000 0.00000 0.00000 MINI CONSTR> 130.94303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 186.90776 0.00110 0.05283 0.00004 MINI INTERN> 6.38011 34.83122 0.00000 27.73636 6.21101 MINI EXTERN> -37.01402 17.81241 0.00000 0.00000 0.00000 MINI CONSTR> 130.95066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11165 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 186.90688 0.00087 0.06722 0.00004 MINI INTERN> 6.37669 34.82696 0.00000 27.73543 6.21086 MINI EXTERN> -37.01706 17.81601 0.00000 0.00000 0.00000 MINI CONSTR> 130.95800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 186.90600 0.00088 0.06178 0.00004 MINI INTERN> 6.37814 34.82307 0.00000 27.73433 6.21066 MINI EXTERN> -37.01972 17.81560 0.00000 0.00000 0.00000 MINI CONSTR> 130.96393 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11165 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 186.90513 0.00088 0.06018 0.00004 MINI INTERN> 6.38179 34.81993 0.00000 27.73305 6.21045 MINI EXTERN> -37.02246 17.81219 0.00000 0.00000 0.00000 MINI CONSTR> 130.97017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 186.90405 0.00108 0.02011 0.00002 MINI INTERN> 6.38576 34.81138 0.00000 27.73224 6.20966 MINI EXTERN> -37.02514 17.81471 0.00000 0.00000 0.00000 MINI CONSTR> 130.97545 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11165 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 186.90361 0.00044 0.06799 0.00005 MINI INTERN> 6.38251 34.81303 0.00000 27.73116 6.21020 MINI EXTERN> -37.02781 17.81218 0.00000 0.00000 0.00000 MINI CONSTR> 130.98234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 186.90295 0.00067 0.07950 0.00005 MINI INTERN> 6.37823 34.80769 0.00000 27.73074 6.21001 MINI EXTERN> -37.03053 17.81836 0.00000 0.00000 0.00000 MINI CONSTR> 130.98844 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11165 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 186.90173 0.00122 0.02193 0.00002 MINI INTERN> 6.38601 34.80108 0.00000 27.72976 6.20927 MINI EXTERN> -37.03302 17.81526 0.00000 0.00000 0.00000 MINI CONSTR> 130.99337 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> 500 186.90173 0.00122 0.02193 0.00002 STPD INTERN> 6.38601 34.80108 0.00000 27.72976 6.20927 STPD EXTERN> -37.03302 17.81526 0.00000 0.00000 0.00000 STPD CONSTR> 130.99337 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 11165 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11165 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 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> 0 186.90173 0.00122 0.02193 0.00000 MINI INTERN> 6.38601 34.80108 0.00000 27.72976 6.20927 MINI EXTERN> -37.03302 17.81526 0.00000 0.00000 0.00000 MINI CONSTR> 130.99337 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 186.88122 0.02051 0.05281 0.00072 MINI INTERN> 6.37309 34.61448 0.00000 27.70792 6.20842 MINI EXTERN> -37.19040 17.83173 0.00000 0.00000 0.00000 MINI CONSTR> 131.33597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 186.86544 0.01578 0.10215 0.03160 MINI INTERN> 6.41664 34.54958 0.00000 27.73041 6.22693 MINI EXTERN> -37.15701 17.80297 0.00000 0.00000 0.00000 MINI CONSTR> 131.29593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 186.85488 0.01056 0.04806 0.00900 MINI INTERN> 6.37851 34.33269 0.00000 27.84845 6.27557 MINI EXTERN> -37.33751 17.90191 0.00000 0.00000 0.00000 MINI CONSTR> 131.45527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 186.85328 0.00160 0.02565 0.00261 MINI INTERN> 6.36230 34.33292 0.00000 27.87632 6.27244 MINI EXTERN> -37.48982 17.93667 0.00000 0.00000 0.00000 MINI CONSTR> 131.56245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 186.85144 0.00184 0.03950 0.00523 MINI INTERN> 6.35696 34.31560 0.00000 27.91364 6.27024 MINI EXTERN> -37.63463 17.96816 0.00000 0.00000 0.00000 MINI CONSTR> 131.66147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 186.84940 0.00205 0.02656 0.00415 MINI INTERN> 6.36395 34.32038 0.00000 27.91188 6.26168 MINI EXTERN> -37.61160 17.95479 0.00000 0.00000 0.00000 MINI CONSTR> 131.64832 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 186.84870 0.00070 0.01687 0.00205 MINI INTERN> 6.37335 34.31474 0.00000 27.89955 6.26129 MINI EXTERN> -37.54400 17.94457 0.00000 0.00000 0.00000 MINI CONSTR> 131.59920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 186.84827 0.00042 0.01714 0.00161 MINI INTERN> 6.37266 34.31363 0.00000 27.89497 6.26325 MINI EXTERN> -37.53535 17.95360 0.00000 0.00000 0.00000 MINI CONSTR> 131.58551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 186.84788 0.00040 0.01356 0.00192 MINI INTERN> 6.37250 34.30957 0.00000 27.89830 6.26533 MINI EXTERN> -37.57990 17.97539 0.00000 0.00000 0.00000 MINI CONSTR> 131.60668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 186.84764 0.00024 0.01030 0.00103 MINI INTERN> 6.36793 34.30702 0.00000 27.89806 6.26723 MINI EXTERN> -37.59437 17.98408 0.00000 0.00000 0.00000 MINI CONSTR> 131.61769 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> 52 186.84757 0.00007 0.00892 0.02000 CONJ INTERN> 6.36578 34.30782 0.00000 27.89394 6.26842 CONJ EXTERN> -37.59040 17.98564 0.00000 0.00000 0.00000 CONJ CONSTR> 131.61637 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "6000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 2.6925 ( PROT LYS 1 HT2 ) 2.6925 ( PROT LYS 1 N ) 3.3657 ( PROT LYS 1 HT3 ) 2.6925 ( PROT LYS 1 CA ) 3.3657 ( PROT LYS 1 CB ) 2.6925 ( PROT LYS 1 CG ) 2.6925 ( PROT LYS 1 CD ) 2.6925 ( PROT LYS 1 CE ) 2.6925 ( PROT LYS 1 NZ ) 2.6925 ( PROT LYS 1 HZ1 ) 2.6925 ( PROT LYS 1 HZ2 ) 2.6925 ( PROT LYS 1 HZ3 ) 2.6925 ( PROT LYS 1 C ) 3.3657 ( PROT LYS 1 O ) 3.3657 ( PROT MET 2 N ) 3.3657 ( PROT MET 2 H ) 2.6925 ( PROT MET 2 CA ) 3.3657 ( PROT MET 2 CB ) 2.6925 ( PROT MET 2 CG ) 2.6925 ( PROT MET 2 SD ) 2.6925 ( PROT MET 2 CE ) 2.6925 ( PROT MET 2 C ) 3.3657 ( PROT MET 2 O ) 3.3657 ( PROT LYS 3 N ) 3.3657 ( PROT LYS 3 H ) 2.6925 ( PROT LYS 3 CA ) 3.3657 ( PROT LYS 3 CB ) 2.6925 ( PROT LYS 3 CG ) 2.6925 ( PROT LYS 3 CD ) 2.6925 ( PROT LYS 3 CE ) 2.6925 ( PROT LYS 3 NZ ) 2.6925 ( PROT LYS 3 HZ1 ) 2.6925 ( PROT LYS 3 HZ2 ) 2.6925 ( PROT LYS 3 HZ3 ) 2.6925 ( PROT LYS 3 C ) 3.3657 ( PROT LYS 3 O ) 3.3657 ( PROT ALA 4 N ) 3.3657 ( PROT ALA 4 H ) 2.6925 ( PROT ALA 4 CA ) 3.3657 ( PROT ALA 4 CB ) 2.6925 ( PROT ALA 4 C ) 3.3657 ( PROT ALA 4 O ) 3.3657 ( PROT VAL 5 N ) 3.3657 ( PROT VAL 5 H ) 2.6925 ( PROT VAL 5 CA ) 3.3657 ( PROT VAL 5 CB ) 2.6925 ( PROT VAL 5 CG1 ) 2.6925 ( PROT VAL 5 CG2 ) 2.6925 ( PROT VAL 5 C ) 3.3657 ( PROT VAL 5 O ) 3.3657 ( PROT MET 6 N ) 3.3657 ( PROT MET 6 H ) 2.6925 ( PROT MET 6 CA ) 3.3657 ( PROT MET 6 CB ) 2.6925 ( PROT MET 6 CG ) 2.6925 ( PROT MET 6 SD ) 2.6925 ( PROT MET 6 CE ) 2.6925 ( PROT MET 6 C ) 3.3657 ( PROT MET 6 O ) 3.3657 ( PROT ILE 7 N ) 3.3657 ( PROT ILE 7 H ) 2.6925 ( PROT ILE 7 CA ) 3.3657 ( PROT ILE 7 CB ) 2.6925 ( PROT ILE 7 CG2 ) 2.6925 ( PROT ILE 7 CG1 ) 2.6925 ( PROT ILE 7 CD ) 2.6925 ( PROT ILE 7 C ) 3.3657 ( PROT ILE 7 O ) 3.3657 ( PROT GLY 8 N ) 3.3657 ( PROT GLY 8 H ) 2.6925 ( PROT GLY 8 CA ) 3.3657 ( PROT GLY 8 C ) 3.3657 ( PROT GLY 8 O ) 3.3657 ( PROT ALA 9 N ) 3.3657 ( PROT ALA 9 H ) 2.6925 ( PROT ALA 9 CA ) 3.3657 ( PROT ALA 9 CB ) 2.6925 ( PROT ALA 9 C ) 3.3657 ( PROT ALA 9 O ) 3.3657 ( PROT CYS 10 N ) 3.3657 ( PROT CYS 10 H ) 2.6925 ( PROT CYS 10 CA ) 3.3657 ( PROT CYS 10 CB ) 2.6925 ( PROT CYS 10 SG ) 2.6925 ( PROT CYS 10 C ) 3.3657 ( PROT CYS 10 O ) 3.3657 ( PROT PHE 11 N ) 3.3657 ( PROT PHE 11 H ) 2.6925 ( PROT PHE 11 CA ) 3.3657 ( PROT PHE 11 CB ) 2.6925 ( PROT PHE 11 CG ) 2.6925 ( PROT PHE 11 CD1 ) 2.6925 ( PROT PHE 11 CD2 ) 2.6925 ( PROT PHE 11 CE1 ) 2.6925 ( PROT PHE 11 CE2 ) 2.6925 ( PROT PHE 11 CZ ) 2.6925 ( PROT PHE 11 C ) 3.3657 ( PROT PHE 11 O ) 3.3657 ( PROT LEU 12 N ) 3.3657 ( PROT LEU 12 H ) 2.6925 ( PROT LEU 12 CA ) 3.3657 ( PROT LEU 12 CB ) 2.6925 ( PROT LEU 12 CG ) 2.6925 ( PROT LEU 12 CD1 ) 2.6925 ( PROT LEU 12 CD2 ) 2.6925 ( PROT LEU 12 C ) 3.3657 ( PROT LEU 12 O ) 3.3657 ( PROT ILE 13 N ) 3.3657 ( PROT ILE 13 H ) 2.6925 ( PROT ILE 13 CA ) 3.3657 ( PROT ILE 13 CB ) 2.6925 ( PROT ILE 13 CG2 ) 2.6925 ( PROT ILE 13 CG1 ) 2.6925 ( PROT ILE 13 CD ) 2.6925 ( PROT ILE 13 C ) 3.3657 ( PROT ILE 13 O ) 3.3657 ( PROT ASP 14 N ) 3.3657 ( PROT ASP 14 H ) 2.6925 ( PROT ASP 14 CA ) 3.3657 ( PROT ASP 14 CB ) 2.6925 ( PROT ASP 14 CG ) 2.6925 ( PROT ASP 14 OD1 ) 2.6925 ( PROT ASP 14 OD2 ) 2.6925 ( PROT ASP 14 C ) 3.3657 ( PROT ASP 14 O ) 3.3657 ( PROT PHE 15 N ) 3.3657 ( PROT PHE 15 H ) 2.6925 ( PROT PHE 15 CA ) 3.3657 ( PROT PHE 15 CB ) 2.6925 ( PROT PHE 15 CG ) 2.6925 ( PROT PHE 15 CD1 ) 2.6925 ( PROT PHE 15 CD2 ) 2.6925 ( PROT PHE 15 CE1 ) 2.6925 ( PROT PHE 15 CE2 ) 2.6925 ( PROT PHE 15 CZ ) 2.6925 ( PROT PHE 15 C ) 3.3657 ( PROT PHE 15 O ) 3.3657 ( PROT MET 16 N ) 3.3657 ( PROT MET 16 H ) 2.6925 ( PROT MET 16 CA ) 3.3657 ( PROT MET 16 CB ) 2.6925 ( PROT MET 16 CG ) 2.6925 ( PROT MET 16 SD ) 2.6925 ( PROT MET 16 CE ) 2.6925 ( PROT MET 16 C ) 3.3657 ( PROT MET 16 O ) 3.3657 ( PROT PHE 17 N ) 3.3657 ( PROT PHE 17 H ) 2.6925 ( PROT PHE 17 CA ) 3.3657 ( PROT PHE 17 CB ) 2.6925 ( PROT PHE 17 CG ) 2.6925 ( PROT PHE 17 CD1 ) 2.6925 ( PROT PHE 17 CD2 ) 2.6925 ( PROT PHE 17 CE1 ) 2.6925 ( PROT PHE 17 CE2 ) 2.6925 ( PROT PHE 17 CZ ) 2.6925 ( PROT PHE 17 C ) 3.3657 ( PROT PHE 17 O ) 3.3657 ( PROT PHE 18 N ) 3.3657 ( PROT PHE 18 H ) 2.6925 ( PROT PHE 18 CA ) 3.3657 ( PROT PHE 18 CB ) 2.6925 ( PROT PHE 18 CG ) 2.6925 ( PROT PHE 18 CD1 ) 2.6925 ( PROT PHE 18 CD2 ) 2.6925 ( PROT PHE 18 CE1 ) 2.6925 ( PROT PHE 18 CE2 ) 2.6925 ( PROT PHE 18 CZ ) 2.6925 ( PROT PHE 18 C ) 3.3657 ( PROT PHE 18 O ) 3.3657 ( PROT GLU 19 N ) 3.3657 ( PROT GLU 19 H ) 2.6925 ( PROT GLU 19 CA ) 3.3657 ( PROT GLU 19 CB ) 2.6925 ( PROT GLU 19 CG ) 2.6925 ( PROT GLU 19 CD ) 2.6925 ( PROT GLU 19 OE1 ) 2.6925 ( PROT GLU 19 OE2 ) 2.6925 ( PROT GLU 19 C ) 3.3657 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41060 5.26150 -8.67065 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00044 -0.00159 -0.00104 ROTATION MATRIX 1.000000 -0.000187 -0.000009 0.000187 1.000000 0.000247 0.000009 -0.000247 1.000000 AXIS OF ROTATION IS 0.798009 0.029426 -0.601927 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 29.0952 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.399830 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.3998" Parameter: A <- "0.3998" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70584 5.22056 -8.77914 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00900 0.04386 -0.01523 ROTATION MATRIX 0.999778 0.016726 0.012804 -0.016529 0.999746 -0.015330 -0.013057 0.015115 0.999801 AXIS OF ROTATION IS -0.585731 -0.497559 0.639807 ANGLE IS 1.49 CENTER OF ROTATION 8.922230 5.120913 -9.602800 SHIFT IS -0.036842 TOTAL SQUARE DIFF IS 0.9189 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.219911 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.3998" RDCMND substituted energy or value "?RMS" to " 0.2199" Parameter: A <- "0.3998 0.2199" 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 0.3998 0.2199 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 " 131.62" Parameter: H <- "131.62" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 55.23120 131.61637 2.10108 ENER INTERN> 6.36578 34.30782 0.00000 27.89394 6.26842 ENER EXTERN> -37.59040 17.98564 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " 55.23" Parameter: B <- "55.23" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 17.99" Parameter: C <- "17.99" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -37.59" Parameter: C <- " -19.60" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -19.60" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 6.37" Parameter: D <- "6.37" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 34.31" Parameter: D <- " 40.68" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 27.89" Parameter: D <- " 68.57" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 6.27" Parameter: D <- " 74.84" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 74.84" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 6000 ENER= 55.23 GRMS= 2.10 ELEC= 17.99 VDW= -37.59 RDTITL> *EXTERNAL= -19.60 INTERNAL= 74.84 USER= 0.00 HARM= 131.62 RDTITL> *BOND= 6.37 ANGL= 34.31 DIHE= 27.89 IMPR= 6.27 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 55.23 GRMS= 2.10 ELEC= 17.99 VDW= -37.59 RDTITL> *EXTERNAL= -19.60 INTERNAL= 74.84 USER= 0.00 HARM= 131.62 RDTITL> *BOND= 6.37 ANGL= 34.31 DIHE= 27.89 IMPR= 6.27 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= 55.23 GRMS= 2.10 ELEC= 17.99 VDW= -37.59 RDTITL> *EXTERNAL= -19.60 INTERNAL= 74.84 USER= 0.00 HARM= 131.62 RDTITL> *BOND= 6.37 ANGL= 34.31 DIHE= 27.89 IMPR= 6.27 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 6000 0.3998 0.2199 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "6000" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11165 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11166 ATOM PAIRS WERE FOUND FOR ATOM LIST 335 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> 0 147.47333 -92.24213 0.82381 0.02000 MINI INTERN> 6.36578 34.30782 0.00000 27.89394 6.26842 MINI EXTERN> -37.59040 17.98564 0.00000 0.00000 0.00000 MINI CONSTR> 92.24213 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 164.35476 -16.88143 15.01972 0.00864 MINI INTERN> 27.00819 31.35282 0.00000 30.26494 5.53786 MINI EXTERN> -48.43384 20.71244 0.00000 0.00000 0.00000 MINI CONSTR> 97.91236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11153 ATOM PAIRS WERE FOUND FOR ATOM LIST 338 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 147.47231 16.88245 6.78832 0.00373 MINI INTERN> 8.41069 36.03434 0.00000 29.09884 6.68205 MINI EXTERN> -50.31777 18.80984 0.00000 0.00000 0.00000 MINI CONSTR> 98.75431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 142.96868 4.50363 0.45080 0.00067 MINI INTERN> 6.13310 33.45676 0.00000 29.52338 6.27489 MINI EXTERN> -50.76713 19.52455 0.00000 0.00000 0.00000 MINI CONSTR> 98.82314 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11146 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 142.62902 0.33966 1.04492 0.00070 MINI INTERN> 6.43286 33.24790 0.00000 29.49370 6.29426 MINI EXTERN> -51.48298 19.51456 0.00000 0.00000 0.00000 MINI CONSTR> 99.12873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 142.29247 0.33655 1.11095 0.00072 MINI INTERN> 6.59317 32.97172 0.00000 29.50807 6.26734 MINI EXTERN> -51.95689 19.56315 0.00000 0.00000 0.00000 MINI CONSTR> 99.34591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11145 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 141.98391 0.30856 1.06497 0.00075 MINI INTERN> 6.50290 32.88523 0.00000 29.51253 6.24636 MINI EXTERN> -52.24405 19.56038 0.00000 0.00000 0.00000 MINI CONSTR> 99.52057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 141.68529 0.29862 1.11689 0.00078 MINI INTERN> 6.48905 32.76516 0.00000 29.50499 6.22843 MINI EXTERN> -52.55904 19.56579 0.00000 0.00000 0.00000 MINI CONSTR> 99.69091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11143 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 141.39331 0.29198 1.12953 0.00080 MINI INTERN> 6.44338 32.66748 0.00000 29.49477 6.20742 MINI EXTERN> -52.82500 19.56374 0.00000 0.00000 0.00000 MINI CONSTR> 99.84151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 141.03556 0.35775 0.36361 0.00035 MINI INTERN> 5.89160 32.65713 0.00000 29.58171 6.10183 MINI EXTERN> -52.73337 19.59612 0.00000 0.00000 0.00000 MINI CONSTR> 99.94053 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11141 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 140.93759 0.09797 1.25179 0.00087 MINI INTERN> 6.51104 32.42735 0.00000 29.44247 6.18225 MINI EXTERN> -53.27287 19.57660 0.00000 0.00000 0.00000 MINI CONSTR> 100.07075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 140.55329 0.38430 0.37822 0.00037 MINI INTERN> 5.85988 32.44550 0.00000 29.53480 6.06411 MINI EXTERN> -53.12086 19.61313 0.00000 0.00000 0.00000 MINI CONSTR> 100.15672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11141 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 140.36444 0.18885 0.32145 0.00039 MINI INTERN> 5.85267 32.37921 0.00000 29.50607 6.05596 MINI EXTERN> -53.27529 19.61034 0.00000 0.00000 0.00000 MINI CONSTR> 100.23548 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 140.16003 0.20441 0.51798 0.00040 MINI INTERN> 5.78133 32.29094 0.00000 29.49365 6.02071 MINI EXTERN> -53.37820 19.62885 0.00000 0.00000 0.00000 MINI CONSTR> 100.32275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11141 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 139.97460 0.18542 0.42447 0.00042 MINI INTERN> 5.80158 32.21792 0.00000 29.45453 6.01668 MINI EXTERN> -53.52939 19.61904 0.00000 0.00000 0.00000 MINI CONSTR> 100.39425 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 139.80875 0.16585 0.48757 0.00043 MINI INTERN> 5.73973 32.16933 0.00000 29.43427 5.99642 MINI EXTERN> -53.61783 19.62620 0.00000 0.00000 0.00000 MINI CONSTR> 100.46062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11138 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 139.66303 0.14572 0.65684 0.00045 MINI INTERN> 5.66472 32.12562 0.00000 29.41882 5.97145 MINI EXTERN> -53.68245 19.64192 0.00000 0.00000 0.00000 MINI CONSTR> 100.52296 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 139.51264 0.15039 0.73281 0.00046 MINI INTERN> 5.70022 32.05405 0.00000 29.38154 5.96049 MINI EXTERN> -53.79183 19.62491 0.00000 0.00000 0.00000 MINI CONSTR> 100.58326 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11136 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 139.37523 0.13742 0.75051 0.00048 MINI INTERN> 5.61061 32.03381 0.00000 29.36334 5.94258 MINI EXTERN> -53.84831 19.63596 0.00000 0.00000 0.00000 MINI CONSTR> 100.63723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 139.23779 0.13744 0.71791 0.00050 MINI INTERN> 5.57550 31.98689 0.00000 29.33256 5.93495 MINI EXTERN> -53.93238 19.65062 0.00000 0.00000 0.00000 MINI CONSTR> 100.68964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11136 ATOM PAIRS WERE FOUND FOR ATOM LIST 337 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 139.10843 0.12936 0.78445 0.00052 MINI INTERN> 5.65445 31.90931 0.00000 29.28697 5.93085 MINI EXTERN> -54.04157 19.62637 0.00000 0.00000 0.00000 MINI CONSTR> 100.74205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 138.94603 0.16241 0.24106 0.00022 MINI INTERN> 5.80662 31.77948 0.00000 29.20743 5.96603 MINI EXTERN> -54.24931 19.64122 0.00000 0.00000 0.00000 MINI CONSTR> 100.79456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11135 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 138.88062 0.06541 0.81750 0.00056 MINI INTERN> 5.49331 31.87138 0.00000 29.24822 5.89969 MINI EXTERN> -54.12332 19.65624 0.00000 0.00000 0.00000 MINI CONSTR> 100.83511 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 138.76944 0.11118 0.88739 0.00058 MINI INTERN> 5.57836 31.79207 0.00000 29.20259 5.89589 MINI EXTERN> -54.22007 19.63761 0.00000 0.00000 0.00000 MINI CONSTR> 100.88300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11134 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 138.59866 0.17078 0.28125 0.00025 MINI INTERN> 5.81919 31.61682 0.00000 29.10100 5.94544 MINI EXTERN> -54.47197 19.65054 0.00000 0.00000 0.00000 MINI CONSTR> 100.93764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 138.50596 0.09270 0.20919 0.00026 MINI INTERN> 5.76565 31.59191 0.00000 29.08414 5.92990 MINI EXTERN> -54.49461 19.65536 0.00000 0.00000 0.00000 MINI CONSTR> 100.97362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11134 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 138.47700 0.02897 0.94806 0.00064 MINI INTERN> 5.44859 31.70180 0.00000 29.12845 5.86065 MINI EXTERN> -54.34988 19.67470 0.00000 0.00000 0.00000 MINI CONSTR> 101.01270 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 138.30224 0.17475 0.35977 0.00028 MINI INTERN> 5.83434 31.47475 0.00000 28.99733 5.92846 MINI EXTERN> -54.66218 19.65938 0.00000 0.00000 0.00000 MINI CONSTR> 101.07017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11134 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 138.21197 0.09027 0.25987 0.00029 MINI INTERN> 5.78287 31.45129 0.00000 28.97829 5.91351 MINI EXTERN> -54.68202 19.66096 0.00000 0.00000 0.00000 MINI CONSTR> 101.10707 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 138.12931 0.08266 0.31990 0.00030 MINI INTERN> 5.79964 31.40224 0.00000 28.94272 5.91126 MINI EXTERN> -54.74547 19.66998 0.00000 0.00000 0.00000 MINI CONSTR> 101.14894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11132 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 138.06256 0.06675 0.44857 0.00031 MINI INTERN> 5.86773 31.34543 0.00000 28.90157 5.91439 MINI EXTERN> -54.81975 19.66498 0.00000 0.00000 0.00000 MINI CONSTR> 101.18821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 137.98584 0.07672 0.47503 0.00032 MINI INTERN> 5.84050 31.31620 0.00000 28.87447 5.90769 MINI EXTERN> -54.86007 19.67883 0.00000 0.00000 0.00000 MINI CONSTR> 101.22822 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11131 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 137.92162 0.06422 0.53002 0.00033 MINI INTERN> 5.88760 31.27181 0.00000 28.84056 5.90495 MINI EXTERN> -54.91087 19.66278 0.00000 0.00000 0.00000 MINI CONSTR> 101.26478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 137.85662 0.06500 0.49668 0.00034 MINI INTERN> 5.87345 31.23347 0.00000 28.81649 5.89948 MINI EXTERN> -54.94666 19.68199 0.00000 0.00000 0.00000 MINI CONSTR> 101.29839 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11132 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 137.79438 0.06224 0.54574 0.00036 MINI INTERN> 5.86867 31.21624 0.00000 28.79317 5.88963 MINI EXTERN> -54.96819 19.66138 0.00000 0.00000 0.00000 MINI CONSTR> 101.33348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 137.71613 0.07825 0.16672 0.00015 MINI INTERN> 5.67923 31.23891 0.00000 28.80510 5.85925 MINI EXTERN> -54.91390 19.68848 0.00000 0.00000 0.00000 MINI CONSTR> 101.35907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11130 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 137.68437 0.03176 0.56212 0.00038 MINI INTERN> 5.90907 31.12681 0.00000 28.73361 5.88817 MINI EXTERN> -55.06342 19.68791 0.00000 0.00000 0.00000 MINI CONSTR> 101.40221 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 137.62827 0.05610 0.58602 0.00040 MINI INTERN> 5.90243 31.10905 0.00000 28.70904 5.88179 MINI EXTERN> -55.08934 19.67761 0.00000 0.00000 0.00000 MINI CONSTR> 101.43768 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11130 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 137.54596 0.08231 0.19245 0.00017 MINI INTERN> 5.65467 31.15735 0.00000 28.73226 5.84124 MINI EXTERN> -55.00175 19.69854 0.00000 0.00000 0.00000 MINI CONSTR> 101.46365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 137.50121 0.04475 0.14597 0.00018 MINI INTERN> 5.67192 31.12851 0.00000 28.70640 5.84224 MINI EXTERN> -55.04110 19.70016 0.00000 0.00000 0.00000 MINI CONSTR> 101.49310 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11130 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 137.45178 0.04943 0.14956 0.00019 MINI INTERN> 5.66557 31.10447 0.00000 28.68333 5.83694 MINI EXTERN> -55.06713 19.70192 0.00000 0.00000 0.00000 MINI CONSTR> 101.52669 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 137.40668 0.04511 0.25977 0.00019 MINI INTERN> 5.62308 31.09236 0.00000 28.66869 5.82413 MINI EXTERN> -55.07082 19.70900 0.00000 0.00000 0.00000 MINI CONSTR> 101.56023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11130 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 137.36690 0.03978 0.13637 0.00020 MINI INTERN> 5.66321 31.05834 0.00000 28.63967 5.83035 MINI EXTERN> -55.12011 19.70780 0.00000 0.00000 0.00000 MINI CONSTR> 101.58764 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 137.32364 0.04326 0.29876 0.00021 MINI INTERN> 5.61248 31.04734 0.00000 28.62630 5.81452 MINI EXTERN> -55.11711 19.71639 0.00000 0.00000 0.00000 MINI CONSTR> 101.62370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11128 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 137.28023 0.04341 0.18258 0.00021 MINI INTERN> 5.64526 31.01326 0.00000 28.59699 5.81815 MINI EXTERN> -55.16226 19.71400 0.00000 0.00000 0.00000 MINI CONSTR> 101.65485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 137.24871 0.03152 0.32476 0.00022 MINI INTERN> 5.60768 31.00152 0.00000 28.58445 5.80719 MINI EXTERN> -55.16444 19.72704 0.00000 0.00000 0.00000 MINI CONSTR> 101.68527 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11128 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 137.21716 0.03155 0.37535 0.00023 MINI INTERN> 5.62018 30.98498 0.00000 28.56462 5.80304 MINI EXTERN> -55.18415 19.71447 0.00000 0.00000 0.00000 MINI CONSTR> 101.71402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 137.18522 0.03194 0.33976 0.00024 MINI INTERN> 5.59275 30.97474 0.00000 28.54953 5.79978 MINI EXTERN> -55.19929 19.72714 0.00000 0.00000 0.00000 MINI CONSTR> 101.74057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11128 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 137.15346 0.03176 0.38882 0.00025 MINI INTERN> 5.59964 30.94747 0.00000 28.52877 5.79455 MINI EXTERN> -55.21984 19.73059 0.00000 0.00000 0.00000 MINI CONSTR> 101.77227 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 137.12437 0.02909 0.37077 0.00026 MINI INTERN> 5.59067 30.93474 0.00000 28.51179 5.79284 MINI EXTERN> -55.23926 19.73496 0.00000 0.00000 0.00000 MINI CONSTR> 101.79863 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11126 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 137.08338 0.04099 0.11315 0.00011 MINI INTERN> 5.65558 30.89499 0.00000 28.47399 5.80739 MINI EXTERN> -55.30752 19.72903 0.00000 0.00000 0.00000 MINI CONSTR> 101.82992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 137.07130 0.01208 0.42941 0.00028 MINI INTERN> 5.59370 30.89144 0.00000 28.47388 5.78925 MINI EXTERN> -55.28493 19.75244 0.00000 0.00000 0.00000 MINI CONSTR> 101.85551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11126 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 137.03141 0.03989 0.13033 0.00012 MINI INTERN> 5.65864 30.86078 0.00000 28.43801 5.80370 MINI EXTERN> -55.34734 19.73373 0.00000 0.00000 0.00000 MINI CONSTR> 101.88390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 137.00943 0.02198 0.10451 0.00012 MINI INTERN> 5.64976 30.84679 0.00000 28.42563 5.79946 MINI EXTERN> -55.35713 19.73855 0.00000 0.00000 0.00000 MINI CONSTR> 101.90638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11126 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 136.98656 0.02286 0.10745 0.00013 MINI INTERN> 5.65175 30.83044 0.00000 28.40902 5.79759 MINI EXTERN> -55.37496 19.74085 0.00000 0.00000 0.00000 MINI CONSTR> 101.93188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 136.96384 0.02273 0.17110 0.00013 MINI INTERN> 5.66694 30.81142 0.00000 28.38760 5.79853 MINI EXTERN> -55.40204 19.74059 0.00000 0.00000 0.00000 MINI CONSTR> 101.96079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11125 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 136.94291 0.02093 0.13750 0.00014 MINI INTERN> 5.65349 30.79886 0.00000 28.37561 5.79448 MINI EXTERN> -55.41135 19.74787 0.00000 0.00000 0.00000 MINI CONSTR> 101.98395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 136.92391 0.01900 0.15685 0.00014 MINI INTERN> 5.66265 30.78145 0.00000 28.35909 5.79359 MINI EXTERN> -55.43011 19.74905 0.00000 0.00000 0.00000 MINI CONSTR> 102.00818 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11125 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 136.90498 0.01893 0.16210 0.00015 MINI INTERN> 5.66584 30.76724 0.00000 28.34411 5.79144 MINI EXTERN> -55.44468 19.74886 0.00000 0.00000 0.00000 MINI CONSTR> 102.03217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 136.88954 0.01543 0.22075 0.00015 MINI INTERN> 5.67847 30.74827 0.00000 28.32712 5.79214 MINI EXTERN> -55.46662 19.75413 0.00000 0.00000 0.00000 MINI CONSTR> 102.05603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11124 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 136.87213 0.01741 0.24497 0.00016 MINI INTERN> 5.68077 30.73803 0.00000 28.31261 5.78954 MINI EXTERN> -55.47896 19.74974 0.00000 0.00000 0.00000 MINI CONSTR> 102.08040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 136.85693 0.01519 0.25549 0.00016 MINI INTERN> 5.68541 30.72001 0.00000 28.29782 5.78927 MINI EXTERN> -55.49706 19.75836 0.00000 0.00000 0.00000 MINI CONSTR> 102.10313 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11124 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 136.84148 0.01545 0.24277 0.00017 MINI INTERN> 5.68302 30.70816 0.00000 28.28591 5.78696 MINI EXTERN> -55.50785 19.76112 0.00000 0.00000 0.00000 MINI CONSTR> 102.12416 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 136.82593 0.01555 0.25540 0.00018 MINI INTERN> 5.67725 30.69860 0.00000 28.27247 5.78509 MINI EXTERN> -55.52021 19.76456 0.00000 0.00000 0.00000 MINI CONSTR> 102.14816 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11124 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 136.81063 0.01530 0.26365 0.00018 MINI INTERN> 5.67312 30.69161 0.00000 28.26005 5.78249 MINI EXTERN> -55.53055 19.76216 0.00000 0.00000 0.00000 MINI CONSTR> 102.17174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 136.79202 0.01861 0.08503 0.00008 MINI INTERN> 5.62627 30.68927 0.00000 28.25904 5.77194 MINI EXTERN> -55.51686 19.77337 0.00000 0.00000 0.00000 MINI CONSTR> 102.18899 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 136.78653 0.00549 0.28649 0.00020 MINI INTERN> 5.67282 30.66508 0.00000 28.23548 5.78026 MINI EXTERN> -55.55553 19.77554 0.00000 0.00000 0.00000 MINI CONSTR> 102.21289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 136.76646 0.02007 0.09273 0.00009 MINI INTERN> 5.62365 30.66737 0.00000 28.23559 5.76820 MINI EXTERN> -55.53861 19.77913 0.00000 0.00000 0.00000 MINI CONSTR> 102.23113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 136.75589 0.01057 0.07258 0.00009 MINI INTERN> 5.62442 30.65843 0.00000 28.22474 5.76800 MINI EXTERN> -55.55050 19.78176 0.00000 0.00000 0.00000 MINI CONSTR> 102.24904 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 136.74484 0.01106 0.07597 0.00009 MINI INTERN> 5.62183 30.64924 0.00000 28.21429 5.76617 MINI EXTERN> -55.55981 19.78453 0.00000 0.00000 0.00000 MINI CONSTR> 102.26859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 136.73419 0.01065 0.12745 0.00010 MINI INTERN> 5.61585 30.64040 0.00000 28.20467 5.76255 MINI EXTERN> -55.56584 19.78720 0.00000 0.00000 0.00000 MINI CONSTR> 102.28936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 136.72390 0.01029 0.09799 0.00010 MINI INTERN> 5.61567 30.63037 0.00000 28.19361 5.76251 MINI EXTERN> -55.57816 19.79208 0.00000 0.00000 0.00000 MINI CONSTR> 102.30781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11122 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 136.71484 0.00906 0.11701 0.00010 MINI INTERN> 5.61085 30.62351 0.00000 28.18472 5.76038 MINI EXTERN> -55.58509 19.79455 0.00000 0.00000 0.00000 MINI CONSTR> 102.32591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 136.70684 0.00800 0.15468 0.00011 MINI INTERN> 5.60849 30.61728 0.00000 28.17637 5.75788 MINI EXTERN> -55.59100 19.79438 0.00000 0.00000 0.00000 MINI CONSTR> 102.34344 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11122 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 136.69848 0.00836 0.17478 0.00011 MINI INTERN> 5.60162 30.60781 0.00000 28.16667 5.75692 MINI EXTERN> -55.60057 19.80410 0.00000 0.00000 0.00000 MINI CONSTR> 102.36193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 136.69076 0.00773 0.17820 0.00011 MINI INTERN> 5.59771 30.60284 0.00000 28.15876 5.75504 MINI EXTERN> -55.60657 19.80457 0.00000 0.00000 0.00000 MINI CONSTR> 102.37840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 136.68299 0.00777 0.17032 0.00012 MINI INTERN> 5.60328 30.59568 0.00000 28.14983 5.75401 MINI EXTERN> -55.61518 19.80096 0.00000 0.00000 0.00000 MINI CONSTR> 102.39441 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 136.67573 0.00725 0.18657 0.00012 MINI INTERN> 5.59602 30.58579 0.00000 28.14045 5.75381 MINI EXTERN> -55.62549 19.81330 0.00000 0.00000 0.00000 MINI CONSTR> 102.41184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 136.66653 0.00921 0.05794 0.00005 MINI INTERN> 5.62034 30.57133 0.00000 28.12782 5.75654 MINI EXTERN> -55.64375 19.80731 0.00000 0.00000 0.00000 MINI CONSTR> 102.42695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 136.66271 0.00382 0.19800 0.00013 MINI INTERN> 5.59895 30.57594 0.00000 28.12535 5.75026 MINI EXTERN> -55.63713 19.80679 0.00000 0.00000 0.00000 MINI CONSTR> 102.44255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 136.65698 0.00573 0.22750 0.00014 MINI INTERN> 5.58951 30.56533 0.00000 28.11638 5.75070 MINI EXTERN> -55.64800 19.82393 0.00000 0.00000 0.00000 MINI CONSTR> 102.45914 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 136.65077 0.00621 0.21762 0.00014 MINI INTERN> 5.58272 30.56368 0.00000 28.11064 5.74797 MINI EXTERN> -55.65016 19.82209 0.00000 0.00000 0.00000 MINI CONSTR> 102.47383 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 136.64076 0.01001 0.06818 0.00006 MINI INTERN> 5.62190 30.54029 0.00000 28.09452 5.75303 MINI EXTERN> -55.67630 19.81729 0.00000 0.00000 0.00000 MINI CONSTR> 102.49003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 136.63548 0.00528 0.05073 0.00006 MINI INTERN> 5.61615 30.53601 0.00000 28.08890 5.75142 MINI EXTERN> -55.68030 19.82034 0.00000 0.00000 0.00000 MINI CONSTR> 102.50297 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 136.62980 0.00568 0.05360 0.00007 MINI INTERN> 5.61726 30.52836 0.00000 28.08086 5.75070 MINI EXTERN> -55.68837 19.82275 0.00000 0.00000 0.00000 MINI CONSTR> 102.51823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 136.62441 0.00539 0.09129 0.00007 MINI INTERN> 5.62477 30.51805 0.00000 28.07102 5.75090 MINI EXTERN> -55.69981 19.82462 0.00000 0.00000 0.00000 MINI CONSTR> 102.53486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 136.61914 0.00527 0.06659 0.00007 MINI INTERN> 5.61710 30.51384 0.00000 28.06539 5.74927 MINI EXTERN> -55.70381 19.82899 0.00000 0.00000 0.00000 MINI CONSTR> 102.54836 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 136.61452 0.00462 0.08280 0.00007 MINI INTERN> 5.62126 30.50578 0.00000 28.05753 5.74898 MINI EXTERN> -55.71234 19.83073 0.00000 0.00000 0.00000 MINI CONSTR> 102.56257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 136.61047 0.00405 0.11059 0.00008 MINI INTERN> 5.62692 30.49788 0.00000 28.04979 5.74882 MINI EXTERN> -55.72092 19.83164 0.00000 0.00000 0.00000 MINI CONSTR> 102.57635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 136.60614 0.00433 0.12331 0.00008 MINI INTERN> 5.62059 30.49213 0.00000 28.04341 5.74796 MINI EXTERN> -55.72694 19.83861 0.00000 0.00000 0.00000 MINI CONSTR> 102.59038 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 136.60224 0.00390 0.12634 0.00008 MINI INTERN> 5.62614 30.48482 0.00000 28.03640 5.74764 MINI EXTERN> -55.73451 19.83870 0.00000 0.00000 0.00000 MINI CONSTR> 102.60303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 136.59830 0.00395 0.12090 0.00008 MINI INTERN> 5.62772 30.47975 0.00000 28.03057 5.74670 MINI EXTERN> -55.73983 19.83836 0.00000 0.00000 0.00000 MINI CONSTR> 102.61503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 136.59459 0.00371 0.13386 0.00009 MINI INTERN> 5.61740 30.47519 0.00000 28.02532 5.74568 MINI EXTERN> -55.74440 19.84742 0.00000 0.00000 0.00000 MINI CONSTR> 102.62797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 136.58988 0.00470 0.04112 0.00004 MINI INTERN> 5.60706 30.47642 0.00000 28.02309 5.74264 MINI EXTERN> -55.74257 19.84548 0.00000 0.00000 0.00000 MINI CONSTR> 102.63774 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 136.58794 0.00194 0.14023 0.00009 MINI INTERN> 5.63024 30.46253 0.00000 28.01258 5.74488 MINI EXTERN> -55.75791 19.84423 0.00000 0.00000 0.00000 MINI CONSTR> 102.65139 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 136.58502 0.00292 0.16290 0.00010 MINI INTERN> 5.61441 30.45919 0.00000 28.00850 5.74374 MINI EXTERN> -55.76105 19.85689 0.00000 0.00000 0.00000 MINI CONSTR> 102.66335 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11123 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 136.57982 0.00521 0.04482 0.00004 MINI INTERN> 5.60416 30.46128 0.00000 28.00651 5.74045 MINI EXTERN> -55.75860 19.85291 0.00000 0.00000 0.00000 MINI CONSTR> 102.67311 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 136.57700 0.00282 0.03760 0.00004 MINI INTERN> 5.60581 30.45610 0.00000 28.00132 5.74016 MINI EXTERN> -55.76421 19.85448 0.00000 0.00000 0.00000 MINI CONSTR> 102.68332 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11122 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 136.57410 0.00290 0.03850 0.00005 MINI INTERN> 5.60456 30.45157 0.00000 27.99633 5.73948 MINI EXTERN> -55.76906 19.85698 0.00000 0.00000 0.00000 MINI CONSTR> 102.69423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 136.57130 0.00280 0.03768 0.00005 MINI INTERN> 5.60383 30.44676 0.00000 27.99130 5.73893 MINI EXTERN> -55.77418 19.85964 0.00000 0.00000 0.00000 MINI CONSTR> 102.70502 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11122 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 136.56858 0.00272 0.06685 0.00005 MINI INTERN> 5.59918 30.44379 0.00000 27.98683 5.73748 MINI EXTERN> -55.77738 19.86196 0.00000 0.00000 0.00000 MINI CONSTR> 102.71672 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> 500 136.56858 0.00272 0.06685 0.00006 STPD INTERN> 5.59918 30.44379 0.00000 27.98683 5.73748 STPD EXTERN> -55.77738 19.86196 0.00000 0.00000 0.00000 STPD CONSTR> 102.71672 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 11122 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11122 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 136.56858 0.00272 0.06685 0.00000 MINI INTERN> 5.59918 30.44379 0.00000 27.98683 5.73748 MINI EXTERN> -55.77738 19.86196 0.00000 0.00000 0.00000 MINI CONSTR> 102.71672 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 136.50805 0.06053 0.02835 0.00049 MINI INTERN> 5.58425 30.23123 0.00000 27.76905 5.71539 MINI EXTERN> -56.03080 19.98023 0.00000 0.00000 0.00000 MINI CONSTR> 103.25870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 136.50228 0.00577 0.07041 0.01251 MINI INTERN> 5.58977 30.22707 0.00000 27.75949 5.68968 MINI EXTERN> -55.84918 19.97623 0.00000 0.00000 0.00000 MINI CONSTR> 103.10923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 136.49654 0.00574 0.04288 0.01109 MINI INTERN> 5.57449 30.18178 0.00000 27.77250 5.73485 MINI EXTERN> -55.95376 20.10164 0.00000 0.00000 0.00000 MINI CONSTR> 103.08503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 136.49482 0.00172 0.02092 0.00192 MINI INTERN> 5.58286 30.17028 0.00000 27.80813 5.73579 MINI EXTERN> -56.10639 20.15021 0.00000 0.00000 0.00000 MINI CONSTR> 103.15392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 136.49415 0.00066 0.02115 0.00161 MINI INTERN> 5.58067 30.15836 0.00000 27.82423 5.73198 MINI EXTERN> -56.17779 20.16522 0.00000 0.00000 0.00000 MINI CONSTR> 103.21149 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 136.49347 0.00069 0.01991 0.00212 MINI INTERN> 5.56825 30.14460 0.00000 27.82990 5.73853 MINI EXTERN> -56.20891 20.16164 0.00000 0.00000 0.00000 MINI CONSTR> 103.25946 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 136.49301 0.00045 0.01345 0.00141 MINI INTERN> 5.56841 30.12608 0.00000 27.82990 5.73949 MINI EXTERN> -56.19597 20.14876 0.00000 0.00000 0.00000 MINI CONSTR> 103.27635 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> 39 136.49282 0.00019 0.00981 0.02000 CONJ INTERN> 5.56583 30.12192 0.00000 27.83783 5.74066 CONJ EXTERN> -56.19584 20.14084 0.00000 0.00000 0.00000 CONJ CONSTR> 103.28158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "6600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 1.7502 ( PROT LYS 1 HT2 ) 1.7502 ( PROT LYS 1 N ) 2.1877 ( PROT LYS 1 HT3 ) 1.7502 ( PROT LYS 1 CA ) 2.1877 ( PROT LYS 1 CB ) 1.7502 ( PROT LYS 1 CG ) 1.7502 ( PROT LYS 1 CD ) 1.7502 ( PROT LYS 1 CE ) 1.7502 ( PROT LYS 1 NZ ) 1.7502 ( PROT LYS 1 HZ1 ) 1.7502 ( PROT LYS 1 HZ2 ) 1.7502 ( PROT LYS 1 HZ3 ) 1.7502 ( PROT LYS 1 C ) 2.1877 ( PROT LYS 1 O ) 2.1877 ( PROT MET 2 N ) 2.1877 ( PROT MET 2 H ) 1.7502 ( PROT MET 2 CA ) 2.1877 ( PROT MET 2 CB ) 1.7502 ( PROT MET 2 CG ) 1.7502 ( PROT MET 2 SD ) 1.7502 ( PROT MET 2 CE ) 1.7502 ( PROT MET 2 C ) 2.1877 ( PROT MET 2 O ) 2.1877 ( PROT LYS 3 N ) 2.1877 ( PROT LYS 3 H ) 1.7502 ( PROT LYS 3 CA ) 2.1877 ( PROT LYS 3 CB ) 1.7502 ( PROT LYS 3 CG ) 1.7502 ( PROT LYS 3 CD ) 1.7502 ( PROT LYS 3 CE ) 1.7502 ( PROT LYS 3 NZ ) 1.7502 ( PROT LYS 3 HZ1 ) 1.7502 ( PROT LYS 3 HZ2 ) 1.7502 ( PROT LYS 3 HZ3 ) 1.7502 ( PROT LYS 3 C ) 2.1877 ( PROT LYS 3 O ) 2.1877 ( PROT ALA 4 N ) 2.1877 ( PROT ALA 4 H ) 1.7502 ( PROT ALA 4 CA ) 2.1877 ( PROT ALA 4 CB ) 1.7502 ( PROT ALA 4 C ) 2.1877 ( PROT ALA 4 O ) 2.1877 ( PROT VAL 5 N ) 2.1877 ( PROT VAL 5 H ) 1.7502 ( PROT VAL 5 CA ) 2.1877 ( PROT VAL 5 CB ) 1.7502 ( PROT VAL 5 CG1 ) 1.7502 ( PROT VAL 5 CG2 ) 1.7502 ( PROT VAL 5 C ) 2.1877 ( PROT VAL 5 O ) 2.1877 ( PROT MET 6 N ) 2.1877 ( PROT MET 6 H ) 1.7502 ( PROT MET 6 CA ) 2.1877 ( PROT MET 6 CB ) 1.7502 ( PROT MET 6 CG ) 1.7502 ( PROT MET 6 SD ) 1.7502 ( PROT MET 6 CE ) 1.7502 ( PROT MET 6 C ) 2.1877 ( PROT MET 6 O ) 2.1877 ( PROT ILE 7 N ) 2.1877 ( PROT ILE 7 H ) 1.7502 ( PROT ILE 7 CA ) 2.1877 ( PROT ILE 7 CB ) 1.7502 ( PROT ILE 7 CG2 ) 1.7502 ( PROT ILE 7 CG1 ) 1.7502 ( PROT ILE 7 CD ) 1.7502 ( PROT ILE 7 C ) 2.1877 ( PROT ILE 7 O ) 2.1877 ( PROT GLY 8 N ) 2.1877 ( PROT GLY 8 H ) 1.7502 ( PROT GLY 8 CA ) 2.1877 ( PROT GLY 8 C ) 2.1877 ( PROT GLY 8 O ) 2.1877 ( PROT ALA 9 N ) 2.1877 ( PROT ALA 9 H ) 1.7502 ( PROT ALA 9 CA ) 2.1877 ( PROT ALA 9 CB ) 1.7502 ( PROT ALA 9 C ) 2.1877 ( PROT ALA 9 O ) 2.1877 ( PROT CYS 10 N ) 2.1877 ( PROT CYS 10 H ) 1.7502 ( PROT CYS 10 CA ) 2.1877 ( PROT CYS 10 CB ) 1.7502 ( PROT CYS 10 SG ) 1.7502 ( PROT CYS 10 C ) 2.1877 ( PROT CYS 10 O ) 2.1877 ( PROT PHE 11 N ) 2.1877 ( PROT PHE 11 H ) 1.7502 ( PROT PHE 11 CA ) 2.1877 ( PROT PHE 11 CB ) 1.7502 ( PROT PHE 11 CG ) 1.7502 ( PROT PHE 11 CD1 ) 1.7502 ( PROT PHE 11 CD2 ) 1.7502 ( PROT PHE 11 CE1 ) 1.7502 ( PROT PHE 11 CE2 ) 1.7502 ( PROT PHE 11 CZ ) 1.7502 ( PROT PHE 11 C ) 2.1877 ( PROT PHE 11 O ) 2.1877 ( PROT LEU 12 N ) 2.1877 ( PROT LEU 12 H ) 1.7502 ( PROT LEU 12 CA ) 2.1877 ( PROT LEU 12 CB ) 1.7502 ( PROT LEU 12 CG ) 1.7502 ( PROT LEU 12 CD1 ) 1.7502 ( PROT LEU 12 CD2 ) 1.7502 ( PROT LEU 12 C ) 2.1877 ( PROT LEU 12 O ) 2.1877 ( PROT ILE 13 N ) 2.1877 ( PROT ILE 13 H ) 1.7502 ( PROT ILE 13 CA ) 2.1877 ( PROT ILE 13 CB ) 1.7502 ( PROT ILE 13 CG2 ) 1.7502 ( PROT ILE 13 CG1 ) 1.7502 ( PROT ILE 13 CD ) 1.7502 ( PROT ILE 13 C ) 2.1877 ( PROT ILE 13 O ) 2.1877 ( PROT ASP 14 N ) 2.1877 ( PROT ASP 14 H ) 1.7502 ( PROT ASP 14 CA ) 2.1877 ( PROT ASP 14 CB ) 1.7502 ( PROT ASP 14 CG ) 1.7502 ( PROT ASP 14 OD1 ) 1.7502 ( PROT ASP 14 OD2 ) 1.7502 ( PROT ASP 14 C ) 2.1877 ( PROT ASP 14 O ) 2.1877 ( PROT PHE 15 N ) 2.1877 ( PROT PHE 15 H ) 1.7502 ( PROT PHE 15 CA ) 2.1877 ( PROT PHE 15 CB ) 1.7502 ( PROT PHE 15 CG ) 1.7502 ( PROT PHE 15 CD1 ) 1.7502 ( PROT PHE 15 CD2 ) 1.7502 ( PROT PHE 15 CE1 ) 1.7502 ( PROT PHE 15 CE2 ) 1.7502 ( PROT PHE 15 CZ ) 1.7502 ( PROT PHE 15 C ) 2.1877 ( PROT PHE 15 O ) 2.1877 ( PROT MET 16 N ) 2.1877 ( PROT MET 16 H ) 1.7502 ( PROT MET 16 CA ) 2.1877 ( PROT MET 16 CB ) 1.7502 ( PROT MET 16 CG ) 1.7502 ( PROT MET 16 SD ) 1.7502 ( PROT MET 16 CE ) 1.7502 ( PROT MET 16 C ) 2.1877 ( PROT MET 16 O ) 2.1877 ( PROT PHE 17 N ) 2.1877 ( PROT PHE 17 H ) 1.7502 ( PROT PHE 17 CA ) 2.1877 ( PROT PHE 17 CB ) 1.7502 ( PROT PHE 17 CG ) 1.7502 ( PROT PHE 17 CD1 ) 1.7502 ( PROT PHE 17 CD2 ) 1.7502 ( PROT PHE 17 CE1 ) 1.7502 ( PROT PHE 17 CE2 ) 1.7502 ( PROT PHE 17 CZ ) 1.7502 ( PROT PHE 17 C ) 2.1877 ( PROT PHE 17 O ) 2.1877 ( PROT PHE 18 N ) 2.1877 ( PROT PHE 18 H ) 1.7502 ( PROT PHE 18 CA ) 2.1877 ( PROT PHE 18 CB ) 1.7502 ( PROT PHE 18 CG ) 1.7502 ( PROT PHE 18 CD1 ) 1.7502 ( PROT PHE 18 CD2 ) 1.7502 ( PROT PHE 18 CE1 ) 1.7502 ( PROT PHE 18 CE2 ) 1.7502 ( PROT PHE 18 CZ ) 1.7502 ( PROT PHE 18 C ) 2.1877 ( PROT PHE 18 O ) 2.1877 ( PROT GLU 19 N ) 2.1877 ( PROT GLU 19 H ) 1.7502 ( PROT GLU 19 CA ) 2.1877 ( PROT GLU 19 CB ) 1.7502 ( PROT GLU 19 CG ) 1.7502 ( PROT GLU 19 CD ) 1.7502 ( PROT GLU 19 OE1 ) 1.7502 ( PROT GLU 19 OE2 ) 1.7502 ( PROT GLU 19 C ) 2.1877 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41039 5.26150 -8.67044 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00064 -0.00159 -0.00126 ROTATION MATRIX 1.000000 -0.000198 0.000009 0.000198 1.000000 0.000266 -0.000009 -0.000266 1.000000 AXIS OF ROTATION IS 0.801946 -0.028118 -0.596735 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 35.1192 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.439275 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4393" Parameter: A <- "0.4393" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70513 5.22039 -8.77977 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00971 0.04403 -0.01460 ROTATION MATRIX 0.999774 0.017067 0.012667 -0.016870 0.999737 -0.015516 -0.012929 0.015298 0.999799 AXIS OF ROTATION IS -0.586920 -0.487538 0.646399 ANGLE IS 1.50 CENTER OF ROTATION 8.897005 5.155088 -9.591102 SHIFT IS -0.036602 TOTAL SQUARE DIFF IS 1.3158 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.263158 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4393" RDCMND substituted energy or value "?RMS" to " 0.2632" Parameter: A <- "0.4393 0.2632" 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 0.4393 0.2632 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 " 103.28" Parameter: H <- "103.28" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 33.21124 103.28158 1.50056 ENER INTERN> 5.56583 30.12192 0.00000 27.83783 5.74066 ENER EXTERN> -56.19584 20.14084 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 " 33.21" Parameter: B <- "33.21" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 20.14" Parameter: C <- "20.14" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -56.20" Parameter: C <- " -36.06" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -36.06" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.57" Parameter: D <- "5.57" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 30.12" Parameter: D <- " 35.69" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 27.84" Parameter: D <- " 63.53" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.74" Parameter: D <- " 69.27" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 69.27" 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= 33.21 GRMS= 1.50 ELEC= 20.14 VDW= -56.20 RDTITL> *EXTERNAL= -36.06 INTERNAL= 69.27 USER= 0.00 HARM= 103.28 RDTITL> *BOND= 5.57 ANGL= 30.12 DIHE= 27.84 IMPR= 5.74 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11122 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11124 ATOM PAIRS WERE FOUND FOR ATOM LIST 336 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 104.80999 -71.59875 0.57933 0.02000 MINI INTERN> 5.56583 30.12192 0.00000 27.83783 5.74066 MINI EXTERN> -56.19584 20.14084 0.00000 0.00000 0.00000 MINI CONSTR> 71.59875 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 124.27936 -19.46937 15.48316 0.00864 MINI INTERN> 27.60055 27.62664 0.00000 29.83091 5.13597 MINI EXTERN> -64.38389 22.80396 0.00000 0.00000 0.00000 MINI CONSTR> 75.66521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11110 ATOM PAIRS WERE FOUND FOR ATOM LIST 334 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 106.20039 18.07897 6.67770 0.00373 MINI INTERN> 7.58414 32.08174 0.00000 28.79012 6.10931 MINI EXTERN> -65.36619 20.83158 0.00000 0.00000 0.00000 MINI CONSTR> 76.16970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 102.66064 3.53975 2.78246 0.00161 MINI INTERN> 6.60569 29.02123 0.00000 29.26282 5.63042 MINI EXTERN> -65.87523 21.81894 0.00000 0.00000 0.00000 MINI CONSTR> 76.19677 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11110 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 101.78674 0.87390 0.31832 0.00029 MINI INTERN> 5.49379 29.54204 0.00000 29.12002 5.73280 MINI EXTERN> -65.99982 21.52887 0.00000 0.00000 0.00000 MINI CONSTR> 76.36903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 101.70663 0.08011 1.13035 0.00072 MINI INTERN> 5.56112 29.66727 0.00000 29.01962 5.78754 MINI EXTERN> -66.27294 21.40467 0.00000 0.00000 0.00000 MINI CONSTR> 76.53935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11102 ATOM PAIRS WERE FOUND FOR ATOM LIST 333 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 101.52778 0.17885 1.13643 0.00075 MINI INTERN> 5.87033 29.36208 0.00000 28.98339 5.77972 MINI EXTERN> -66.60005 21.44501 0.00000 0.00000 0.00000 MINI CONSTR> 76.68730 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 101.24143 0.28635 0.35698 0.00032 MINI INTERN> 5.38664 29.33358 0.00000 29.07791 5.67749 MINI EXTERN> -66.54211 21.49843 0.00000 0.00000 0.00000 MINI CONSTR> 76.80948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11101 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 101.09386 0.14757 0.26532 0.00034 MINI INTERN> 5.43109 29.24710 0.00000 29.04358 5.67624 MINI EXTERN> -66.71981 21.49262 0.00000 0.00000 0.00000 MINI CONSTR> 76.92304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 100.92549 0.16837 0.26000 0.00035 MINI INTERN> 5.41571 29.16966 0.00000 29.01575 5.66209 MINI EXTERN> -66.88293 21.49032 0.00000 0.00000 0.00000 MINI CONSTR> 77.05490 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11100 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 100.75824 0.16725 0.47219 0.00036 MINI INTERN> 5.31854 29.11477 0.00000 29.00583 5.62603 MINI EXTERN> -66.99405 21.49328 0.00000 0.00000 0.00000 MINI CONSTR> 77.19383 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 100.61681 0.14143 0.38171 0.00037 MINI INTERN> 5.32308 29.04684 0.00000 28.96909 5.62257 MINI EXTERN> -67.13679 21.49478 0.00000 0.00000 0.00000 MINI CONSTR> 77.29724 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11099 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 100.49993 0.11688 0.56746 0.00039 MINI INTERN> 5.25221 29.01904 0.00000 28.95615 5.59649 MINI EXTERN> -67.21134 21.49018 0.00000 0.00000 0.00000 MINI CONSTR> 77.39720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 100.35923 0.14070 0.41149 0.00040 MINI INTERN> 5.28476 28.93733 0.00000 28.90917 5.59916 MINI EXTERN> -67.35852 21.49418 0.00000 0.00000 0.00000 MINI CONSTR> 77.49316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11099 ATOM PAIRS WERE FOUND FOR ATOM LIST 331 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 100.26163 0.09760 0.60891 0.00042 MINI INTERN> 5.19132 28.93064 0.00000 28.89814 5.57495 MINI EXTERN> -67.40868 21.49597 0.00000 0.00000 0.00000 MINI CONSTR> 77.57929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 100.15447 0.10716 0.70287 0.00043 MINI INTERN> 5.19287 28.88810 0.00000 28.86712 5.56095 MINI EXTERN> -67.49730 21.47677 0.00000 0.00000 0.00000 MINI CONSTR> 77.66597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11098 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 100.04432 0.11015 0.64384 0.00045 MINI INTERN> 5.14155 28.85565 0.00000 28.83995 5.55145 MINI EXTERN> -67.57250 21.48529 0.00000 0.00000 0.00000 MINI CONSTR> 77.74292 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 99.93224 0.11208 0.68650 0.00046 MINI INTERN> 5.13433 28.80269 0.00000 28.80477 5.53858 MINI EXTERN> -67.65957 21.48232 0.00000 0.00000 0.00000 MINI CONSTR> 77.82913 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11097 ATOM PAIRS WERE FOUND FOR ATOM LIST 330 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 99.83653 0.09572 0.81168 0.00048 MINI INTERN> 5.09245 28.76547 0.00000 28.77582 5.52381 MINI EXTERN> -67.73102 21.49762 0.00000 0.00000 0.00000 MINI CONSTR> 77.91238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 99.73691 0.09962 0.73678 0.00050 MINI INTERN> 5.08327 28.73030 0.00000 28.74201 5.51878 MINI EXTERN> -67.80235 21.48737 0.00000 0.00000 0.00000 MINI CONSTR> 77.97754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11095 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 99.64413 0.09279 0.80626 0.00052 MINI INTERN> 5.16081 28.66205 0.00000 28.69344 5.51480 MINI EXTERN> -67.89585 21.45852 0.00000 0.00000 0.00000 MINI CONSTR> 78.05035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 99.50054 0.14359 0.24511 0.00022 MINI INTERN> 5.38432 28.48276 0.00000 28.59768 5.55372 MINI EXTERN> -68.10920 21.46975 0.00000 0.00000 0.00000 MINI CONSTR> 78.12150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11094 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 99.47433 0.02621 0.82756 0.00056 MINI INTERN> 5.07310 28.62120 0.00000 28.64031 5.49171 MINI EXTERN> -67.99187 21.46094 0.00000 0.00000 0.00000 MINI CONSTR> 78.17894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 99.32923 0.14510 0.29665 0.00024 MINI INTERN> 5.40986 28.38760 0.00000 28.52183 5.54225 MINI EXTERN> -68.24524 21.46260 0.00000 0.00000 0.00000 MINI CONSTR> 78.25034 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11092 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 99.25627 0.07296 0.20007 0.00025 MINI INTERN> 5.34028 28.38010 0.00000 28.50632 5.52725 MINI EXTERN> -68.26364 21.46615 0.00000 0.00000 0.00000 MINI CONSTR> 78.29982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 99.17519 0.08108 0.35303 0.00026 MINI INTERN> 5.43700 28.29650 0.00000 28.44839 5.53226 MINI EXTERN> -68.36768 21.46031 0.00000 0.00000 0.00000 MINI CONSTR> 78.36842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11091 ATOM PAIRS WERE FOUND FOR ATOM LIST 329 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 99.10296 0.07223 0.18478 0.00027 MINI INTERN> 5.32038 28.31417 0.00000 28.44230 5.51180 MINI EXTERN> -68.36095 21.46136 0.00000 0.00000 0.00000 MINI CONSTR> 78.41389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 99.02374 0.07922 0.40408 0.00028 MINI INTERN> 5.45309 28.21461 0.00000 28.37418 5.52110 MINI EXTERN> -68.47994 21.45455 0.00000 0.00000 0.00000 MINI CONSTR> 78.48614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11089 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 98.94289 0.08086 0.24121 0.00029 MINI INTERN> 5.35250 28.22070 0.00000 28.35897 5.50307 MINI EXTERN> -68.48651 21.45577 0.00000 0.00000 0.00000 MINI CONSTR> 78.53838 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 98.87267 0.07021 0.33211 0.00030 MINI INTERN> 5.40065 28.16686 0.00000 28.31380 5.50169 MINI EXTERN> -68.55361 21.44610 0.00000 0.00000 0.00000 MINI CONSTR> 78.59718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11088 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 98.81789 0.05478 0.44239 0.00031 MINI INTERN> 5.45934 28.10960 0.00000 28.27103 5.50348 MINI EXTERN> -68.61985 21.44642 0.00000 0.00000 0.00000 MINI CONSTR> 78.64789 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 98.75014 0.06776 0.47626 0.00032 MINI INTERN> 5.45378 28.07798 0.00000 28.23479 5.49811 MINI EXTERN> -68.66606 21.44739 0.00000 0.00000 0.00000 MINI CONSTR> 78.70415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11088 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 98.69347 0.05667 0.55453 0.00033 MINI INTERN> 5.48623 28.04319 0.00000 28.19837 5.49292 MINI EXTERN> -68.71009 21.42800 0.00000 0.00000 0.00000 MINI CONSTR> 78.75484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 98.63568 0.05779 0.50328 0.00034 MINI INTERN> 5.47729 28.01239 0.00000 28.17018 5.48795 MINI EXTERN> -68.74435 21.43414 0.00000 0.00000 0.00000 MINI CONSTR> 78.79808 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11087 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 98.55803 0.07765 0.16279 0.00015 MINI INTERN> 5.23683 28.08430 0.00000 28.18500 5.45343 MINI EXTERN> -68.68189 21.44115 0.00000 0.00000 0.00000 MINI CONSTR> 78.83920 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 98.52806 0.02997 0.55796 0.00037 MINI INTERN> 5.48796 27.95682 0.00000 28.10735 5.47735 MINI EXTERN> -68.81456 21.42227 0.00000 0.00000 0.00000 MINI CONSTR> 78.89088 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11084 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 98.48095 0.04711 0.63280 0.00038 MINI INTERN> 5.40982 27.95361 0.00000 28.08864 5.46775 MINI EXTERN> -68.82842 21.45365 0.00000 0.00000 0.00000 MINI CONSTR> 78.93591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 98.42996 0.05100 0.59921 0.00040 MINI INTERN> 5.50466 27.88990 0.00000 28.04303 5.47168 MINI EXTERN> -68.89155 21.43258 0.00000 0.00000 0.00000 MINI CONSTR> 78.97967 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11084 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 98.34820 0.08176 0.18998 0.00017 MINI INTERN> 5.19822 27.99905 0.00000 28.07134 5.42904 MINI EXTERN> -68.79633 21.42989 0.00000 0.00000 0.00000 MINI CONSTR> 79.01699 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 98.30463 0.04357 0.14555 0.00018 MINI INTERN> 5.22449 27.96433 0.00000 28.03990 5.42922 MINI EXTERN> -68.83538 21.42761 0.00000 0.00000 0.00000 MINI CONSTR> 79.05445 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11084 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 98.25658 0.04805 0.15158 0.00019 MINI INTERN> 5.21371 27.94594 0.00000 28.01251 5.42306 MINI EXTERN> -68.85973 21.42393 0.00000 0.00000 0.00000 MINI CONSTR> 79.09716 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 98.21041 0.04617 0.25463 0.00019 MINI INTERN> 5.15614 27.94959 0.00000 27.99311 5.41026 MINI EXTERN> -68.86431 21.42381 0.00000 0.00000 0.00000 MINI CONSTR> 79.14181 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11083 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 98.16604 0.04437 0.18557 0.00020 MINI INTERN> 5.19130 27.91189 0.00000 27.95941 5.41073 MINI EXTERN> -68.90435 21.41683 0.00000 0.00000 0.00000 MINI CONSTR> 79.18023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 98.12503 0.04101 0.21970 0.00021 MINI INTERN> 5.16349 27.90323 0.00000 27.93696 5.40352 MINI EXTERN> -68.91940 21.41760 0.00000 0.00000 0.00000 MINI CONSTR> 79.21963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11082 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 98.08387 0.04116 0.22083 0.00021 MINI INTERN> 5.16467 27.88300 0.00000 27.90972 5.39913 MINI EXTERN> -68.94355 21.41224 0.00000 0.00000 0.00000 MINI CONSTR> 79.25866 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 98.05051 0.03335 0.32197 0.00022 MINI INTERN> 5.11637 27.88827 0.00000 27.89344 5.38911 MINI EXTERN> -68.94615 21.41387 0.00000 0.00000 0.00000 MINI CONSTR> 79.29560 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11082 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 98.01182 0.03869 0.34515 0.00023 MINI INTERN> 5.12972 27.86552 0.00000 27.86488 5.38487 MINI EXTERN> -68.97098 21.40320 0.00000 0.00000 0.00000 MINI CONSTR> 79.33460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 97.97827 0.03356 0.37554 0.00024 MINI INTERN> 5.09464 27.86022 0.00000 27.84513 5.37877 MINI EXTERN> -68.98300 21.41189 0.00000 0.00000 0.00000 MINI CONSTR> 79.37061 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11082 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 97.94402 0.03425 0.35539 0.00025 MINI INTERN> 5.10510 27.84170 0.00000 27.82044 5.37561 MINI EXTERN> -69.00392 21.40130 0.00000 0.00000 0.00000 MINI CONSTR> 79.40378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 97.91094 0.03307 0.39260 0.00026 MINI INTERN> 5.10221 27.81791 0.00000 27.79358 5.37403 MINI EXTERN> -69.03072 21.41321 0.00000 0.00000 0.00000 MINI CONSTR> 79.44071 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11082 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 97.87791 0.03303 0.36755 0.00027 MINI INTERN> 5.09129 27.81317 0.00000 27.77376 5.36721 MINI EXTERN> -69.03935 21.39819 0.00000 0.00000 0.00000 MINI CONSTR> 79.47364 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 97.83586 0.04205 0.12346 0.00011 MINI INTERN> 5.22763 27.72149 0.00000 27.72150 5.38302 MINI EXTERN> -69.12068 21.39465 0.00000 0.00000 0.00000 MINI CONSTR> 79.50824 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11082 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 97.81986 0.01599 0.41886 0.00029 MINI INTERN> 5.07536 27.79183 0.00000 27.73085 5.35775 MINI EXTERN> -69.06750 21.39133 0.00000 0.00000 0.00000 MINI CONSTR> 79.54025 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 97.79171 0.02816 0.46874 0.00030 MINI INTERN> 5.07963 27.76429 0.00000 27.70345 5.35778 MINI EXTERN> -69.09650 21.40730 0.00000 0.00000 0.00000 MINI CONSTR> 79.57576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11079 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 97.74572 0.04599 0.13986 0.00013 MINI INTERN> 5.23622 27.66876 0.00000 27.64948 5.37394 MINI EXTERN> -69.17821 21.38673 0.00000 0.00000 0.00000 MINI CONSTR> 79.60880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 97.72053 0.02519 0.11132 0.00013 MINI INTERN> 5.21352 27.66566 0.00000 27.63415 5.36843 MINI EXTERN> -69.18397 21.38619 0.00000 0.00000 0.00000 MINI CONSTR> 79.63654 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11079 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 97.69337 0.02716 0.11513 0.00014 MINI INTERN> 5.21850 27.64849 0.00000 27.61102 5.36577 MINI EXTERN> -69.20206 21.38324 0.00000 0.00000 0.00000 MINI CONSTR> 79.66842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 97.66719 0.02617 0.11053 0.00014 MINI INTERN> 5.21375 27.63622 0.00000 27.59027 5.36215 MINI EXTERN> -69.21587 21.38132 0.00000 0.00000 0.00000 MINI CONSTR> 79.69936 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11077 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 97.64065 0.02654 0.20012 0.00015 MINI INTERN> 5.25976 27.59868 0.00000 27.55672 5.36414 MINI EXTERN> -69.25164 21.37718 0.00000 0.00000 0.00000 MINI CONSTR> 79.73580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 97.61503 0.02562 0.13472 0.00015 MINI INTERN> 5.22450 27.60108 0.00000 27.54302 5.35736 MINI EXTERN> -69.25255 21.37741 0.00000 0.00000 0.00000 MINI CONSTR> 79.76421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11077 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 97.59109 0.02393 0.16667 0.00016 MINI INTERN> 5.23960 27.58189 0.00000 27.51898 5.35542 MINI EXTERN> -69.27161 21.37121 0.00000 0.00000 0.00000 MINI CONSTR> 79.79561 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 97.57181 0.01928 0.23811 0.00016 MINI INTERN> 5.27084 27.55370 0.00000 27.49304 5.35666 MINI EXTERN> -69.29823 21.37094 0.00000 0.00000 0.00000 MINI CONSTR> 79.82487 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11077 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 97.54612 0.02569 0.14593 0.00017 MINI INTERN> 5.22667 27.56056 0.00000 27.48107 5.34892 MINI EXTERN> -69.29512 21.37096 0.00000 0.00000 0.00000 MINI CONSTR> 79.85306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 97.52809 0.01803 0.25304 0.00018 MINI INTERN> 5.27188 27.52822 0.00000 27.45243 5.35096 MINI EXTERN> -69.32506 21.36608 0.00000 0.00000 0.00000 MINI CONSTR> 79.88357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11076 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 97.50733 0.02076 0.28762 0.00018 MINI INTERN> 5.26407 27.51660 0.00000 27.43208 5.34826 MINI EXTERN> -69.33843 21.37044 0.00000 0.00000 0.00000 MINI CONSTR> 79.91432 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 97.48821 0.01913 0.27904 0.00019 MINI INTERN> 5.27402 27.50584 0.00000 27.41406 5.34494 MINI EXTERN> -69.34844 21.35809 0.00000 0.00000 0.00000 MINI CONSTR> 79.93970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11076 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 97.46979 0.01841 0.29217 0.00020 MINI INTERN> 5.25182 27.49864 0.00000 27.39818 5.34197 MINI EXTERN> -69.35741 21.36997 0.00000 0.00000 0.00000 MINI CONSTR> 79.96663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 97.44645 0.02335 0.09215 0.00009 MINI INTERN> 5.17514 27.52758 0.00000 27.39796 5.32914 MINI EXTERN> -69.33376 21.36263 0.00000 0.00000 0.00000 MINI CONSTR> 79.98775 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11076 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 97.43624 0.01021 0.31073 0.00021 MINI INTERN> 5.28900 27.46476 0.00000 27.35795 5.33946 MINI EXTERN> -69.38828 21.35575 0.00000 0.00000 0.00000 MINI CONSTR> 80.01760 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 97.41921 0.01703 0.33793 0.00022 MINI INTERN> 5.26137 27.46193 0.00000 27.34324 5.33559 MINI EXTERN> -69.39378 21.36606 0.00000 0.00000 0.00000 MINI CONSTR> 80.04481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11076 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 97.39346 0.02576 0.10543 0.00010 MINI INTERN> 5.16297 27.50118 0.00000 27.34643 5.31997 MINI EXTERN> -69.36157 21.35785 0.00000 0.00000 0.00000 MINI CONSTR> 80.06663 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 97.38819 0.00526 0.34281 0.00024 MINI INTERN> 5.29040 27.43108 0.00000 27.30545 5.33310 MINI EXTERN> -69.42182 21.35610 0.00000 0.00000 0.00000 MINI CONSTR> 80.09388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11075 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 97.36087 0.02732 0.11614 0.00010 MINI INTERN> 5.15681 27.48372 0.00000 27.31297 5.31429 MINI EXTERN> -69.37950 21.35494 0.00000 0.00000 0.00000 MINI CONSTR> 80.11763 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 97.34703 0.01384 0.08135 0.00011 MINI INTERN> 5.17216 27.46710 0.00000 27.29541 5.31447 MINI EXTERN> -69.39465 21.35353 0.00000 0.00000 0.00000 MINI CONSTR> 80.13901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11075 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 97.33112 0.01591 0.08559 0.00011 MINI INTERN> 5.16852 27.45903 0.00000 27.27868 5.31140 MINI EXTERN> -69.40286 21.35143 0.00000 0.00000 0.00000 MINI CONSTR> 80.16492 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 97.31703 0.01409 0.15944 0.00011 MINI INTERN> 5.14121 27.46308 0.00000 27.26660 5.30521 MINI EXTERN> -69.40122 21.35130 0.00000 0.00000 0.00000 MINI CONSTR> 80.19086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11075 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 97.30209 0.01494 0.09865 0.00012 MINI INTERN> 5.15969 27.44404 0.00000 27.24733 5.30570 MINI EXTERN> -69.41808 21.34955 0.00000 0.00000 0.00000 MINI CONSTR> 80.21387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 97.28725 0.01484 0.09980 0.00012 MINI INTERN> 5.16094 27.43385 0.00000 27.23001 5.30324 MINI EXTERN> -69.42766 21.34739 0.00000 0.00000 0.00000 MINI CONSTR> 80.23949 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11073 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 97.27397 0.01329 0.13804 0.00013 MINI INTERN> 5.14849 27.42933 0.00000 27.21548 5.29969 MINI EXTERN> -69.43280 21.34942 0.00000 0.00000 0.00000 MINI CONSTR> 80.26436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 97.26378 0.01019 0.18796 0.00013 MINI INTERN> 5.13473 27.42961 0.00000 27.20445 5.29553 MINI EXTERN> -69.43377 21.34791 0.00000 0.00000 0.00000 MINI CONSTR> 80.28532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11074 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 97.25225 0.01153 0.22190 0.00014 MINI INTERN> 5.14561 27.41979 0.00000 27.18819 5.29317 MINI EXTERN> -69.44239 21.33958 0.00000 0.00000 0.00000 MINI CONSTR> 80.30830 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 97.24087 0.01137 0.20096 0.00014 MINI INTERN> 5.13194 27.41570 0.00000 27.17643 5.29089 MINI EXTERN> -69.44730 21.34480 0.00000 0.00000 0.00000 MINI CONSTR> 80.32842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11073 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 97.22938 0.01150 0.23043 0.00015 MINI INTERN> 5.13405 27.40749 0.00000 27.16066 5.28806 MINI EXTERN> -69.45455 21.34123 0.00000 0.00000 0.00000 MINI CONSTR> 80.35245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 97.21872 0.01065 0.22013 0.00015 MINI INTERN> 5.12904 27.40040 0.00000 27.14775 5.28655 MINI EXTERN> -69.46175 21.34439 0.00000 0.00000 0.00000 MINI CONSTR> 80.37234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11073 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 97.20425 0.01448 0.07169 0.00007 MINI INTERN> 5.17416 27.36963 0.00000 27.12470 5.29118 MINI EXTERN> -69.48813 21.33944 0.00000 0.00000 0.00000 MINI CONSTR> 80.39327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 97.19885 0.00540 0.23642 0.00016 MINI INTERN> 5.12686 27.38765 0.00000 27.12134 5.28213 MINI EXTERN> -69.47381 21.34142 0.00000 0.00000 0.00000 MINI CONSTR> 80.41324 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11072 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 97.18858 0.01027 0.24646 0.00017 MINI INTERN> 5.13665 27.37743 0.00000 27.10594 5.28031 MINI EXTERN> -69.48233 21.33572 0.00000 0.00000 0.00000 MINI CONSTR> 80.43486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 97.17423 0.01435 0.07470 0.00007 MINI INTERN> 5.17382 27.34784 0.00000 27.08426 5.28548 MINI EXTERN> -69.50825 21.33648 0.00000 0.00000 0.00000 MINI CONSTR> 80.45461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11072 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 97.16566 0.00857 0.06404 0.00008 MINI INTERN> 5.16888 27.34358 0.00000 27.07348 5.28323 MINI EXTERN> -69.51218 21.33635 0.00000 0.00000 0.00000 MINI CONSTR> 80.47232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 97.15662 0.00905 0.06609 0.00008 MINI INTERN> 5.17025 27.33626 0.00000 27.06042 5.28154 MINI EXTERN> -69.51877 21.33504 0.00000 0.00000 0.00000 MINI CONSTR> 80.49187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11072 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 97.14796 0.00866 0.06499 0.00008 MINI INTERN> 5.16888 27.33004 0.00000 27.04819 5.27971 MINI EXTERN> -69.52442 21.33474 0.00000 0.00000 0.00000 MINI CONSTR> 80.51081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 97.13944 0.00851 0.11478 0.00008 MINI INTERN> 5.18129 27.31758 0.00000 27.03204 5.27933 MINI EXTERN> -69.53556 21.33257 0.00000 0.00000 0.00000 MINI CONSTR> 80.53219 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11072 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 97.13099 0.00845 0.08016 0.00009 MINI INTERN> 5.17038 27.31562 0.00000 27.02240 5.27656 MINI EXTERN> -69.53745 21.33382 0.00000 0.00000 0.00000 MINI CONSTR> 80.54966 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 97.12332 0.00767 0.09777 0.00009 MINI INTERN> 5.17621 27.30715 0.00000 27.00933 5.27540 MINI EXTERN> -69.54480 21.33174 0.00000 0.00000 0.00000 MINI CONSTR> 80.56828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11071 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 97.11655 0.00677 0.13721 0.00009 MINI INTERN> 5.18309 27.29795 0.00000 26.99612 5.27468 MINI EXTERN> -69.55300 21.33099 0.00000 0.00000 0.00000 MINI CONSTR> 80.58671 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 97.10792 0.00863 0.08128 0.00010 MINI INTERN> 5.17112 27.29755 0.00000 26.98699 5.27137 MINI EXTERN> -69.55333 21.33012 0.00000 0.00000 0.00000 MINI CONSTR> 80.60408 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11071 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 97.10175 0.00617 0.14592 0.00010 MINI INTERN> 5.17975 27.28687 0.00000 26.97287 5.27118 MINI EXTERN> -69.56302 21.33087 0.00000 0.00000 0.00000 MINI CONSTR> 80.62322 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 97.09538 0.00637 0.17454 0.00011 MINI INTERN> 5.18615 27.28134 0.00000 26.96111 5.26918 MINI EXTERN> -69.56753 21.32430 0.00000 0.00000 0.00000 MINI CONSTR> 80.64083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11071 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 97.08890 0.00648 0.15660 0.00011 MINI INTERN> 5.18411 27.27529 0.00000 26.95105 5.26811 MINI EXTERN> -69.57274 21.32680 0.00000 0.00000 0.00000 MINI CONSTR> 80.65628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 97.08266 0.00624 0.17472 0.00011 MINI INTERN> 5.17126 27.27244 0.00000 26.94151 5.26619 MINI EXTERN> -69.57587 21.33366 0.00000 0.00000 0.00000 MINI CONSTR> 80.67348 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11070 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 97.07467 0.00799 0.05354 0.00005 MINI INTERN> 5.15735 27.27584 0.00000 26.93583 5.26192 MINI EXTERN> -69.57193 21.32875 0.00000 0.00000 0.00000 MINI CONSTR> 80.68690 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 97.07467 0.00799 0.05354 0.00006 STPD INTERN> 5.15735 27.27584 0.00000 26.93583 5.26192 STPD EXTERN> -69.57193 21.32875 0.00000 0.00000 0.00000 STPD CONSTR> 80.68690 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 11070 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11070 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 97.07467 0.00799 0.05354 0.00000 MINI INTERN> 5.15735 27.27584 0.00000 26.93583 5.26192 MINI EXTERN> -69.57193 21.32875 0.00000 0.00000 0.00000 MINI CONSTR> 80.68690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 96.88363 0.19103 0.01294 0.00035 MINI INTERN> 5.13065 26.96095 0.00000 26.29954 5.17005 MINI EXTERN> -69.87437 21.31177 0.00000 0.00000 0.00000 MINI CONSTR> 81.88505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 96.88210 0.00154 0.03224 0.00481 MINI INTERN> 5.13692 26.96488 0.00000 26.26974 5.14452 MINI EXTERN> -69.68343 21.29227 0.00000 0.00000 0.00000 MINI CONSTR> 81.75721 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 96.88074 0.00135 0.02052 0.00289 MINI INTERN> 5.13003 26.98552 0.00000 26.24796 5.16195 MINI EXTERN> -69.67998 21.35729 0.00000 0.00000 0.00000 MINI CONSTR> 81.67798 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 96.88033 0.00041 0.01263 0.00125 MINI INTERN> 5.14046 27.00126 0.00000 26.25181 5.15620 MINI EXTERN> -69.72018 21.36393 0.00000 0.00000 0.00000 MINI CONSTR> 81.68685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 96.88009 0.00024 0.01078 0.00124 MINI INTERN> 5.14478 26.99597 0.00000 26.25515 5.16015 MINI EXTERN> -69.76204 21.37014 0.00000 0.00000 0.00000 MINI CONSTR> 81.71593 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 96.87987 0.00023 0.01089 0.00131 MINI INTERN> 5.14042 26.98834 0.00000 26.24722 5.16052 MINI EXTERN> -69.77731 21.37164 0.00000 0.00000 0.00000 MINI CONSTR> 81.74904 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> 34 96.87969 0.00017 0.00940 0.02000 CONJ INTERN> 5.13575 26.98098 0.00000 26.23727 5.15872 CONJ EXTERN> -69.77905 21.37599 0.00000 0.00000 0.00000 CONJ CONSTR> 81.77002 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "7200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 1.1376 ( PROT LYS 1 HT2 ) 1.1376 ( PROT LYS 1 N ) 1.4220 ( PROT LYS 1 HT3 ) 1.1376 ( PROT LYS 1 CA ) 1.4220 ( PROT LYS 1 CB ) 1.1376 ( PROT LYS 1 CG ) 1.1376 ( PROT LYS 1 CD ) 1.1376 ( PROT LYS 1 CE ) 1.1376 ( PROT LYS 1 NZ ) 1.1376 ( PROT LYS 1 HZ1 ) 1.1376 ( PROT LYS 1 HZ2 ) 1.1376 ( PROT LYS 1 HZ3 ) 1.1376 ( PROT LYS 1 C ) 1.4220 ( PROT LYS 1 O ) 1.4220 ( PROT MET 2 N ) 1.4220 ( PROT MET 2 H ) 1.1376 ( PROT MET 2 CA ) 1.4220 ( PROT MET 2 CB ) 1.1376 ( PROT MET 2 CG ) 1.1376 ( PROT MET 2 SD ) 1.1376 ( PROT MET 2 CE ) 1.1376 ( PROT MET 2 C ) 1.4220 ( PROT MET 2 O ) 1.4220 ( PROT LYS 3 N ) 1.4220 ( PROT LYS 3 H ) 1.1376 ( PROT LYS 3 CA ) 1.4220 ( PROT LYS 3 CB ) 1.1376 ( PROT LYS 3 CG ) 1.1376 ( PROT LYS 3 CD ) 1.1376 ( PROT LYS 3 CE ) 1.1376 ( PROT LYS 3 NZ ) 1.1376 ( PROT LYS 3 HZ1 ) 1.1376 ( PROT LYS 3 HZ2 ) 1.1376 ( PROT LYS 3 HZ3 ) 1.1376 ( PROT LYS 3 C ) 1.4220 ( PROT LYS 3 O ) 1.4220 ( PROT ALA 4 N ) 1.4220 ( PROT ALA 4 H ) 1.1376 ( PROT ALA 4 CA ) 1.4220 ( PROT ALA 4 CB ) 1.1376 ( PROT ALA 4 C ) 1.4220 ( PROT ALA 4 O ) 1.4220 ( PROT VAL 5 N ) 1.4220 ( PROT VAL 5 H ) 1.1376 ( PROT VAL 5 CA ) 1.4220 ( PROT VAL 5 CB ) 1.1376 ( PROT VAL 5 CG1 ) 1.1376 ( PROT VAL 5 CG2 ) 1.1376 ( PROT VAL 5 C ) 1.4220 ( PROT VAL 5 O ) 1.4220 ( PROT MET 6 N ) 1.4220 ( PROT MET 6 H ) 1.1376 ( PROT MET 6 CA ) 1.4220 ( PROT MET 6 CB ) 1.1376 ( PROT MET 6 CG ) 1.1376 ( PROT MET 6 SD ) 1.1376 ( PROT MET 6 CE ) 1.1376 ( PROT MET 6 C ) 1.4220 ( PROT MET 6 O ) 1.4220 ( PROT ILE 7 N ) 1.4220 ( PROT ILE 7 H ) 1.1376 ( PROT ILE 7 CA ) 1.4220 ( PROT ILE 7 CB ) 1.1376 ( PROT ILE 7 CG2 ) 1.1376 ( PROT ILE 7 CG1 ) 1.1376 ( PROT ILE 7 CD ) 1.1376 ( PROT ILE 7 C ) 1.4220 ( PROT ILE 7 O ) 1.4220 ( PROT GLY 8 N ) 1.4220 ( PROT GLY 8 H ) 1.1376 ( PROT GLY 8 CA ) 1.4220 ( PROT GLY 8 C ) 1.4220 ( PROT GLY 8 O ) 1.4220 ( PROT ALA 9 N ) 1.4220 ( PROT ALA 9 H ) 1.1376 ( PROT ALA 9 CA ) 1.4220 ( PROT ALA 9 CB ) 1.1376 ( PROT ALA 9 C ) 1.4220 ( PROT ALA 9 O ) 1.4220 ( PROT CYS 10 N ) 1.4220 ( PROT CYS 10 H ) 1.1376 ( PROT CYS 10 CA ) 1.4220 ( PROT CYS 10 CB ) 1.1376 ( PROT CYS 10 SG ) 1.1376 ( PROT CYS 10 C ) 1.4220 ( PROT CYS 10 O ) 1.4220 ( PROT PHE 11 N ) 1.4220 ( PROT PHE 11 H ) 1.1376 ( PROT PHE 11 CA ) 1.4220 ( PROT PHE 11 CB ) 1.1376 ( PROT PHE 11 CG ) 1.1376 ( PROT PHE 11 CD1 ) 1.1376 ( PROT PHE 11 CD2 ) 1.1376 ( PROT PHE 11 CE1 ) 1.1376 ( PROT PHE 11 CE2 ) 1.1376 ( PROT PHE 11 CZ ) 1.1376 ( PROT PHE 11 C ) 1.4220 ( PROT PHE 11 O ) 1.4220 ( PROT LEU 12 N ) 1.4220 ( PROT LEU 12 H ) 1.1376 ( PROT LEU 12 CA ) 1.4220 ( PROT LEU 12 CB ) 1.1376 ( PROT LEU 12 CG ) 1.1376 ( PROT LEU 12 CD1 ) 1.1376 ( PROT LEU 12 CD2 ) 1.1376 ( PROT LEU 12 C ) 1.4220 ( PROT LEU 12 O ) 1.4220 ( PROT ILE 13 N ) 1.4220 ( PROT ILE 13 H ) 1.1376 ( PROT ILE 13 CA ) 1.4220 ( PROT ILE 13 CB ) 1.1376 ( PROT ILE 13 CG2 ) 1.1376 ( PROT ILE 13 CG1 ) 1.1376 ( PROT ILE 13 CD ) 1.1376 ( PROT ILE 13 C ) 1.4220 ( PROT ILE 13 O ) 1.4220 ( PROT ASP 14 N ) 1.4220 ( PROT ASP 14 H ) 1.1376 ( PROT ASP 14 CA ) 1.4220 ( PROT ASP 14 CB ) 1.1376 ( PROT ASP 14 CG ) 1.1376 ( PROT ASP 14 OD1 ) 1.1376 ( PROT ASP 14 OD2 ) 1.1376 ( PROT ASP 14 C ) 1.4220 ( PROT ASP 14 O ) 1.4220 ( PROT PHE 15 N ) 1.4220 ( PROT PHE 15 H ) 1.1376 ( PROT PHE 15 CA ) 1.4220 ( PROT PHE 15 CB ) 1.1376 ( PROT PHE 15 CG ) 1.1376 ( PROT PHE 15 CD1 ) 1.1376 ( PROT PHE 15 CD2 ) 1.1376 ( PROT PHE 15 CE1 ) 1.1376 ( PROT PHE 15 CE2 ) 1.1376 ( PROT PHE 15 CZ ) 1.1376 ( PROT PHE 15 C ) 1.4220 ( PROT PHE 15 O ) 1.4220 ( PROT MET 16 N ) 1.4220 ( PROT MET 16 H ) 1.1376 ( PROT MET 16 CA ) 1.4220 ( PROT MET 16 CB ) 1.1376 ( PROT MET 16 CG ) 1.1376 ( PROT MET 16 SD ) 1.1376 ( PROT MET 16 CE ) 1.1376 ( PROT MET 16 C ) 1.4220 ( PROT MET 16 O ) 1.4220 ( PROT PHE 17 N ) 1.4220 ( PROT PHE 17 H ) 1.1376 ( PROT PHE 17 CA ) 1.4220 ( PROT PHE 17 CB ) 1.1376 ( PROT PHE 17 CG ) 1.1376 ( PROT PHE 17 CD1 ) 1.1376 ( PROT PHE 17 CD2 ) 1.1376 ( PROT PHE 17 CE1 ) 1.1376 ( PROT PHE 17 CE2 ) 1.1376 ( PROT PHE 17 CZ ) 1.1376 ( PROT PHE 17 C ) 1.4220 ( PROT PHE 17 O ) 1.4220 ( PROT PHE 18 N ) 1.4220 ( PROT PHE 18 H ) 1.1376 ( PROT PHE 18 CA ) 1.4220 ( PROT PHE 18 CB ) 1.1376 ( PROT PHE 18 CG ) 1.1376 ( PROT PHE 18 CD1 ) 1.1376 ( PROT PHE 18 CD2 ) 1.1376 ( PROT PHE 18 CE1 ) 1.1376 ( PROT PHE 18 CE2 ) 1.1376 ( PROT PHE 18 CZ ) 1.1376 ( PROT PHE 18 C ) 1.4220 ( PROT PHE 18 O ) 1.4220 ( PROT GLU 19 N ) 1.4220 ( PROT GLU 19 H ) 1.1376 ( PROT GLU 19 CA ) 1.4220 ( PROT GLU 19 CB ) 1.1376 ( PROT GLU 19 CG ) 1.1376 ( PROT GLU 19 CD ) 1.1376 ( PROT GLU 19 OE1 ) 1.1376 ( PROT GLU 19 OE2 ) 1.1376 ( PROT GLU 19 C ) 1.4220 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41026 5.26110 -8.67001 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00078 -0.00118 -0.00169 ROTATION MATRIX 1.000000 -0.000152 0.000042 0.000152 1.000000 0.000256 -0.000042 -0.000256 1.000000 AXIS OF ROTATION IS 0.851504 -0.141068 -0.505015 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 42.8425 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.485179 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.4852" Parameter: A <- "0.4852" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70569 5.22088 -8.78165 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00916 0.04354 -0.01272 ROTATION MATRIX 0.999770 0.017344 0.012582 -0.017144 0.999728 -0.015784 -0.012853 0.015564 0.999796 AXIS OF ROTATION IS -0.590416 -0.479048 0.649556 ANGLE IS 1.52 CENTER OF ROTATION 8.874633 5.183869 -9.590913 SHIFT IS -0.034521 TOTAL SQUARE DIFF IS 1.8524 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.312240 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.4852" RDCMND substituted energy or value "?RMS" to " 0.3122" Parameter: A <- "0.4852 0.3122" 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 0.4852 0.3122 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 81.77" Parameter: H <- "81.77" 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 15.10967 81.77002 1.07555 ENER INTERN> 5.13575 26.98098 0.00000 26.23727 5.15872 ENER EXTERN> -69.77905 21.37599 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 " 15.11" Parameter: B <- "15.11" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 21.38" Parameter: C <- "21.38" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -69.78" Parameter: C <- " -48.40" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -48.40" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 5.14" Parameter: D <- "5.14" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 26.98" Parameter: D <- " 32.12" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 26.24" Parameter: D <- " 58.36" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 5.16" Parameter: D <- " 63.52" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 63.52" 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= 7200 ENER= 15.11 GRMS= 1.08 ELEC= 21.38 VDW= -69.78 RDTITL> *EXTERNAL= -48.40 INTERNAL= 63.52 USER= 0.00 HARM= 81.77 RDTITL> *BOND= 5.14 ANGL= 26.98 DIHE= 26.24 IMPR= 5.16 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "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= 15.11 GRMS= 1.08 ELEC= 21.38 VDW= -69.78 RDTITL> *EXTERNAL= -48.40 INTERNAL= 63.52 USER= 0.00 HARM= 81.77 RDTITL> *BOND= 5.14 ANGL= 26.98 DIHE= 26.24 IMPR= 5.16 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= 15.11 GRMS= 1.08 ELEC= 21.38 VDW= -69.78 RDTITL> *EXTERNAL= -48.40 INTERNAL= 63.52 USER= 0.00 HARM= 81.77 RDTITL> *BOND= 5.14 ANGL= 26.98 DIHE= 26.24 IMPR= 5.16 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 7200 0.4852 0.3122 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "7200" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11070 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11068 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 71.21950 -56.10982 0.40926 0.02000 MINI INTERN> 5.13575 26.98098 0.00000 26.23727 5.15872 MINI EXTERN> -69.77905 21.37599 0.00000 0.00000 0.00000 MINI CONSTR> 56.10982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 92.36417 -21.14468 15.75747 0.00864 MINI INTERN> 27.63473 25.27439 0.00000 27.89889 4.67463 MINI EXTERN> -76.03656 23.84334 0.00000 0.00000 0.00000 MINI CONSTR> 59.07475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11061 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 69.49638 22.86779 0.38690 0.00156 MINI INTERN> 5.13671 26.74609 0.00000 27.20831 5.22665 MINI EXTERN> -76.73317 22.59713 0.00000 0.00000 0.00000 MINI CONSTR> 59.31466 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 69.37342 0.12297 1.03329 0.00067 MINI INTERN> 5.39120 26.75537 0.00000 27.07047 5.22816 MINI EXTERN> -77.10326 22.51640 0.00000 0.00000 0.00000 MINI CONSTR> 59.51507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11058 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 69.24818 0.12524 0.97208 0.00070 MINI INTERN> 5.39967 26.66429 0.00000 27.03209 5.21958 MINI EXTERN> -77.16195 22.47772 0.00000 0.00000 0.00000 MINI CONSTR> 59.61678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 69.04282 0.20536 0.33706 0.00030 MINI INTERN> 5.20594 26.50215 0.00000 27.05425 5.16421 MINI EXTERN> -77.11344 22.50462 0.00000 0.00000 0.00000 MINI CONSTR> 59.72509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11057 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 68.94094 0.10188 0.33759 0.00031 MINI INTERN> 5.20609 26.44964 0.00000 27.01985 5.15329 MINI EXTERN> -77.19846 22.48211 0.00000 0.00000 0.00000 MINI CONSTR> 59.82842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 68.84723 0.09371 0.35840 0.00032 MINI INTERN> 5.19131 26.40297 0.00000 26.98961 5.14152 MINI EXTERN> -77.27636 22.47094 0.00000 0.00000 0.00000 MINI CONSTR> 59.92723 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11057 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 68.76168 0.08554 0.45300 0.00034 MINI INTERN> 5.17671 26.33648 0.00000 26.96424 5.12521 MINI EXTERN> -77.34504 22.47735 0.00000 0.00000 0.00000 MINI CONSTR> 60.02673 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 68.65402 0.10766 0.29456 0.00035 MINI INTERN> 5.17066 26.29948 0.00000 26.91859 5.12585 MINI EXTERN> -77.45326 22.46300 0.00000 0.00000 0.00000 MINI CONSTR> 60.12970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11055 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 68.57686 0.07716 0.53110 0.00036 MINI INTERN> 5.22491 26.20386 0.00000 26.88449 5.11218 MINI EXTERN> -77.54442 22.46298 0.00000 0.00000 0.00000 MINI CONSTR> 60.23284 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 68.49763 0.07923 0.57014 0.00037 MINI INTERN> 5.21780 26.15080 0.00000 26.85512 5.09947 MINI EXTERN> -77.61429 22.46418 0.00000 0.00000 0.00000 MINI CONSTR> 60.32456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11055 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 68.41956 0.07807 0.58992 0.00039 MINI INTERN> 5.16714 26.14063 0.00000 26.82118 5.09389 MINI EXTERN> -77.67856 22.46403 0.00000 0.00000 0.00000 MINI CONSTR> 60.41124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 68.33883 0.08073 0.54939 0.00040 MINI INTERN> 5.15880 26.08831 0.00000 26.79353 5.08067 MINI EXTERN> -77.74323 22.46335 0.00000 0.00000 0.00000 MINI CONSTR> 60.49741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11054 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 68.24164 0.09719 0.19432 0.00017 MINI INTERN> 5.07971 26.15518 0.00000 26.74875 5.09671 MINI EXTERN> -77.84068 22.42468 0.00000 0.00000 0.00000 MINI CONSTR> 60.57729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 68.19733 0.04431 0.62990 0.00043 MINI INTERN> 5.13924 26.01359 0.00000 26.72956 5.06343 MINI EXTERN> -77.87300 22.46068 0.00000 0.00000 0.00000 MINI CONSTR> 60.66384 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11052 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 68.13984 0.05749 0.77582 0.00045 MINI INTERN> 5.17411 26.00446 0.00000 26.68875 5.06856 MINI EXTERN> -77.97003 22.43134 0.00000 0.00000 0.00000 MINI CONSTR> 60.74265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 68.02788 0.11196 0.21540 0.00019 MINI INTERN> 5.06025 26.04808 0.00000 26.64714 5.07828 MINI EXTERN> -78.03820 22.41552 0.00000 0.00000 0.00000 MINI CONSTR> 60.81682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11049 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 67.96714 0.06074 0.18108 0.00020 MINI INTERN> 5.06547 26.00233 0.00000 26.61880 5.07042 MINI EXTERN> -78.08955 22.41667 0.00000 0.00000 0.00000 MINI CONSTR> 60.88300 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 67.94249 0.02465 0.72515 0.00050 MINI INTERN> 5.04295 25.93334 0.00000 26.61800 5.02753 MINI EXTERN> -78.08325 22.44099 0.00000 0.00000 0.00000 MINI CONSTR> 60.96293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11048 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 67.83094 0.11156 0.25916 0.00022 MINI INTERN> 5.05496 25.94554 0.00000 26.54320 5.06217 MINI EXTERN> -78.22075 22.40453 0.00000 0.00000 0.00000 MINI CONSTR> 61.04129 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 67.77456 0.05638 0.17810 0.00022 MINI INTERN> 5.05335 25.89833 0.00000 26.51860 5.05156 MINI EXTERN> -78.25741 22.40984 0.00000 0.00000 0.00000 MINI CONSTR> 61.10030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11047 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 67.71060 0.06396 0.30179 0.00023 MINI INTERN> 5.06100 25.87665 0.00000 26.47350 5.05264 MINI EXTERN> -78.33242 22.39820 0.00000 0.00000 0.00000 MINI CONSTR> 61.18102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 67.65050 0.06009 0.24767 0.00024 MINI INTERN> 5.04826 25.83914 0.00000 26.44465 5.04302 MINI EXTERN> -78.37146 22.40129 0.00000 0.00000 0.00000 MINI CONSTR> 61.24562 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11045 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 67.59545 0.05505 0.27920 0.00025 MINI INTERN> 5.06217 25.80236 0.00000 26.40862 5.03983 MINI EXTERN> -78.42614 22.39757 0.00000 0.00000 0.00000 MINI CONSTR> 61.31105 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 67.54516 0.05029 0.37620 0.00026 MINI INTERN> 5.08436 25.77025 0.00000 26.37062 5.03883 MINI EXTERN> -78.48555 22.38983 0.00000 0.00000 0.00000 MINI CONSTR> 61.37682 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11045 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 67.49273 0.05243 0.41046 0.00027 MINI INTERN> 5.07582 25.74178 0.00000 26.33720 5.03305 MINI EXTERN> -78.52645 22.39097 0.00000 0.00000 0.00000 MINI CONSTR> 61.44036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 67.44215 0.05058 0.41814 0.00028 MINI INTERN> 5.10403 25.69882 0.00000 26.30128 5.03044 MINI EXTERN> -78.57965 22.38640 0.00000 0.00000 0.00000 MINI CONSTR> 61.50081 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11043 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 67.38903 0.05311 0.43896 0.00029 MINI INTERN> 5.10044 25.67294 0.00000 26.26788 5.02511 MINI EXTERN> -78.62408 22.38171 0.00000 0.00000 0.00000 MINI CONSTR> 61.56503 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 67.33883 0.05020 0.42451 0.00030 MINI INTERN> 5.09059 25.64570 0.00000 26.23759 5.01848 MINI EXTERN> -78.65789 22.38211 0.00000 0.00000 0.00000 MINI CONSTR> 61.62225 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11043 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 67.29148 0.04734 0.46988 0.00031 MINI INTERN> 5.08834 25.61859 0.00000 26.21063 5.01051 MINI EXTERN> -78.69454 22.37695 0.00000 0.00000 0.00000 MINI CONSTR> 61.68101 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 67.24366 0.04782 0.44288 0.00032 MINI INTERN> 5.10636 25.58116 0.00000 26.17364 5.00885 MINI EXTERN> -78.73917 22.37573 0.00000 0.00000 0.00000 MINI CONSTR> 61.73709 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11042 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 67.18231 0.06135 0.15027 0.00014 MINI INTERN> 4.99594 25.57862 0.00000 26.17082 4.98217 MINI EXTERN> -78.71834 22.38616 0.00000 0.00000 0.00000 MINI CONSTR> 61.78695 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 67.15790 0.02441 0.50650 0.00034 MINI INTERN> 5.12356 25.52285 0.00000 26.10977 5.00055 MINI EXTERN> -78.81558 22.36956 0.00000 0.00000 0.00000 MINI CONSTR> 61.84720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11042 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 67.11769 0.04021 0.58207 0.00036 MINI INTERN> 5.08156 25.51624 0.00000 26.08316 4.99037 MINI EXTERN> -78.82975 22.37401 0.00000 0.00000 0.00000 MINI CONSTR> 61.90211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 67.07429 0.04341 0.55097 0.00037 MINI INTERN> 5.13664 25.46733 0.00000 26.04390 4.99298 MINI EXTERN> -78.88762 22.36558 0.00000 0.00000 0.00000 MINI CONSTR> 61.95547 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11042 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 67.00386 0.07042 0.17245 0.00016 MINI INTERN> 4.97375 25.48645 0.00000 26.05063 4.95986 MINI EXTERN> -78.84699 22.37568 0.00000 0.00000 0.00000 MINI CONSTR> 62.00448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 66.96605 0.03781 0.13487 0.00017 MINI INTERN> 4.98016 25.46568 0.00000 26.02093 4.95882 MINI EXTERN> -78.88097 22.37133 0.00000 0.00000 0.00000 MINI CONSTR> 62.05010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11041 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 66.92401 0.04204 0.14042 0.00017 MINI INTERN> 4.97412 25.44405 0.00000 25.99157 4.95314 MINI EXTERN> -78.90999 22.36857 0.00000 0.00000 0.00000 MINI CONSTR> 62.10255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 66.88333 0.04068 0.23278 0.00018 MINI INTERN> 4.95221 25.42527 0.00000 25.96537 4.94242 MINI EXTERN> -78.92869 22.36926 0.00000 0.00000 0.00000 MINI CONSTR> 62.15748 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11038 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 66.84454 0.03879 0.17686 0.00019 MINI INTERN> 4.96177 25.40236 0.00000 25.93485 4.94146 MINI EXTERN> -78.96346 22.36371 0.00000 0.00000 0.00000 MINI CONSTR> 62.20385 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 66.80815 0.03638 0.20121 0.00019 MINI INTERN> 4.94752 25.38779 0.00000 25.90900 4.93526 MINI EXTERN> -78.98483 22.36209 0.00000 0.00000 0.00000 MINI CONSTR> 62.25133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11036 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 66.77026 0.03789 0.18984 0.00020 MINI INTERN> 4.94763 25.36618 0.00000 25.87939 4.93142 MINI EXTERN> -79.01317 22.35931 0.00000 0.00000 0.00000 MINI CONSTR> 62.29951 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 66.73840 0.03187 0.30139 0.00021 MINI INTERN> 4.92985 25.35218 0.00000 25.85666 4.92198 MINI EXTERN> -79.02829 22.35852 0.00000 0.00000 0.00000 MINI CONSTR> 62.34750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11036 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 66.70345 0.03494 0.32051 0.00021 MINI INTERN> 4.92902 25.33163 0.00000 25.82650 4.91827 MINI EXTERN> -79.05418 22.35776 0.00000 0.00000 0.00000 MINI CONSTR> 62.39446 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 66.67173 0.03173 0.33768 0.00022 MINI INTERN> 4.91730 25.31991 0.00000 25.80408 4.91228 MINI EXTERN> -79.07331 22.35349 0.00000 0.00000 0.00000 MINI CONSTR> 62.43798 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11036 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 66.63924 0.03248 0.36166 0.00023 MINI INTERN> 4.91203 25.30293 0.00000 25.77611 4.90789 MINI EXTERN> -79.09555 22.35260 0.00000 0.00000 0.00000 MINI CONSTR> 62.48323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 66.60779 0.03145 0.34063 0.00024 MINI INTERN> 4.90995 25.28815 0.00000 25.75247 4.90461 MINI EXTERN> -79.11841 22.34749 0.00000 0.00000 0.00000 MINI CONSTR> 62.52352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11036 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 66.57714 0.03065 0.37713 0.00025 MINI INTERN> 4.91237 25.26839 0.00000 25.72190 4.90205 MINI EXTERN> -79.14293 22.34765 0.00000 0.00000 0.00000 MINI CONSTR> 62.56771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 66.54618 0.03096 0.35240 0.00026 MINI INTERN> 4.89920 25.25798 0.00000 25.70128 4.89627 MINI EXTERN> -79.15984 22.34288 0.00000 0.00000 0.00000 MINI CONSTR> 62.60840 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11036 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 66.50650 0.03968 0.11841 0.00011 MINI INTERN> 4.95477 25.21617 0.00000 25.65980 4.90597 MINI EXTERN> -79.21369 22.33451 0.00000 0.00000 0.00000 MINI CONSTR> 62.64898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 66.49047 0.01603 0.40185 0.00028 MINI INTERN> 4.89110 25.22887 0.00000 25.65289 4.88735 MINI EXTERN> -79.19806 22.33794 0.00000 0.00000 0.00000 MINI CONSTR> 62.69039 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11035 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 66.46301 0.02746 0.44485 0.00029 MINI INTERN> 4.89867 25.20796 0.00000 25.62184 4.88562 MINI EXTERN> -79.22212 22.33846 0.00000 0.00000 0.00000 MINI CONSTR> 62.73257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 66.41949 0.04351 0.13348 0.00012 MINI INTERN> 4.95356 25.16574 0.00000 25.58304 4.89551 MINI EXTERN> -79.27664 22.32675 0.00000 0.00000 0.00000 MINI CONSTR> 62.77154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11034 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 66.41147 0.00803 0.45940 0.00031 MINI INTERN> 4.87968 25.18793 0.00000 25.57858 4.87654 MINI EXTERN> -79.25296 22.33336 0.00000 0.00000 0.00000 MINI CONSTR> 62.80833 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 66.36707 0.04440 0.15983 0.00013 MINI INTERN> 4.95715 25.13244 0.00000 25.53386 4.88946 MINI EXTERN> -79.31616 22.32232 0.00000 0.00000 0.00000 MINI CONSTR> 62.84799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11033 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 66.34400 0.02306 0.11144 0.00014 MINI INTERN> 4.94400 25.12311 0.00000 25.51746 4.88399 MINI EXTERN> -79.32536 22.32156 0.00000 0.00000 0.00000 MINI CONSTR> 62.87923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 66.31782 0.02619 0.18816 0.00014 MINI INTERN> 4.96334 25.09922 0.00000 25.48644 4.88364 MINI EXTERN> -79.35416 22.31779 0.00000 0.00000 0.00000 MINI CONSTR> 62.92154 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11033 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 66.29474 0.02308 0.10456 0.00015 MINI INTERN> 4.93792 25.09578 0.00000 25.47284 4.87677 MINI EXTERN> -79.35789 22.31782 0.00000 0.00000 0.00000 MINI CONSTR> 62.95150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 66.26776 0.02698 0.21327 0.00015 MINI INTERN> 4.96177 25.06995 0.00000 25.43820 4.87706 MINI EXTERN> -79.39015 22.31322 0.00000 0.00000 0.00000 MINI CONSTR> 62.99771 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11032 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 66.24259 0.02518 0.15176 0.00016 MINI INTERN> 4.94581 25.06095 0.00000 25.42032 4.87129 MINI EXTERN> -79.39992 22.31224 0.00000 0.00000 0.00000 MINI CONSTR> 63.03190 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 66.22242 0.02017 0.23808 0.00016 MINI INTERN> 4.96439 25.04040 0.00000 25.39297 4.87103 MINI EXTERN> -79.42390 22.30911 0.00000 0.00000 0.00000 MINI CONSTR> 63.06842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11032 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 66.19644 0.02598 0.15333 0.00017 MINI INTERN> 4.94204 25.03393 0.00000 25.37583 4.86464 MINI EXTERN> -79.43150 22.30874 0.00000 0.00000 0.00000 MINI CONSTR> 63.10277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 66.17805 0.01839 0.25155 0.00018 MINI INTERN> 4.96324 25.01293 0.00000 25.34914 4.86459 MINI EXTERN> -79.45543 22.30537 0.00000 0.00000 0.00000 MINI CONSTR> 63.13821 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11032 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 66.15569 0.02236 0.27751 0.00018 MINI INTERN> 4.95714 25.00280 0.00000 25.32561 4.86100 MINI EXTERN> -79.46959 22.30341 0.00000 0.00000 0.00000 MINI CONSTR> 63.17532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 66.13622 0.01947 0.29890 0.00019 MINI INTERN> 4.96613 24.98528 0.00000 25.30421 4.85881 MINI EXTERN> -79.48814 22.30134 0.00000 0.00000 0.00000 MINI CONSTR> 63.20859 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11030 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 66.11604 0.02017 0.28228 0.00020 MINI INTERN> 4.96323 24.97338 0.00000 25.28438 4.85546 MINI EXTERN> -79.49984 22.30006 0.00000 0.00000 0.00000 MINI CONSTR> 63.23938 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 66.09588 0.02017 0.30782 0.00020 MINI INTERN> 4.95652 24.96287 0.00000 25.26546 4.85142 MINI EXTERN> -79.51337 22.29933 0.00000 0.00000 0.00000 MINI CONSTR> 63.27365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11029 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 66.07032 0.02556 0.09554 0.00009 MINI INTERN> 4.91261 24.96583 0.00000 25.25527 4.84191 MINI EXTERN> -79.50689 22.30054 0.00000 0.00000 0.00000 MINI CONSTR> 63.30106 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 66.05948 0.01084 0.32093 0.00022 MINI INTERN> 4.96594 24.93413 0.00000 25.22318 4.84703 MINI EXTERN> -79.54298 22.29624 0.00000 0.00000 0.00000 MINI CONSTR> 63.33594 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11029 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 66.04148 0.01800 0.35614 0.00023 MINI INTERN> 4.95917 24.92829 0.00000 25.20297 4.84224 MINI EXTERN> -79.55006 22.29064 0.00000 0.00000 0.00000 MINI CONSTR> 63.36823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 66.02491 0.01657 0.37853 0.00024 MINI INTERN> 4.95774 24.91284 0.00000 25.18535 4.84046 MINI EXTERN> -79.56793 22.29714 0.00000 0.00000 0.00000 MINI CONSTR> 63.39932 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11029 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 65.99565 0.02926 0.10784 0.00010 MINI INTERN> 4.90360 24.92119 0.00000 25.17677 4.82940 MINI EXTERN> -79.55672 22.29471 0.00000 0.00000 0.00000 MINI CONSTR> 63.42670 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 65.97954 0.01610 0.08825 0.00011 MINI INTERN> 4.90632 24.90951 0.00000 25.15859 4.82778 MINI EXTERN> -79.56992 22.29338 0.00000 0.00000 0.00000 MINI CONSTR> 63.45387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11028 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 65.96203 0.01751 0.09168 0.00011 MINI INTERN> 4.90386 24.89915 0.00000 25.13960 4.82461 MINI EXTERN> -79.58129 22.29171 0.00000 0.00000 0.00000 MINI CONSTR> 63.48439 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 65.94523 0.01680 0.09107 0.00011 MINI INTERN> 4.90204 24.88855 0.00000 25.12102 4.82187 MINI EXTERN> -79.59301 22.29086 0.00000 0.00000 0.00000 MINI CONSTR> 63.51390 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11027 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 65.92855 0.01667 0.15926 0.00012 MINI INTERN> 4.89161 24.88180 0.00000 25.10302 4.81668 MINI EXTERN> -79.60039 22.28952 0.00000 0.00000 0.00000 MINI CONSTR> 63.54631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 65.91190 0.01665 0.11231 0.00012 MINI INTERN> 4.89542 24.86839 0.00000 25.08390 4.81560 MINI EXTERN> -79.61493 22.28944 0.00000 0.00000 0.00000 MINI CONSTR> 63.57407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11025 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 65.89654 0.01536 0.13454 0.00013 MINI INTERN> 4.89143 24.86032 0.00000 25.06660 4.81204 MINI EXTERN> -79.62384 22.28714 0.00000 0.00000 0.00000 MINI CONSTR> 63.60285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 65.88063 0.01591 0.12854 0.00013 MINI INTERN> 4.89077 24.84945 0.00000 25.04809 4.80956 MINI EXTERN> -79.63543 22.28644 0.00000 0.00000 0.00000 MINI CONSTR> 63.63177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11025 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 65.86748 0.01315 0.19783 0.00014 MINI INTERN> 4.88425 24.84336 0.00000 25.03205 4.80525 MINI EXTERN> -79.64218 22.28459 0.00000 0.00000 0.00000 MINI CONSTR> 63.66016 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 65.85250 0.01498 0.21103 0.00014 MINI INTERN> 4.87988 24.83257 0.00000 25.01361 4.80306 MINI EXTERN> -79.65399 22.28817 0.00000 0.00000 0.00000 MINI CONSTR> 63.68919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11025 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 65.83922 0.01328 0.22592 0.00015 MINI INTERN> 4.88194 24.82491 0.00000 24.99751 4.79959 MINI EXTERN> -79.66187 22.28158 0.00000 0.00000 0.00000 MINI CONSTR> 63.71555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 65.82585 0.01337 0.24214 0.00015 MINI INTERN> 4.87381 24.81683 0.00000 24.98098 4.79732 MINI EXTERN> -79.67174 22.28606 0.00000 0.00000 0.00000 MINI CONSTR> 63.74260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11024 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 65.81249 0.01336 0.22540 0.00016 MINI INTERN> 4.87826 24.80806 0.00000 24.96528 4.79478 MINI EXTERN> -79.68050 22.27970 0.00000 0.00000 0.00000 MINI CONSTR> 63.76691 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 65.79936 0.01313 0.25074 0.00016 MINI INTERN> 4.87234 24.79741 0.00000 24.94758 4.79336 MINI EXTERN> -79.69263 22.28682 0.00000 0.00000 0.00000 MINI CONSTR> 63.79449 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11023 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 65.78614 0.01322 0.23189 0.00017 MINI INTERN> 4.87320 24.79068 0.00000 24.93251 4.78988 MINI EXTERN> -79.69925 22.27976 0.00000 0.00000 0.00000 MINI CONSTR> 63.81935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 65.76909 0.01705 0.07789 0.00007 MINI INTERN> 4.89572 24.76914 0.00000 24.91094 4.79206 MINI EXTERN> -79.71990 22.27687 0.00000 0.00000 0.00000 MINI CONSTR> 63.84427 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11023 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 65.76235 0.00674 0.26371 0.00018 MINI INTERN> 4.86866 24.77478 0.00000 24.90110 4.78471 MINI EXTERN> -79.71624 22.27909 0.00000 0.00000 0.00000 MINI CONSTR> 63.87024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 65.74993 0.01242 0.28160 0.00019 MINI INTERN> 4.88124 24.76227 0.00000 24.88315 4.78228 MINI EXTERN> -79.72711 22.27133 0.00000 0.00000 0.00000 MINI CONSTR> 63.89678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11023 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 65.73150 0.01844 0.09267 0.00008 MINI INTERN> 4.89548 24.74177 0.00000 24.86185 4.78522 MINI EXTERN> -79.74812 22.27384 0.00000 0.00000 0.00000 MINI CONSTR> 63.92147 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 65.72846 0.00304 0.30711 0.00020 MINI INTERN> 4.86230 24.74969 0.00000 24.85435 4.77836 MINI EXTERN> -79.74307 22.28232 0.00000 0.00000 0.00000 MINI CONSTR> 63.94452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11023 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 65.70922 0.01924 0.10539 0.00009 MINI INTERN> 4.89494 24.72480 0.00000 24.83181 4.78112 MINI EXTERN> -79.76526 22.27313 0.00000 0.00000 0.00000 MINI CONSTR> 63.96869 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 65.69921 0.01002 0.07289 0.00009 MINI INTERN> 4.89031 24.71980 0.00000 24.82030 4.77836 MINI EXTERN> -79.77000 22.27192 0.00000 0.00000 0.00000 MINI CONSTR> 63.98852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11022 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 65.68802 0.01118 0.12639 0.00009 MINI INTERN> 4.89760 24.70763 0.00000 24.80206 4.77711 MINI EXTERN> -79.78221 22.27074 0.00000 0.00000 0.00000 MINI CONSTR> 64.01509 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 65.67807 0.00995 0.07073 0.00010 MINI INTERN> 4.88720 24.70466 0.00000 24.79184 4.77410 MINI EXTERN> -79.78535 22.27159 0.00000 0.00000 0.00000 MINI CONSTR> 64.03403 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11021 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 65.66761 0.01046 0.14624 0.00010 MINI INTERN> 4.89567 24.69174 0.00000 24.77309 4.77318 MINI EXTERN> -79.79831 22.27134 0.00000 0.00000 0.00000 MINI CONSTR> 64.06089 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 65.65705 0.01056 0.11124 0.00011 MINI INTERN> 4.89424 24.68565 0.00000 24.76045 4.77038 MINI EXTERN> -79.80376 22.26807 0.00000 0.00000 0.00000 MINI CONSTR> 64.08202 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11021 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 65.64839 0.00867 0.15676 0.00011 MINI INTERN> 4.89800 24.67577 0.00000 24.74529 4.76930 MINI EXTERN> -79.81363 22.26916 0.00000 0.00000 0.00000 MINI CONSTR> 64.10450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 65.63710 0.01128 0.10307 0.00011 MINI INTERN> 4.89105 24.67144 0.00000 24.73286 4.76602 MINI EXTERN> -79.81787 22.26711 0.00000 0.00000 0.00000 MINI CONSTR> 64.12649 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11021 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 65.62915 0.00795 0.16634 0.00012 MINI INTERN> 4.89872 24.66069 0.00000 24.71732 4.76511 MINI EXTERN> -79.82828 22.26667 0.00000 0.00000 0.00000 MINI CONSTR> 64.14892 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 65.62915 0.00795 0.16634 0.00014 STPD INTERN> 4.89872 24.66069 0.00000 24.71732 4.76511 STPD EXTERN> -79.82828 22.26667 0.00000 0.00000 0.00000 STPD CONSTR> 64.14892 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 11021 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11021 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 65.62915 0.00795 0.16634 0.00000 MINI INTERN> 4.89872 24.66069 0.00000 24.71732 4.76511 MINI EXTERN> -79.82828 22.26667 0.00000 0.00000 0.00000 MINI CONSTR> 64.14892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 65.19353 0.43562 0.02746 0.00347 MINI INTERN> 4.82478 24.01664 0.00000 23.51598 4.58968 MINI EXTERN> -80.56320 22.26730 0.00000 0.00000 0.00000 MINI CONSTR> 66.54236 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 65.19104 0.00249 0.04822 0.00401 MINI INTERN> 4.79975 24.03670 0.00000 23.49998 4.55996 MINI EXTERN> -80.35857 22.21380 0.00000 0.00000 0.00000 MINI CONSTR> 66.43943 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 65.18657 0.00447 0.05218 0.00783 MINI INTERN> 4.80121 24.02653 0.00000 23.47316 4.58179 MINI EXTERN> -80.17298 22.25406 0.00000 0.00000 0.00000 MINI CONSTR> 66.22280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 65.18380 0.00277 0.02830 0.00299 MINI INTERN> 4.82348 24.07600 0.00000 23.47877 4.57430 MINI EXTERN> -80.18279 22.29245 0.00000 0.00000 0.00000 MINI CONSTR> 66.12158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 65.18277 0.00103 0.02156 0.00169 MINI INTERN> 4.83001 24.09682 0.00000 23.49571 4.57729 MINI EXTERN> -80.25083 22.31981 0.00000 0.00000 0.00000 MINI CONSTR> 66.11395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 65.18222 0.00056 0.01657 0.00151 MINI INTERN> 4.83438 24.08983 0.00000 23.50922 4.58292 MINI EXTERN> -80.28323 22.32564 0.00000 0.00000 0.00000 MINI CONSTR> 66.12345 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 65.18186 0.00036 0.01323 0.00139 MINI INTERN> 4.82605 24.08592 0.00000 23.51284 4.58788 MINI EXTERN> -80.29587 22.33310 0.00000 0.00000 0.00000 MINI CONSTR> 66.13194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 65.18156 0.00030 0.01262 0.00147 MINI INTERN> 4.82292 24.08026 0.00000 23.51260 4.58555 MINI EXTERN> -80.29121 22.33087 0.00000 0.00000 0.00000 MINI CONSTR> 66.14057 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 65.18135 0.00021 0.01059 0.00129 MINI INTERN> 4.82437 24.07573 0.00000 23.50004 4.58380 MINI EXTERN> -80.28812 22.33574 0.00000 0.00000 0.00000 MINI CONSTR> 66.14979 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> 46 65.18131 0.00004 0.00957 0.02000 CONJ INTERN> 4.82833 24.07237 0.00000 23.49826 4.58344 CONJ EXTERN> -80.29346 22.34069 0.00000 0.00000 0.00000 CONJ CONSTR> 66.15168 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "7800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.73944 ( PROT LYS 1 HT2 ) 0.73944 ( PROT LYS 1 N ) 0.92430 ( PROT LYS 1 HT3 ) 0.73944 ( PROT LYS 1 CA ) 0.92430 ( PROT LYS 1 CB ) 0.73944 ( PROT LYS 1 CG ) 0.73944 ( PROT LYS 1 CD ) 0.73944 ( PROT LYS 1 CE ) 0.73944 ( PROT LYS 1 NZ ) 0.73944 ( PROT LYS 1 HZ1 ) 0.73944 ( PROT LYS 1 HZ2 ) 0.73944 ( PROT LYS 1 HZ3 ) 0.73944 ( PROT LYS 1 C ) 0.92430 ( PROT LYS 1 O ) 0.92430 ( PROT MET 2 N ) 0.92430 ( PROT MET 2 H ) 0.73944 ( PROT MET 2 CA ) 0.92430 ( PROT MET 2 CB ) 0.73944 ( PROT MET 2 CG ) 0.73944 ( PROT MET 2 SD ) 0.73944 ( PROT MET 2 CE ) 0.73944 ( PROT MET 2 C ) 0.92430 ( PROT MET 2 O ) 0.92430 ( PROT LYS 3 N ) 0.92430 ( PROT LYS 3 H ) 0.73944 ( PROT LYS 3 CA ) 0.92430 ( PROT LYS 3 CB ) 0.73944 ( PROT LYS 3 CG ) 0.73944 ( PROT LYS 3 CD ) 0.73944 ( PROT LYS 3 CE ) 0.73944 ( PROT LYS 3 NZ ) 0.73944 ( PROT LYS 3 HZ1 ) 0.73944 ( PROT LYS 3 HZ2 ) 0.73944 ( PROT LYS 3 HZ3 ) 0.73944 ( PROT LYS 3 C ) 0.92430 ( PROT LYS 3 O ) 0.92430 ( PROT ALA 4 N ) 0.92430 ( PROT ALA 4 H ) 0.73944 ( PROT ALA 4 CA ) 0.92430 ( PROT ALA 4 CB ) 0.73944 ( PROT ALA 4 C ) 0.92430 ( PROT ALA 4 O ) 0.92430 ( PROT VAL 5 N ) 0.92430 ( PROT VAL 5 H ) 0.73944 ( PROT VAL 5 CA ) 0.92430 ( PROT VAL 5 CB ) 0.73944 ( PROT VAL 5 CG1 ) 0.73944 ( PROT VAL 5 CG2 ) 0.73944 ( PROT VAL 5 C ) 0.92430 ( PROT VAL 5 O ) 0.92430 ( PROT MET 6 N ) 0.92430 ( PROT MET 6 H ) 0.73944 ( PROT MET 6 CA ) 0.92430 ( PROT MET 6 CB ) 0.73944 ( PROT MET 6 CG ) 0.73944 ( PROT MET 6 SD ) 0.73944 ( PROT MET 6 CE ) 0.73944 ( PROT MET 6 C ) 0.92430 ( PROT MET 6 O ) 0.92430 ( PROT ILE 7 N ) 0.92430 ( PROT ILE 7 H ) 0.73944 ( PROT ILE 7 CA ) 0.92430 ( PROT ILE 7 CB ) 0.73944 ( PROT ILE 7 CG2 ) 0.73944 ( PROT ILE 7 CG1 ) 0.73944 ( PROT ILE 7 CD ) 0.73944 ( PROT ILE 7 C ) 0.92430 ( PROT ILE 7 O ) 0.92430 ( PROT GLY 8 N ) 0.92430 ( PROT GLY 8 H ) 0.73944 ( PROT GLY 8 CA ) 0.92430 ( PROT GLY 8 C ) 0.92430 ( PROT GLY 8 O ) 0.92430 ( PROT ALA 9 N ) 0.92430 ( PROT ALA 9 H ) 0.73944 ( PROT ALA 9 CA ) 0.92430 ( PROT ALA 9 CB ) 0.73944 ( PROT ALA 9 C ) 0.92430 ( PROT ALA 9 O ) 0.92430 ( PROT CYS 10 N ) 0.92430 ( PROT CYS 10 H ) 0.73944 ( PROT CYS 10 CA ) 0.92430 ( PROT CYS 10 CB ) 0.73944 ( PROT CYS 10 SG ) 0.73944 ( PROT CYS 10 C ) 0.92430 ( PROT CYS 10 O ) 0.92430 ( PROT PHE 11 N ) 0.92430 ( PROT PHE 11 H ) 0.73944 ( PROT PHE 11 CA ) 0.92430 ( PROT PHE 11 CB ) 0.73944 ( PROT PHE 11 CG ) 0.73944 ( PROT PHE 11 CD1 ) 0.73944 ( PROT PHE 11 CD2 ) 0.73944 ( PROT PHE 11 CE1 ) 0.73944 ( PROT PHE 11 CE2 ) 0.73944 ( PROT PHE 11 CZ ) 0.73944 ( PROT PHE 11 C ) 0.92430 ( PROT PHE 11 O ) 0.92430 ( PROT LEU 12 N ) 0.92430 ( PROT LEU 12 H ) 0.73944 ( PROT LEU 12 CA ) 0.92430 ( PROT LEU 12 CB ) 0.73944 ( PROT LEU 12 CG ) 0.73944 ( PROT LEU 12 CD1 ) 0.73944 ( PROT LEU 12 CD2 ) 0.73944 ( PROT LEU 12 C ) 0.92430 ( PROT LEU 12 O ) 0.92430 ( PROT ILE 13 N ) 0.92430 ( PROT ILE 13 H ) 0.73944 ( PROT ILE 13 CA ) 0.92430 ( PROT ILE 13 CB ) 0.73944 ( PROT ILE 13 CG2 ) 0.73944 ( PROT ILE 13 CG1 ) 0.73944 ( PROT ILE 13 CD ) 0.73944 ( PROT ILE 13 C ) 0.92430 ( PROT ILE 13 O ) 0.92430 ( PROT ASP 14 N ) 0.92430 ( PROT ASP 14 H ) 0.73944 ( PROT ASP 14 CA ) 0.92430 ( PROT ASP 14 CB ) 0.73944 ( PROT ASP 14 CG ) 0.73944 ( PROT ASP 14 OD1 ) 0.73944 ( PROT ASP 14 OD2 ) 0.73944 ( PROT ASP 14 C ) 0.92430 ( PROT ASP 14 O ) 0.92430 ( PROT PHE 15 N ) 0.92430 ( PROT PHE 15 H ) 0.73944 ( PROT PHE 15 CA ) 0.92430 ( PROT PHE 15 CB ) 0.73944 ( PROT PHE 15 CG ) 0.73944 ( PROT PHE 15 CD1 ) 0.73944 ( PROT PHE 15 CD2 ) 0.73944 ( PROT PHE 15 CE1 ) 0.73944 ( PROT PHE 15 CE2 ) 0.73944 ( PROT PHE 15 CZ ) 0.73944 ( PROT PHE 15 C ) 0.92430 ( PROT PHE 15 O ) 0.92430 ( PROT MET 16 N ) 0.92430 ( PROT MET 16 H ) 0.73944 ( PROT MET 16 CA ) 0.92430 ( PROT MET 16 CB ) 0.73944 ( PROT MET 16 CG ) 0.73944 ( PROT MET 16 SD ) 0.73944 ( PROT MET 16 CE ) 0.73944 ( PROT MET 16 C ) 0.92430 ( PROT MET 16 O ) 0.92430 ( PROT PHE 17 N ) 0.92430 ( PROT PHE 17 H ) 0.73944 ( PROT PHE 17 CA ) 0.92430 ( PROT PHE 17 CB ) 0.73944 ( PROT PHE 17 CG ) 0.73944 ( PROT PHE 17 CD1 ) 0.73944 ( PROT PHE 17 CD2 ) 0.73944 ( PROT PHE 17 CE1 ) 0.73944 ( PROT PHE 17 CE2 ) 0.73944 ( PROT PHE 17 CZ ) 0.73944 ( PROT PHE 17 C ) 0.92430 ( PROT PHE 17 O ) 0.92430 ( PROT PHE 18 N ) 0.92430 ( PROT PHE 18 H ) 0.73944 ( PROT PHE 18 CA ) 0.92430 ( PROT PHE 18 CB ) 0.73944 ( PROT PHE 18 CG ) 0.73944 ( PROT PHE 18 CD1 ) 0.73944 ( PROT PHE 18 CD2 ) 0.73944 ( PROT PHE 18 CE1 ) 0.73944 ( PROT PHE 18 CE2 ) 0.73944 ( PROT PHE 18 CZ ) 0.73944 ( PROT PHE 18 C ) 0.92430 ( PROT PHE 18 O ) 0.92430 ( PROT GLU 19 N ) 0.92430 ( PROT GLU 19 H ) 0.73944 ( PROT GLU 19 CA ) 0.92430 ( PROT GLU 19 CB ) 0.73944 ( PROT GLU 19 CG ) 0.73944 ( PROT GLU 19 CD ) 0.73944 ( PROT GLU 19 OE1 ) 0.73944 ( PROT GLU 19 OE2 ) 0.73944 ( PROT GLU 19 C ) 0.92430 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.41004 5.26031 -8.66946 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00099 -0.00040 -0.00223 ROTATION MATRIX 1.000000 -0.000115 0.000057 0.000115 1.000000 0.000268 -0.000057 -0.000268 1.000000 AXIS OF ROTATION IS 0.902360 -0.190861 -0.386417 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 53.4636 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.541993 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.5420" Parameter: A <- "0.5420" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.70713 5.22390 -8.78430 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00771 0.04052 -0.01007 ROTATION MATRIX 0.999777 0.017274 0.012158 -0.017080 0.999728 -0.015884 -0.012429 0.015672 0.999800 AXIS OF ROTATION IS -0.598442 -0.466281 0.651498 ANGLE IS 1.51 CENTER OF ROTATION 8.888059 5.206032 -9.572536 SHIFT IS -0.030066 TOTAL SQUARE DIFF IS 2.6083 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.370510 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.5420" RDCMND substituted energy or value "?RMS" to " 0.3705" Parameter: A <- "0.5420 0.3705" 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 0.5420 0.3705 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 " 66.15" Parameter: H <- "66.15" 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 -0.97037 66.15168 0.77904 ENER INTERN> 4.82833 24.07237 0.00000 23.49826 4.58344 ENER EXTERN> -80.29346 22.34069 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 " -0.97" Parameter: B <- "-0.97" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 22.34" Parameter: C <- "22.34" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -80.29" Parameter: C <- " -57.95" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -57.95" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.83" Parameter: D <- "4.83" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 24.07" Parameter: D <- " 28.90" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 23.50" Parameter: D <- " 52.40" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.58" Parameter: D <- " 56.98" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 56.98" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 7800 ENER= -0.97 GRMS= 0.78 ELEC= 22.34 VDW= -80.29 RDTITL> *EXTERNAL= -57.95 INTERNAL= 56.98 USER= 0.00 HARM= 66.15 RDTITL> *BOND= 4.83 ANGL= 24.07 DIHE= 23.50 IMPR= 4.58 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 11021 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 11006 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 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 43.90980 -44.88017 0.29165 0.02000 MINI INTERN> 4.82833 24.07237 0.00000 23.49826 4.58344 MINI EXTERN> -80.29346 22.34069 0.00000 0.00000 0.00000 MINI CONSTR> 44.88017 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 67.49507 -23.58527 16.51017 0.00864 MINI INTERN> 30.01156 22.51599 0.00000 24.72709 4.22939 MINI EXTERN> -85.79756 24.70106 0.00000 0.00000 0.00000 MINI CONSTR> 47.10755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10997 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 42.78091 24.71416 0.56579 0.00156 MINI INTERN> 5.04046 23.83676 0.00000 24.21603 4.63559 MINI EXTERN> -85.67179 23.47975 0.00000 0.00000 0.00000 MINI CONSTR> 47.24412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 42.68989 0.09102 0.57590 0.00067 MINI INTERN> 4.94066 24.06461 0.00000 24.08691 4.66273 MINI EXTERN> -85.73169 23.34223 0.00000 0.00000 0.00000 MINI CONSTR> 47.32444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10995 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 42.60662 0.08327 0.38565 0.00029 MINI INTERN> 4.93521 23.87800 0.00000 24.09663 4.61136 MINI EXTERN> -85.64198 23.34643 0.00000 0.00000 0.00000 MINI CONSTR> 47.38097 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 42.53665 0.06997 0.32237 0.00030 MINI INTERN> 4.88506 23.87571 0.00000 24.05214 4.60601 MINI EXTERN> -85.62149 23.28882 0.00000 0.00000 0.00000 MINI CONSTR> 47.45041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10993 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 42.48367 0.05298 0.44409 0.00031 MINI INTERN> 4.84519 23.85292 0.00000 24.02251 4.59221 MINI EXTERN> -85.60619 23.25607 0.00000 0.00000 0.00000 MINI CONSTR> 47.52095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 42.41947 0.06420 0.48323 0.00032 MINI INTERN> 4.82586 23.81734 0.00000 23.98306 4.58153 MINI EXTERN> -85.61837 23.22687 0.00000 0.00000 0.00000 MINI CONSTR> 47.60319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10991 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 42.36114 0.05833 0.53003 0.00034 MINI INTERN> 4.83019 23.76327 0.00000 23.94899 4.57116 MINI EXTERN> -85.64948 23.21396 0.00000 0.00000 0.00000 MINI CONSTR> 47.68305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 42.30464 0.05650 0.49935 0.00035 MINI INTERN> 4.80324 23.74807 0.00000 23.91720 4.56783 MINI EXTERN> -85.68142 23.19679 0.00000 0.00000 0.00000 MINI CONSTR> 47.75293 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10990 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 42.24428 0.06036 0.50900 0.00036 MINI INTERN> 4.80858 23.70421 0.00000 23.87949 4.56088 MINI EXTERN> -85.72602 23.18160 0.00000 0.00000 0.00000 MINI CONSTR> 47.83555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 42.16784 0.07645 0.16436 0.00016 MINI INTERN> 4.86571 23.66204 0.00000 23.81742 4.58487 MINI EXTERN> -85.83366 23.16162 0.00000 0.00000 0.00000 MINI CONSTR> 47.90985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10987 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 42.14267 0.02517 0.57053 0.00039 MINI INTERN> 4.81294 23.63119 0.00000 23.81787 4.54785 MINI EXTERN> -85.81565 23.16408 0.00000 0.00000 0.00000 MINI CONSTR> 47.98438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 42.06358 0.07908 0.18266 0.00017 MINI INTERN> 4.85796 23.59985 0.00000 23.75343 4.57618 MINI EXTERN> -85.92797 23.14664 0.00000 0.00000 0.00000 MINI CONSTR> 48.05749 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10985 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 42.04731 0.01627 0.60529 0.00042 MINI INTERN> 4.77246 23.59408 0.00000 23.76207 4.53592 MINI EXTERN> -85.89437 23.15069 0.00000 0.00000 0.00000 MINI CONSTR> 48.12646 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 41.96503 0.08228 0.21177 0.00018 MINI INTERN> 4.85445 23.54072 0.00000 23.69076 4.56806 MINI EXTERN> -86.02415 23.13400 0.00000 0.00000 0.00000 MINI CONSTR> 48.20119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10984 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 41.92216 0.04287 0.14958 0.00019 MINI INTERN> 4.84071 23.50941 0.00000 23.67071 4.55839 MINI EXTERN> -86.05351 23.13652 0.00000 0.00000 0.00000 MINI CONSTR> 48.25992 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 41.87424 0.04792 0.25360 0.00019 MINI INTERN> 4.85994 23.47936 0.00000 23.62966 4.56100 MINI EXTERN> -86.11984 23.12680 0.00000 0.00000 0.00000 MINI CONSTR> 48.33732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10984 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 41.83197 0.04227 0.14276 0.00020 MINI INTERN> 4.83303 23.45482 0.00000 23.61435 4.54830 MINI EXTERN> -86.13906 23.12809 0.00000 0.00000 0.00000 MINI CONSTR> 48.39245 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 41.78486 0.04711 0.29032 0.00021 MINI INTERN> 4.85750 23.42574 0.00000 23.56896 4.55322 MINI EXTERN> -86.21163 23.11779 0.00000 0.00000 0.00000 MINI CONSTR> 48.47327 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10984 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 41.73704 0.04783 0.17982 0.00022 MINI INTERN> 4.82954 23.40128 0.00000 23.54870 4.54160 MINI EXTERN> -86.23850 23.11805 0.00000 0.00000 0.00000 MINI CONSTR> 48.53635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 41.69146 0.04557 0.21666 0.00022 MINI INTERN> 4.81648 23.38166 0.00000 23.51681 4.53833 MINI EXTERN> -86.28469 23.11550 0.00000 0.00000 0.00000 MINI CONSTR> 48.60739 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10983 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 41.65641 0.03505 0.32813 0.00023 MINI INTERN> 4.83903 23.35699 0.00000 23.48124 4.54063 MINI EXTERN> -86.33825 23.10610 0.00000 0.00000 0.00000 MINI CONSTR> 48.67067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 41.61503 0.04138 0.36055 0.00024 MINI INTERN> 4.83938 23.33295 0.00000 23.45331 4.53433 MINI EXTERN> -86.37768 23.09665 0.00000 0.00000 0.00000 MINI CONSTR> 48.73609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10980 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 41.57810 0.03693 0.37818 0.00025 MINI INTERN> 4.84997 23.30096 0.00000 23.42218 4.53324 MINI EXTERN> -86.42355 23.09940 0.00000 0.00000 0.00000 MINI CONSTR> 48.79591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 41.53936 0.03873 0.36117 0.00026 MINI INTERN> 4.84231 23.27978 0.00000 23.39599 4.52822 MINI EXTERN> -86.45621 23.09587 0.00000 0.00000 0.00000 MINI CONSTR> 48.85342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10980 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 41.49937 0.03999 0.40461 0.00027 MINI INTERN> 4.82646 23.27025 0.00000 23.36581 4.52479 MINI EXTERN> -86.49642 23.08782 0.00000 0.00000 0.00000 MINI CONSTR> 48.92067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 41.46224 0.03713 0.39589 0.00028 MINI INTERN> 4.81381 23.24919 0.00000 23.34049 4.51999 MINI EXTERN> -86.52791 23.08970 0.00000 0.00000 0.00000 MINI CONSTR> 48.97696 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10980 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 41.41464 0.04760 0.13413 0.00012 MINI INTERN> 4.79438 23.19683 0.00000 23.33027 4.49662 MINI EXTERN> -86.53048 23.09948 0.00000 0.00000 0.00000 MINI CONSTR> 49.02755 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 41.39433 0.02032 0.42705 0.00030 MINI INTERN> 4.83255 23.19555 0.00000 23.28449 4.51283 MINI EXTERN> -86.59972 23.08108 0.00000 0.00000 0.00000 MINI CONSTR> 49.08757 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10980 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 41.34130 0.05303 0.12858 0.00013 MINI INTERN> 4.79010 23.15254 0.00000 23.27448 4.48837 MINI EXTERN> -86.59918 23.09248 0.00000 0.00000 0.00000 MINI CONSTR> 49.14250 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 41.32464 0.01666 0.46664 0.00032 MINI INTERN> 4.80163 23.17125 0.00000 23.23045 4.50487 MINI EXTERN> -86.66217 23.07562 0.00000 0.00000 0.00000 MINI CONSTR> 49.20298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10980 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 41.27143 0.05321 0.15069 0.00014 MINI INTERN> 4.79040 23.10267 0.00000 23.22063 4.47788 MINI EXTERN> -86.66202 23.08773 0.00000 0.00000 0.00000 MINI CONSTR> 49.25412 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 41.26219 0.00924 0.51057 0.00034 MINI INTERN> 4.79571 23.13212 0.00000 23.17796 4.49714 MINI EXTERN> -86.72202 23.07277 0.00000 0.00000 0.00000 MINI CONSTR> 49.30852 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10979 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 41.20776 0.05442 0.17897 0.00015 MINI INTERN> 4.78122 23.06402 0.00000 23.17053 4.46858 MINI EXTERN> -86.71758 23.08354 0.00000 0.00000 0.00000 MINI CONSTR> 49.35745 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 41.17966 0.02810 0.12501 0.00015 MINI INTERN> 4.77152 23.06058 0.00000 23.14776 4.46879 MINI EXTERN> -86.74447 23.07530 0.00000 0.00000 0.00000 MINI CONSTR> 49.40019 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10978 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 41.14765 0.03201 0.20927 0.00016 MINI INTERN> 4.76897 23.03131 0.00000 23.12265 4.45964 MINI EXTERN> -86.76878 23.07749 0.00000 0.00000 0.00000 MINI CONSTR> 49.45638 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 41.11684 0.03081 0.16284 0.00017 MINI INTERN> 4.76882 23.01858 0.00000 23.09691 4.45861 MINI EXTERN> -86.79826 23.06856 0.00000 0.00000 0.00000 MINI CONSTR> 49.50362 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10978 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 41.08818 0.02866 0.18410 0.00017 MINI INTERN> 4.75914 23.00399 0.00000 23.07402 4.45365 MINI EXTERN> -86.82100 23.06669 0.00000 0.00000 0.00000 MINI CONSTR> 49.55169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 41.05943 0.02874 0.19673 0.00018 MINI INTERN> 4.74930 22.98970 0.00000 23.04998 4.44976 MINI EXTERN> -86.84527 23.06624 0.00000 0.00000 0.00000 MINI CONSTR> 49.59974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10978 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 41.03418 0.02525 0.26889 0.00019 MINI INTERN> 4.74575 22.97359 0.00000 23.02875 4.44298 MINI EXTERN> -86.86437 23.06073 0.00000 0.00000 0.00000 MINI CONSTR> 49.64676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 41.00684 0.02734 0.29728 0.00019 MINI INTERN> 4.73504 22.95866 0.00000 23.00339 4.44038 MINI EXTERN> -86.89048 23.06538 0.00000 0.00000 0.00000 MINI CONSTR> 49.69447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10977 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 40.98084 0.02600 0.30308 0.00020 MINI INTERN> 4.72471 22.94948 0.00000 22.98276 4.43531 MINI EXTERN> -86.90875 23.05850 0.00000 0.00000 0.00000 MINI CONSTR> 49.73882 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 40.95470 0.02614 0.32682 0.00021 MINI INTERN> 4.73047 22.93297 0.00000 22.95928 4.43109 MINI EXTERN> -86.93165 23.04790 0.00000 0.00000 0.00000 MINI CONSTR> 49.78463 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10977 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 40.92860 0.02609 0.30559 0.00021 MINI INTERN> 4.71308 22.92396 0.00000 22.93726 4.42876 MINI EXTERN> -86.95287 23.05161 0.00000 0.00000 0.00000 MINI CONSTR> 49.82680 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 40.90340 0.02520 0.34353 0.00022 MINI INTERN> 4.73459 22.90189 0.00000 22.91162 4.42560 MINI EXTERN> -86.97882 23.03643 0.00000 0.00000 0.00000 MINI CONSTR> 49.87211 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10977 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 40.87738 0.02602 0.31799 0.00023 MINI INTERN> 4.70787 22.89595 0.00000 22.89164 4.42116 MINI EXTERN> -86.99542 23.04112 0.00000 0.00000 0.00000 MINI CONSTR> 49.91506 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 40.85166 0.02572 0.33320 0.00024 MINI INTERN> 4.70261 22.87973 0.00000 22.86681 4.41799 MINI EXTERN> -87.01872 23.04257 0.00000 0.00000 0.00000 MINI CONSTR> 49.96068 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10976 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 40.81907 0.03259 0.11136 0.00010 MINI INTERN> 4.74384 22.84822 0.00000 22.83321 4.42532 MINI EXTERN> -87.06275 23.03088 0.00000 0.00000 0.00000 MINI CONSTR> 50.00036 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 40.80644 0.01263 0.37193 0.00026 MINI INTERN> 4.68911 22.85832 0.00000 22.82498 4.41017 MINI EXTERN> -87.05507 23.03544 0.00000 0.00000 0.00000 MINI CONSTR> 50.04350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10976 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 40.78357 0.02288 0.41954 0.00027 MINI INTERN> 4.72129 22.83244 0.00000 22.79858 4.40745 MINI EXTERN> -87.08147 23.01797 0.00000 0.00000 0.00000 MINI CONSTR> 50.08729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 40.74613 0.03743 0.12372 0.00011 MINI INTERN> 4.74086 22.80220 0.00000 22.76399 4.41574 MINI EXTERN> -87.12606 23.02166 0.00000 0.00000 0.00000 MINI CONSTR> 50.12773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10975 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 40.72506 0.02108 0.10292 0.00012 MINI INTERN> 4.73553 22.79022 0.00000 22.74581 4.41150 MINI EXTERN> -87.14064 23.01886 0.00000 0.00000 0.00000 MINI CONSTR> 50.16378 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 40.70262 0.02244 0.10580 0.00012 MINI INTERN> 4.73550 22.77529 0.00000 22.72381 4.40859 MINI EXTERN> -87.16036 23.01621 0.00000 0.00000 0.00000 MINI CONSTR> 50.20357 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10974 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 40.68019 0.02243 0.10276 0.00013 MINI INTERN> 4.73214 22.76183 0.00000 22.70246 4.40520 MINI EXTERN> -87.17860 23.01387 0.00000 0.00000 0.00000 MINI CONSTR> 50.24329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 40.65687 0.02332 0.17214 0.00013 MINI INTERN> 4.74673 22.74106 0.00000 22.67444 4.40410 MINI EXTERN> -87.20607 23.00795 0.00000 0.00000 0.00000 MINI CONSTR> 50.28866 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10974 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 40.63529 0.02158 0.13618 0.00014 MINI INTERN> 4.73416 22.73108 0.00000 22.65614 4.39988 MINI EXTERN> -87.21988 23.00859 0.00000 0.00000 0.00000 MINI CONSTR> 50.32532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 40.61482 0.02047 0.15049 0.00014 MINI INTERN> 4.74001 22.71487 0.00000 22.63428 4.39737 MINI EXTERN> -87.23930 23.00441 0.00000 0.00000 0.00000 MINI CONSTR> 50.36317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10973 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 40.59338 0.02144 0.14563 0.00015 MINI INTERN> 4.73845 22.70195 0.00000 22.61353 4.39374 MINI EXTERN> -87.25598 22.99991 0.00000 0.00000 0.00000 MINI CONSTR> 50.40178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 40.57356 0.01983 0.17529 0.00015 MINI INTERN> 4.74226 22.68584 0.00000 22.59106 4.39173 MINI EXTERN> -87.27620 22.99886 0.00000 0.00000 0.00000 MINI CONSTR> 50.44000 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10973 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 40.55573 0.01783 0.23106 0.00016 MINI INTERN> 4.75494 22.66827 0.00000 22.56849 4.38995 MINI EXTERN> -87.29675 22.99369 0.00000 0.00000 0.00000 MINI CONSTR> 50.47714 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 40.53583 0.01990 0.25192 0.00016 MINI INTERN> 4.74396 22.65801 0.00000 22.54791 4.38697 MINI EXTERN> -87.31332 22.99672 0.00000 0.00000 0.00000 MINI CONSTR> 50.51557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10973 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 40.51753 0.01829 0.26067 0.00017 MINI INTERN> 4.75720 22.64036 0.00000 22.52660 4.38462 MINI EXTERN> -87.33181 22.98961 0.00000 0.00000 0.00000 MINI CONSTR> 50.55096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 40.49804 0.01950 0.27328 0.00018 MINI INTERN> 4.75771 22.62730 0.00000 22.50556 4.38157 MINI EXTERN> -87.34870 22.98584 0.00000 0.00000 0.00000 MINI CONSTR> 50.58876 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10973 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 40.47937 0.01867 0.25985 0.00018 MINI INTERN> 4.75259 22.61635 0.00000 22.48712 4.37850 MINI EXTERN> -87.36278 22.98505 0.00000 0.00000 0.00000 MINI CONSTR> 50.62255 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 40.46058 0.01879 0.28347 0.00019 MINI INTERN> 4.75517 22.60436 0.00000 22.46682 4.37485 MINI EXTERN> -87.37805 22.97725 0.00000 0.00000 0.00000 MINI CONSTR> 50.66018 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10973 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 40.43691 0.02367 0.09391 0.00008 MINI INTERN> 4.70471 22.61104 0.00000 22.45784 4.36633 MINI EXTERN> -87.37530 22.98109 0.00000 0.00000 0.00000 MINI CONSTR> 50.69120 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 40.42647 0.01044 0.29945 0.00020 MINI INTERN> 4.75025 22.58014 0.00000 22.42794 4.37028 MINI EXTERN> -87.40929 22.97950 0.00000 0.00000 0.00000 MINI CONSTR> 50.72765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 40.40178 0.02469 0.09791 0.00009 MINI INTERN> 4.70012 22.58909 0.00000 22.42034 4.36051 MINI EXTERN> -87.40371 22.97651 0.00000 0.00000 0.00000 MINI CONSTR> 50.75891 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 40.39431 0.00747 0.33690 0.00022 MINI INTERN> 4.76133 22.55545 0.00000 22.39222 4.36350 MINI EXTERN> -87.43591 22.96450 0.00000 0.00000 0.00000 MINI CONSTR> 50.79323 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 40.36827 0.02604 0.10405 0.00010 MINI INTERN> 4.69563 22.56825 0.00000 22.38414 4.35478 MINI EXTERN> -87.43059 22.97169 0.00000 0.00000 0.00000 MINI CONSTR> 50.82437 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 40.36257 0.00570 0.34858 0.00024 MINI INTERN> 4.76611 22.52970 0.00000 22.35409 4.35920 MINI EXTERN> -87.46621 22.96181 0.00000 0.00000 0.00000 MINI CONSTR> 50.85786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 40.33550 0.02708 0.12161 0.00010 MINI INTERN> 4.69089 22.54810 0.00000 22.34828 4.34874 MINI EXTERN> -87.45637 22.96618 0.00000 0.00000 0.00000 MINI CONSTR> 50.88968 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 40.32111 0.01439 0.08840 0.00011 MINI INTERN> 4.69483 22.53595 0.00000 22.33142 4.34760 MINI EXTERN> -87.47067 22.96497 0.00000 0.00000 0.00000 MINI CONSTR> 50.91700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10971 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 40.30541 0.01570 0.09220 0.00011 MINI INTERN> 4.69212 22.52643 0.00000 22.31409 4.34470 MINI EXTERN> -87.48291 22.96247 0.00000 0.00000 0.00000 MINI CONSTR> 50.94850 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 40.28917 0.01624 0.14618 0.00011 MINI INTERN> 4.68219 22.52005 0.00000 22.29653 4.34020 MINI EXTERN> -87.49301 22.95955 0.00000 0.00000 0.00000 MINI CONSTR> 50.98366 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10971 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 40.27341 0.01576 0.11228 0.00012 MINI INTERN> 4.68529 22.50674 0.00000 22.27798 4.33880 MINI EXTERN> -87.50833 22.95905 0.00000 0.00000 0.00000 MINI CONSTR> 51.01387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 40.25853 0.01488 0.12854 0.00012 MINI INTERN> 4.68142 22.49865 0.00000 22.26139 4.33549 MINI EXTERN> -87.51904 22.95564 0.00000 0.00000 0.00000 MINI CONSTR> 51.04497 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10971 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 40.24285 0.01568 0.11926 0.00013 MINI INTERN> 4.68229 22.48701 0.00000 22.24312 4.33307 MINI EXTERN> -87.53264 22.95332 0.00000 0.00000 0.00000 MINI CONSTR> 51.07667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 40.22729 0.01556 0.12812 0.00013 MINI INTERN> 4.68023 22.47687 0.00000 22.22482 4.33018 MINI EXTERN> -87.54521 22.95117 0.00000 0.00000 0.00000 MINI CONSTR> 51.10922 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10971 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 40.21466 0.01263 0.19671 0.00014 MINI INTERN> 4.67089 22.47209 0.00000 22.20975 4.32615 MINI EXTERN> -87.55348 22.94919 0.00000 0.00000 0.00000 MINI CONSTR> 51.14007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 40.19983 0.01483 0.20880 0.00014 MINI INTERN> 4.67185 22.46100 0.00000 22.19063 4.32369 MINI EXTERN> -87.56657 22.94732 0.00000 0.00000 0.00000 MINI CONSTR> 51.17191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10971 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 40.18676 0.01307 0.22866 0.00015 MINI INTERN> 4.66786 22.45299 0.00000 22.17587 4.32065 MINI EXTERN> -87.57693 22.94497 0.00000 0.00000 0.00000 MINI CONSTR> 51.20136 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 40.17326 0.01350 0.21728 0.00015 MINI INTERN> 4.66731 22.44416 0.00000 22.15917 4.31848 MINI EXTERN> -87.58788 22.94311 0.00000 0.00000 0.00000 MINI CONSTR> 51.22891 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10971 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 40.16027 0.01299 0.24285 0.00016 MINI INTERN> 4.66958 22.43227 0.00000 22.14337 4.31640 MINI EXTERN> -87.60090 22.94108 0.00000 0.00000 0.00000 MINI CONSTR> 51.25847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 40.14679 0.01348 0.22662 0.00016 MINI INTERN> 4.66366 22.42648 0.00000 22.12740 4.31330 MINI EXTERN> -87.60953 22.93895 0.00000 0.00000 0.00000 MINI CONSTR> 51.28651 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 40.13326 0.01352 0.23689 0.00017 MINI INTERN> 4.66107 22.41715 0.00000 22.11033 4.31078 MINI EXTERN> -87.62082 22.93799 0.00000 0.00000 0.00000 MINI CONSTR> 51.31676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 40.11583 0.01743 0.07910 0.00007 MINI INTERN> 4.68740 22.39239 0.00000 22.08880 4.31245 MINI EXTERN> -87.64333 22.93416 0.00000 0.00000 0.00000 MINI CONSTR> 51.34396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 40.10904 0.00679 0.26770 0.00018 MINI INTERN> 4.65564 22.40101 0.00000 22.07910 4.30586 MINI EXTERN> -87.64107 22.93565 0.00000 0.00000 0.00000 MINI CONSTR> 51.37285 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 40.09785 0.01119 0.31011 0.00019 MINI INTERN> 4.68304 22.38279 0.00000 22.06045 4.30392 MINI EXTERN> -87.65769 22.92467 0.00000 0.00000 0.00000 MINI CONSTR> 51.40068 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 40.08550 0.01235 0.29265 0.00020 MINI INTERN> 4.66059 22.38268 0.00000 22.04800 4.30048 MINI EXTERN> -87.66212 22.92800 0.00000 0.00000 0.00000 MINI CONSTR> 51.42787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 40.06575 0.01975 0.09279 0.00008 MINI INTERN> 4.68609 22.35550 0.00000 22.02522 4.30333 MINI EXTERN> -87.68629 22.92676 0.00000 0.00000 0.00000 MINI CONSTR> 51.45514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 40.05486 0.01089 0.07326 0.00009 MINI INTERN> 4.68190 22.34961 0.00000 22.01256 4.30073 MINI EXTERN> -87.69366 22.92500 0.00000 0.00000 0.00000 MINI CONSTR> 51.47872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 40.04296 0.01190 0.07633 0.00009 MINI INTERN> 4.68174 22.34055 0.00000 21.99704 4.29859 MINI EXTERN> -87.70405 22.92338 0.00000 0.00000 0.00000 MINI CONSTR> 51.50572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 40.03125 0.01172 0.07356 0.00009 MINI INTERN> 4.67998 22.33251 0.00000 21.98212 4.29622 MINI EXTERN> -87.71353 22.92171 0.00000 0.00000 0.00000 MINI CONSTR> 51.53223 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 40.01884 0.01241 0.12626 0.00010 MINI INTERN> 4.68777 22.31908 0.00000 21.96304 4.29457 MINI EXTERN> -87.72796 22.91913 0.00000 0.00000 0.00000 MINI CONSTR> 51.56321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10972 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 40.00730 0.01154 0.09369 0.00010 MINI INTERN> 4.67991 22.31399 0.00000 21.94992 4.29186 MINI EXTERN> -87.73478 22.91837 0.00000 0.00000 0.00000 MINI CONSTR> 51.58804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 39.99637 0.01093 0.10961 0.00011 MINI INTERN> 4.68382 22.30385 0.00000 21.93447 4.28990 MINI EXTERN> -87.74572 22.91585 0.00000 0.00000 0.00000 MINI CONSTR> 51.61419 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10970 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 39.98535 0.01101 0.11320 0.00011 MINI INTERN> 4.68076 22.29641 0.00000 21.91990 4.28772 MINI EXTERN> -87.75460 22.91506 0.00000 0.00000 0.00000 MINI CONSTR> 51.64010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 39.97604 0.00931 0.16332 0.00011 MINI INTERN> 4.68969 22.28496 0.00000 21.90422 4.28624 MINI EXTERN> -87.76650 22.91207 0.00000 0.00000 0.00000 MINI CONSTR> 51.66537 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10970 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 39.96436 0.01169 0.12002 0.00012 MINI INTERN> 4.67777 22.28120 0.00000 21.89175 4.28345 MINI EXTERN> -87.77219 22.91247 0.00000 0.00000 0.00000 MINI CONSTR> 51.68991 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 39.96436 0.01169 0.12002 0.00014 STPD INTERN> 4.67777 22.28120 0.00000 21.89175 4.28345 STPD EXTERN> -87.77219 22.91247 0.00000 0.00000 0.00000 STPD CONSTR> 51.68991 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 10970 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10970 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 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 39.96436 0.01169 0.12002 0.00000 MINI INTERN> 4.67777 22.28120 0.00000 21.89175 4.28345 MINI EXTERN> -87.77219 22.91247 0.00000 0.00000 0.00000 MINI CONSTR> 51.68991 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 39.29623 0.66813 0.06325 0.01103 MINI INTERN> 4.60383 21.33161 0.00000 20.20618 4.03613 MINI EXTERN> -89.05326 22.80290 0.00000 0.00000 0.00000 MINI CONSTR> 55.36885 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 39.29012 0.00611 0.07757 0.00594 MINI INTERN> 4.55680 21.35162 0.00000 20.17813 3.98749 MINI EXTERN> -88.81434 22.73560 0.00000 0.00000 0.00000 MINI CONSTR> 55.29482 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 39.27738 0.01275 0.09206 0.01323 MINI INTERN> 4.54591 21.30929 0.00000 20.09308 4.00886 MINI EXTERN> -88.42521 22.70852 0.00000 0.00000 0.00000 MINI CONSTR> 55.03692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 39.26767 0.00971 0.06049 0.00765 MINI INTERN> 4.59338 21.41026 0.00000 20.08613 3.98770 MINI EXTERN> -88.38717 22.71755 0.00000 0.00000 0.00000 MINI CONSTR> 54.85982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 39.26263 0.00504 0.04975 0.00458 MINI INTERN> 4.60955 21.46077 0.00000 20.10972 3.98441 MINI EXTERN> -88.48287 22.77830 0.00000 0.00000 0.00000 MINI CONSTR> 54.80274 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 39.25987 0.00276 0.03534 0.00339 MINI INTERN> 4.62624 21.44571 0.00000 20.13950 3.99586 MINI EXTERN> -88.53598 22.79856 0.00000 0.00000 0.00000 MINI CONSTR> 54.78998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 39.25816 0.00171 0.02868 0.00339 MINI INTERN> 4.61226 21.43475 0.00000 20.15490 4.00502 MINI EXTERN> -88.55135 22.81234 0.00000 0.00000 0.00000 MINI CONSTR> 54.79023 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 39.25681 0.00135 0.02703 0.00307 MINI INTERN> 4.60202 21.43396 0.00000 20.17492 4.00984 MINI EXTERN> -88.57157 22.81136 0.00000 0.00000 0.00000 MINI CONSTR> 54.79627 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 39.25592 0.00089 0.02057 0.00255 MINI INTERN> 4.60755 21.42999 0.00000 20.16213 4.00870 MINI EXTERN> -88.55980 22.80414 0.00000 0.00000 0.00000 MINI CONSTR> 54.80321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 39.25531 0.00061 0.01911 0.00217 MINI INTERN> 4.60390 21.42800 0.00000 20.15523 4.01195 MINI EXTERN> -88.58437 22.83363 0.00000 0.00000 0.00000 MINI CONSTR> 54.80697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 39.25488 0.00043 0.01261 0.00150 MINI INTERN> 4.60540 21.41185 0.00000 20.14850 4.00837 MINI EXTERN> -88.54941 22.82532 0.00000 0.00000 0.00000 MINI CONSTR> 54.80484 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 39.25461 0.00026 0.01171 0.00123 MINI INTERN> 4.60533 21.41113 0.00000 20.13827 4.00826 MINI EXTERN> -88.53234 22.82127 0.00000 0.00000 0.00000 MINI CONSTR> 54.80269 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> 64 39.25444 0.00017 0.00984 0.02000 CONJ INTERN> 4.60537 21.41692 0.00000 20.13085 4.00741 CONJ EXTERN> -88.54005 22.83087 0.00000 0.00000 0.00000 CONJ CONSTR> 54.80308 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "8400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.48064 ( PROT LYS 1 HT2 ) 0.48064 ( PROT LYS 1 N ) 0.60080 ( PROT LYS 1 HT3 ) 0.48064 ( PROT LYS 1 CA ) 0.60080 ( PROT LYS 1 CB ) 0.48064 ( PROT LYS 1 CG ) 0.48064 ( PROT LYS 1 CD ) 0.48064 ( PROT LYS 1 CE ) 0.48064 ( PROT LYS 1 NZ ) 0.48064 ( PROT LYS 1 HZ1 ) 0.48064 ( PROT LYS 1 HZ2 ) 0.48064 ( PROT LYS 1 HZ3 ) 0.48064 ( PROT LYS 1 C ) 0.60080 ( PROT LYS 1 O ) 0.60080 ( PROT MET 2 N ) 0.60080 ( PROT MET 2 H ) 0.48064 ( PROT MET 2 CA ) 0.60080 ( PROT MET 2 CB ) 0.48064 ( PROT MET 2 CG ) 0.48064 ( PROT MET 2 SD ) 0.48064 ( PROT MET 2 CE ) 0.48064 ( PROT MET 2 C ) 0.60080 ( PROT MET 2 O ) 0.60080 ( PROT LYS 3 N ) 0.60080 ( PROT LYS 3 H ) 0.48064 ( PROT LYS 3 CA ) 0.60080 ( PROT LYS 3 CB ) 0.48064 ( PROT LYS 3 CG ) 0.48064 ( PROT LYS 3 CD ) 0.48064 ( PROT LYS 3 CE ) 0.48064 ( PROT LYS 3 NZ ) 0.48064 ( PROT LYS 3 HZ1 ) 0.48064 ( PROT LYS 3 HZ2 ) 0.48064 ( PROT LYS 3 HZ3 ) 0.48064 ( PROT LYS 3 C ) 0.60080 ( PROT LYS 3 O ) 0.60080 ( PROT ALA 4 N ) 0.60080 ( PROT ALA 4 H ) 0.48064 ( PROT ALA 4 CA ) 0.60080 ( PROT ALA 4 CB ) 0.48064 ( PROT ALA 4 C ) 0.60080 ( PROT ALA 4 O ) 0.60080 ( PROT VAL 5 N ) 0.60080 ( PROT VAL 5 H ) 0.48064 ( PROT VAL 5 CA ) 0.60080 ( PROT VAL 5 CB ) 0.48064 ( PROT VAL 5 CG1 ) 0.48064 ( PROT VAL 5 CG2 ) 0.48064 ( PROT VAL 5 C ) 0.60080 ( PROT VAL 5 O ) 0.60080 ( PROT MET 6 N ) 0.60080 ( PROT MET 6 H ) 0.48064 ( PROT MET 6 CA ) 0.60080 ( PROT MET 6 CB ) 0.48064 ( PROT MET 6 CG ) 0.48064 ( PROT MET 6 SD ) 0.48064 ( PROT MET 6 CE ) 0.48064 ( PROT MET 6 C ) 0.60080 ( PROT MET 6 O ) 0.60080 ( PROT ILE 7 N ) 0.60080 ( PROT ILE 7 H ) 0.48064 ( PROT ILE 7 CA ) 0.60080 ( PROT ILE 7 CB ) 0.48064 ( PROT ILE 7 CG2 ) 0.48064 ( PROT ILE 7 CG1 ) 0.48064 ( PROT ILE 7 CD ) 0.48064 ( PROT ILE 7 C ) 0.60080 ( PROT ILE 7 O ) 0.60080 ( PROT GLY 8 N ) 0.60080 ( PROT GLY 8 H ) 0.48064 ( PROT GLY 8 CA ) 0.60080 ( PROT GLY 8 C ) 0.60080 ( PROT GLY 8 O ) 0.60080 ( PROT ALA 9 N ) 0.60080 ( PROT ALA 9 H ) 0.48064 ( PROT ALA 9 CA ) 0.60080 ( PROT ALA 9 CB ) 0.48064 ( PROT ALA 9 C ) 0.60080 ( PROT ALA 9 O ) 0.60080 ( PROT CYS 10 N ) 0.60080 ( PROT CYS 10 H ) 0.48064 ( PROT CYS 10 CA ) 0.60080 ( PROT CYS 10 CB ) 0.48064 ( PROT CYS 10 SG ) 0.48064 ( PROT CYS 10 C ) 0.60080 ( PROT CYS 10 O ) 0.60080 ( PROT PHE 11 N ) 0.60080 ( PROT PHE 11 H ) 0.48064 ( PROT PHE 11 CA ) 0.60080 ( PROT PHE 11 CB ) 0.48064 ( PROT PHE 11 CG ) 0.48064 ( PROT PHE 11 CD1 ) 0.48064 ( PROT PHE 11 CD2 ) 0.48064 ( PROT PHE 11 CE1 ) 0.48064 ( PROT PHE 11 CE2 ) 0.48064 ( PROT PHE 11 CZ ) 0.48064 ( PROT PHE 11 C ) 0.60080 ( PROT PHE 11 O ) 0.60080 ( PROT LEU 12 N ) 0.60080 ( PROT LEU 12 H ) 0.48064 ( PROT LEU 12 CA ) 0.60080 ( PROT LEU 12 CB ) 0.48064 ( PROT LEU 12 CG ) 0.48064 ( PROT LEU 12 CD1 ) 0.48064 ( PROT LEU 12 CD2 ) 0.48064 ( PROT LEU 12 C ) 0.60080 ( PROT LEU 12 O ) 0.60080 ( PROT ILE 13 N ) 0.60080 ( PROT ILE 13 H ) 0.48064 ( PROT ILE 13 CA ) 0.60080 ( PROT ILE 13 CB ) 0.48064 ( PROT ILE 13 CG2 ) 0.48064 ( PROT ILE 13 CG1 ) 0.48064 ( PROT ILE 13 CD ) 0.48064 ( PROT ILE 13 C ) 0.60080 ( PROT ILE 13 O ) 0.60080 ( PROT ASP 14 N ) 0.60080 ( PROT ASP 14 H ) 0.48064 ( PROT ASP 14 CA ) 0.60080 ( PROT ASP 14 CB ) 0.48064 ( PROT ASP 14 CG ) 0.48064 ( PROT ASP 14 OD1 ) 0.48064 ( PROT ASP 14 OD2 ) 0.48064 ( PROT ASP 14 C ) 0.60080 ( PROT ASP 14 O ) 0.60080 ( PROT PHE 15 N ) 0.60080 ( PROT PHE 15 H ) 0.48064 ( PROT PHE 15 CA ) 0.60080 ( PROT PHE 15 CB ) 0.48064 ( PROT PHE 15 CG ) 0.48064 ( PROT PHE 15 CD1 ) 0.48064 ( PROT PHE 15 CD2 ) 0.48064 ( PROT PHE 15 CE1 ) 0.48064 ( PROT PHE 15 CE2 ) 0.48064 ( PROT PHE 15 CZ ) 0.48064 ( PROT PHE 15 C ) 0.60080 ( PROT PHE 15 O ) 0.60080 ( PROT MET 16 N ) 0.60080 ( PROT MET 16 H ) 0.48064 ( PROT MET 16 CA ) 0.60080 ( PROT MET 16 CB ) 0.48064 ( PROT MET 16 CG ) 0.48064 ( PROT MET 16 SD ) 0.48064 ( PROT MET 16 CE ) 0.48064 ( PROT MET 16 C ) 0.60080 ( PROT MET 16 O ) 0.60080 ( PROT PHE 17 N ) 0.60080 ( PROT PHE 17 H ) 0.48064 ( PROT PHE 17 CA ) 0.60080 ( PROT PHE 17 CB ) 0.48064 ( PROT PHE 17 CG ) 0.48064 ( PROT PHE 17 CD1 ) 0.48064 ( PROT PHE 17 CD2 ) 0.48064 ( PROT PHE 17 CE1 ) 0.48064 ( PROT PHE 17 CE2 ) 0.48064 ( PROT PHE 17 CZ ) 0.48064 ( PROT PHE 17 C ) 0.60080 ( PROT PHE 17 O ) 0.60080 ( PROT PHE 18 N ) 0.60080 ( PROT PHE 18 H ) 0.48064 ( PROT PHE 18 CA ) 0.60080 ( PROT PHE 18 CB ) 0.48064 ( PROT PHE 18 CG ) 0.48064 ( PROT PHE 18 CD1 ) 0.48064 ( PROT PHE 18 CD2 ) 0.48064 ( PROT PHE 18 CE1 ) 0.48064 ( PROT PHE 18 CE2 ) 0.48064 ( PROT PHE 18 CZ ) 0.48064 ( PROT PHE 18 C ) 0.60080 ( PROT PHE 18 O ) 0.60080 ( PROT GLU 19 N ) 0.60080 ( PROT GLU 19 H ) 0.48064 ( PROT GLU 19 CA ) 0.60080 ( PROT GLU 19 CB ) 0.48064 ( PROT GLU 19 CG ) 0.48064 ( PROT GLU 19 CD ) 0.48064 ( PROT GLU 19 OE1 ) 0.48064 ( PROT GLU 19 OE2 ) 0.48064 ( PROT GLU 19 C ) 0.60080 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.40972 5.25918 -8.66899 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00132 0.00073 -0.00270 ROTATION MATRIX 1.000000 -0.000074 0.000099 0.000074 1.000000 0.000281 -0.000099 -0.000281 1.000000 AXIS OF ROTATION IS 0.915713 -0.321408 -0.241180 ANGLE IS 0.02 TOTAL SQUARE DIFF IS 68.3638 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.612883 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.6129" Parameter: A <- "0.6129" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.71024 5.23005 -8.78711 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS 0.00460 0.03437 -0.00725 ROTATION MATRIX 0.999796 0.016797 0.011197 -0.016620 0.999738 -0.015712 -0.011458 0.015523 0.999814 AXIS OF ROTATION IS -0.611907 -0.443840 0.654657 ANGLE IS 1.46 CENTER OF ROTATION 8.957170 5.191458 -9.534600 SHIFT IS -0.022822 TOTAL SQUARE DIFF IS 3.6764 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.439878 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.6129" RDCMND substituted energy or value "?RMS" to " 0.4399" Parameter: A <- "0.6129 0.4399" 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 0.6129 0.4399 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 " 54.80" Parameter: H <- "54.80" 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 -15.54864 54.80308 0.57093 ENER INTERN> 4.60537 21.41692 0.00000 20.13085 4.00741 ENER EXTERN> -88.54005 22.83087 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 " -15.55" Parameter: B <- "-15.55" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 22.83" Parameter: C <- "22.83" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -88.54" Parameter: C <- " -65.71" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -65.71" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.61" Parameter: D <- "4.61" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 21.42" Parameter: D <- " 26.03" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 20.13" Parameter: D <- " 46.16" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 4.01" Parameter: D <- " 50.17" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 50.17" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 8400 ENER= -15.55 GRMS= 0.57 ELEC= 22.83 VDW= -88.54 RDTITL> *EXTERNAL= -65.71 INTERNAL= 50.17 USER= 0.00 HARM= 54.80 RDTITL> *BOND= 4.61 ANGL= 21.42 DIHE= 20.13 IMPR= 4.01 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= -15.55 GRMS= 0.57 ELEC= 22.83 VDW= -88.54 RDTITL> *EXTERNAL= -65.71 INTERNAL= 50.17 USER= 0.00 HARM= 54.80 RDTITL> *BOND= 4.61 ANGL= 21.42 DIHE= 20.13 IMPR= 4.01 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= -15.55 GRMS= 0.57 ELEC= 22.83 VDW= -88.54 RDTITL> *EXTERNAL= -65.71 INTERNAL= 50.17 USER= 0.00 HARM= 54.80 RDTITL> *BOND= 4.61 ANGL= 21.42 DIHE= 20.13 IMPR= 4.01 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 8400 0.6129 0.4399 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "8400" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 10970 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10947 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 21.21386 -36.76249 0.21032 0.02000 MINI INTERN> 4.60537 21.41692 0.00000 20.13085 4.00741 MINI EXTERN> -88.54005 22.83087 0.00000 0.00000 0.00000 MINI CONSTR> 36.76249 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 20.56398 0.64988 0.66604 0.00150 MINI INTERN> 4.87053 21.84469 0.00000 20.69206 4.07549 MINI EXTERN> -93.65739 24.19770 0.00000 0.00000 0.00000 MINI CONSTR> 38.54091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10946 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 20.43629 0.12769 0.34853 0.00065 MINI INTERN> 4.84162 21.47913 0.00000 20.63099 4.05959 MINI EXTERN> -93.07700 23.94651 0.00000 0.00000 0.00000 MINI CONSTR> 38.55546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 20.36385 0.07244 0.25850 0.00028 MINI INTERN> 4.72871 21.47789 0.00000 20.55132 4.05914 MINI EXTERN> -92.80628 23.75657 0.00000 0.00000 0.00000 MINI CONSTR> 38.59650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10944 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 20.31703 0.04683 0.39650 0.00029 MINI INTERN> 4.77191 21.36822 0.00000 20.49382 4.04429 MINI EXTERN> -92.68626 23.67922 0.00000 0.00000 0.00000 MINI CONSTR> 38.64583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 20.27630 0.04073 0.45247 0.00030 MINI INTERN> 4.68685 21.40836 0.00000 20.44442 4.04362 MINI EXTERN> -92.58659 23.58548 0.00000 0.00000 0.00000 MINI CONSTR> 38.69417 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10944 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 20.22319 0.05311 0.13945 0.00013 MINI INTERN> 4.71523 21.29784 0.00000 20.41632 4.03783 MINI EXTERN> -92.54819 23.56790 0.00000 0.00000 0.00000 MINI CONSTR> 38.73625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 20.20501 0.01818 0.52454 0.00032 MINI INTERN> 4.65320 21.34752 0.00000 20.37897 4.03460 MINI EXTERN> -92.52349 23.52138 0.00000 0.00000 0.00000 MINI CONSTR> 38.79283 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10942 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 20.16741 0.03759 0.48989 0.00034 MINI INTERN> 4.63836 21.34243 0.00000 20.34377 4.03240 MINI EXTERN> -92.52732 23.49223 0.00000 0.00000 0.00000 MINI CONSTR> 38.84555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 20.13087 0.03654 0.50217 0.00035 MINI INTERN> 4.62835 21.30868 0.00000 20.31609 4.02847 MINI EXTERN> -92.53006 23.47677 0.00000 0.00000 0.00000 MINI CONSTR> 38.90257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10942 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 20.07299 0.05788 0.16007 0.00015 MINI INTERN> 4.69579 21.16841 0.00000 20.28650 4.01667 MINI EXTERN> -92.52686 23.47817 0.00000 0.00000 0.00000 MINI CONSTR> 38.95431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 20.04292 0.03007 0.12914 0.00016 MINI INTERN> 4.68090 21.15820 0.00000 20.26302 4.01349 MINI EXTERN> -92.53948 23.46607 0.00000 0.00000 0.00000 MINI CONSTR> 39.00073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10941 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 20.01015 0.03277 0.13363 0.00016 MINI INTERN> 4.67889 21.13138 0.00000 20.23701 4.00893 MINI EXTERN> -92.55786 23.45758 0.00000 0.00000 0.00000 MINI CONSTR> 39.05421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 19.97728 0.03287 0.12590 0.00017 MINI INTERN> 4.67197 21.11106 0.00000 20.21167 4.00499 MINI EXTERN> -92.58056 23.44978 0.00000 0.00000 0.00000 MINI CONSTR> 39.10838 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10939 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 19.94365 0.03363 0.22450 0.00017 MINI INTERN> 4.70010 21.05406 0.00000 20.18148 3.99738 MINI EXTERN> -92.61078 23.45036 0.00000 0.00000 0.00000 MINI CONSTR> 39.17104 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 19.91291 0.03073 0.18506 0.00018 MINI INTERN> 4.68743 21.04175 0.00000 20.15943 3.99419 MINI EXTERN> -92.63417 23.44344 0.00000 0.00000 0.00000 MINI CONSTR> 39.22086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10938 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 19.88129 0.03162 0.19328 0.00019 MINI INTERN> 4.68630 21.01818 0.00000 20.13583 3.98975 MINI EXTERN> -92.66455 23.43980 0.00000 0.00000 0.00000 MINI CONSTR> 39.27597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 19.85456 0.02674 0.26346 0.00019 MINI INTERN> 4.70748 20.97552 0.00000 20.11057 3.98361 MINI EXTERN> -92.69398 23.44266 0.00000 0.00000 0.00000 MINI CONSTR> 39.32870 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10938 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 19.82757 0.02699 0.31030 0.00020 MINI INTERN> 4.70344 20.95944 0.00000 20.08960 3.98010 MINI EXTERN> -92.72115 23.43606 0.00000 0.00000 0.00000 MINI CONSTR> 39.38007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 19.80175 0.02582 0.33846 0.00021 MINI INTERN> 4.70125 20.94182 0.00000 20.06837 3.97628 MINI EXTERN> -92.74714 23.43254 0.00000 0.00000 0.00000 MINI CONSTR> 39.42864 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10938 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 19.77261 0.02915 0.28715 0.00022 MINI INTERN> 4.70778 20.91172 0.00000 20.04532 3.97115 MINI EXTERN> -92.77442 23.43419 0.00000 0.00000 0.00000 MINI CONSTR> 39.47685 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 19.74771 0.02489 0.38143 0.00022 MINI INTERN> 4.70571 20.89580 0.00000 20.02015 3.96775 MINI EXTERN> -92.80847 23.43600 0.00000 0.00000 0.00000 MINI CONSTR> 39.53076 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10937 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 19.72165 0.02607 0.36302 0.00023 MINI INTERN> 4.69560 20.88572 0.00000 20.00085 3.96475 MINI EXTERN> -92.83323 23.43254 0.00000 0.00000 0.00000 MINI CONSTR> 39.57542 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 19.69463 0.02702 0.34840 0.00024 MINI INTERN> 4.70322 20.85685 0.00000 19.98009 3.95957 MINI EXTERN> -92.86183 23.43308 0.00000 0.00000 0.00000 MINI CONSTR> 39.62365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10934 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 19.66825 0.02638 0.33224 0.00025 MINI INTERN> 4.71521 20.82465 0.00000 19.95970 3.95399 MINI EXTERN> -92.89003 23.43336 0.00000 0.00000 0.00000 MINI CONSTR> 39.67137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 19.63386 0.03439 0.11319 0.00011 MINI INTERN> 4.60683 20.91238 0.00000 19.93992 3.96242 MINI EXTERN> -92.90611 23.40228 0.00000 0.00000 0.00000 MINI CONSTR> 39.71615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10933 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 19.62171 0.01215 0.41793 0.00027 MINI INTERN> 4.69844 20.80771 0.00000 19.91523 3.94814 MINI EXTERN> -92.94089 23.42663 0.00000 0.00000 0.00000 MINI CONSTR> 39.76645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 19.59805 0.02366 0.43264 0.00028 MINI INTERN> 4.71297 20.78148 0.00000 19.89630 3.94372 MINI EXTERN> -92.96907 23.41976 0.00000 0.00000 0.00000 MINI CONSTR> 39.81289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10931 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 19.57489 0.02316 0.44823 0.00029 MINI INTERN> 4.70098 20.77040 0.00000 19.87245 3.93998 MINI EXTERN> -92.99122 23.42346 0.00000 0.00000 0.00000 MINI CONSTR> 39.85884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 19.53377 0.04113 0.12761 0.00012 MINI INTERN> 4.59141 20.85498 0.00000 19.85528 3.94868 MINI EXTERN> -93.01167 23.39210 0.00000 0.00000 0.00000 MINI CONSTR> 39.90298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10930 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 19.51235 0.02142 0.10892 0.00013 MINI INTERN> 4.59842 20.83207 0.00000 19.83680 3.94460 MINI EXTERN> -93.03466 23.39284 0.00000 0.00000 0.00000 MINI CONSTR> 39.94228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 19.48911 0.02324 0.11192 0.00013 MINI INTERN> 4.59507 20.81886 0.00000 19.81636 3.94136 MINI EXTERN> -93.05929 23.39051 0.00000 0.00000 0.00000 MINI CONSTR> 39.98624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10929 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 19.46597 0.02314 0.11319 0.00014 MINI INTERN> 4.59265 20.80455 0.00000 19.79578 3.93795 MINI EXTERN> -93.08370 23.38866 0.00000 0.00000 0.00000 MINI CONSTR> 40.03010 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 19.44179 0.02418 0.18091 0.00014 MINI INTERN> 4.57257 20.80942 0.00000 19.77307 3.93649 MINI EXTERN> -93.11023 23.38033 0.00000 0.00000 0.00000 MINI CONSTR> 40.08013 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10928 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 19.41960 0.02218 0.15446 0.00015 MINI INTERN> 4.57729 20.78818 0.00000 19.75332 3.93246 MINI EXTERN> -93.13328 23.38094 0.00000 0.00000 0.00000 MINI CONSTR> 40.12070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 19.39563 0.02397 0.13804 0.00015 MINI INTERN> 4.57579 20.77052 0.00000 19.73232 3.92807 MINI EXTERN> -93.15681 23.38017 0.00000 0.00000 0.00000 MINI CONSTR> 40.16556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10927 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 19.37344 0.02219 0.17753 0.00016 MINI INTERN> 4.56764 20.76452 0.00000 19.71133 3.92549 MINI EXTERN> -93.18124 23.37501 0.00000 0.00000 0.00000 MINI CONSTR> 40.21069 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 19.35412 0.01932 0.23417 0.00017 MINI INTERN> 4.55165 20.76640 0.00000 19.69080 3.92386 MINI EXTERN> -93.20223 23.37089 0.00000 0.00000 0.00000 MINI CONSTR> 40.25275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10926 ATOM PAIRS WERE FOUND FOR ATOM LIST 318 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 19.33384 0.02028 0.25620 0.00017 MINI INTERN> 4.55566 20.75098 0.00000 19.67156 3.92050 MINI EXTERN> -93.22600 23.36723 0.00000 0.00000 0.00000 MINI CONSTR> 40.29391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 19.31351 0.02033 0.25832 0.00018 MINI INTERN> 4.55122 20.74067 0.00000 19.65125 3.91777 MINI EXTERN> -93.24742 23.36589 0.00000 0.00000 0.00000 MINI CONSTR> 40.33414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10926 ATOM PAIRS WERE FOUND FOR ATOM LIST 319 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 19.29135 0.02216 0.26697 0.00019 MINI INTERN> 4.54166 20.73358 0.00000 19.63071 3.91440 MINI EXTERN> -93.26925 23.36193 0.00000 0.00000 0.00000 MINI CONSTR> 40.37832 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 19.27129 0.02005 0.30262 0.00019 MINI INTERN> 4.53227 20.72503 0.00000 19.60976 3.91089 MINI EXTERN> -93.28922 23.36165 0.00000 0.00000 0.00000 MINI CONSTR> 40.42091 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10926 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 19.25088 0.02042 0.27748 0.00020 MINI INTERN> 4.54152 20.70527 0.00000 19.59174 3.90720 MINI EXTERN> -93.31153 23.35827 0.00000 0.00000 0.00000 MINI CONSTR> 40.45842 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 19.22570 0.02518 0.09828 0.00009 MINI INTERN> 4.59909 20.62332 0.00000 19.57263 3.89543 MINI EXTERN> -93.33407 23.37554 0.00000 0.00000 0.00000 MINI CONSTR> 40.49376 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10927 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 19.21269 0.01301 0.29543 0.00021 MINI INTERN> 4.53214 20.68630 0.00000 19.55310 3.90116 MINI EXTERN> -93.35084 23.35462 0.00000 0.00000 0.00000 MINI CONSTR> 40.53622 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 19.19081 0.02188 0.30370 0.00022 MINI INTERN> 4.51075 20.68672 0.00000 19.53327 3.89797 MINI EXTERN> -93.37003 23.35156 0.00000 0.00000 0.00000 MINI CONSTR> 40.58056 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10926 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 19.16459 0.02622 0.10257 0.00010 MINI INTERN> 4.59965 20.57884 0.00000 19.51217 3.88412 MINI EXTERN> -93.39702 23.37187 0.00000 0.00000 0.00000 MINI CONSTR> 40.61496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 19.15575 0.00884 0.34984 0.00024 MINI INTERN> 4.52053 20.65800 0.00000 19.49419 3.89050 MINI EXTERN> -93.40856 23.34579 0.00000 0.00000 0.00000 MINI CONSTR> 40.65529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10923 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 19.12724 0.02851 0.11274 0.00010 MINI INTERN> 4.60285 20.54884 0.00000 19.47426 3.87663 MINI EXTERN> -93.43559 23.37027 0.00000 0.00000 0.00000 MINI CONSTR> 40.68998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 19.12096 0.00628 0.37197 0.00026 MINI INTERN> 4.50700 20.64110 0.00000 19.45927 3.88507 MINI EXTERN> -93.44526 23.34512 0.00000 0.00000 0.00000 MINI CONSTR> 40.72865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10922 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 19.09099 0.02997 0.12736 0.00011 MINI INTERN> 4.60505 20.52011 0.00000 19.43703 3.86926 MINI EXTERN> -93.47298 23.36896 0.00000 0.00000 0.00000 MINI CONSTR> 40.76356 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 19.07487 0.01612 0.09547 0.00011 MINI INTERN> 4.58846 20.52488 0.00000 19.42171 3.86791 MINI EXTERN> -93.48683 23.36412 0.00000 0.00000 0.00000 MINI CONSTR> 40.79462 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10922 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 19.05651 0.01836 0.09274 0.00012 MINI INTERN> 4.58541 20.51424 0.00000 19.40294 3.86462 MINI EXTERN> -93.50515 23.36276 0.00000 0.00000 0.00000 MINI CONSTR> 40.83169 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 19.03787 0.01864 0.15741 0.00012 MINI INTERN> 4.61309 20.47499 0.00000 19.38055 3.85772 MINI EXTERN> -93.52813 23.36677 0.00000 0.00000 0.00000 MINI CONSTR> 40.87288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10920 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 19.02068 0.01719 0.13480 0.00013 MINI INTERN> 4.59901 20.47413 0.00000 19.36410 3.85568 MINI EXTERN> -93.54354 23.36478 0.00000 0.00000 0.00000 MINI CONSTR> 40.90652 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 19.00406 0.01662 0.14271 0.00013 MINI INTERN> 4.60143 20.46062 0.00000 19.34613 3.85192 MINI EXTERN> -93.56052 23.36350 0.00000 0.00000 0.00000 MINI CONSTR> 40.94098 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10920 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 18.98584 0.01822 0.12450 0.00014 MINI INTERN> 4.59513 20.45307 0.00000 19.32741 3.84899 MINI EXTERN> -93.57788 23.36184 0.00000 0.00000 0.00000 MINI CONSTR> 40.97728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 18.96847 0.01737 0.15344 0.00014 MINI INTERN> 4.60543 20.43321 0.00000 19.30772 3.84437 MINI EXTERN> -93.59697 23.36023 0.00000 0.00000 0.00000 MINI CONSTR> 41.01448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10920 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 18.95392 0.01455 0.20217 0.00015 MINI INTERN> 4.61819 20.40746 0.00000 19.28957 3.83937 MINI EXTERN> -93.61470 23.36556 0.00000 0.00000 0.00000 MINI CONSTR> 41.04848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 18.93504 0.01888 0.15221 0.00015 MINI INTERN> 4.60222 20.41220 0.00000 19.27171 3.83766 MINI EXTERN> -93.62994 23.35782 0.00000 0.00000 0.00000 MINI CONSTR> 41.08336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10919 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 18.92196 0.01308 0.22489 0.00016 MINI INTERN> 4.62274 20.38391 0.00000 19.25379 3.83218 MINI EXTERN> -93.64746 23.36057 0.00000 0.00000 0.00000 MINI CONSTR> 41.11624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 18.90712 0.01485 0.24813 0.00016 MINI INTERN> 4.61910 20.37052 0.00000 19.23645 3.82871 MINI EXTERN> -93.66368 23.36619 0.00000 0.00000 0.00000 MINI CONSTR> 41.14982 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10917 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 18.89177 0.01535 0.25291 0.00017 MINI INTERN> 4.61908 20.36711 0.00000 19.21973 3.82581 MINI EXTERN> -93.67797 23.35665 0.00000 0.00000 0.00000 MINI CONSTR> 41.18136 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 18.87622 0.01555 0.24322 0.00018 MINI INTERN> 4.60912 20.35746 0.00000 19.20316 3.82289 MINI EXTERN> -93.69318 23.36299 0.00000 0.00000 0.00000 MINI CONSTR> 41.21377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 18.85670 0.01952 0.08635 0.00008 MINI INTERN> 4.55096 20.40181 0.00000 19.18922 3.82619 MINI EXTERN> -93.70171 23.34671 0.00000 0.00000 0.00000 MINI CONSTR> 41.24353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 18.84772 0.00897 0.28574 0.00019 MINI INTERN> 4.60120 20.34144 0.00000 19.16967 3.81690 MINI EXTERN> -93.72293 23.36379 0.00000 0.00000 0.00000 MINI CONSTR> 41.27765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 18.83489 0.01284 0.33154 0.00020 MINI INTERN> 4.60746 20.34141 0.00000 19.15301 3.81394 MINI EXTERN> -93.73587 23.34685 0.00000 0.00000 0.00000 MINI CONSTR> 41.30809 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 18.82052 0.01437 0.32830 0.00020 MINI INTERN> 4.60764 20.32835 0.00000 19.13671 3.81016 MINI EXTERN> -93.75050 23.34911 0.00000 0.00000 0.00000 MINI CONSTR> 41.33905 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10916 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 18.80569 0.01483 0.31234 0.00021 MINI INTERN> 4.59461 20.31854 0.00000 19.12077 3.80724 MINI EXTERN> -93.76517 23.35923 0.00000 0.00000 0.00000 MINI CONSTR> 41.37046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 18.78225 0.02344 0.09866 0.00009 MINI INTERN> 4.54414 20.35346 0.00000 19.10508 3.81008 MINI EXTERN> -93.77536 23.34376 0.00000 0.00000 0.00000 MINI CONSTR> 41.40109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10915 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 18.76905 0.01320 0.08359 0.00010 MINI INTERN> 4.54809 20.33888 0.00000 19.09015 3.80651 MINI EXTERN> -93.78876 23.34566 0.00000 0.00000 0.00000 MINI CONSTR> 41.42851 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 18.75510 0.01395 0.08514 0.00010 MINI INTERN> 4.54773 20.32910 0.00000 19.07405 3.80332 MINI EXTERN> -93.80260 23.34525 0.00000 0.00000 0.00000 MINI CONSTR> 41.45825 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10915 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 18.74083 0.01427 0.08173 0.00010 MINI INTERN> 4.54821 20.31818 0.00000 19.05763 3.79987 MINI EXTERN> -93.81673 23.34513 0.00000 0.00000 0.00000 MINI CONSTR> 41.48855 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 18.72646 0.01437 0.08697 0.00011 MINI INTERN> 4.54596 20.30930 0.00000 19.04087 3.79672 MINI EXTERN> -93.83097 23.34511 0.00000 0.00000 0.00000 MINI CONSTR> 41.51947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10915 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 18.71197 0.01449 0.14085 0.00011 MINI INTERN> 4.53851 20.30683 0.00000 19.02264 3.79417 MINI EXTERN> -93.84576 23.34234 0.00000 0.00000 0.00000 MINI CONSTR> 41.55325 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 18.69776 0.01421 0.10859 0.00011 MINI INTERN> 4.53970 20.29283 0.00000 19.00701 3.79045 MINI EXTERN> -93.85946 23.34528 0.00000 0.00000 0.00000 MINI CONSTR> 41.58195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10913 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 18.68449 0.01327 0.12619 0.00012 MINI INTERN> 4.53942 20.28408 0.00000 18.99078 3.78736 MINI EXTERN> -93.87300 23.34443 0.00000 0.00000 0.00000 MINI CONSTR> 41.61143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 18.67072 0.01377 0.12756 0.00012 MINI INTERN> 4.54131 20.27328 0.00000 18.97443 3.78381 MINI EXTERN> -93.88667 23.34347 0.00000 0.00000 0.00000 MINI CONSTR> 41.64109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10912 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 18.65900 0.01172 0.18268 0.00013 MINI INTERN> 4.53585 20.26830 0.00000 18.95845 3.78145 MINI EXTERN> -93.89986 23.34454 0.00000 0.00000 0.00000 MINI CONSTR> 41.67027 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 18.64585 0.01315 0.20140 0.00013 MINI INTERN> 4.54207 20.25680 0.00000 18.94201 3.77751 MINI EXTERN> -93.91327 23.34100 0.00000 0.00000 0.00000 MINI CONSTR> 41.69974 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10911 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 18.63343 0.01242 0.20611 0.00014 MINI INTERN> 4.54009 20.24745 0.00000 18.92659 3.77466 MINI EXTERN> -93.92630 23.34342 0.00000 0.00000 0.00000 MINI CONSTR> 41.72751 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 18.62085 0.01258 0.22354 0.00014 MINI INTERN> 4.53445 20.23902 0.00000 18.91089 3.77182 MINI EXTERN> -93.93961 23.34797 0.00000 0.00000 0.00000 MINI CONSTR> 41.75631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10911 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 18.60820 0.01265 0.20938 0.00015 MINI INTERN> 4.54224 20.22652 0.00000 18.89598 3.76804 MINI EXTERN> -93.95180 23.34475 0.00000 0.00000 0.00000 MINI CONSTR> 41.78247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 18.59680 0.01140 0.25663 0.00015 MINI INTERN> 4.53390 20.21961 0.00000 18.88016 3.76549 MINI EXTERN> -93.96523 23.35126 0.00000 0.00000 0.00000 MINI CONSTR> 41.81161 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10911 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 18.58441 0.01240 0.23274 0.00016 MINI INTERN> 4.53758 20.20811 0.00000 18.86606 3.76217 MINI EXTERN> -93.97693 23.35099 0.00000 0.00000 0.00000 MINI CONSTR> 41.83643 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 18.56829 0.01612 0.07762 0.00007 MINI INTERN> 4.54100 20.19290 0.00000 18.85278 3.75736 MINI EXTERN> -93.98818 23.35133 0.00000 0.00000 0.00000 MINI CONSTR> 41.86109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10910 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 18.56068 0.00761 0.24551 0.00017 MINI INTERN> 4.54107 20.18836 0.00000 18.83594 3.75574 MINI EXTERN> -94.00163 23.35144 0.00000 0.00000 0.00000 MINI CONSTR> 41.88976 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 18.54313 0.01755 0.07990 0.00007 MINI INTERN> 4.53902 20.17514 0.00000 18.82204 3.75094 MINI EXTERN> -94.01331 23.35321 0.00000 0.00000 0.00000 MINI CONSTR> 41.91610 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10909 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 18.53681 0.00632 0.26400 0.00018 MINI INTERN> 4.54584 20.16878 0.00000 18.80532 3.74895 MINI EXTERN> -94.02637 23.35041 0.00000 0.00000 0.00000 MINI CONSTR> 41.94388 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 18.52542 0.01139 0.30364 0.00019 MINI INTERN> 4.53248 20.16340 0.00000 18.79019 3.74645 MINI EXTERN> -94.03925 23.35995 0.00000 0.00000 0.00000 MINI CONSTR> 41.97220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10908 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 18.51339 0.01203 0.29216 0.00020 MINI INTERN> 4.54649 20.15045 0.00000 18.77439 3.74246 MINI EXTERN> -94.05146 23.35247 0.00000 0.00000 0.00000 MINI CONSTR> 41.99858 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 18.49372 0.01967 0.09283 0.00008 MINI INTERN> 4.53525 20.13986 0.00000 18.76094 3.73800 MINI EXTERN> -94.06303 23.35794 0.00000 0.00000 0.00000 MINI CONSTR> 42.02475 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10908 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 18.48283 0.01089 0.07350 0.00009 MINI INTERN> 4.53424 20.13286 0.00000 18.74773 3.73541 MINI EXTERN> -94.07359 23.35833 0.00000 0.00000 0.00000 MINI CONSTR> 42.04784 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 18.47089 0.01194 0.07675 0.00009 MINI INTERN> 4.53293 20.12441 0.00000 18.73287 3.73224 MINI EXTERN> -94.08565 23.35994 0.00000 0.00000 0.00000 MINI CONSTR> 42.07414 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10907 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 18.45901 0.01188 0.07462 0.00009 MINI INTERN> 4.53165 20.11603 0.00000 18.71808 3.72916 MINI EXTERN> -94.09761 23.36157 0.00000 0.00000 0.00000 MINI CONSTR> 42.10012 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 18.44646 0.01255 0.12667 0.00010 MINI INTERN> 4.53285 20.10545 0.00000 18.70125 3.72509 MINI EXTERN> -94.11134 23.36317 0.00000 0.00000 0.00000 MINI CONSTR> 42.12999 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10907 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 18.43484 0.01162 0.10083 0.00010 MINI INTERN> 4.52889 20.09845 0.00000 18.68742 3.72254 MINI EXTERN> -94.12254 23.36592 0.00000 0.00000 0.00000 MINI CONSTR> 42.15415 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 18.42372 0.01112 0.11101 0.00011 MINI INTERN> 4.52869 20.09039 0.00000 18.67324 3.71937 MINI EXTERN> -94.13394 23.36695 0.00000 0.00000 0.00000 MINI CONSTR> 42.17903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10907 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 18.41196 0.01176 0.10767 0.00011 MINI INTERN> 4.52937 20.08150 0.00000 18.65849 3.71613 MINI EXTERN> -94.14578 23.36770 0.00000 0.00000 0.00000 MINI CONSTR> 42.20457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 18.40097 0.01099 0.12820 0.00011 MINI INTERN> 4.52666 20.07403 0.00000 18.64417 3.71309 MINI EXTERN> -94.15744 23.37066 0.00000 0.00000 0.00000 MINI CONSTR> 42.22981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10907 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 18.39083 0.01014 0.17011 0.00012 MINI INTERN> 4.52745 20.06593 0.00000 18.62990 3.70976 MINI EXTERN> -94.16896 23.37195 0.00000 0.00000 0.00000 MINI CONSTR> 42.25480 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 18.39083 0.01014 0.17011 0.00014 STPD INTERN> 4.52745 20.06593 0.00000 18.62990 3.70976 STPD EXTERN> -94.16896 23.37195 0.00000 0.00000 0.00000 STPD CONSTR> 42.25480 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 10907 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10907 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 18.39083 0.01014 0.17011 0.00000 MINI INTERN> 4.52745 20.06593 0.00000 18.62990 3.70976 MINI EXTERN> -94.16896 23.37195 0.00000 0.00000 0.00000 MINI CONSTR> 42.25480 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 17.49459 0.89625 0.46120 0.11681 MINI INTERN> 4.48667 18.81067 0.00000 16.97664 3.47349 MINI EXTERN> -96.55545 24.34705 0.00000 0.00000 0.00000 MINI CONSTR> 45.95551 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 17.38006 0.11453 0.30142 0.03036 MINI INTERN> 4.37837 18.57829 0.00000 16.79528 3.49862 MINI EXTERN> -96.73851 24.31559 0.00000 0.00000 0.00000 MINI CONSTR> 46.55242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 17.31243 0.06763 0.25474 0.02068 MINI INTERN> 4.34364 18.43970 0.00000 16.63980 3.47429 MINI EXTERN> -96.61447 24.18100 0.00000 0.00000 0.00000 MINI CONSTR> 46.84848 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 17.25747 0.05496 0.22063 0.02397 MINI INTERN> 4.29271 18.43396 0.00000 16.52106 3.51753 MINI EXTERN> -96.58335 24.06251 0.00000 0.00000 0.00000 MINI CONSTR> 47.01306 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 17.20782 0.04964 0.21547 0.01923 MINI INTERN> 4.29184 18.40367 0.00000 16.40347 3.42471 MINI EXTERN> -96.40533 23.99145 0.00000 0.00000 0.00000 MINI CONSTR> 47.09800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 17.17021 0.03761 0.21298 0.01573 MINI INTERN> 4.29287 18.35211 0.00000 16.36346 3.41804 MINI EXTERN> -96.20680 23.83119 0.00000 0.00000 0.00000 MINI CONSTR> 47.11933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 17.13765 0.03256 0.17970 0.01429 MINI INTERN> 4.30504 18.48678 0.00000 16.31962 3.37644 MINI EXTERN> -96.34422 23.89082 0.00000 0.00000 0.00000 MINI CONSTR> 47.10316 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 17.10779 0.02986 0.18603 0.01573 MINI INTERN> 4.31411 18.50509 0.00000 16.30318 3.37769 MINI EXTERN> -96.42261 23.99013 0.00000 0.00000 0.00000 MINI CONSTR> 47.04020 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 17.07842 0.02937 0.18910 0.01774 MINI INTERN> 4.34908 18.48366 0.00000 16.25742 3.37722 MINI EXTERN> -96.37958 24.06414 0.00000 0.00000 0.00000 MINI CONSTR> 46.92648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 17.04774 0.03068 0.17857 0.02226 MINI INTERN> 4.39065 18.52843 0.00000 16.26217 3.36672 MINI EXTERN> -96.37911 24.11173 0.00000 0.00000 0.00000 MINI CONSTR> 46.76715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 17.02762 0.02012 0.12809 0.00992 MINI INTERN> 4.36281 18.51125 0.00000 16.24368 3.42066 MINI EXTERN> -96.25785 24.10677 0.00000 0.00000 0.00000 MINI CONSTR> 46.64030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 17.01176 0.01586 0.14063 0.01288 MINI INTERN> 4.33179 18.47393 0.00000 16.17844 3.42146 MINI EXTERN> -96.17941 24.26630 0.00000 0.00000 0.00000 MINI CONSTR> 46.51925 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 16.99964 0.01212 0.10779 0.00757 MINI INTERN> 4.32769 18.46741 0.00000 16.25592 3.41633 MINI EXTERN> -96.15969 24.27295 0.00000 0.00000 0.00000 MINI CONSTR> 46.41903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 16.99076 0.00888 0.10712 0.00675 MINI INTERN> 4.33799 18.50003 0.00000 16.28787 3.37374 MINI EXTERN> -96.16527 24.31941 0.00000 0.00000 0.00000 MINI CONSTR> 46.33698 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 16.98164 0.00913 0.10070 0.00772 MINI INTERN> 4.33676 18.45872 0.00000 16.29562 3.40736 MINI EXTERN> -96.08843 24.33043 0.00000 0.00000 0.00000 MINI CONSTR> 46.24117 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 16.97516 0.00648 0.07941 0.00572 MINI INTERN> 4.32846 18.45595 0.00000 16.30510 3.40604 MINI EXTERN> -96.04023 24.35036 0.00000 0.00000 0.00000 MINI CONSTR> 46.16947 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 16.97062 0.00453 0.07222 0.00575 MINI INTERN> 4.35003 18.52382 0.00000 16.32627 3.40736 MINI EXTERN> -96.08339 24.32756 0.00000 0.00000 0.00000 MINI CONSTR> 46.11898 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 16.96505 0.00558 0.08006 0.00680 MINI INTERN> 4.33929 18.52579 0.00000 16.36841 3.42624 MINI EXTERN> -95.99819 24.25304 0.00000 0.00000 0.00000 MINI CONSTR> 46.05046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 16.96049 0.00456 0.06763 0.00502 MINI INTERN> 4.33993 18.52330 0.00000 16.37479 3.44042 MINI EXTERN> -95.96930 24.25782 0.00000 0.00000 0.00000 MINI CONSTR> 45.99353 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 16.95733 0.00316 0.05503 0.00402 MINI INTERN> 4.36040 18.52735 0.00000 16.40871 3.45916 MINI EXTERN> -95.99863 24.24557 0.00000 0.00000 0.00000 MINI CONSTR> 45.95477 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 16.95733 0.00316 0.05503 0.02000 CONJ INTERN> 4.36040 18.52735 0.00000 16.40871 3.45916 CONJ EXTERN> -95.99863 24.24557 0.00000 0.00000 0.00000 CONJ CONSTR> 45.95477 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "9000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.31241 ( PROT LYS 1 HT2 ) 0.31241 ( PROT LYS 1 N ) 0.39052 ( PROT LYS 1 HT3 ) 0.31241 ( PROT LYS 1 CA ) 0.39052 ( PROT LYS 1 CB ) 0.31241 ( PROT LYS 1 CG ) 0.31241 ( PROT LYS 1 CD ) 0.31241 ( PROT LYS 1 CE ) 0.31241 ( PROT LYS 1 NZ ) 0.31241 ( PROT LYS 1 HZ1 ) 0.31241 ( PROT LYS 1 HZ2 ) 0.31241 ( PROT LYS 1 HZ3 ) 0.31241 ( PROT LYS 1 C ) 0.39052 ( PROT LYS 1 O ) 0.39052 ( PROT MET 2 N ) 0.39052 ( PROT MET 2 H ) 0.31241 ( PROT MET 2 CA ) 0.39052 ( PROT MET 2 CB ) 0.31241 ( PROT MET 2 CG ) 0.31241 ( PROT MET 2 SD ) 0.31241 ( PROT MET 2 CE ) 0.31241 ( PROT MET 2 C ) 0.39052 ( PROT MET 2 O ) 0.39052 ( PROT LYS 3 N ) 0.39052 ( PROT LYS 3 H ) 0.31241 ( PROT LYS 3 CA ) 0.39052 ( PROT LYS 3 CB ) 0.31241 ( PROT LYS 3 CG ) 0.31241 ( PROT LYS 3 CD ) 0.31241 ( PROT LYS 3 CE ) 0.31241 ( PROT LYS 3 NZ ) 0.31241 ( PROT LYS 3 HZ1 ) 0.31241 ( PROT LYS 3 HZ2 ) 0.31241 ( PROT LYS 3 HZ3 ) 0.31241 ( PROT LYS 3 C ) 0.39052 ( PROT LYS 3 O ) 0.39052 ( PROT ALA 4 N ) 0.39052 ( PROT ALA 4 H ) 0.31241 ( PROT ALA 4 CA ) 0.39052 ( PROT ALA 4 CB ) 0.31241 ( PROT ALA 4 C ) 0.39052 ( PROT ALA 4 O ) 0.39052 ( PROT VAL 5 N ) 0.39052 ( PROT VAL 5 H ) 0.31241 ( PROT VAL 5 CA ) 0.39052 ( PROT VAL 5 CB ) 0.31241 ( PROT VAL 5 CG1 ) 0.31241 ( PROT VAL 5 CG2 ) 0.31241 ( PROT VAL 5 C ) 0.39052 ( PROT VAL 5 O ) 0.39052 ( PROT MET 6 N ) 0.39052 ( PROT MET 6 H ) 0.31241 ( PROT MET 6 CA ) 0.39052 ( PROT MET 6 CB ) 0.31241 ( PROT MET 6 CG ) 0.31241 ( PROT MET 6 SD ) 0.31241 ( PROT MET 6 CE ) 0.31241 ( PROT MET 6 C ) 0.39052 ( PROT MET 6 O ) 0.39052 ( PROT ILE 7 N ) 0.39052 ( PROT ILE 7 H ) 0.31241 ( PROT ILE 7 CA ) 0.39052 ( PROT ILE 7 CB ) 0.31241 ( PROT ILE 7 CG2 ) 0.31241 ( PROT ILE 7 CG1 ) 0.31241 ( PROT ILE 7 CD ) 0.31241 ( PROT ILE 7 C ) 0.39052 ( PROT ILE 7 O ) 0.39052 ( PROT GLY 8 N ) 0.39052 ( PROT GLY 8 H ) 0.31241 ( PROT GLY 8 CA ) 0.39052 ( PROT GLY 8 C ) 0.39052 ( PROT GLY 8 O ) 0.39052 ( PROT ALA 9 N ) 0.39052 ( PROT ALA 9 H ) 0.31241 ( PROT ALA 9 CA ) 0.39052 ( PROT ALA 9 CB ) 0.31241 ( PROT ALA 9 C ) 0.39052 ( PROT ALA 9 O ) 0.39052 ( PROT CYS 10 N ) 0.39052 ( PROT CYS 10 H ) 0.31241 ( PROT CYS 10 CA ) 0.39052 ( PROT CYS 10 CB ) 0.31241 ( PROT CYS 10 SG ) 0.31241 ( PROT CYS 10 C ) 0.39052 ( PROT CYS 10 O ) 0.39052 ( PROT PHE 11 N ) 0.39052 ( PROT PHE 11 H ) 0.31241 ( PROT PHE 11 CA ) 0.39052 ( PROT PHE 11 CB ) 0.31241 ( PROT PHE 11 CG ) 0.31241 ( PROT PHE 11 CD1 ) 0.31241 ( PROT PHE 11 CD2 ) 0.31241 ( PROT PHE 11 CE1 ) 0.31241 ( PROT PHE 11 CE2 ) 0.31241 ( PROT PHE 11 CZ ) 0.31241 ( PROT PHE 11 C ) 0.39052 ( PROT PHE 11 O ) 0.39052 ( PROT LEU 12 N ) 0.39052 ( PROT LEU 12 H ) 0.31241 ( PROT LEU 12 CA ) 0.39052 ( PROT LEU 12 CB ) 0.31241 ( PROT LEU 12 CG ) 0.31241 ( PROT LEU 12 CD1 ) 0.31241 ( PROT LEU 12 CD2 ) 0.31241 ( PROT LEU 12 C ) 0.39052 ( PROT LEU 12 O ) 0.39052 ( PROT ILE 13 N ) 0.39052 ( PROT ILE 13 H ) 0.31241 ( PROT ILE 13 CA ) 0.39052 ( PROT ILE 13 CB ) 0.31241 ( PROT ILE 13 CG2 ) 0.31241 ( PROT ILE 13 CG1 ) 0.31241 ( PROT ILE 13 CD ) 0.31241 ( PROT ILE 13 C ) 0.39052 ( PROT ILE 13 O ) 0.39052 ( PROT ASP 14 N ) 0.39052 ( PROT ASP 14 H ) 0.31241 ( PROT ASP 14 CA ) 0.39052 ( PROT ASP 14 CB ) 0.31241 ( PROT ASP 14 CG ) 0.31241 ( PROT ASP 14 OD1 ) 0.31241 ( PROT ASP 14 OD2 ) 0.31241 ( PROT ASP 14 C ) 0.39052 ( PROT ASP 14 O ) 0.39052 ( PROT PHE 15 N ) 0.39052 ( PROT PHE 15 H ) 0.31241 ( PROT PHE 15 CA ) 0.39052 ( PROT PHE 15 CB ) 0.31241 ( PROT PHE 15 CG ) 0.31241 ( PROT PHE 15 CD1 ) 0.31241 ( PROT PHE 15 CD2 ) 0.31241 ( PROT PHE 15 CE1 ) 0.31241 ( PROT PHE 15 CE2 ) 0.31241 ( PROT PHE 15 CZ ) 0.31241 ( PROT PHE 15 C ) 0.39052 ( PROT PHE 15 O ) 0.39052 ( PROT MET 16 N ) 0.39052 ( PROT MET 16 H ) 0.31241 ( PROT MET 16 CA ) 0.39052 ( PROT MET 16 CB ) 0.31241 ( PROT MET 16 CG ) 0.31241 ( PROT MET 16 SD ) 0.31241 ( PROT MET 16 CE ) 0.31241 ( PROT MET 16 C ) 0.39052 ( PROT MET 16 O ) 0.39052 ( PROT PHE 17 N ) 0.39052 ( PROT PHE 17 H ) 0.31241 ( PROT PHE 17 CA ) 0.39052 ( PROT PHE 17 CB ) 0.31241 ( PROT PHE 17 CG ) 0.31241 ( PROT PHE 17 CD1 ) 0.31241 ( PROT PHE 17 CD2 ) 0.31241 ( PROT PHE 17 CE1 ) 0.31241 ( PROT PHE 17 CE2 ) 0.31241 ( PROT PHE 17 CZ ) 0.31241 ( PROT PHE 17 C ) 0.39052 ( PROT PHE 17 O ) 0.39052 ( PROT PHE 18 N ) 0.39052 ( PROT PHE 18 H ) 0.31241 ( PROT PHE 18 CA ) 0.39052 ( PROT PHE 18 CB ) 0.31241 ( PROT PHE 18 CG ) 0.31241 ( PROT PHE 18 CD1 ) 0.31241 ( PROT PHE 18 CD2 ) 0.31241 ( PROT PHE 18 CE1 ) 0.31241 ( PROT PHE 18 CE2 ) 0.31241 ( PROT PHE 18 CZ ) 0.31241 ( PROT PHE 18 C ) 0.39052 ( PROT PHE 18 O ) 0.39052 ( PROT GLU 19 N ) 0.39052 ( PROT GLU 19 H ) 0.31241 ( PROT GLU 19 CA ) 0.39052 ( PROT GLU 19 CB ) 0.31241 ( PROT GLU 19 CG ) 0.31241 ( PROT GLU 19 CD ) 0.31241 ( PROT GLU 19 OE1 ) 0.31241 ( PROT GLU 19 OE2 ) 0.31241 ( PROT GLU 19 C ) 0.39052 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.40906 5.25544 -8.66785 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00198 0.00447 -0.00385 ROTATION MATRIX 0.999999 0.000995 0.000897 -0.000994 0.999999 -0.000627 -0.000898 0.000626 0.999999 AXIS OF ROTATION IS -0.423510 -0.606900 0.672541 ANGLE IS 0.08 TOTAL SQUARE DIFF IS 88.5873 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.697670 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.6977" Parameter: A <- "0.6977" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.71538 5.24005 -8.78956 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.00054 0.02437 -0.00481 ROTATION MATRIX 0.999839 0.015586 0.008933 -0.015454 0.999772 -0.014738 -0.009160 0.014597 0.999851 AXIS OF ROTATION IS -0.632452 -0.390082 0.669209 ANGLE IS 1.33 CENTER OF ROTATION 9.092828 5.105508 -9.465595 SHIFT IS -0.012384 TOTAL SQUARE DIFF IS 4.9550 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.510676 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.6977" RDCMND substituted energy or value "?RMS" to " 0.5107" Parameter: A <- "0.6977 0.5107" 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 0.6977 0.5107 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 45.95" Parameter: H <- "45.95" 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 -28.99744 45.95477 0.42156 ENER INTERN> 4.36040 18.52735 0.00000 16.40871 3.45916 ENER EXTERN> -95.99863 24.24557 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 " -29.00" Parameter: B <- "-29.00" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 24.25" Parameter: C <- "24.25" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -96.00" Parameter: C <- " -71.75" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -71.75" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.36" Parameter: D <- "4.36" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 18.53" Parameter: D <- " 22.89" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 16.41" Parameter: D <- " 39.30" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.46" Parameter: D <- " 42.76" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 42.76" 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= -29.00 GRMS= 0.42 ELEC= 24.25 VDW= -96.00 RDTITL> *EXTERNAL= -71.75 INTERNAL= 42.76 USER= 0.00 HARM= 45.95 RDTITL> *BOND= 4.36 ANGL= 18.53 DIHE= 16.41 IMPR= 3.46 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 10907 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10891 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 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 1.50595 -30.50339 0.15978 0.02000 MINI INTERN> 4.36040 18.52735 0.00000 16.40871 3.45916 MINI EXTERN> -95.99863 24.24557 0.00000 0.00000 0.00000 MINI CONSTR> 30.50339 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 7.90704 -6.40109 8.75250 0.00360 MINI INTERN> 10.25643 19.82562 0.00000 16.82613 3.45181 MINI EXTERN> -100.02349 25.78657 0.00000 0.00000 0.00000 MINI CONSTR> 31.78396 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10880 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 2.31198 5.59506 3.86208 0.00156 MINI INTERN> 5.79492 18.93722 0.00000 16.71442 3.46822 MINI EXTERN> -99.62778 25.23346 0.00000 0.00000 0.00000 MINI CONSTR> 31.79151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 1.16706 1.14492 1.57429 0.00067 MINI INTERN> 4.67903 18.67175 0.00000 16.70902 3.45932 MINI EXTERN> -99.36359 25.20683 0.00000 0.00000 0.00000 MINI CONSTR> 31.80470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10878 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 0.94243 0.22463 0.52109 0.00029 MINI INTERN> 4.54647 18.59313 0.00000 16.65252 3.46643 MINI EXTERN> -99.20740 25.06558 0.00000 0.00000 0.00000 MINI CONSTR> 31.82571 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 0.91468 0.02775 0.48639 0.00030 MINI INTERN> 4.51832 18.56142 0.00000 16.62387 3.46582 MINI EXTERN> -99.09947 24.99688 0.00000 0.00000 0.00000 MINI CONSTR> 31.84782 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10875 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 0.86998 0.04470 0.16233 0.00013 MINI INTERN> 4.46607 18.53095 0.00000 16.60113 3.46330 MINI EXTERN> -99.00556 24.93835 0.00000 0.00000 0.00000 MINI CONSTR> 31.87574 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 0.84920 0.02077 0.10266 0.00013 MINI INTERN> 4.46201 18.50756 0.00000 16.57807 3.46392 MINI EXTERN> -98.96076 24.89806 0.00000 0.00000 0.00000 MINI CONSTR> 31.90035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10875 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 0.82508 0.02412 0.20130 0.00014 MINI INTERN> 4.43669 18.48857 0.00000 16.55264 3.46184 MINI EXTERN> -98.90477 24.85154 0.00000 0.00000 0.00000 MINI CONSTR> 31.93856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 0.80281 0.02227 0.13348 0.00014 MINI INTERN> 4.43434 18.46623 0.00000 16.53119 3.46163 MINI EXTERN> -98.88382 24.82362 0.00000 0.00000 0.00000 MINI CONSTR> 31.96963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10875 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 0.78139 0.02142 0.14647 0.00015 MINI INTERN> 4.42338 18.44851 0.00000 16.51134 3.46023 MINI EXTERN> -98.86605 24.79867 0.00000 0.00000 0.00000 MINI CONSTR> 32.00532 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 0.76438 0.01701 0.23521 0.00016 MINI INTERN> 4.40535 18.43819 0.00000 16.49588 3.45816 MINI EXTERN> -98.85297 24.77956 0.00000 0.00000 0.00000 MINI CONSTR> 32.04021 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10874 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 0.74416 0.02022 0.23793 0.00016 MINI INTERN> 4.39568 18.42279 0.00000 16.47911 3.45647 MINI EXTERN> -98.85043 24.76397 0.00000 0.00000 0.00000 MINI CONSTR> 32.07656 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 0.72417 0.01999 0.24820 0.00017 MINI INTERN> 4.38458 18.40906 0.00000 16.46332 3.45439 MINI EXTERN> -98.85237 24.75089 0.00000 0.00000 0.00000 MINI CONSTR> 32.11431 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10873 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 0.70506 0.01911 0.26847 0.00017 MINI INTERN> 4.37277 18.39726 0.00000 16.44867 3.45203 MINI EXTERN> -98.85801 24.73995 0.00000 0.00000 0.00000 MINI CONSTR> 32.15238 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 0.68693 0.01814 0.25939 0.00018 MINI INTERN> 4.36956 18.38355 0.00000 16.43458 3.45073 MINI EXTERN> -98.86950 24.73159 0.00000 0.00000 0.00000 MINI CONSTR> 32.18642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10872 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 0.66875 0.01817 0.27396 0.00019 MINI INTERN> 4.35969 18.37308 0.00000 16.42125 3.44842 MINI EXTERN> -98.88107 24.72379 0.00000 0.00000 0.00000 MINI CONSTR> 32.22358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 0.65008 0.01867 0.28417 0.00019 MINI INTERN> 4.34996 18.36278 0.00000 16.40790 3.44582 MINI EXTERN> -98.89524 24.71691 0.00000 0.00000 0.00000 MINI CONSTR> 32.26194 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10870 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 0.63116 0.01892 0.28899 0.00020 MINI INTERN> 4.34240 18.35167 0.00000 16.39436 3.44326 MINI EXTERN> -98.91196 24.71070 0.00000 0.00000 0.00000 MINI CONSTR> 32.30075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 0.60662 0.02455 0.08989 0.00009 MINI INTERN> 4.41537 18.29906 0.00000 16.36520 3.44935 MINI EXTERN> -98.96443 24.70653 0.00000 0.00000 0.00000 MINI CONSTR> 32.33554 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10867 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 0.59804 0.00858 0.31598 0.00022 MINI INTERN> 4.32909 18.33216 0.00000 16.37021 3.43921 MINI EXTERN> -98.94565 24.70098 0.00000 0.00000 0.00000 MINI CONSTR> 32.37204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 0.58196 0.01607 0.34537 0.00022 MINI INTERN> 4.33942 18.31536 0.00000 16.35367 3.43841 MINI EXTERN> -98.97344 24.70009 0.00000 0.00000 0.00000 MINI CONSTR> 32.40845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10867 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 0.55608 0.02589 0.10680 0.00010 MINI INTERN> 4.41971 18.25729 0.00000 16.32453 3.44589 MINI EXTERN> -99.02839 24.69565 0.00000 0.00000 0.00000 MINI CONSTR> 32.44140 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 0.55165 0.00443 0.35158 0.00024 MINI INTERN> 4.31569 18.30424 0.00000 16.33425 3.43433 MINI EXTERN> -99.00296 24.69189 0.00000 0.00000 0.00000 MINI CONSTR> 32.47421 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10866 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 0.52437 0.02727 0.12428 0.00010 MINI INTERN> 4.42471 18.23038 0.00000 16.29828 3.44372 MINI EXTERN> -99.07260 24.69031 0.00000 0.00000 0.00000 MINI CONSTR> 32.50958 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 0.51043 0.01394 0.08400 0.00011 MINI INTERN> 4.40443 18.22993 0.00000 16.29201 3.44061 MINI EXTERN> -99.08179 24.68771 0.00000 0.00000 0.00000 MINI CONSTR> 32.53753 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10864 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 0.49421 0.01622 0.14808 0.00011 MINI INTERN> 4.43162 18.20375 0.00000 16.27262 3.44167 MINI EXTERN> -99.11690 24.68553 0.00000 0.00000 0.00000 MINI CONSTR> 32.57591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 0.48024 0.01397 0.08139 0.00012 MINI INTERN> 4.40134 18.20882 0.00000 16.26855 3.43776 MINI EXTERN> -99.12198 24.68305 0.00000 0.00000 0.00000 MINI CONSTR> 32.60269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10864 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 0.46350 0.01674 0.16518 0.00012 MINI INTERN> 4.43398 18.17946 0.00000 16.24702 3.43933 MINI EXTERN> -99.16127 24.68100 0.00000 0.00000 0.00000 MINI CONSTR> 32.64398 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 0.44778 0.01572 0.11077 0.00012 MINI INTERN> 4.41271 18.17878 0.00000 16.23981 3.43601 MINI EXTERN> -99.17238 24.67785 0.00000 0.00000 0.00000 MINI CONSTR> 32.67500 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10863 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 0.43352 0.01426 0.14274 0.00013 MINI INTERN> 4.42363 18.16241 0.00000 16.22503 3.43578 MINI EXTERN> -99.19867 24.67698 0.00000 0.00000 0.00000 MINI CONSTR> 32.70836 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 0.42130 0.01222 0.19352 0.00013 MINI INTERN> 4.44116 18.14380 0.00000 16.21079 3.43576 MINI EXTERN> -99.22415 24.67456 0.00000 0.00000 0.00000 MINI CONSTR> 32.73940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10863 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 0.40701 0.01430 0.20657 0.00014 MINI INTERN> 4.43720 18.13533 0.00000 16.19845 3.43454 MINI EXTERN> -99.24528 24.67453 0.00000 0.00000 0.00000 MINI CONSTR> 32.77222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 0.39421 0.01280 0.22287 0.00014 MINI INTERN> 4.44780 18.11987 0.00000 16.18636 3.43347 MINI EXTERN> -99.26624 24.67026 0.00000 0.00000 0.00000 MINI CONSTR> 32.80268 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 0.38125 0.01296 0.23613 0.00015 MINI INTERN> 4.44942 18.10916 0.00000 16.17373 3.43268 MINI EXTERN> -99.28811 24.67117 0.00000 0.00000 0.00000 MINI CONSTR> 32.83319 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 0.36822 0.01304 0.22125 0.00015 MINI INTERN> 4.44835 18.09994 0.00000 16.16430 3.43081 MINI EXTERN> -99.30366 24.66730 0.00000 0.00000 0.00000 MINI CONSTR> 32.86119 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 0.35517 0.01305 0.24381 0.00016 MINI INTERN> 4.44098 18.09404 0.00000 16.15253 3.42960 MINI EXTERN> -99.32336 24.66874 0.00000 0.00000 0.00000 MINI CONSTR> 32.89265 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 0.34213 0.01304 0.23506 0.00017 MINI INTERN> 4.44708 18.08112 0.00000 16.14224 3.42776 MINI EXTERN> -99.34018 24.66237 0.00000 0.00000 0.00000 MINI CONSTR> 32.92174 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10861 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 0.32585 0.01628 0.07818 0.00007 MINI INTERN> 4.37553 18.10769 0.00000 16.14472 3.42111 MINI EXTERN> -99.33132 24.66052 0.00000 0.00000 0.00000 MINI CONSTR> 32.94759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 0.31893 0.00692 0.26270 0.00018 MINI INTERN> 4.45883 18.05712 0.00000 16.11861 3.42604 MINI EXTERN> -99.38000 24.65997 0.00000 0.00000 0.00000 MINI CONSTR> 32.97837 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10860 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 0.30735 0.01158 0.29605 0.00019 MINI INTERN> 4.44045 18.05773 0.00000 16.10859 3.42455 MINI EXTERN> -99.39598 24.66409 0.00000 0.00000 0.00000 MINI CONSTR> 33.00792 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 0.29532 0.01203 0.28884 0.00019 MINI INTERN> 4.46572 18.03552 0.00000 16.09545 3.42377 MINI EXTERN> -99.41800 24.65650 0.00000 0.00000 0.00000 MINI CONSTR> 33.03635 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10860 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 0.27597 0.01935 0.09065 0.00008 MINI INTERN> 4.36533 18.07615 0.00000 16.10220 3.41519 MINI EXTERN> -99.39966 24.65331 0.00000 0.00000 0.00000 MINI CONSTR> 33.06345 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 0.27259 0.00338 0.30497 0.00021 MINI INTERN> 4.46817 18.01705 0.00000 16.07418 3.42113 MINI EXTERN> -99.45199 24.65266 0.00000 0.00000 0.00000 MINI CONSTR> 33.09138 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10860 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 0.25264 0.01995 0.10902 0.00009 MINI INTERN> 4.35762 18.06298 0.00000 16.08238 3.41195 MINI EXTERN> -99.43038 24.64918 0.00000 0.00000 0.00000 MINI CONSTR> 33.11891 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 0.24235 0.01029 0.07510 0.00009 MINI INTERN> 4.37006 18.04865 0.00000 16.07073 3.41219 MINI EXTERN> -99.45000 24.64900 0.00000 0.00000 0.00000 MINI CONSTR> 33.14172 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10859 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 0.23046 0.01189 0.12630 0.00010 MINI INTERN> 4.34942 18.05084 0.00000 16.06303 3.40895 MINI EXTERN> -99.45995 24.64596 0.00000 0.00000 0.00000 MINI CONSTR> 33.17222 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 0.21996 0.01050 0.07182 0.00010 MINI INTERN> 4.37057 18.03162 0.00000 16.04987 3.40983 MINI EXTERN> -99.48250 24.64599 0.00000 0.00000 0.00000 MINI CONSTR> 33.19460 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10859 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 0.20821 0.01175 0.14584 0.00010 MINI INTERN> 4.34227 18.03792 0.00000 16.04293 3.40597 MINI EXTERN> -99.49034 24.64307 0.00000 0.00000 0.00000 MINI CONSTR> 33.22640 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 0.19628 0.01193 0.09615 0.00011 MINI INTERN> 4.35962 18.01981 0.00000 16.02962 3.40604 MINI EXTERN> -99.51220 24.64140 0.00000 0.00000 0.00000 MINI CONSTR> 33.25200 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10858 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 0.18559 0.01069 0.12236 0.00011 MINI INTERN> 4.34800 18.01794 0.00000 16.02092 3.40397 MINI EXTERN> -99.52431 24.64000 0.00000 0.00000 0.00000 MINI CONSTR> 33.27907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 0.17606 0.00953 0.16693 0.00011 MINI INTERN> 4.33473 18.01778 0.00000 16.01316 3.40164 MINI EXTERN> -99.53453 24.63811 0.00000 0.00000 0.00000 MINI CONSTR> 33.30517 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10857 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 0.16451 0.01154 0.16307 0.00012 MINI INTERN> 4.33723 18.00765 0.00000 16.00182 3.40038 MINI EXTERN> -99.55158 24.63626 0.00000 0.00000 0.00000 MINI CONSTR> 33.33275 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 0.15291 0.01161 0.13037 0.00012 MINI INTERN> 4.34632 17.99395 0.00000 15.98904 3.40025 MINI EXTERN> -99.57184 24.63662 0.00000 0.00000 0.00000 MINI CONSTR> 33.35856 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10857 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 0.14458 0.00833 0.18195 0.00013 MINI INTERN> 4.33055 17.99606 0.00000 15.98254 3.39772 MINI EXTERN> -99.57948 24.63438 0.00000 0.00000 0.00000 MINI CONSTR> 33.38281 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 0.13500 0.00958 0.22201 0.00013 MINI INTERN> 4.33310 17.98726 0.00000 15.97279 3.39576 MINI EXTERN> -99.59296 24.62948 0.00000 0.00000 0.00000 MINI CONSTR> 33.40957 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10857 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 0.12515 0.00985 0.20137 0.00014 MINI INTERN> 4.32830 17.98247 0.00000 15.96392 3.39469 MINI EXTERN> -99.60566 24.62939 0.00000 0.00000 0.00000 MINI CONSTR> 33.43204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 0.11541 0.00973 0.21568 0.00014 MINI INTERN> 4.33333 17.97190 0.00000 15.95111 3.39484 MINI EXTERN> -99.62578 24.63308 0.00000 0.00000 0.00000 MINI CONSTR> 33.45693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10855 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 0.10295 0.01246 0.06803 0.00006 MINI INTERN> 4.37609 17.93969 0.00000 15.93491 3.39680 MINI EXTERN> -99.65333 24.63066 0.00000 0.00000 0.00000 MINI CONSTR> 33.47813 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 0.09733 0.00562 0.22787 0.00015 MINI INTERN> 4.32030 17.96543 0.00000 15.93645 3.39050 MINI EXTERN> -99.64370 24.62488 0.00000 0.00000 0.00000 MINI CONSTR> 33.50347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10854 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 0.08854 0.00879 0.25706 0.00016 MINI INTERN> 4.32962 17.95286 0.00000 15.92256 3.39126 MINI EXTERN> -99.66592 24.63043 0.00000 0.00000 0.00000 MINI CONSTR> 33.52773 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 0.07891 0.00962 0.24239 0.00016 MINI INTERN> 4.31114 17.95605 0.00000 15.91797 3.38768 MINI EXTERN> -99.66886 24.62356 0.00000 0.00000 0.00000 MINI CONSTR> 33.55137 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10854 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 0.06938 0.00953 0.25280 0.00017 MINI INTERN> 4.30968 17.94901 0.00000 15.90729 3.38672 MINI EXTERN> -99.68398 24.62422 0.00000 0.00000 0.00000 MINI CONSTR> 33.57645 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 0.05422 0.01517 0.08065 0.00007 MINI INTERN> 4.37969 17.89986 0.00000 15.88390 3.39097 MINI EXTERN> -99.72490 24.62450 0.00000 0.00000 0.00000 MINI CONSTR> 33.60019 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10854 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 0.04584 0.00838 0.06437 0.00008 MINI INTERN> 4.37094 17.89809 0.00000 15.87686 3.38933 MINI EXTERN> -99.73355 24.62350 0.00000 0.00000 0.00000 MINI CONSTR> 33.62067 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 0.03662 0.00922 0.06688 0.00008 MINI INTERN> 4.37278 17.88986 0.00000 15.86681 3.38824 MINI EXTERN> -99.74739 24.62226 0.00000 0.00000 0.00000 MINI CONSTR> 33.64407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 0.02751 0.00911 0.06476 0.00008 MINI INTERN> 4.37093 17.88370 0.00000 15.85746 3.38695 MINI EXTERN> -99.75981 24.62119 0.00000 0.00000 0.00000 MINI CONSTR> 33.66710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 0.01819 0.00932 0.06640 0.00009 MINI INTERN> 4.37164 17.87599 0.00000 15.84740 3.38573 MINI EXTERN> -99.77333 24.61989 0.00000 0.00000 0.00000 MINI CONSTR> 33.69086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10854 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 0.00923 0.00896 0.12150 0.00009 MINI INTERN> 4.38943 17.85885 0.00000 15.83330 3.38583 MINI EXTERN> -99.79439 24.61966 0.00000 0.00000 0.00000 MINI CONSTR> 33.71655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -0.00002 0.00925 0.07991 0.00009 MINI INTERN> 4.37599 17.85920 0.00000 15.82679 3.38357 MINI EXTERN> -99.80117 24.61763 0.00000 0.00000 0.00000 MINI CONSTR> 33.73797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10854 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -0.00879 0.00877 0.09877 0.00010 MINI INTERN> 4.37900 17.85019 0.00000 15.81593 3.38291 MINI EXTERN> -99.81618 24.61791 0.00000 0.00000 0.00000 MINI CONSTR> 33.76143 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -0.01619 0.00740 0.14238 0.00010 MINI INTERN> 4.39360 17.83632 0.00000 15.80439 3.38254 MINI EXTERN> -99.83274 24.61634 0.00000 0.00000 0.00000 MINI CONSTR> 33.78337 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10854 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -0.02575 0.00956 0.09229 0.00010 MINI INTERN> 4.37587 17.83837 0.00000 15.79797 3.38040 MINI EXTERN> -99.83915 24.61587 0.00000 0.00000 0.00000 MINI CONSTR> 33.80492 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -0.03280 0.00705 0.15120 0.00011 MINI INTERN> 4.39369 17.82276 0.00000 15.78556 3.38038 MINI EXTERN> -99.85725 24.61493 0.00000 0.00000 0.00000 MINI CONSTR> 33.82713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10853 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -0.04165 0.00885 0.15664 0.00011 MINI INTERN> 4.39338 17.81614 0.00000 15.77597 3.37881 MINI EXTERN> -99.86913 24.61268 0.00000 0.00000 0.00000 MINI CONSTR> 33.85052 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -0.04909 0.00745 0.18916 0.00011 MINI INTERN> 4.38912 17.81131 0.00000 15.76620 3.37832 MINI EXTERN> -99.88208 24.61544 0.00000 0.00000 0.00000 MINI CONSTR> 33.87260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10852 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -0.05691 0.00782 0.17040 0.00012 MINI INTERN> 4.39305 17.80328 0.00000 15.75764 3.37717 MINI EXTERN> -99.89302 24.61324 0.00000 0.00000 0.00000 MINI CONSTR> 33.89172 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -0.06454 0.00762 0.18917 0.00012 MINI INTERN> 4.39325 17.79799 0.00000 15.74998 3.37479 MINI EXTERN> -99.90120 24.60787 0.00000 0.00000 0.00000 MINI CONSTR> 33.91279 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10851 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -0.07238 0.00785 0.17703 0.00013 MINI INTERN> 4.39717 17.78890 0.00000 15.73974 3.37463 MINI EXTERN> -99.91532 24.60945 0.00000 0.00000 0.00000 MINI CONSTR> 33.93305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -0.08234 0.00995 0.06082 0.00005 MINI INTERN> 4.35495 17.80418 0.00000 15.73863 3.37077 MINI EXTERN> -99.91129 24.60863 0.00000 0.00000 0.00000 MINI CONSTR> 33.95179 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10850 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -0.08671 0.00438 0.20133 0.00014 MINI INTERN> 4.40184 17.77454 0.00000 15.72166 3.37258 MINI EXTERN> -99.93812 24.60741 0.00000 0.00000 0.00000 MINI CONSTR> 33.97338 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -0.09744 0.01073 0.06508 0.00006 MINI INTERN> 4.35247 17.79315 0.00000 15.72158 3.36836 MINI EXTERN> -99.93194 24.60690 0.00000 0.00000 0.00000 MINI CONSTR> 33.99204 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10850 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -0.10052 0.00308 0.22580 0.00015 MINI INTERN> 4.39362 17.76615 0.00000 15.70456 3.37122 MINI EXTERN> -99.95952 24.61099 0.00000 0.00000 0.00000 MINI CONSTR> 34.01247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -0.11201 0.01149 0.06943 0.00006 MINI INTERN> 4.34991 17.78248 0.00000 15.70490 3.36604 MINI EXTERN> -99.95196 24.60548 0.00000 0.00000 0.00000 MINI CONSTR> 34.03114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10850 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -0.11446 0.00244 0.23194 0.00016 MINI INTERN> 4.40289 17.74964 0.00000 15.68634 3.36944 MINI EXTERN> -99.98257 24.60868 0.00000 0.00000 0.00000 MINI CONSTR> 34.05114 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -0.12649 0.01203 0.08094 0.00007 MINI INTERN> 4.34564 17.77264 0.00000 15.68825 3.36365 MINI EXTERN> -99.97157 24.60439 0.00000 0.00000 0.00000 MINI CONSTR> 34.07052 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10849 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -0.13290 0.00641 0.05872 0.00007 MINI INTERN> 4.35280 17.76358 0.00000 15.67973 3.36320 MINI EXTERN> -99.98277 24.60359 0.00000 0.00000 0.00000 MINI CONSTR> 34.08697 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -0.13992 0.00702 0.06152 0.00007 MINI INTERN> 4.35065 17.75884 0.00000 15.67165 3.36201 MINI EXTERN> -99.99214 24.60300 0.00000 0.00000 0.00000 MINI CONSTR> 34.10607 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10847 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -0.14718 0.00727 0.09778 0.00008 MINI INTERN> 4.34016 17.75823 0.00000 15.66410 3.36009 MINI EXTERN> -99.99954 24.60242 0.00000 0.00000 0.00000 MINI CONSTR> 34.12736 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -0.15425 0.00707 0.07584 0.00008 MINI INTERN> 4.34715 17.74877 0.00000 15.65493 3.35940 MINI EXTERN> -100.01121 24.60118 0.00000 0.00000 0.00000 MINI CONSTR> 34.14552 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10846 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -0.16100 0.00675 0.08509 0.00008 MINI INTERN> 4.34250 17.74543 0.00000 15.64721 3.35815 MINI EXTERN> -100.01973 24.60104 0.00000 0.00000 0.00000 MINI CONSTR> 34.16440 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -0.16817 0.00717 0.07832 0.00008 MINI INTERN> 4.34401 17.73851 0.00000 15.63824 3.35722 MINI EXTERN> -100.03052 24.60064 0.00000 0.00000 0.00000 MINI CONSTR> 34.18373 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10846 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -0.17537 0.00720 0.08275 0.00009 MINI INTERN> 4.34351 17.73269 0.00000 15.62951 3.35596 MINI EXTERN> -100.04045 24.59970 0.00000 0.00000 0.00000 MINI CONSTR> 34.20370 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -0.18131 0.00594 0.13263 0.00009 MINI INTERN> 4.33274 17.73304 0.00000 15.62271 3.35418 MINI EXTERN> -100.04675 24.59974 0.00000 0.00000 0.00000 MINI CONSTR> 34.22304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10846 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -0.18788 0.00657 0.14501 0.00009 MINI INTERN> 4.33667 17.72566 0.00000 15.61433 3.35276 MINI EXTERN> -100.05613 24.59695 0.00000 0.00000 0.00000 MINI CONSTR> 34.24188 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -0.19407 0.00619 0.14862 0.00010 MINI INTERN> 4.33001 17.72364 0.00000 15.60710 3.35164 MINI EXTERN> -100.06387 24.59780 0.00000 0.00000 0.00000 MINI CONSTR> 34.25961 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10846 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -0.20063 0.00656 0.15705 0.00010 MINI INTERN> 4.32836 17.71858 0.00000 15.59847 3.35075 MINI EXTERN> -100.07385 24.59854 0.00000 0.00000 0.00000 MINI CONSTR> 34.27853 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -0.20694 0.00631 0.15039 0.00011 MINI INTERN> 4.33126 17.71198 0.00000 15.59087 3.34952 MINI EXTERN> -100.08228 24.59623 0.00000 0.00000 0.00000 MINI CONSTR> 34.29549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10845 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -0.21304 0.00610 0.16713 0.00011 MINI INTERN> 4.33073 17.70617 0.00000 15.58154 3.34940 MINI EXTERN> -100.09402 24.59949 0.00000 0.00000 0.00000 MINI CONSTR> 34.31365 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -0.21935 0.00631 0.15646 0.00011 MINI INTERN> 4.32731 17.70308 0.00000 15.57511 3.34754 MINI EXTERN> -100.09985 24.59662 0.00000 0.00000 0.00000 MINI CONSTR> 34.33084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10844 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -0.22570 0.00635 0.16449 0.00012 MINI INTERN> 4.32897 17.69678 0.00000 15.56693 3.34622 MINI EXTERN> -100.10871 24.59482 0.00000 0.00000 0.00000 MINI CONSTR> 34.34929 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 -0.22570 0.00635 0.16449 0.00014 STPD INTERN> 4.32897 17.69678 0.00000 15.56693 3.34622 STPD EXTERN> -100.10871 24.59482 0.00000 0.00000 0.00000 STPD CONSTR> 34.34929 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 10844 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10844 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 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 -0.22570 0.00635 0.16449 0.00000 MINI INTERN> 4.32897 17.69678 0.00000 15.56693 3.34622 MINI EXTERN> -100.10871 24.59482 0.00000 0.00000 0.00000 MINI CONSTR> 34.34929 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -0.83331 0.60761 0.09448 0.03850 MINI INTERN> 4.35208 16.78264 0.00000 14.22327 3.19870 MINI EXTERN> -101.96165 24.66025 0.00000 0.00000 0.00000 MINI CONSTR> 37.91141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -0.84678 0.01347 0.11630 0.00950 MINI INTERN> 4.28997 16.78133 0.00000 14.17311 3.15473 MINI EXTERN> -101.85331 24.67370 0.00000 0.00000 0.00000 MINI CONSTR> 37.93368 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -0.88630 0.03952 0.19445 0.03073 MINI INTERN> 4.19405 16.61359 0.00000 14.03990 3.17656 MINI EXTERN> -101.47050 24.69521 0.00000 0.00000 0.00000 MINI CONSTR> 37.86489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -0.94051 0.05421 0.14102 0.03526 MINI INTERN> 4.27417 16.62131 0.00000 13.89419 3.13067 MINI EXTERN> -101.26660 24.64816 0.00000 0.00000 0.00000 MINI CONSTR> 37.75758 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -0.97403 0.03352 0.12652 0.01961 MINI INTERN> 4.31898 16.66003 0.00000 13.80361 3.13655 MINI EXTERN> -101.41445 24.81499 0.00000 0.00000 0.00000 MINI CONSTR> 37.70626 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -0.99240 0.01837 0.08472 0.01188 MINI INTERN> 4.34864 16.61218 0.00000 13.76400 3.14315 MINI EXTERN> -101.36593 24.82072 0.00000 0.00000 0.00000 MINI CONSTR> 37.68485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -1.00349 0.01110 0.07836 0.01100 MINI INTERN> 4.30517 16.55590 0.00000 13.74011 3.14844 MINI EXTERN> -101.30404 24.87131 0.00000 0.00000 0.00000 MINI CONSTR> 37.67963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -1.01425 0.01075 0.08678 0.01198 MINI INTERN> 4.29236 16.56840 0.00000 13.75691 3.16073 MINI EXTERN> -101.38520 24.90542 0.00000 0.00000 0.00000 MINI CONSTR> 37.68712 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -1.02393 0.00968 0.06694 0.01024 MINI INTERN> 4.32033 16.53653 0.00000 13.75455 3.15207 MINI EXTERN> -101.33869 24.85214 0.00000 0.00000 0.00000 MINI CONSTR> 37.69914 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -1.03078 0.00685 0.06438 0.00894 MINI INTERN> 4.29362 16.55388 0.00000 13.75752 3.15124 MINI EXTERN> -101.38429 24.89356 0.00000 0.00000 0.00000 MINI CONSTR> 37.70369 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -1.03723 0.00645 0.05721 0.00914 MINI INTERN> 4.30709 16.53230 0.00000 13.76475 3.15409 MINI EXTERN> -101.36798 24.88080 0.00000 0.00000 0.00000 MINI CONSTR> 37.69172 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -1.04184 0.00462 0.05252 0.00727 MINI INTERN> 4.32501 16.51924 0.00000 13.75323 3.17308 MINI EXTERN> -101.31374 24.83408 0.00000 0.00000 0.00000 MINI CONSTR> 37.66726 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -1.04577 0.00393 0.04243 0.00546 MINI INTERN> 4.31088 16.52629 0.00000 13.74176 3.17913 MINI EXTERN> -101.26299 24.82464 0.00000 0.00000 0.00000 MINI CONSTR> 37.63452 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -1.04815 0.00238 0.03886 0.00415 MINI INTERN> 4.30851 16.53729 0.00000 13.75272 3.16647 MINI EXTERN> -101.22466 24.80375 0.00000 0.00000 0.00000 MINI CONSTR> 37.60777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -1.05049 0.00233 0.03444 0.00515 MINI INTERN> 4.30725 16.54771 0.00000 13.75757 3.17087 MINI EXTERN> -101.19920 24.78907 0.00000 0.00000 0.00000 MINI CONSTR> 37.57624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -1.05221 0.00172 0.03410 0.00449 MINI INTERN> 4.31764 16.55697 0.00000 13.76589 3.17048 MINI EXTERN> -101.18608 24.77112 0.00000 0.00000 0.00000 MINI CONSTR> 37.55178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -1.05362 0.00141 0.02796 0.00284 MINI INTERN> 4.31062 16.56304 0.00000 13.77338 3.17547 MINI EXTERN> -101.16286 24.75409 0.00000 0.00000 0.00000 MINI CONSTR> 37.53263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -1.05508 0.00146 0.02946 0.00516 MINI INTERN> 4.31188 16.56748 0.00000 13.79910 3.17113 MINI EXTERN> -101.14977 24.72928 0.00000 0.00000 0.00000 MINI CONSTR> 37.51582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -1.05644 0.00136 0.02820 0.00495 MINI INTERN> 4.31479 16.58498 0.00000 13.83746 3.16238 MINI EXTERN> -101.18602 24.72517 0.00000 0.00000 0.00000 MINI CONSTR> 37.50479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -1.05774 0.00131 0.02490 0.00521 MINI INTERN> 4.31715 16.58191 0.00000 13.85113 3.17260 MINI EXTERN> -101.17729 24.69888 0.00000 0.00000 0.00000 MINI CONSTR> 37.49787 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 -1.05774 0.00131 0.02490 0.02000 CONJ INTERN> 4.31715 16.58191 0.00000 13.85113 3.17260 CONJ EXTERN> -101.17729 24.69888 0.00000 0.00000 0.00000 CONJ CONSTR> 37.49787 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "9600" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.20307 ( PROT LYS 1 HT2 ) 0.20307 ( PROT LYS 1 N ) 0.25384 ( PROT LYS 1 HT3 ) 0.20307 ( PROT LYS 1 CA ) 0.25384 ( PROT LYS 1 CB ) 0.20307 ( PROT LYS 1 CG ) 0.20307 ( PROT LYS 1 CD ) 0.20307 ( PROT LYS 1 CE ) 0.20307 ( PROT LYS 1 NZ ) 0.20307 ( PROT LYS 1 HZ1 ) 0.20307 ( PROT LYS 1 HZ2 ) 0.20307 ( PROT LYS 1 HZ3 ) 0.20307 ( PROT LYS 1 C ) 0.25384 ( PROT LYS 1 O ) 0.25384 ( PROT MET 2 N ) 0.25384 ( PROT MET 2 H ) 0.20307 ( PROT MET 2 CA ) 0.25384 ( PROT MET 2 CB ) 0.20307 ( PROT MET 2 CG ) 0.20307 ( PROT MET 2 SD ) 0.20307 ( PROT MET 2 CE ) 0.20307 ( PROT MET 2 C ) 0.25384 ( PROT MET 2 O ) 0.25384 ( PROT LYS 3 N ) 0.25384 ( PROT LYS 3 H ) 0.20307 ( PROT LYS 3 CA ) 0.25384 ( PROT LYS 3 CB ) 0.20307 ( PROT LYS 3 CG ) 0.20307 ( PROT LYS 3 CD ) 0.20307 ( PROT LYS 3 CE ) 0.20307 ( PROT LYS 3 NZ ) 0.20307 ( PROT LYS 3 HZ1 ) 0.20307 ( PROT LYS 3 HZ2 ) 0.20307 ( PROT LYS 3 HZ3 ) 0.20307 ( PROT LYS 3 C ) 0.25384 ( PROT LYS 3 O ) 0.25384 ( PROT ALA 4 N ) 0.25384 ( PROT ALA 4 H ) 0.20307 ( PROT ALA 4 CA ) 0.25384 ( PROT ALA 4 CB ) 0.20307 ( PROT ALA 4 C ) 0.25384 ( PROT ALA 4 O ) 0.25384 ( PROT VAL 5 N ) 0.25384 ( PROT VAL 5 H ) 0.20307 ( PROT VAL 5 CA ) 0.25384 ( PROT VAL 5 CB ) 0.20307 ( PROT VAL 5 CG1 ) 0.20307 ( PROT VAL 5 CG2 ) 0.20307 ( PROT VAL 5 C ) 0.25384 ( PROT VAL 5 O ) 0.25384 ( PROT MET 6 N ) 0.25384 ( PROT MET 6 H ) 0.20307 ( PROT MET 6 CA ) 0.25384 ( PROT MET 6 CB ) 0.20307 ( PROT MET 6 CG ) 0.20307 ( PROT MET 6 SD ) 0.20307 ( PROT MET 6 CE ) 0.20307 ( PROT MET 6 C ) 0.25384 ( PROT MET 6 O ) 0.25384 ( PROT ILE 7 N ) 0.25384 ( PROT ILE 7 H ) 0.20307 ( PROT ILE 7 CA ) 0.25384 ( PROT ILE 7 CB ) 0.20307 ( PROT ILE 7 CG2 ) 0.20307 ( PROT ILE 7 CG1 ) 0.20307 ( PROT ILE 7 CD ) 0.20307 ( PROT ILE 7 C ) 0.25384 ( PROT ILE 7 O ) 0.25384 ( PROT GLY 8 N ) 0.25384 ( PROT GLY 8 H ) 0.20307 ( PROT GLY 8 CA ) 0.25384 ( PROT GLY 8 C ) 0.25384 ( PROT GLY 8 O ) 0.25384 ( PROT ALA 9 N ) 0.25384 ( PROT ALA 9 H ) 0.20307 ( PROT ALA 9 CA ) 0.25384 ( PROT ALA 9 CB ) 0.20307 ( PROT ALA 9 C ) 0.25384 ( PROT ALA 9 O ) 0.25384 ( PROT CYS 10 N ) 0.25384 ( PROT CYS 10 H ) 0.20307 ( PROT CYS 10 CA ) 0.25384 ( PROT CYS 10 CB ) 0.20307 ( PROT CYS 10 SG ) 0.20307 ( PROT CYS 10 C ) 0.25384 ( PROT CYS 10 O ) 0.25384 ( PROT PHE 11 N ) 0.25384 ( PROT PHE 11 H ) 0.20307 ( PROT PHE 11 CA ) 0.25384 ( PROT PHE 11 CB ) 0.20307 ( PROT PHE 11 CG ) 0.20307 ( PROT PHE 11 CD1 ) 0.20307 ( PROT PHE 11 CD2 ) 0.20307 ( PROT PHE 11 CE1 ) 0.20307 ( PROT PHE 11 CE2 ) 0.20307 ( PROT PHE 11 CZ ) 0.20307 ( PROT PHE 11 C ) 0.25384 ( PROT PHE 11 O ) 0.25384 ( PROT LEU 12 N ) 0.25384 ( PROT LEU 12 H ) 0.20307 ( PROT LEU 12 CA ) 0.25384 ( PROT LEU 12 CB ) 0.20307 ( PROT LEU 12 CG ) 0.20307 ( PROT LEU 12 CD1 ) 0.20307 ( PROT LEU 12 CD2 ) 0.20307 ( PROT LEU 12 C ) 0.25384 ( PROT LEU 12 O ) 0.25384 ( PROT ILE 13 N ) 0.25384 ( PROT ILE 13 H ) 0.20307 ( PROT ILE 13 CA ) 0.25384 ( PROT ILE 13 CB ) 0.20307 ( PROT ILE 13 CG2 ) 0.20307 ( PROT ILE 13 CG1 ) 0.20307 ( PROT ILE 13 CD ) 0.20307 ( PROT ILE 13 C ) 0.25384 ( PROT ILE 13 O ) 0.25384 ( PROT ASP 14 N ) 0.25384 ( PROT ASP 14 H ) 0.20307 ( PROT ASP 14 CA ) 0.25384 ( PROT ASP 14 CB ) 0.20307 ( PROT ASP 14 CG ) 0.20307 ( PROT ASP 14 OD1 ) 0.20307 ( PROT ASP 14 OD2 ) 0.20307 ( PROT ASP 14 C ) 0.25384 ( PROT ASP 14 O ) 0.25384 ( PROT PHE 15 N ) 0.25384 ( PROT PHE 15 H ) 0.20307 ( PROT PHE 15 CA ) 0.25384 ( PROT PHE 15 CB ) 0.20307 ( PROT PHE 15 CG ) 0.20307 ( PROT PHE 15 CD1 ) 0.20307 ( PROT PHE 15 CD2 ) 0.20307 ( PROT PHE 15 CE1 ) 0.20307 ( PROT PHE 15 CE2 ) 0.20307 ( PROT PHE 15 CZ ) 0.20307 ( PROT PHE 15 C ) 0.25384 ( PROT PHE 15 O ) 0.25384 ( PROT MET 16 N ) 0.25384 ( PROT MET 16 H ) 0.20307 ( PROT MET 16 CA ) 0.25384 ( PROT MET 16 CB ) 0.20307 ( PROT MET 16 CG ) 0.20307 ( PROT MET 16 SD ) 0.20307 ( PROT MET 16 CE ) 0.20307 ( PROT MET 16 C ) 0.25384 ( PROT MET 16 O ) 0.25384 ( PROT PHE 17 N ) 0.25384 ( PROT PHE 17 H ) 0.20307 ( PROT PHE 17 CA ) 0.25384 ( PROT PHE 17 CB ) 0.20307 ( PROT PHE 17 CG ) 0.20307 ( PROT PHE 17 CD1 ) 0.20307 ( PROT PHE 17 CD2 ) 0.20307 ( PROT PHE 17 CE1 ) 0.20307 ( PROT PHE 17 CE2 ) 0.20307 ( PROT PHE 17 CZ ) 0.20307 ( PROT PHE 17 C ) 0.25384 ( PROT PHE 17 O ) 0.25384 ( PROT PHE 18 N ) 0.25384 ( PROT PHE 18 H ) 0.20307 ( PROT PHE 18 CA ) 0.25384 ( PROT PHE 18 CB ) 0.20307 ( PROT PHE 18 CG ) 0.20307 ( PROT PHE 18 CD1 ) 0.20307 ( PROT PHE 18 CD2 ) 0.20307 ( PROT PHE 18 CE1 ) 0.20307 ( PROT PHE 18 CE2 ) 0.20307 ( PROT PHE 18 CZ ) 0.20307 ( PROT PHE 18 C ) 0.25384 ( PROT PHE 18 O ) 0.25384 ( PROT GLU 19 N ) 0.25384 ( PROT GLU 19 H ) 0.20307 ( PROT GLU 19 CA ) 0.25384 ( PROT GLU 19 CB ) 0.20307 ( PROT GLU 19 CG ) 0.20307 ( PROT GLU 19 CD ) 0.20307 ( PROT GLU 19 OE1 ) 0.20307 ( PROT GLU 19 OE2 ) 0.20307 ( PROT GLU 19 C ) 0.25384 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.40891 5.25524 -8.66798 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00212 0.00468 -0.00372 ROTATION MATRIX 1.000000 0.000499 0.000577 -0.000499 1.000000 -0.000133 -0.000577 0.000133 1.000000 AXIS OF ROTATION IS -0.171387 -0.745559 0.644025 ANGLE IS 0.04 TOTAL SQUARE DIFF IS 111.4980 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.782704 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.7827" Parameter: A <- "0.7827" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.72126 5.24997 -8.79100 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.00642 0.01445 -0.00337 ROTATION MATRIX 0.999890 0.013478 0.006140 -0.013397 0.999825 -0.013050 -0.006315 0.012966 0.999896 AXIS OF ROTATION IS -0.659907 -0.315918 0.681703 ANGLE IS 1.13 CENTER OF ROTATION 9.272371 4.922577 -9.379186 SHIFT IS -0.002625 TOTAL SQUARE DIFF IS 6.5069 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.585207 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.7827" RDCMND substituted energy or value "?RMS" to " 0.5852" Parameter: A <- "0.7827 0.5852" 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 0.7827 0.5852 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 37.50" Parameter: H <- "37.50" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -38.55561 37.49787 0.30693 ENER INTERN> 4.31715 16.58191 0.00000 13.85113 3.17260 ENER EXTERN> -101.17729 24.69888 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 " -38.56" Parameter: B <- "-38.56" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 24.70" Parameter: C <- "24.70" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -101.18" Parameter: C <- " -76.48" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -76.48" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.32" Parameter: D <- "4.32" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 16.58" Parameter: D <- " 20.90" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 13.85" Parameter: D <- " 34.75" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.17" Parameter: D <- " 37.92" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 37.92" 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= -38.56 GRMS= 0.31 ELEC= 24.70 VDW= -101.18 RDTITL> *EXTERNAL= -76.48 INTERNAL= 37.92 USER= 0.00 HARM= 37.50 RDTITL> *BOND= 4.32 ANGL= 16.58 DIHE= 13.85 IMPR= 3.17 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../pdb/@output_@1.pdb Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= -38.56 GRMS= 0.31 ELEC= 24.70 VDW= -101.18 RDTITL> *EXTERNAL= -76.48 INTERNAL= 37.92 USER= 0.00 HARM= 37.50 RDTITL> *BOND= 4.32 ANGL= 16.58 DIHE= 13.85 IMPR= 3.17 UREY= 0.00 RDTITL> * Write CHARMM-pdb format CHARMM> close unit 12 CLOLGU> ***** WARNING ***** Attempt to close unit that was not open. CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "1200" and "800". IF test evaluated as false. Skipping command CHARMM> open unit 1 card write name ../crd/@output_@1.crd Parameter: OUTPUT -> "MINI_"helix_allh"" Parameter: 1 -> "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= -38.56 GRMS= 0.31 ELEC= 24.70 VDW= -101.18 RDTITL> *EXTERNAL= -76.48 INTERNAL= 37.92 USER= 0.00 HARM= 37.50 RDTITL> *BOND= 4.32 ANGL= 16.58 DIHE= 13.85 IMPR= 3.17 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 9600 0.7827 0.5852 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "9600" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 10844 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10811 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -13.85376 -24.70186 0.11242 0.02000 MINI INTERN> 4.31715 16.58191 0.00000 13.85113 3.17260 MINI EXTERN> -101.17729 24.69888 0.00000 0.00000 0.00000 MINI CONSTR> 24.70186 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -13.87519 0.02144 1.61353 0.00150 MINI INTERN> 4.63126 17.32328 0.00000 14.13450 3.20440 MINI EXTERN> -104.89259 26.03372 0.00000 0.00000 0.00000 MINI CONSTR> 25.69024 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10799 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -14.12844 0.25325 0.92899 0.00065 MINI INTERN> 4.77111 16.72036 0.00000 14.03512 3.16972 MINI EXTERN> -104.20242 25.69057 0.00000 0.00000 0.00000 MINI CONSTR> 25.68710 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -14.24602 0.11759 0.33591 0.00028 MINI INTERN> 4.48814 16.75963 0.00000 13.99386 3.19092 MINI EXTERN> -103.90192 25.52583 0.00000 0.00000 0.00000 MINI CONSTR> 25.69752 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10799 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -14.27930 0.03328 0.11469 0.00012 MINI INTERN> 4.47570 16.67866 0.00000 13.96106 3.19132 MINI EXTERN> -103.72848 25.43337 0.00000 0.00000 0.00000 MINI CONSTR> 25.70906 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -14.29666 0.01736 0.16073 0.00013 MINI INTERN> 4.45847 16.64471 0.00000 13.93432 3.19370 MINI EXTERN> -103.61196 25.35962 0.00000 0.00000 0.00000 MINI CONSTR> 25.72447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10799 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -14.31154 0.01487 0.14505 0.00013 MINI INTERN> 4.44671 16.62431 0.00000 13.91452 3.19355 MINI EXTERN> -103.54038 25.31020 0.00000 0.00000 0.00000 MINI CONSTR> 25.73955 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -14.32130 0.00976 0.22023 0.00013 MINI INTERN> 4.44194 16.60616 0.00000 13.89812 3.19384 MINI EXTERN> -103.48998 25.27405 0.00000 0.00000 0.00000 MINI CONSTR> 25.75457 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10799 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -14.33287 0.01157 0.23487 0.00014 MINI INTERN> 4.43472 16.58933 0.00000 13.88268 3.19369 MINI EXTERN> -103.44861 25.24387 0.00000 0.00000 0.00000 MINI CONSTR> 25.77144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -14.34446 0.01159 0.24384 0.00014 MINI INTERN> 4.42849 16.57350 0.00000 13.86821 3.19335 MINI EXTERN> -103.41684 25.21912 0.00000 0.00000 0.00000 MINI CONSTR> 25.78971 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10799 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -14.35596 0.01150 0.24417 0.00015 MINI INTERN> 4.42305 16.55909 0.00000 13.85499 3.19282 MINI EXTERN> -103.39402 25.19943 0.00000 0.00000 0.00000 MINI CONSTR> 25.80867 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -14.37036 0.01440 0.07786 0.00006 MINI INTERN> 4.40674 16.55257 0.00000 13.84565 3.19048 MINI EXTERN> -103.37745 25.18615 0.00000 0.00000 0.00000 MINI CONSTR> 25.82549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10799 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -14.37441 0.00404 0.26891 0.00016 MINI INTERN> 4.41648 16.53651 0.00000 13.83411 3.19183 MINI EXTERN> -103.37047 25.17362 0.00000 0.00000 0.00000 MINI CONSTR> 25.84352 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -14.38423 0.00982 0.28216 0.00017 MINI INTERN> 4.41442 16.52484 0.00000 13.82349 3.19121 MINI EXTERN> -103.36481 25.16331 0.00000 0.00000 0.00000 MINI CONSTR> 25.86331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10799 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -14.40025 0.01602 0.09112 0.00007 MINI INTERN> 4.39565 16.52141 0.00000 13.81569 3.18812 MINI EXTERN> -103.35931 25.15596 0.00000 0.00000 0.00000 MINI CONSTR> 25.88223 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -14.40847 0.00821 0.06721 0.00007 MINI INTERN> 4.39484 16.51268 0.00000 13.80812 3.18778 MINI EXTERN> -103.36049 25.15063 0.00000 0.00000 0.00000 MINI CONSTR> 25.89797 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10797 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -14.41817 0.00970 0.06674 0.00008 MINI INTERN> 4.39251 16.50358 0.00000 13.79936 3.18699 MINI EXTERN> -103.36351 25.14515 0.00000 0.00000 0.00000 MINI CONSTR> 25.91775 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -14.42780 0.00964 0.06764 0.00008 MINI INTERN> 4.39032 16.49495 0.00000 13.79090 3.18618 MINI EXTERN> -103.36872 25.14074 0.00000 0.00000 0.00000 MINI CONSTR> 25.93784 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10797 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -14.43704 0.00924 0.13186 0.00008 MINI INTERN> 4.38561 16.48847 0.00000 13.78259 3.18470 MINI EXTERN> -103.37525 25.13697 0.00000 0.00000 0.00000 MINI CONSTR> 25.95988 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -14.44616 0.00912 0.08431 0.00009 MINI INTERN> 4.38586 16.47982 0.00000 13.77531 3.18442 MINI EXTERN> -103.38372 25.13462 0.00000 0.00000 0.00000 MINI CONSTR> 25.97754 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10797 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -14.45538 0.00921 0.08478 0.00009 MINI INTERN> 4.38435 16.47225 0.00000 13.76770 3.18368 MINI EXTERN> -103.39348 25.13248 0.00000 0.00000 0.00000 MINI CONSTR> 25.99766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -14.46452 0.00915 0.09147 0.00009 MINI INTERN> 4.38268 16.46508 0.00000 13.76023 3.18288 MINI EXTERN> -103.40435 25.13082 0.00000 0.00000 0.00000 MINI CONSTR> 26.01812 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10797 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -14.47195 0.00742 0.15948 0.00010 MINI INTERN> 4.37912 16.46055 0.00000 13.75365 3.18170 MINI EXTERN> -103.41475 25.12959 0.00000 0.00000 0.00000 MINI CONSTR> 26.03819 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -14.48057 0.00862 0.15941 0.00010 MINI INTERN> 4.37813 16.45382 0.00000 13.74678 3.18106 MINI EXTERN> -103.42680 25.12876 0.00000 0.00000 0.00000 MINI CONSTR> 26.05768 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10797 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -14.48928 0.00871 0.16327 0.00010 MINI INTERN> 4.37721 16.44704 0.00000 13.73984 3.18046 MINI EXTERN> -103.43985 25.12818 0.00000 0.00000 0.00000 MINI CONSTR> 26.07783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -14.49790 0.00861 0.17245 0.00011 MINI INTERN> 4.37646 16.44035 0.00000 13.73291 3.17986 MINI EXTERN> -103.45364 25.12786 0.00000 0.00000 0.00000 MINI CONSTR> 26.09832 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10796 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -14.50606 0.00816 0.18910 0.00011 MINI INTERN> 4.37574 16.43412 0.00000 13.72618 3.17922 MINI EXTERN> -103.46764 25.12775 0.00000 0.00000 0.00000 MINI CONSTR> 26.11857 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -14.51381 0.00776 0.18161 0.00012 MINI INTERN> 4.37538 16.42843 0.00000 13.72016 3.17865 MINI EXTERN> -103.48031 25.12778 0.00000 0.00000 0.00000 MINI CONSTR> 26.13609 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10796 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -14.52180 0.00799 0.19096 0.00012 MINI INTERN> 4.37484 16.42258 0.00000 13.71369 3.17805 MINI EXTERN> -103.49455 25.12791 0.00000 0.00000 0.00000 MINI CONSTR> 26.15567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -14.52999 0.00819 0.19727 0.00012 MINI INTERN> 4.37440 16.41666 0.00000 13.70710 3.17747 MINI EXTERN> -103.50939 25.12815 0.00000 0.00000 0.00000 MINI CONSTR> 26.17564 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10796 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -14.53825 0.00826 0.19880 0.00013 MINI INTERN> 4.37398 16.41084 0.00000 13.70052 3.17687 MINI EXTERN> -103.52442 25.12846 0.00000 0.00000 0.00000 MINI CONSTR> 26.19550 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -14.54878 0.01053 0.06404 0.00006 MINI INTERN> 4.37995 16.40088 0.00000 13.69259 3.17656 MINI EXTERN> -103.54017 25.12859 0.00000 0.00000 0.00000 MINI CONSTR> 26.21282 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10794 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -14.55235 0.00356 0.22005 0.00014 MINI INTERN> 4.37300 16.40115 0.00000 13.68885 3.17564 MINI EXTERN> -103.55175 25.12931 0.00000 0.00000 0.00000 MINI CONSTR> 26.23145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -14.56003 0.00769 0.22661 0.00014 MINI INTERN> 4.37267 16.39590 0.00000 13.68254 3.17504 MINI EXTERN> -103.56684 25.12982 0.00000 0.00000 0.00000 MINI CONSTR> 26.25083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10794 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -14.56762 0.00759 0.23613 0.00015 MINI INTERN> 4.37230 16.39084 0.00000 13.67620 3.17444 MINI EXTERN> -103.58220 25.13035 0.00000 0.00000 0.00000 MINI CONSTR> 26.27045 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -14.57994 0.01232 0.07254 0.00006 MINI INTERN> 4.37915 16.37934 0.00000 13.66735 3.17405 MINI EXTERN> -103.59941 25.13058 0.00000 0.00000 0.00000 MINI CONSTR> 26.28900 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10794 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -14.58648 0.00654 0.05807 0.00007 MINI INTERN> 4.37756 16.37569 0.00000 13.66249 3.17353 MINI EXTERN> -103.61152 25.13105 0.00000 0.00000 0.00000 MINI CONSTR> 26.30470 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -14.59405 0.00758 0.05729 0.00007 MINI INTERN> 4.37716 16.37070 0.00000 13.65635 3.17292 MINI EXTERN> -103.62636 25.13168 0.00000 0.00000 0.00000 MINI CONSTR> 26.32350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10793 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -14.60179 0.00774 0.05696 0.00007 MINI INTERN> 4.37682 16.36559 0.00000 13.65002 3.17228 MINI EXTERN> -103.64167 25.13236 0.00000 0.00000 0.00000 MINI CONSTR> 26.34280 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -14.60956 0.00777 0.05738 0.00007 MINI INTERN> 4.37660 16.36044 0.00000 13.64361 3.17163 MINI EXTERN> -103.65721 25.13308 0.00000 0.00000 0.00000 MINI CONSTR> 26.36229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10793 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -14.61734 0.00778 0.10740 0.00008 MINI INTERN> 4.37951 16.35342 0.00000 13.63582 3.17077 MINI EXTERN> -103.67503 25.13424 0.00000 0.00000 0.00000 MINI CONSTR> 26.38392 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -14.62458 0.00723 0.07287 0.00008 MINI INTERN> 4.37719 16.34993 0.00000 13.63069 3.17030 MINI EXTERN> -103.68816 25.13472 0.00000 0.00000 0.00000 MINI CONSTR> 26.40075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10791 ATOM PAIRS WERE FOUND FOR ATOM LIST 326 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -14.63199 0.00741 0.07148 0.00008 MINI INTERN> 4.37677 16.34522 0.00000 13.62451 3.16966 MINI EXTERN> -103.70328 25.13553 0.00000 0.00000 0.00000 MINI CONSTR> 26.41959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -14.63947 0.00748 0.07359 0.00009 MINI INTERN> 4.37656 16.34036 0.00000 13.61815 3.16899 MINI EXTERN> -103.71880 25.13644 0.00000 0.00000 0.00000 MINI CONSTR> 26.43882 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10789 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -14.64677 0.00730 0.08356 0.00009 MINI INTERN> 4.37677 16.33539 0.00000 13.61170 3.16829 MINI EXTERN> -103.73441 25.13747 0.00000 0.00000 0.00000 MINI CONSTR> 26.45801 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -14.65243 0.00566 0.13865 0.00009 MINI INTERN> 4.37943 16.33011 0.00000 13.60529 3.16746 MINI EXTERN> -103.74933 25.13890 0.00000 0.00000 0.00000 MINI CONSTR> 26.47572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10789 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -14.65939 0.00695 0.14183 0.00010 MINI INTERN> 4.37921 16.32568 0.00000 13.59923 3.16678 MINI EXTERN> -103.76428 25.13999 0.00000 0.00000 0.00000 MINI CONSTR> 26.49402 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -14.66626 0.00688 0.14978 0.00010 MINI INTERN> 4.37915 16.32125 0.00000 13.59305 3.16605 MINI EXTERN> -103.77960 25.14128 0.00000 0.00000 0.00000 MINI CONSTR> 26.51257 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10788 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -14.67278 0.00652 0.16413 0.00010 MINI INTERN> 4.37944 16.31688 0.00000 13.58691 3.16529 MINI EXTERN> -103.79479 25.14267 0.00000 0.00000 0.00000 MINI CONSTR> 26.53083 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -14.67897 0.00619 0.15743 0.00011 MINI INTERN> 4.37905 16.31294 0.00000 13.58168 3.16481 MINI EXTERN> -103.80725 25.14320 0.00000 0.00000 0.00000 MINI CONSTR> 26.54659 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10787 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -14.68537 0.00640 0.16574 0.00011 MINI INTERN> 4.37897 16.30887 0.00000 13.57579 3.16410 MINI EXTERN> -103.82186 25.14453 0.00000 0.00000 0.00000 MINI CONSTR> 26.56423 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -14.69194 0.00656 0.17146 0.00011 MINI INTERN> 4.37845 16.30501 0.00000 13.56986 3.16334 MINI EXTERN> -103.83686 25.14606 0.00000 0.00000 0.00000 MINI CONSTR> 26.58220 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10787 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -14.69857 0.00664 0.17305 0.00012 MINI INTERN> 4.37765 16.30130 0.00000 13.56400 3.16258 MINI EXTERN> -103.85171 25.14750 0.00000 0.00000 0.00000 MINI CONSTR> 26.60009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -14.70708 0.00850 0.05536 0.00005 MINI INTERN> 4.37311 16.29702 0.00000 13.55966 3.16352 MINI EXTERN> -103.85903 25.14280 0.00000 0.00000 0.00000 MINI CONSTR> 26.61585 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10787 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -14.70997 0.00289 0.19058 0.00013 MINI INTERN> 4.37789 16.29376 0.00000 13.55306 3.16130 MINI EXTERN> -103.87823 25.14985 0.00000 0.00000 0.00000 MINI CONSTR> 26.63241 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -14.71615 0.00618 0.19605 0.00013 MINI INTERN> 4.37686 16.29056 0.00000 13.54740 3.16050 MINI EXTERN> -103.89277 25.15158 0.00000 0.00000 0.00000 MINI CONSTR> 26.64972 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -14.72227 0.00612 0.20396 0.00014 MINI INTERN> 4.37545 16.28776 0.00000 13.54175 3.15962 MINI EXTERN> -103.90765 25.15356 0.00000 0.00000 0.00000 MINI CONSTR> 26.66725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -14.73217 0.00991 0.06208 0.00006 MINI INTERN> 4.37356 16.27967 0.00000 13.53639 3.16140 MINI EXTERN> -103.91253 25.14525 0.00000 0.00000 0.00000 MINI CONSTR> 26.68407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -14.73745 0.00527 0.05048 0.00006 MINI INTERN> 4.37281 16.27694 0.00000 13.53164 3.16065 MINI EXTERN> -103.92458 25.14698 0.00000 0.00000 0.00000 MINI CONSTR> 26.69814 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -14.74353 0.00608 0.04978 0.00006 MINI INTERN> 4.37269 16.27293 0.00000 13.52591 3.16006 MINI EXTERN> -103.93786 25.14791 0.00000 0.00000 0.00000 MINI CONSTR> 26.71483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -14.74971 0.00618 0.05023 0.00007 MINI INTERN> 4.37297 16.26862 0.00000 13.52004 3.15944 MINI EXTERN> -103.95129 25.14858 0.00000 0.00000 0.00000 MINI CONSTR> 26.73191 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -14.75577 0.00606 0.09191 0.00007 MINI INTERN> 4.37615 16.26143 0.00000 13.51323 3.15965 MINI EXTERN> -103.96348 25.14684 0.00000 0.00000 0.00000 MINI CONSTR> 26.75041 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -14.76148 0.00571 0.06407 0.00007 MINI INTERN> 4.37468 16.25925 0.00000 13.50844 3.15856 MINI EXTERN> -103.97641 25.14896 0.00000 0.00000 0.00000 MINI CONSTR> 26.76504 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -14.76696 0.00548 0.07602 0.00007 MINI INTERN> 4.37437 16.25522 0.00000 13.50282 3.15838 MINI EXTERN> -103.98835 25.14976 0.00000 0.00000 0.00000 MINI CONSTR> 26.78084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -14.77211 0.00516 0.08640 0.00008 MINI INTERN> 4.37609 16.25056 0.00000 13.49756 3.15792 MINI EXTERN> -103.99938 25.14933 0.00000 0.00000 0.00000 MINI CONSTR> 26.79580 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -14.77684 0.00473 0.11585 0.00008 MINI INTERN> 4.37806 16.24547 0.00000 13.49206 3.15786 MINI EXTERN> -104.00994 25.14881 0.00000 0.00000 0.00000 MINI CONSTR> 26.81084 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -14.78295 0.00611 0.07110 0.00008 MINI INTERN> 4.37529 16.24413 0.00000 13.48730 3.15650 MINI EXTERN> -104.02364 25.15181 0.00000 0.00000 0.00000 MINI CONSTR> 26.82566 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -14.78739 0.00445 0.12207 0.00009 MINI INTERN> 4.37879 16.23767 0.00000 13.48133 3.15686 MINI EXTERN> -104.03360 25.15040 0.00000 0.00000 0.00000 MINI CONSTR> 26.84116 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -14.79276 0.00537 0.13190 0.00009 MINI INTERN> 4.38152 16.23268 0.00000 13.47570 3.15598 MINI EXTERN> -104.04605 25.15033 0.00000 0.00000 0.00000 MINI CONSTR> 26.85706 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -14.79745 0.00469 0.14624 0.00009 MINI INTERN> 4.37916 16.22994 0.00000 13.47035 3.15618 MINI EXTERN> -104.05716 25.15242 0.00000 0.00000 0.00000 MINI CONSTR> 26.87166 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -14.80236 0.00491 0.13586 0.00010 MINI INTERN> 4.38115 16.22590 0.00000 13.46578 3.15529 MINI EXTERN> -104.06736 25.15191 0.00000 0.00000 0.00000 MINI CONSTR> 26.88496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -14.80701 0.00465 0.16562 0.00010 MINI INTERN> 4.37917 16.22298 0.00000 13.45995 3.15537 MINI EXTERN> -104.07977 25.15454 0.00000 0.00000 0.00000 MINI CONSTR> 26.90075 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10786 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -14.81182 0.00481 0.15028 0.00010 MINI INTERN> 4.37976 16.21960 0.00000 13.45555 3.15471 MINI EXTERN> -104.08943 25.15457 0.00000 0.00000 0.00000 MINI CONSTR> 26.91342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -14.81834 0.00652 0.04945 0.00004 MINI INTERN> 4.36895 16.22485 0.00000 13.45261 3.15201 MINI EXTERN> -104.10456 25.16136 0.00000 0.00000 0.00000 MINI CONSTR> 26.92644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10784 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -14.82090 0.00256 0.16194 0.00011 MINI INTERN> 4.38447 16.21099 0.00000 13.44582 3.15326 MINI EXTERN> -104.11001 25.15379 0.00000 0.00000 0.00000 MINI CONSTR> 26.94079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -14.82768 0.00679 0.05188 0.00005 MINI INTERN> 4.36860 16.21872 0.00000 13.44299 3.15089 MINI EXTERN> -104.12581 25.16318 0.00000 0.00000 0.00000 MINI CONSTR> 26.95375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10784 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -14.82952 0.00184 0.18030 0.00012 MINI INTERN> 4.37874 16.20737 0.00000 13.43618 3.15312 MINI EXTERN> -104.13114 25.15861 0.00000 0.00000 0.00000 MINI CONSTR> 26.96759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -14.83679 0.00727 0.05698 0.00005 MINI INTERN> 4.36766 16.21309 0.00000 13.43350 3.14978 MINI EXTERN> -104.14683 25.16536 0.00000 0.00000 0.00000 MINI CONSTR> 26.98066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10784 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -14.83825 0.00146 0.18264 0.00013 MINI INTERN> 4.38481 16.19767 0.00000 13.42644 3.15202 MINI EXTERN> -104.15002 25.15675 0.00000 0.00000 0.00000 MINI CONSTR> 26.99407 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -14.84637 0.00811 0.05620 0.00005 MINI INTERN> 4.36749 16.20648 0.00000 13.42338 3.14872 MINI EXTERN> -104.16840 25.16702 0.00000 0.00000 0.00000 MINI CONSTR> 27.00894 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10782 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -14.85053 0.00416 0.04490 0.00006 MINI INTERN> 4.36873 16.20239 0.00000 13.41881 3.14856 MINI EXTERN> -104.17698 25.16701 0.00000 0.00000 0.00000 MINI CONSTR> 27.02095 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -14.85520 0.00468 0.04752 0.00006 MINI INTERN> 4.36841 16.19947 0.00000 13.41385 3.14790 MINI EXTERN> -104.18787 25.16807 0.00000 0.00000 0.00000 MINI CONSTR> 27.03496 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10782 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -14.85970 0.00449 0.08184 0.00006 MINI INTERN> 4.36470 16.19928 0.00000 13.40906 3.14684 MINI EXTERN> -104.20046 25.17111 0.00000 0.00000 0.00000 MINI CONSTR> 27.04978 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -14.86421 0.00451 0.05827 0.00006 MINI INTERN> 4.36760 16.19396 0.00000 13.40418 3.14661 MINI EXTERN> -104.20904 25.17022 0.00000 0.00000 0.00000 MINI CONSTR> 27.06228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10782 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -14.86847 0.00426 0.06844 0.00007 MINI INTERN> 4.36555 16.19230 0.00000 13.39955 3.14602 MINI EXTERN> -104.21961 25.17217 0.00000 0.00000 0.00000 MINI CONSTR> 27.07555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -14.87284 0.00437 0.06864 0.00007 MINI INTERN> 4.36632 16.18886 0.00000 13.39476 3.14542 MINI EXTERN> -104.22953 25.17260 0.00000 0.00000 0.00000 MINI CONSTR> 27.08873 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -14.87653 0.00369 0.10272 0.00007 MINI INTERN> 4.36256 16.18892 0.00000 13.39047 3.14464 MINI EXTERN> -104.24045 25.17556 0.00000 0.00000 0.00000 MINI CONSTR> 27.10177 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -14.88071 0.00418 0.11030 0.00007 MINI INTERN> 4.36572 16.18445 0.00000 13.38568 3.14380 MINI EXTERN> -104.24998 25.17481 0.00000 0.00000 0.00000 MINI CONSTR> 27.11481 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -14.88462 0.00391 0.11416 0.00008 MINI INTERN> 4.36214 16.18374 0.00000 13.38135 3.14340 MINI EXTERN> -104.25995 25.17750 0.00000 0.00000 0.00000 MINI CONSTR> 27.12720 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -14.88886 0.00424 0.11780 0.00008 MINI INTERN> 4.36216 16.18080 0.00000 13.37655 3.14282 MINI EXTERN> -104.26991 25.17827 0.00000 0.00000 0.00000 MINI CONSTR> 27.14046 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10781 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -14.89296 0.00410 0.12633 0.00008 MINI INTERN> 4.36060 16.17867 0.00000 13.37174 3.14242 MINI EXTERN> -104.27999 25.17988 0.00000 0.00000 0.00000 MINI CONSTR> 27.15372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -14.89690 0.00394 0.12070 0.00008 MINI INTERN> 4.36277 16.17478 0.00000 13.36739 3.14174 MINI EXTERN> -104.28854 25.17955 0.00000 0.00000 0.00000 MINI CONSTR> 27.16540 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10779 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -14.90076 0.00386 0.13361 0.00009 MINI INTERN> 4.35971 16.17284 0.00000 13.36250 3.14201 MINI EXTERN> -104.29791 25.18200 0.00000 0.00000 0.00000 MINI CONSTR> 27.17809 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -14.90470 0.00394 0.12515 0.00009 MINI INTERN> 4.36130 16.17001 0.00000 13.35841 3.14081 MINI EXTERN> -104.30712 25.18194 0.00000 0.00000 0.00000 MINI CONSTR> 27.18995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -14.90982 0.00512 0.04220 0.00004 MINI INTERN> 4.36980 16.15897 0.00000 13.35253 3.14180 MINI EXTERN> -104.31293 25.17856 0.00000 0.00000 0.00000 MINI CONSTR> 27.20144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -14.91206 0.00224 0.14241 0.00010 MINI INTERN> 4.36111 16.16515 0.00000 13.34956 3.13959 MINI EXTERN> -104.32553 25.18372 0.00000 0.00000 0.00000 MINI CONSTR> 27.21434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10778 ATOM PAIRS WERE FOUND FOR ATOM LIST 328 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -14.91583 0.00376 0.15423 0.00010 MINI INTERN> 4.35806 16.16312 0.00000 13.34464 3.13995 MINI EXTERN> -104.33462 25.18615 0.00000 0.00000 0.00000 MINI CONSTR> 27.22688 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -14.91902 0.00319 0.17599 0.00011 MINI INTERN> 4.36879 16.15564 0.00000 13.34022 3.13835 MINI EXTERN> -104.34247 25.18201 0.00000 0.00000 0.00000 MINI CONSTR> 27.23845 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -14.92503 0.00601 0.04890 0.00005 MINI INTERN> 4.37084 16.14706 0.00000 13.33451 3.13999 MINI EXTERN> -104.34839 25.18164 0.00000 0.00000 0.00000 MINI CONSTR> 27.24933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -14.92838 0.00335 0.04103 0.00005 MINI INTERN> 4.36917 16.14583 0.00000 13.33082 3.13946 MINI EXTERN> -104.35641 25.18305 0.00000 0.00000 0.00000 MINI CONSTR> 27.25970 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -14.93199 0.00360 0.04210 0.00005 MINI INTERN> 4.36960 16.14289 0.00000 13.32647 3.13902 MINI EXTERN> -104.36483 25.18371 0.00000 0.00000 0.00000 MINI CONSTR> 27.27115 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 -14.93199 0.00360 0.04210 0.00006 STPD INTERN> 4.36960 16.14289 0.00000 13.32647 3.13902 STPD EXTERN> -104.36483 25.18371 0.00000 0.00000 0.00000 STPD CONSTR> 27.27115 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 10777 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10777 ATOM PAIRS WERE FOUND FOR ATOM LIST 327 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -14.93199 0.00360 0.04210 0.00000 MINI INTERN> 4.36960 16.14289 0.00000 13.32647 3.13902 MINI EXTERN> -104.36483 25.18371 0.00000 0.00000 0.00000 MINI CONSTR> 27.27115 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -15.28971 0.35773 0.04416 0.00500 MINI INTERN> 4.38578 15.70602 0.00000 12.54084 3.06629 MINI EXTERN> -106.01078 25.40535 0.00000 0.00000 0.00000 MINI CONSTR> 29.61679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -15.30460 0.01489 0.12936 0.01860 MINI INTERN> 4.32714 15.65900 0.00000 12.50851 3.00731 MINI EXTERN> -105.87471 25.45607 0.00000 0.00000 0.00000 MINI CONSTR> 29.61208 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -15.34549 0.04089 0.15757 0.03466 MINI INTERN> 4.28939 15.62441 0.00000 12.42497 3.02243 MINI EXTERN> -105.78101 25.50625 0.00000 0.00000 0.00000 MINI CONSTR> 29.56807 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -15.37941 0.03391 0.11707 0.03128 MINI INTERN> 4.35643 15.72169 0.00000 12.35299 3.01963 MINI EXTERN> -105.69702 25.33556 0.00000 0.00000 0.00000 MINI CONSTR> 29.53131 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -15.39387 0.01447 0.07910 0.01498 MINI INTERN> 4.38154 15.70097 0.00000 12.28774 3.01569 MINI EXTERN> -105.69561 25.39952 0.00000 0.00000 0.00000 MINI CONSTR> 29.51628 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -15.40169 0.00782 0.05945 0.00956 MINI INTERN> 4.39244 15.69674 0.00000 12.26902 3.01547 MINI EXTERN> -105.65294 25.36692 0.00000 0.00000 0.00000 MINI CONSTR> 29.51066 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -15.40949 0.00779 0.06781 0.00941 MINI INTERN> 4.35138 15.64228 0.00000 12.24475 3.01595 MINI EXTERN> -105.58039 25.40438 0.00000 0.00000 0.00000 MINI CONSTR> 29.51217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -15.41919 0.00971 0.06443 0.01415 MINI INTERN> 4.33196 15.64949 0.00000 12.22204 3.01527 MINI EXTERN> -105.62743 25.46557 0.00000 0.00000 0.00000 MINI CONSTR> 29.52391 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -15.42582 0.00663 0.05622 0.01028 MINI INTERN> 4.37589 15.63867 0.00000 12.20533 3.01680 MINI EXTERN> -105.57185 25.37451 0.00000 0.00000 0.00000 MINI CONSTR> 29.53483 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -15.43051 0.00470 0.04456 0.00647 MINI INTERN> 4.35002 15.67846 0.00000 12.20325 3.01423 MINI EXTERN> -105.59576 25.37807 0.00000 0.00000 0.00000 MINI CONSTR> 29.54121 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -15.43367 0.00315 0.04324 0.00553 MINI INTERN> 4.35382 15.66986 0.00000 12.22201 3.01014 MINI EXTERN> -105.59913 25.36839 0.00000 0.00000 0.00000 MINI CONSTR> 29.54124 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -15.43626 0.00260 0.03825 0.00521 MINI INTERN> 4.37142 15.67032 0.00000 12.22138 3.02646 MINI EXTERN> -105.60489 25.34261 0.00000 0.00000 0.00000 MINI CONSTR> 29.53644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -15.43813 0.00186 0.02996 0.00393 MINI INTERN> 4.36274 15.68032 0.00000 12.23262 3.03416 MINI EXTERN> -105.62313 25.34648 0.00000 0.00000 0.00000 MINI CONSTR> 29.52868 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -15.43975 0.00162 0.03077 0.00352 MINI INTERN> 4.36455 15.67910 0.00000 12.25056 3.02562 MINI EXTERN> -105.60985 25.33366 0.00000 0.00000 0.00000 MINI CONSTR> 29.51661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -15.44122 0.00147 0.02786 0.00505 MINI INTERN> 4.36461 15.68915 0.00000 12.26091 3.02537 MINI EXTERN> -105.59730 25.31497 0.00000 0.00000 0.00000 MINI CONSTR> 29.50108 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -15.44247 0.00126 0.02528 0.00446 MINI INTERN> 4.36136 15.70059 0.00000 12.26825 3.02936 MINI EXTERN> -105.58257 25.29587 0.00000 0.00000 0.00000 MINI CONSTR> 29.48467 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -15.44338 0.00090 0.02073 0.00232 MINI INTERN> 4.36132 15.69377 0.00000 12.27704 3.03191 MINI EXTERN> -105.57370 25.29471 0.00000 0.00000 0.00000 MINI CONSTR> 29.47157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -15.44420 0.00082 0.02196 0.00271 MINI INTERN> 4.36481 15.69879 0.00000 12.29236 3.02703 MINI EXTERN> -105.57473 25.28870 0.00000 0.00000 0.00000 MINI CONSTR> 29.45884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -15.44484 0.00065 0.01795 0.00258 MINI INTERN> 4.36120 15.70766 0.00000 12.31146 3.02583 MINI EXTERN> -105.61028 25.31027 0.00000 0.00000 0.00000 MINI CONSTR> 29.44903 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -15.44542 0.00058 0.01775 0.00301 MINI INTERN> 4.36152 15.70370 0.00000 12.31740 3.02785 MINI EXTERN> -105.59711 25.30117 0.00000 0.00000 0.00000 MINI CONSTR> 29.44006 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 -15.44542 0.00058 0.01775 0.02000 CONJ INTERN> 4.36152 15.70370 0.00000 12.31740 3.02785 CONJ EXTERN> -105.59711 25.30117 0.00000 0.00000 0.00000 CONJ CONSTR> 29.44006 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "10200" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.13199 ( PROT LYS 1 HT2 ) 0.13199 ( PROT LYS 1 N ) 0.16499 ( PROT LYS 1 HT3 ) 0.13199 ( PROT LYS 1 CA ) 0.16499 ( PROT LYS 1 CB ) 0.13199 ( PROT LYS 1 CG ) 0.13199 ( PROT LYS 1 CD ) 0.13199 ( PROT LYS 1 CE ) 0.13199 ( PROT LYS 1 NZ ) 0.13199 ( PROT LYS 1 HZ1 ) 0.13199 ( PROT LYS 1 HZ2 ) 0.13199 ( PROT LYS 1 HZ3 ) 0.13199 ( PROT LYS 1 C ) 0.16499 ( PROT LYS 1 O ) 0.16499 ( PROT MET 2 N ) 0.16499 ( PROT MET 2 H ) 0.13199 ( PROT MET 2 CA ) 0.16499 ( PROT MET 2 CB ) 0.13199 ( PROT MET 2 CG ) 0.13199 ( PROT MET 2 SD ) 0.13199 ( PROT MET 2 CE ) 0.13199 ( PROT MET 2 C ) 0.16499 ( PROT MET 2 O ) 0.16499 ( PROT LYS 3 N ) 0.16499 ( PROT LYS 3 H ) 0.13199 ( PROT LYS 3 CA ) 0.16499 ( PROT LYS 3 CB ) 0.13199 ( PROT LYS 3 CG ) 0.13199 ( PROT LYS 3 CD ) 0.13199 ( PROT LYS 3 CE ) 0.13199 ( PROT LYS 3 NZ ) 0.13199 ( PROT LYS 3 HZ1 ) 0.13199 ( PROT LYS 3 HZ2 ) 0.13199 ( PROT LYS 3 HZ3 ) 0.13199 ( PROT LYS 3 C ) 0.16499 ( PROT LYS 3 O ) 0.16499 ( PROT ALA 4 N ) 0.16499 ( PROT ALA 4 H ) 0.13199 ( PROT ALA 4 CA ) 0.16499 ( PROT ALA 4 CB ) 0.13199 ( PROT ALA 4 C ) 0.16499 ( PROT ALA 4 O ) 0.16499 ( PROT VAL 5 N ) 0.16499 ( PROT VAL 5 H ) 0.13199 ( PROT VAL 5 CA ) 0.16499 ( PROT VAL 5 CB ) 0.13199 ( PROT VAL 5 CG1 ) 0.13199 ( PROT VAL 5 CG2 ) 0.13199 ( PROT VAL 5 C ) 0.16499 ( PROT VAL 5 O ) 0.16499 ( PROT MET 6 N ) 0.16499 ( PROT MET 6 H ) 0.13199 ( PROT MET 6 CA ) 0.16499 ( PROT MET 6 CB ) 0.13199 ( PROT MET 6 CG ) 0.13199 ( PROT MET 6 SD ) 0.13199 ( PROT MET 6 CE ) 0.13199 ( PROT MET 6 C ) 0.16499 ( PROT MET 6 O ) 0.16499 ( PROT ILE 7 N ) 0.16499 ( PROT ILE 7 H ) 0.13199 ( PROT ILE 7 CA ) 0.16499 ( PROT ILE 7 CB ) 0.13199 ( PROT ILE 7 CG2 ) 0.13199 ( PROT ILE 7 CG1 ) 0.13199 ( PROT ILE 7 CD ) 0.13199 ( PROT ILE 7 C ) 0.16499 ( PROT ILE 7 O ) 0.16499 ( PROT GLY 8 N ) 0.16499 ( PROT GLY 8 H ) 0.13199 ( PROT GLY 8 CA ) 0.16499 ( PROT GLY 8 C ) 0.16499 ( PROT GLY 8 O ) 0.16499 ( PROT ALA 9 N ) 0.16499 ( PROT ALA 9 H ) 0.13199 ( PROT ALA 9 CA ) 0.16499 ( PROT ALA 9 CB ) 0.13199 ( PROT ALA 9 C ) 0.16499 ( PROT ALA 9 O ) 0.16499 ( PROT CYS 10 N ) 0.16499 ( PROT CYS 10 H ) 0.13199 ( PROT CYS 10 CA ) 0.16499 ( PROT CYS 10 CB ) 0.13199 ( PROT CYS 10 SG ) 0.13199 ( PROT CYS 10 C ) 0.16499 ( PROT CYS 10 O ) 0.16499 ( PROT PHE 11 N ) 0.16499 ( PROT PHE 11 H ) 0.13199 ( PROT PHE 11 CA ) 0.16499 ( PROT PHE 11 CB ) 0.13199 ( PROT PHE 11 CG ) 0.13199 ( PROT PHE 11 CD1 ) 0.13199 ( PROT PHE 11 CD2 ) 0.13199 ( PROT PHE 11 CE1 ) 0.13199 ( PROT PHE 11 CE2 ) 0.13199 ( PROT PHE 11 CZ ) 0.13199 ( PROT PHE 11 C ) 0.16499 ( PROT PHE 11 O ) 0.16499 ( PROT LEU 12 N ) 0.16499 ( PROT LEU 12 H ) 0.13199 ( PROT LEU 12 CA ) 0.16499 ( PROT LEU 12 CB ) 0.13199 ( PROT LEU 12 CG ) 0.13199 ( PROT LEU 12 CD1 ) 0.13199 ( PROT LEU 12 CD2 ) 0.13199 ( PROT LEU 12 C ) 0.16499 ( PROT LEU 12 O ) 0.16499 ( PROT ILE 13 N ) 0.16499 ( PROT ILE 13 H ) 0.13199 ( PROT ILE 13 CA ) 0.16499 ( PROT ILE 13 CB ) 0.13199 ( PROT ILE 13 CG2 ) 0.13199 ( PROT ILE 13 CG1 ) 0.13199 ( PROT ILE 13 CD ) 0.13199 ( PROT ILE 13 C ) 0.16499 ( PROT ILE 13 O ) 0.16499 ( PROT ASP 14 N ) 0.16499 ( PROT ASP 14 H ) 0.13199 ( PROT ASP 14 CA ) 0.16499 ( PROT ASP 14 CB ) 0.13199 ( PROT ASP 14 CG ) 0.13199 ( PROT ASP 14 OD1 ) 0.13199 ( PROT ASP 14 OD2 ) 0.13199 ( PROT ASP 14 C ) 0.16499 ( PROT ASP 14 O ) 0.16499 ( PROT PHE 15 N ) 0.16499 ( PROT PHE 15 H ) 0.13199 ( PROT PHE 15 CA ) 0.16499 ( PROT PHE 15 CB ) 0.13199 ( PROT PHE 15 CG ) 0.13199 ( PROT PHE 15 CD1 ) 0.13199 ( PROT PHE 15 CD2 ) 0.13199 ( PROT PHE 15 CE1 ) 0.13199 ( PROT PHE 15 CE2 ) 0.13199 ( PROT PHE 15 CZ ) 0.13199 ( PROT PHE 15 C ) 0.16499 ( PROT PHE 15 O ) 0.16499 ( PROT MET 16 N ) 0.16499 ( PROT MET 16 H ) 0.13199 ( PROT MET 16 CA ) 0.16499 ( PROT MET 16 CB ) 0.13199 ( PROT MET 16 CG ) 0.13199 ( PROT MET 16 SD ) 0.13199 ( PROT MET 16 CE ) 0.13199 ( PROT MET 16 C ) 0.16499 ( PROT MET 16 O ) 0.16499 ( PROT PHE 17 N ) 0.16499 ( PROT PHE 17 H ) 0.13199 ( PROT PHE 17 CA ) 0.16499 ( PROT PHE 17 CB ) 0.13199 ( PROT PHE 17 CG ) 0.13199 ( PROT PHE 17 CD1 ) 0.13199 ( PROT PHE 17 CD2 ) 0.13199 ( PROT PHE 17 CE1 ) 0.13199 ( PROT PHE 17 CE2 ) 0.13199 ( PROT PHE 17 CZ ) 0.13199 ( PROT PHE 17 C ) 0.16499 ( PROT PHE 17 O ) 0.16499 ( PROT PHE 18 N ) 0.16499 ( PROT PHE 18 H ) 0.13199 ( PROT PHE 18 CA ) 0.16499 ( PROT PHE 18 CB ) 0.13199 ( PROT PHE 18 CG ) 0.13199 ( PROT PHE 18 CD1 ) 0.13199 ( PROT PHE 18 CD2 ) 0.13199 ( PROT PHE 18 CE1 ) 0.13199 ( PROT PHE 18 CE2 ) 0.13199 ( PROT PHE 18 CZ ) 0.13199 ( PROT PHE 18 C ) 0.16499 ( PROT PHE 18 O ) 0.16499 ( PROT GLU 19 N ) 0.16499 ( PROT GLU 19 H ) 0.13199 ( PROT GLU 19 CA ) 0.16499 ( PROT GLU 19 CB ) 0.13199 ( PROT GLU 19 CG ) 0.13199 ( PROT GLU 19 CD ) 0.13199 ( PROT GLU 19 OE1 ) 0.13199 ( PROT GLU 19 OE2 ) 0.13199 ( PROT GLU 19 C ) 0.16499 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.40803 5.25520 -8.66815 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00300 0.00471 -0.00354 ROTATION MATRIX 1.000000 -0.000249 0.000270 0.000249 1.000000 0.000634 -0.000270 -0.000634 1.000000 AXIS OF ROTATION IS 0.864951 -0.369076 -0.340063 ANGLE IS 0.04 TOTAL SQUARE DIFF IS 134.9348 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.861046 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.8610" Parameter: A <- "0.8610" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.72996 5.25897 -8.79451 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.01512 0.00545 0.00014 ROTATION MATRIX 0.999947 0.010039 0.002276 -0.010015 0.999895 -0.010485 -0.002381 0.010462 0.999942 AXIS OF ROTATION IS -0.713210 -0.158550 0.682784 ANGLE IS 0.84 TOTAL SQUARE DIFF IS 8.0590 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.651273 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.8610" RDCMND substituted energy or value "?RMS" to " 0.6513" Parameter: A <- "0.8610 0.6513" 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 0.8610 0.6513 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 " 29.44" Parameter: H <- "29.44" 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 -44.88548 29.44006 0.21895 ENER INTERN> 4.36152 15.70370 0.00000 12.31740 3.02785 ENER EXTERN> -105.59711 25.30117 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 " -44.89" Parameter: B <- "-44.89" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 25.30" Parameter: C <- "25.30" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -105.60" Parameter: C <- " -80.30" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -80.30" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.36" Parameter: D <- "4.36" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 15.70" Parameter: D <- " 20.06" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 12.32" Parameter: D <- " 32.38" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 3.03" Parameter: D <- " 35.41" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 35.41" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 10200 ENER= -44.89 GRMS= 0.22 ELEC= 25.30 VDW= -105.60 RDTITL> *EXTERNAL= -80.30 INTERNAL= 35.41 USER= 0.00 HARM= 29.44 RDTITL> *BOND= 4.36 ANGL= 15.70 DIHE= 12.32 IMPR= 3.03 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 10777 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10744 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -25.59498 -19.29050 0.07947 0.02000 MINI INTERN> 4.36152 15.70370 0.00000 12.31740 3.02785 MINI EXTERN> -105.59711 25.30117 0.00000 0.00000 0.00000 MINI CONSTR> 19.29050 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -25.33104 -0.26394 2.03365 0.00150 MINI INTERN> 5.12426 16.30321 0.00000 12.49524 3.05775 MINI EXTERN> -108.80970 26.49366 0.00000 0.00000 0.00000 MINI CONSTR> 20.00456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10731 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -25.77027 0.43924 0.76257 0.00065 MINI INTERN> 4.63025 15.97345 0.00000 12.47541 3.02161 MINI EXTERN> -108.06461 26.19580 0.00000 0.00000 0.00000 MINI CONSTR> 19.99781 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -25.85875 0.08848 0.10445 0.00012 MINI INTERN> 4.55544 15.90666 0.00000 12.42061 3.04276 MINI EXTERN> -107.83296 26.04790 0.00000 0.00000 0.00000 MINI CONSTR> 20.00085 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10731 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -25.87437 0.01561 0.12189 0.00012 MINI INTERN> 4.53516 15.85873 0.00000 12.39153 3.04630 MINI EXTERN> -107.66376 25.95155 0.00000 0.00000 0.00000 MINI CONSTR> 20.00614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -25.88364 0.00927 0.20324 0.00013 MINI INTERN> 4.52141 15.82836 0.00000 12.37079 3.04785 MINI EXTERN> -107.55191 25.88722 0.00000 0.00000 0.00000 MINI CONSTR> 20.01263 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10730 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -25.89273 0.00909 0.20392 0.00013 MINI INTERN> 4.52251 15.79870 0.00000 12.35081 3.04942 MINI EXTERN> -107.47936 25.84526 0.00000 0.00000 0.00000 MINI CONSTR> 20.01994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -25.90051 0.00778 0.20199 0.00013 MINI INTERN> 4.52317 15.77469 0.00000 12.33411 3.05033 MINI EXTERN> -107.42604 25.81549 0.00000 0.00000 0.00000 MINI CONSTR> 20.02775 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10730 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -25.91064 0.01013 0.06053 0.00006 MINI INTERN> 4.47086 15.77649 0.00000 12.33327 3.04576 MINI EXTERN> -107.35742 25.78506 0.00000 0.00000 0.00000 MINI CONSTR> 20.03535 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -25.91334 0.00270 0.21133 0.00014 MINI INTERN> 4.52233 15.73680 0.00000 12.30948 3.04963 MINI EXTERN> -107.34766 25.77130 0.00000 0.00000 0.00000 MINI CONSTR> 20.04478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10731 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -25.92420 0.01086 0.06218 0.00006 MINI INTERN> 4.45624 15.74904 0.00000 12.31148 3.04463 MINI EXTERN> -107.28561 25.74515 0.00000 0.00000 0.00000 MINI CONSTR> 20.05488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -25.92968 0.00548 0.05109 0.00006 MINI INTERN> 4.45573 15.73800 0.00000 12.30224 3.04471 MINI EXTERN> -107.26806 25.73394 0.00000 0.00000 0.00000 MINI CONSTR> 20.06377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10731 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -25.93566 0.00598 0.05213 0.00007 MINI INTERN> 4.45088 15.72806 0.00000 12.29388 3.04392 MINI EXTERN> -107.24956 25.72279 0.00000 0.00000 0.00000 MINI CONSTR> 20.07436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -25.94117 0.00551 0.09691 0.00007 MINI INTERN> 4.43373 15.72436 0.00000 12.28892 3.04168 MINI EXTERN> -107.22785 25.71201 0.00000 0.00000 0.00000 MINI CONSTR> 20.08597 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10731 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -25.94684 0.00567 0.06133 0.00007 MINI INTERN> 4.44090 15.71246 0.00000 12.27985 3.04206 MINI EXTERN> -107.22564 25.70751 0.00000 0.00000 0.00000 MINI CONSTR> 20.09602 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -25.95249 0.00565 0.06378 0.00007 MINI INTERN> 4.43904 15.70408 0.00000 12.27274 3.04130 MINI EXTERN> -107.22011 25.70286 0.00000 0.00000 0.00000 MINI CONSTR> 20.10762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10731 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -25.95749 0.00500 0.08637 0.00008 MINI INTERN> 4.43026 15.70066 0.00000 12.26829 3.03976 MINI EXTERN> -107.21303 25.69769 0.00000 0.00000 0.00000 MINI CONSTR> 20.11889 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -25.96174 0.00425 0.11647 0.00008 MINI INTERN> 4.41986 15.69966 0.00000 12.26467 3.03853 MINI EXTERN> -107.20802 25.69413 0.00000 0.00000 0.00000 MINI CONSTR> 20.12944 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10729 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -25.96681 0.00508 0.12222 0.00008 MINI INTERN> 4.42109 15.69210 0.00000 12.25902 3.03741 MINI EXTERN> -107.20910 25.69172 0.00000 0.00000 0.00000 MINI CONSTR> 20.14094 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -25.97120 0.00438 0.14041 0.00009 MINI INTERN> 4.41453 15.69027 0.00000 12.25410 3.03730 MINI EXTERN> -107.21093 25.69167 0.00000 0.00000 0.00000 MINI CONSTR> 20.15187 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10729 ATOM PAIRS WERE FOUND FOR ATOM LIST 322 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -25.97575 0.00456 0.12834 0.00009 MINI INTERN> 4.41171 15.68770 0.00000 12.25021 3.03658 MINI EXTERN> -107.21287 25.68920 0.00000 0.00000 0.00000 MINI CONSTR> 20.16173 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -25.98051 0.00476 0.14472 0.00009 MINI INTERN> 4.40897 15.68305 0.00000 12.24566 3.03537 MINI EXTERN> -107.21626 25.68882 0.00000 0.00000 0.00000 MINI CONSTR> 20.17389 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10728 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -25.98499 0.00448 0.13882 0.00010 MINI INTERN> 4.40857 15.67958 0.00000 12.24111 3.03510 MINI EXTERN> -107.22184 25.68841 0.00000 0.00000 0.00000 MINI CONSTR> 20.18409 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -25.98973 0.00474 0.14403 0.00010 MINI INTERN> 4.40775 15.67482 0.00000 12.23624 3.03455 MINI EXTERN> -107.22850 25.68962 0.00000 0.00000 0.00000 MINI CONSTR> 20.19579 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10728 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -25.99574 0.00601 0.04733 0.00004 MINI INTERN> 4.44255 15.65418 0.00000 12.22367 3.03769 MINI EXTERN> -107.25396 25.69424 0.00000 0.00000 0.00000 MINI CONSTR> 20.20589 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -25.99797 0.00223 0.15617 0.00011 MINI INTERN> 4.40253 15.67104 0.00000 12.22896 3.03325 MINI EXTERN> -107.23946 25.68892 0.00000 0.00000 0.00000 MINI CONSTR> 20.21679 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10728 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -26.00245 0.00449 0.16232 0.00011 MINI INTERN> 4.40208 15.66677 0.00000 12.22427 3.03289 MINI EXTERN> -107.24793 25.69115 0.00000 0.00000 0.00000 MINI CONSTR> 20.22831 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -26.00881 0.00636 0.04982 0.00005 MINI INTERN> 4.44360 15.64247 0.00000 12.21081 3.03633 MINI EXTERN> -107.27716 25.69686 0.00000 0.00000 0.00000 MINI CONSTR> 20.23828 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10728 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -26.01020 0.00139 0.17594 0.00012 MINI INTERN> 4.39962 15.66333 0.00000 12.21745 3.03162 MINI EXTERN> -107.26133 25.69028 0.00000 0.00000 0.00000 MINI CONSTR> 20.24884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -26.01714 0.00694 0.06156 0.00005 MINI INTERN> 4.44843 15.63350 0.00000 12.20187 3.03573 MINI EXTERN> -107.29585 25.69948 0.00000 0.00000 0.00000 MINI CONSTR> 20.25969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10728 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -26.02077 0.00363 0.04367 0.00005 MINI INTERN> 4.44110 15.63417 0.00000 12.20027 3.03468 MINI EXTERN> -107.29924 25.69980 0.00000 0.00000 0.00000 MINI CONSTR> 20.26846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -26.02500 0.00423 0.07207 0.00006 MINI INTERN> 4.45279 15.62515 0.00000 12.19356 3.03510 MINI EXTERN> -107.31439 25.70254 0.00000 0.00000 0.00000 MINI CONSTR> 20.28026 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10726 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -26.02865 0.00365 0.04208 0.00006 MINI INTERN> 4.44057 15.62871 0.00000 12.19308 3.03377 MINI EXTERN> -107.31571 25.70213 0.00000 0.00000 0.00000 MINI CONSTR> 20.28880 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -26.03297 0.00432 0.08245 0.00006 MINI INTERN> 4.45619 15.61774 0.00000 12.18535 3.03446 MINI EXTERN> -107.33367 25.70552 0.00000 0.00000 0.00000 MINI CONSTR> 20.30144 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10725 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -26.03706 0.00409 0.05721 0.00006 MINI INTERN> 4.44653 15.61986 0.00000 12.18374 3.03352 MINI EXTERN> -107.33795 25.70602 0.00000 0.00000 0.00000 MINI CONSTR> 20.31123 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -26.04082 0.00376 0.07020 0.00006 MINI INTERN> 4.45321 15.61370 0.00000 12.17893 3.03334 MINI EXTERN> -107.34960 25.70798 0.00000 0.00000 0.00000 MINI CONSTR> 20.32164 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10725 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -26.04418 0.00336 0.09750 0.00007 MINI INTERN> 4.46201 15.60666 0.00000 12.17362 3.03355 MINI EXTERN> -107.36251 25.71065 0.00000 0.00000 0.00000 MINI CONSTR> 20.33184 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -26.04854 0.00437 0.05833 0.00007 MINI INTERN> 4.44923 15.61078 0.00000 12.17275 3.03223 MINI EXTERN> -107.36550 25.71011 0.00000 0.00000 0.00000 MINI CONSTR> 20.34185 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10724 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -26.05178 0.00324 0.10405 0.00007 MINI INTERN> 4.46291 15.60126 0.00000 12.16615 3.03297 MINI EXTERN> -107.38162 25.71391 0.00000 0.00000 0.00000 MINI CONSTR> 20.35264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -26.05536 0.00358 0.11817 0.00007 MINI INTERN> 4.46612 15.59755 0.00000 12.16249 3.03217 MINI EXTERN> -107.39107 25.71434 0.00000 0.00000 0.00000 MINI CONSTR> 20.36305 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10724 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -26.05889 0.00352 0.11059 0.00008 MINI INTERN> 4.46490 15.59547 0.00000 12.15902 3.03232 MINI EXTERN> -107.40018 25.71726 0.00000 0.00000 0.00000 MINI CONSTR> 20.37232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -26.06211 0.00322 0.13552 0.00008 MINI INTERN> 4.47091 15.59050 0.00000 12.15517 3.03141 MINI EXTERN> -107.41020 25.71749 0.00000 0.00000 0.00000 MINI CONSTR> 20.38260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10724 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -26.06552 0.00341 0.12371 0.00008 MINI INTERN> 4.47117 15.58781 0.00000 12.15210 3.03109 MINI EXTERN> -107.41839 25.71944 0.00000 0.00000 0.00000 MINI CONSTR> 20.39127 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -26.07001 0.00449 0.04062 0.00004 MINI INTERN> 4.43458 15.60507 0.00000 12.15578 3.02904 MINI EXTERN> -107.41150 25.71708 0.00000 0.00000 0.00000 MINI CONSTR> 20.39993 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10724 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -26.07208 0.00207 0.13055 0.00009 MINI INTERN> 4.47630 15.58058 0.00000 12.14466 3.03074 MINI EXTERN> -107.43798 25.72355 0.00000 0.00000 0.00000 MINI CONSTR> 20.41007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -26.07693 0.00485 0.04199 0.00004 MINI INTERN> 4.43378 15.60138 0.00000 12.14936 3.02829 MINI EXTERN> -107.42892 25.71995 0.00000 0.00000 0.00000 MINI CONSTR> 20.41923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10724 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -26.07860 0.00167 0.14048 0.00010 MINI INTERN> 4.47700 15.57590 0.00000 12.13768 3.03054 MINI EXTERN> -107.45670 25.72788 0.00000 0.00000 0.00000 MINI CONSTR> 20.42909 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -26.08168 0.00308 0.16057 0.00010 MINI INTERN> 4.47564 15.57548 0.00000 12.13583 3.02883 MINI EXTERN> -107.46236 25.72606 0.00000 0.00000 0.00000 MINI CONSTR> 20.43884 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10724 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -26.08700 0.00532 0.04549 0.00004 MINI INTERN> 4.43200 15.59643 0.00000 12.13999 3.02720 MINI EXTERN> -107.45463 25.72430 0.00000 0.00000 0.00000 MINI CONSTR> 20.44772 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -26.08809 0.00109 0.15399 0.00011 MINI INTERN> 4.48560 15.56539 0.00000 12.12702 3.02944 MINI EXTERN> -107.48524 25.73251 0.00000 0.00000 0.00000 MINI CONSTR> 20.45718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10724 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -26.09384 0.00575 0.04804 0.00005 MINI INTERN> 4.43131 15.59274 0.00000 12.13346 3.02646 MINI EXTERN> -107.47259 25.72749 0.00000 0.00000 0.00000 MINI CONSTR> 20.46729 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -26.09676 0.00292 0.03864 0.00005 MINI INTERN> 4.43638 15.58825 0.00000 12.12974 3.02642 MINI EXTERN> -107.48232 25.72932 0.00000 0.00000 0.00000 MINI CONSTR> 20.47546 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10724 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -26.10012 0.00336 0.06410 0.00005 MINI INTERN> 4.42588 15.59212 0.00000 12.12819 3.02550 MINI EXTERN> -107.48761 25.72989 0.00000 0.00000 0.00000 MINI CONSTR> 20.48591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -26.10299 0.00287 0.03804 0.00005 MINI INTERN> 4.43693 15.58431 0.00000 12.12351 3.02581 MINI EXTERN> -107.49936 25.73237 0.00000 0.00000 0.00000 MINI CONSTR> 20.49345 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10723 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -26.10617 0.00319 0.07557 0.00005 MINI INTERN> 4.42341 15.59010 0.00000 12.12266 3.02460 MINI EXTERN> -107.50313 25.73224 0.00000 0.00000 0.00000 MINI CONSTR> 20.50395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -26.10936 0.00319 0.05466 0.00006 MINI INTERN> 4.42971 15.58459 0.00000 12.11825 3.02493 MINI EXTERN> -107.51445 25.73513 0.00000 0.00000 0.00000 MINI CONSTR> 20.51247 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10723 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -26.11224 0.00288 0.06520 0.00006 MINI INTERN> 4.42549 15.58539 0.00000 12.11609 3.02437 MINI EXTERN> -107.52083 25.73594 0.00000 0.00000 0.00000 MINI CONSTR> 20.52130 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -26.11488 0.00264 0.08688 0.00006 MINI INTERN> 4.41988 15.58719 0.00000 12.11441 3.02355 MINI EXTERN> -107.52612 25.73614 0.00000 0.00000 0.00000 MINI CONSTR> 20.53007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10722 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -26.11788 0.00300 0.09195 0.00006 MINI INTERN> 4.41938 15.58550 0.00000 12.11099 3.02365 MINI EXTERN> -107.53535 25.73878 0.00000 0.00000 0.00000 MINI CONSTR> 20.53916 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -26.12067 0.00278 0.09665 0.00006 MINI INTERN> 4.41717 15.58540 0.00000 12.10888 3.02280 MINI EXTERN> -107.54156 25.73886 0.00000 0.00000 0.00000 MINI CONSTR> 20.54777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10722 ATOM PAIRS WERE FOUND FOR ATOM LIST 320 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -26.12356 0.00290 0.10331 0.00007 MINI INTERN> 4.41530 15.58460 0.00000 12.10581 3.02277 MINI EXTERN> -107.54997 25.74114 0.00000 0.00000 0.00000 MINI CONSTR> 20.55678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -26.12630 0.00274 0.10717 0.00007 MINI INTERN> 4.41498 15.58345 0.00000 12.10338 3.02202 MINI EXTERN> -107.55685 25.74147 0.00000 0.00000 0.00000 MINI CONSTR> 20.56525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10721 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -26.12911 0.00280 0.10175 0.00007 MINI INTERN> 4.41490 15.58174 0.00000 12.10030 3.02206 MINI EXTERN> -107.56509 25.74361 0.00000 0.00000 0.00000 MINI CONSTR> 20.57336 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -26.13190 0.00279 0.11214 0.00007 MINI INTERN> 4.42013 15.57736 0.00000 12.09689 3.02132 MINI EXTERN> -107.57422 25.74433 0.00000 0.00000 0.00000 MINI CONSTR> 20.58229 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10720 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -26.13470 0.00281 0.10886 0.00008 MINI INTERN> 4.41459 15.57854 0.00000 12.09423 3.02163 MINI EXTERN> -107.58156 25.74716 0.00000 0.00000 0.00000 MINI CONSTR> 20.59070 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -26.13821 0.00351 0.03626 0.00003 MINI INTERN> 4.44576 15.55866 0.00000 12.08601 3.02255 MINI EXTERN> -107.60105 25.75164 0.00000 0.00000 0.00000 MINI CONSTR> 20.59823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10720 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -26.13975 0.00154 0.12122 0.00008 MINI INTERN> 4.41027 15.57818 0.00000 12.08952 3.02078 MINI EXTERN> -107.59478 25.74928 0.00000 0.00000 0.00000 MINI CONSTR> 20.60700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -26.14365 0.00390 0.03913 0.00004 MINI INTERN> 4.44775 15.55428 0.00000 12.07986 3.02207 MINI EXTERN> -107.61750 25.75494 0.00000 0.00000 0.00000 MINI CONSTR> 20.61494 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10720 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -26.14471 0.00106 0.13619 0.00009 MINI INTERN> 4.41687 15.57191 0.00000 12.08365 3.01956 MINI EXTERN> -107.61050 25.75068 0.00000 0.00000 0.00000 MINI CONSTR> 20.62312 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -26.14886 0.00415 0.04212 0.00004 MINI INTERN> 4.44982 15.55000 0.00000 12.07393 3.02156 MINI EXTERN> -107.63330 25.75806 0.00000 0.00000 0.00000 MINI CONSTR> 20.63107 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10719 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -26.14972 0.00086 0.13841 0.00010 MINI INTERN> 4.40791 15.57402 0.00000 12.07943 3.01897 MINI EXTERN> -107.62248 25.75334 0.00000 0.00000 0.00000 MINI CONSTR> 20.63910 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -26.15415 0.00443 0.04732 0.00004 MINI INTERN> 4.45239 15.54539 0.00000 12.06775 3.02104 MINI EXTERN> -107.64968 25.76130 0.00000 0.00000 0.00000 MINI CONSTR> 20.64766 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10719 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -26.15649 0.00234 0.03376 0.00004 MINI INTERN> 4.44545 15.54797 0.00000 12.06657 3.02049 MINI EXTERN> -107.65341 25.76181 0.00000 0.00000 0.00000 MINI CONSTR> 20.65461 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -26.15921 0.00271 0.03559 0.00004 MINI INTERN> 4.44730 15.54531 0.00000 12.06331 3.02022 MINI EXTERN> -107.66197 25.76347 0.00000 0.00000 0.00000 MINI CONSTR> 20.66315 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10719 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -26.16181 0.00261 0.06100 0.00005 MINI INTERN> 4.45727 15.53798 0.00000 12.05832 3.02042 MINI EXTERN> -107.67442 25.76645 0.00000 0.00000 0.00000 MINI CONSTR> 20.67216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -26.16414 0.00233 0.03418 0.00005 MINI INTERN> 4.44671 15.54269 0.00000 12.05804 3.01961 MINI EXTERN> -107.67606 25.76622 0.00000 0.00000 0.00000 MINI CONSTR> 20.67865 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10719 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -26.16665 0.00251 0.07100 0.00005 MINI INTERN> 4.46113 15.53292 0.00000 12.05230 3.01985 MINI EXTERN> -107.69011 25.76940 0.00000 0.00000 0.00000 MINI CONSTR> 20.68786 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -26.16921 0.00256 0.05226 0.00005 MINI INTERN> 4.45337 15.53572 0.00000 12.05087 3.01949 MINI EXTERN> -107.69441 25.77050 0.00000 0.00000 0.00000 MINI CONSTR> 20.69525 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10719 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -26.17132 0.00211 0.07644 0.00005 MINI INTERN> 4.46320 15.52883 0.00000 12.04652 3.01950 MINI EXTERN> -107.70515 25.77275 0.00000 0.00000 0.00000 MINI CONSTR> 20.70303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -26.17412 0.00280 0.04552 0.00005 MINI INTERN> 4.45290 15.53310 0.00000 12.04567 3.01873 MINI EXTERN> -107.70818 25.77292 0.00000 0.00000 0.00000 MINI CONSTR> 20.71073 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10717 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -26.17630 0.00218 0.08344 0.00006 MINI INTERN> 4.46462 15.52503 0.00000 12.04051 3.01902 MINI EXTERN> -107.72080 25.77597 0.00000 0.00000 0.00000 MINI CONSTR> 20.71935 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -26.17876 0.00247 0.08761 0.00006 MINI INTERN> 4.46583 15.52297 0.00000 12.03765 3.01853 MINI EXTERN> -107.72828 25.77703 0.00000 0.00000 0.00000 MINI CONSTR> 20.72750 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10717 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -26.18096 0.00219 0.09841 0.00006 MINI INTERN> 4.46493 15.52191 0.00000 12.03465 3.01873 MINI EXTERN> -107.73600 25.77960 0.00000 0.00000 0.00000 MINI CONSTR> 20.73521 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -26.18323 0.00227 0.09026 0.00006 MINI INTERN> 4.46726 15.51933 0.00000 12.03210 3.01818 MINI EXTERN> -107.74256 25.78029 0.00000 0.00000 0.00000 MINI CONSTR> 20.74216 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10717 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -26.18556 0.00233 0.10423 0.00007 MINI INTERN> 4.46790 15.51747 0.00000 12.02876 3.01822 MINI EXTERN> -107.75110 25.78258 0.00000 0.00000 0.00000 MINI CONSTR> 20.75062 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -26.18780 0.00224 0.09820 0.00007 MINI INTERN> 4.46936 15.51540 0.00000 12.02636 3.01763 MINI EXTERN> -107.75730 25.78320 0.00000 0.00000 0.00000 MINI CONSTR> 20.75756 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10717 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -26.19012 0.00232 0.10526 0.00007 MINI INTERN> 4.46383 15.51692 0.00000 12.02404 3.01768 MINI EXTERN> -107.76349 25.78541 0.00000 0.00000 0.00000 MINI CONSTR> 20.76549 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -26.19306 0.00294 0.03262 0.00003 MINI INTERN> 4.44228 15.52758 0.00000 12.02601 3.01591 MINI EXTERN> -107.76001 25.78324 0.00000 0.00000 0.00000 MINI CONSTR> 20.77193 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10717 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -26.19427 0.00121 0.11047 0.00008 MINI INTERN> 4.47173 15.50995 0.00000 12.01787 3.01714 MINI EXTERN> -107.77888 25.78818 0.00000 0.00000 0.00000 MINI CONSTR> 20.77973 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -26.19648 0.00220 0.11877 0.00008 MINI INTERN> 4.47209 15.50869 0.00000 12.01568 3.01621 MINI EXTERN> -107.78468 25.78811 0.00000 0.00000 0.00000 MINI CONSTR> 20.78741 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10717 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -26.19979 0.00331 0.03760 0.00003 MINI INTERN> 4.44047 15.52441 0.00000 12.01837 3.01495 MINI EXTERN> -107.77963 25.78732 0.00000 0.00000 0.00000 MINI CONSTR> 20.79430 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -26.20056 0.00077 0.12165 0.00008 MINI INTERN> 4.47524 15.50410 0.00000 12.00958 3.01639 MINI EXTERN> -107.79982 25.79245 0.00000 0.00000 0.00000 MINI CONSTR> 20.80151 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10715 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -26.20276 0.00220 0.13002 0.00009 MINI INTERN> 4.47686 15.50201 0.00000 12.00670 3.01588 MINI EXTERN> -107.80713 25.79339 0.00000 0.00000 0.00000 MINI CONSTR> 20.80953 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -26.20642 0.00366 0.04446 0.00004 MINI INTERN> 4.43901 15.52106 0.00000 12.01065 3.01400 MINI EXTERN> -107.79928 25.79147 0.00000 0.00000 0.00000 MINI CONSTR> 20.81667 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10715 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -26.20833 0.00191 0.03018 0.00004 MINI INTERN> 4.44450 15.51677 0.00000 12.00744 3.01406 MINI EXTERN> -107.80704 25.79323 0.00000 0.00000 0.00000 MINI CONSTR> 20.82272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -26.21063 0.00230 0.03037 0.00004 MINI INTERN> 4.44471 15.51519 0.00000 12.00463 3.01374 MINI EXTERN> -107.81408 25.79469 0.00000 0.00000 0.00000 MINI CONSTR> 20.83049 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10715 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -26.21291 0.00228 0.05633 0.00004 MINI INTERN> 4.43707 15.51794 0.00000 12.00294 3.01309 MINI EXTERN> -107.81870 25.79579 0.00000 0.00000 0.00000 MINI CONSTR> 20.83897 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -26.21497 0.00206 0.04357 0.00004 MINI INTERN> 4.44147 15.51426 0.00000 11.99990 3.01288 MINI EXTERN> -107.82608 25.79708 0.00000 0.00000 0.00000 MINI CONSTR> 20.84553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10715 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -26.21691 0.00193 0.04965 0.00005 MINI INTERN> 4.43909 15.51433 0.00000 11.99783 3.01256 MINI EXTERN> -107.83136 25.79832 0.00000 0.00000 0.00000 MINI CONSTR> 20.85232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -26.21894 0.00204 0.04834 0.00005 MINI INTERN> 4.43924 15.51290 0.00000 11.99518 3.01242 MINI EXTERN> -107.83788 25.79996 0.00000 0.00000 0.00000 MINI CONSTR> 20.85924 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10715 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -26.22067 0.00172 0.07073 0.00005 MINI INTERN> 4.43513 15.51413 0.00000 11.99365 3.01176 MINI EXTERN> -107.84190 25.80050 0.00000 0.00000 0.00000 MINI CONSTR> 20.86606 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 -26.22067 0.00172 0.07073 0.00006 STPD INTERN> 4.43513 15.51413 0.00000 11.99365 3.01176 STPD EXTERN> -107.84190 25.80050 0.00000 0.00000 0.00000 STPD CONSTR> 20.86606 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 10715 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10715 ATOM PAIRS WERE FOUND FOR ATOM LIST 321 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -26.22067 0.00172 0.07073 0.00000 MINI INTERN> 4.43513 15.51413 0.00000 11.99365 3.01176 MINI EXTERN> -107.84190 25.80050 0.00000 0.00000 0.00000 MINI CONSTR> 20.86606 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -26.44205 0.22138 0.03585 0.01331 MINI INTERN> 4.49881 15.25156 0.00000 11.46805 2.96253 MINI EXTERN> -109.16320 26.11791 0.00000 0.00000 0.00000 MINI CONSTR> 22.42230 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -26.45008 0.00803 0.12221 0.01212 MINI INTERN> 4.47472 15.19885 0.00000 11.44663 2.93571 MINI EXTERN> -109.13125 26.19026 0.00000 0.00000 0.00000 MINI CONSTR> 22.43501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -26.47694 0.02686 0.14522 0.03794 MINI INTERN> 4.40296 15.16497 0.00000 11.39660 2.93479 MINI EXTERN> -109.11119 26.27567 0.00000 0.00000 0.00000 MINI CONSTR> 22.45926 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -26.50632 0.02938 0.10758 0.02002 MINI INTERN> 4.44983 15.21698 0.00000 11.32416 2.93580 MINI EXTERN> -109.06363 26.14732 0.00000 0.00000 0.00000 MINI CONSTR> 22.48321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -26.51732 0.01100 0.06436 0.01069 MINI INTERN> 4.47446 15.21582 0.00000 11.27420 2.92375 MINI EXTERN> -109.01665 26.12129 0.00000 0.00000 0.00000 MINI CONSTR> 22.48981 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -26.52319 0.00587 0.06226 0.00814 MINI INTERN> 4.49117 15.23622 0.00000 11.26164 2.93527 MINI EXTERN> -109.00797 26.06890 0.00000 0.00000 0.00000 MINI CONSTR> 22.49158 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -26.52939 0.00620 0.06020 0.01003 MINI INTERN> 4.47265 15.18814 0.00000 11.23593 2.93110 MINI EXTERN> -108.91076 26.05867 0.00000 0.00000 0.00000 MINI CONSTR> 22.49488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -26.53714 0.00774 0.06512 0.01511 MINI INTERN> 4.45253 15.15152 0.00000 11.20702 2.91560 MINI EXTERN> -108.86850 26.10041 0.00000 0.00000 0.00000 MINI CONSTR> 22.50429 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -26.54288 0.00575 0.05864 0.00908 MINI INTERN> 4.47559 15.16247 0.00000 11.19981 2.92473 MINI EXTERN> -108.85355 26.03318 0.00000 0.00000 0.00000 MINI CONSTR> 22.51489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -26.54786 0.00498 0.04801 0.00873 MINI INTERN> 4.45571 15.19764 0.00000 11.18942 2.92092 MINI EXTERN> -108.84290 26.00521 0.00000 0.00000 0.00000 MINI CONSTR> 22.52614 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -26.55182 0.00396 0.05026 0.00902 MINI INTERN> 4.46118 15.16836 0.00000 11.19737 2.92177 MINI EXTERN> -108.85792 26.02053 0.00000 0.00000 0.00000 MINI CONSTR> 22.53690 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -26.55513 0.00331 0.04151 0.00526 MINI INTERN> 4.47211 15.16390 0.00000 11.18933 2.93645 MINI EXTERN> -108.88486 26.02216 0.00000 0.00000 0.00000 MINI CONSTR> 22.54577 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -26.55766 0.00253 0.03849 0.00637 MINI INTERN> 4.46923 15.17322 0.00000 11.20354 2.94717 MINI EXTERN> -108.92826 26.02664 0.00000 0.00000 0.00000 MINI CONSTR> 22.55079 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -26.55988 0.00222 0.03347 0.00566 MINI INTERN> 4.47153 15.17060 0.00000 11.22305 2.93487 MINI EXTERN> -108.95212 26.03976 0.00000 0.00000 0.00000 MINI CONSTR> 22.55242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -26.56224 0.00236 0.04283 0.00618 MINI INTERN> 4.46856 15.18547 0.00000 11.24020 2.93444 MINI EXTERN> -108.96586 26.02562 0.00000 0.00000 0.00000 MINI CONSTR> 22.54933 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -26.56437 0.00213 0.03098 0.00680 MINI INTERN> 4.46749 15.20387 0.00000 11.25016 2.94036 MINI EXTERN> -108.94576 25.97651 0.00000 0.00000 0.00000 MINI CONSTR> 22.54301 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -26.56582 0.00145 0.02704 0.00450 MINI INTERN> 4.46861 15.20129 0.00000 11.24856 2.93853 MINI EXTERN> -108.94244 25.98376 0.00000 0.00000 0.00000 MINI CONSTR> 22.53588 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -26.56707 0.00125 0.02327 0.00393 MINI INTERN> 4.47009 15.19948 0.00000 11.25961 2.93427 MINI EXTERN> -108.91934 25.96191 0.00000 0.00000 0.00000 MINI CONSTR> 22.52692 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -26.56809 0.00102 0.02199 0.00366 MINI INTERN> 4.47008 15.19732 0.00000 11.27554 2.93635 MINI EXTERN> -108.94122 25.97562 0.00000 0.00000 0.00000 MINI CONSTR> 22.51823 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -26.56888 0.00078 0.02142 0.00329 MINI INTERN> 4.46542 15.19324 0.00000 11.27949 2.93542 MINI EXTERN> -108.92723 25.97386 0.00000 0.00000 0.00000 MINI CONSTR> 22.51093 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 -26.56888 0.00078 0.02142 0.02000 CONJ INTERN> 4.46542 15.19324 0.00000 11.27949 2.93542 CONJ EXTERN> -108.92723 25.97386 0.00000 0.00000 0.00000 CONJ CONSTR> 22.51093 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "10800" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.85797E-01 ( PROT LYS 1 HT2 ) 0.85797E-01 ( PROT LYS 1 N ) 0.10725 ( PROT LYS 1 HT3 ) 0.85797E-01 ( PROT LYS 1 CA ) 0.10725 ( PROT LYS 1 CB ) 0.85797E-01 ( PROT LYS 1 CG ) 0.85797E-01 ( PROT LYS 1 CD ) 0.85797E-01 ( PROT LYS 1 CE ) 0.85797E-01 ( PROT LYS 1 NZ ) 0.85797E-01 ( PROT LYS 1 HZ1 ) 0.85797E-01 ( PROT LYS 1 HZ2 ) 0.85797E-01 ( PROT LYS 1 HZ3 ) 0.85797E-01 ( PROT LYS 1 C ) 0.10725 ( PROT LYS 1 O ) 0.10725 ( PROT MET 2 N ) 0.10725 ( PROT MET 2 H ) 0.85797E-01 ( PROT MET 2 CA ) 0.10725 ( PROT MET 2 CB ) 0.85797E-01 ( PROT MET 2 CG ) 0.85797E-01 ( PROT MET 2 SD ) 0.85797E-01 ( PROT MET 2 CE ) 0.85797E-01 ( PROT MET 2 C ) 0.10725 ( PROT MET 2 O ) 0.10725 ( PROT LYS 3 N ) 0.10725 ( PROT LYS 3 H ) 0.85797E-01 ( PROT LYS 3 CA ) 0.10725 ( PROT LYS 3 CB ) 0.85797E-01 ( PROT LYS 3 CG ) 0.85797E-01 ( PROT LYS 3 CD ) 0.85797E-01 ( PROT LYS 3 CE ) 0.85797E-01 ( PROT LYS 3 NZ ) 0.85797E-01 ( PROT LYS 3 HZ1 ) 0.85797E-01 ( PROT LYS 3 HZ2 ) 0.85797E-01 ( PROT LYS 3 HZ3 ) 0.85797E-01 ( PROT LYS 3 C ) 0.10725 ( PROT LYS 3 O ) 0.10725 ( PROT ALA 4 N ) 0.10725 ( PROT ALA 4 H ) 0.85797E-01 ( PROT ALA 4 CA ) 0.10725 ( PROT ALA 4 CB ) 0.85797E-01 ( PROT ALA 4 C ) 0.10725 ( PROT ALA 4 O ) 0.10725 ( PROT VAL 5 N ) 0.10725 ( PROT VAL 5 H ) 0.85797E-01 ( PROT VAL 5 CA ) 0.10725 ( PROT VAL 5 CB ) 0.85797E-01 ( PROT VAL 5 CG1 ) 0.85797E-01 ( PROT VAL 5 CG2 ) 0.85797E-01 ( PROT VAL 5 C ) 0.10725 ( PROT VAL 5 O ) 0.10725 ( PROT MET 6 N ) 0.10725 ( PROT MET 6 H ) 0.85797E-01 ( PROT MET 6 CA ) 0.10725 ( PROT MET 6 CB ) 0.85797E-01 ( PROT MET 6 CG ) 0.85797E-01 ( PROT MET 6 SD ) 0.85797E-01 ( PROT MET 6 CE ) 0.85797E-01 ( PROT MET 6 C ) 0.10725 ( PROT MET 6 O ) 0.10725 ( PROT ILE 7 N ) 0.10725 ( PROT ILE 7 H ) 0.85797E-01 ( PROT ILE 7 CA ) 0.10725 ( PROT ILE 7 CB ) 0.85797E-01 ( PROT ILE 7 CG2 ) 0.85797E-01 ( PROT ILE 7 CG1 ) 0.85797E-01 ( PROT ILE 7 CD ) 0.85797E-01 ( PROT ILE 7 C ) 0.10725 ( PROT ILE 7 O ) 0.10725 ( PROT GLY 8 N ) 0.10725 ( PROT GLY 8 H ) 0.85797E-01 ( PROT GLY 8 CA ) 0.10725 ( PROT GLY 8 C ) 0.10725 ( PROT GLY 8 O ) 0.10725 ( PROT ALA 9 N ) 0.10725 ( PROT ALA 9 H ) 0.85797E-01 ( PROT ALA 9 CA ) 0.10725 ( PROT ALA 9 CB ) 0.85797E-01 ( PROT ALA 9 C ) 0.10725 ( PROT ALA 9 O ) 0.10725 ( PROT CYS 10 N ) 0.10725 ( PROT CYS 10 H ) 0.85797E-01 ( PROT CYS 10 CA ) 0.10725 ( PROT CYS 10 CB ) 0.85797E-01 ( PROT CYS 10 SG ) 0.85797E-01 ( PROT CYS 10 C ) 0.10725 ( PROT CYS 10 O ) 0.10725 ( PROT PHE 11 N ) 0.10725 ( PROT PHE 11 H ) 0.85797E-01 ( PROT PHE 11 CA ) 0.10725 ( PROT PHE 11 CB ) 0.85797E-01 ( PROT PHE 11 CG ) 0.85797E-01 ( PROT PHE 11 CD1 ) 0.85797E-01 ( PROT PHE 11 CD2 ) 0.85797E-01 ( PROT PHE 11 CE1 ) 0.85797E-01 ( PROT PHE 11 CE2 ) 0.85797E-01 ( PROT PHE 11 CZ ) 0.85797E-01 ( PROT PHE 11 C ) 0.10725 ( PROT PHE 11 O ) 0.10725 ( PROT LEU 12 N ) 0.10725 ( PROT LEU 12 H ) 0.85797E-01 ( PROT LEU 12 CA ) 0.10725 ( PROT LEU 12 CB ) 0.85797E-01 ( PROT LEU 12 CG ) 0.85797E-01 ( PROT LEU 12 CD1 ) 0.85797E-01 ( PROT LEU 12 CD2 ) 0.85797E-01 ( PROT LEU 12 C ) 0.10725 ( PROT LEU 12 O ) 0.10725 ( PROT ILE 13 N ) 0.10725 ( PROT ILE 13 H ) 0.85797E-01 ( PROT ILE 13 CA ) 0.10725 ( PROT ILE 13 CB ) 0.85797E-01 ( PROT ILE 13 CG2 ) 0.85797E-01 ( PROT ILE 13 CG1 ) 0.85797E-01 ( PROT ILE 13 CD ) 0.85797E-01 ( PROT ILE 13 C ) 0.10725 ( PROT ILE 13 O ) 0.10725 ( PROT ASP 14 N ) 0.10725 ( PROT ASP 14 H ) 0.85797E-01 ( PROT ASP 14 CA ) 0.10725 ( PROT ASP 14 CB ) 0.85797E-01 ( PROT ASP 14 CG ) 0.85797E-01 ( PROT ASP 14 OD1 ) 0.85797E-01 ( PROT ASP 14 OD2 ) 0.85797E-01 ( PROT ASP 14 C ) 0.10725 ( PROT ASP 14 O ) 0.10725 ( PROT PHE 15 N ) 0.10725 ( PROT PHE 15 H ) 0.85797E-01 ( PROT PHE 15 CA ) 0.10725 ( PROT PHE 15 CB ) 0.85797E-01 ( PROT PHE 15 CG ) 0.85797E-01 ( PROT PHE 15 CD1 ) 0.85797E-01 ( PROT PHE 15 CD2 ) 0.85797E-01 ( PROT PHE 15 CE1 ) 0.85797E-01 ( PROT PHE 15 CE2 ) 0.85797E-01 ( PROT PHE 15 CZ ) 0.85797E-01 ( PROT PHE 15 C ) 0.10725 ( PROT PHE 15 O ) 0.10725 ( PROT MET 16 N ) 0.10725 ( PROT MET 16 H ) 0.85797E-01 ( PROT MET 16 CA ) 0.10725 ( PROT MET 16 CB ) 0.85797E-01 ( PROT MET 16 CG ) 0.85797E-01 ( PROT MET 16 SD ) 0.85797E-01 ( PROT MET 16 CE ) 0.85797E-01 ( PROT MET 16 C ) 0.10725 ( PROT MET 16 O ) 0.10725 ( PROT PHE 17 N ) 0.10725 ( PROT PHE 17 H ) 0.85797E-01 ( PROT PHE 17 CA ) 0.10725 ( PROT PHE 17 CB ) 0.85797E-01 ( PROT PHE 17 CG ) 0.85797E-01 ( PROT PHE 17 CD1 ) 0.85797E-01 ( PROT PHE 17 CD2 ) 0.85797E-01 ( PROT PHE 17 CE1 ) 0.85797E-01 ( PROT PHE 17 CE2 ) 0.85797E-01 ( PROT PHE 17 CZ ) 0.85797E-01 ( PROT PHE 17 C ) 0.10725 ( PROT PHE 17 O ) 0.10725 ( PROT PHE 18 N ) 0.10725 ( PROT PHE 18 H ) 0.85797E-01 ( PROT PHE 18 CA ) 0.10725 ( PROT PHE 18 CB ) 0.85797E-01 ( PROT PHE 18 CG ) 0.85797E-01 ( PROT PHE 18 CD1 ) 0.85797E-01 ( PROT PHE 18 CD2 ) 0.85797E-01 ( PROT PHE 18 CE1 ) 0.85797E-01 ( PROT PHE 18 CE2 ) 0.85797E-01 ( PROT PHE 18 CZ ) 0.85797E-01 ( PROT PHE 18 C ) 0.10725 ( PROT PHE 18 O ) 0.10725 ( PROT GLU 19 N ) 0.10725 ( PROT GLU 19 H ) 0.85797E-01 ( PROT GLU 19 CA ) 0.10725 ( PROT GLU 19 CB ) 0.85797E-01 ( PROT GLU 19 CG ) 0.85797E-01 ( PROT GLU 19 CD ) 0.85797E-01 ( PROT GLU 19 OE1 ) 0.85797E-01 ( PROT GLU 19 OE2 ) 0.85797E-01 ( PROT GLU 19 C ) 0.10725 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.40665 5.25446 -8.66775 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00439 0.00545 -0.00395 ROTATION MATRIX 1.000000 -0.000493 0.000448 0.000493 0.999999 0.001003 -0.000449 -0.001003 0.999999 AXIS OF ROTATION IS 0.832825 -0.372629 -0.409329 ANGLE IS 0.07 TOTAL SQUARE DIFF IS 159.0342 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 0.934780 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 0.9348" Parameter: A <- "0.9348" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.73828 5.26976 -8.79902 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.02344 -0.00534 0.00465 ROTATION MATRIX 0.999978 0.006184 -0.002265 -0.006201 0.999954 -0.007289 0.002220 0.007303 0.999971 AXIS OF ROTATION IS -0.742321 0.228175 0.629997 ANGLE IS 0.56 TOTAL SQUARE DIFF IS 9.5315 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.708278 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "0.9348" RDCMND substituted energy or value "?RMS" to " 0.7083" Parameter: A <- "0.9348 0.7083" 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 0.9348 0.7083 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 22.51" Parameter: H <- "22.51" 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 -49.07980 22.51093 0.15515 ENER INTERN> 4.46542 15.19324 0.00000 11.27949 2.93542 ENER EXTERN> -108.92723 25.97386 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 " -49.08" Parameter: B <- "-49.08" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 25.97" Parameter: C <- "25.97" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -108.93" Parameter: C <- " -82.96" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -82.96" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.47" Parameter: D <- "4.47" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 15.19" Parameter: D <- " 19.66" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 11.28" Parameter: D <- " 30.94" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.94" Parameter: D <- " 33.88" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 33.88" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 10800 ENER= -49.08 GRMS= 0.16 ELEC= 25.97 VDW= -108.93 RDTITL> *EXTERNAL= -82.96 INTERNAL= 33.88 USER= 0.00 HARM= 22.51 RDTITL> *BOND= 4.47 ANGL= 15.19 DIHE= 11.28 IMPR= 2.94 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= -49.08 GRMS= 0.16 ELEC= 25.97 VDW= -108.93 RDTITL> *EXTERNAL= -82.96 INTERNAL= 33.88 USER= 0.00 HARM= 22.51 RDTITL> *BOND= 4.47 ANGL= 15.19 DIHE= 11.28 IMPR= 2.94 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= -49.08 GRMS= 0.16 ELEC= 25.97 VDW= -108.93 RDTITL> *EXTERNAL= -82.96 INTERNAL= 33.88 USER= 0.00 HARM= 22.51 RDTITL> *BOND= 4.47 ANGL= 15.19 DIHE= 11.28 IMPR= 2.94 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 10800 0.9348 0.7083 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "10800" and "12000". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 10715 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10695 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES STEEPD> An energy minimization has been requested. NSTEP = 500 NPRINT = 5 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -34.36800 -14.71180 0.05838 0.02000 MINI INTERN> 4.46542 15.19324 0.00000 11.27949 2.93542 MINI EXTERN> -108.92723 25.97386 0.00000 0.00000 0.00000 MINI CONSTR> 14.71180 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -28.99482 -5.37318 7.72892 0.00360 MINI INTERN> 9.37367 16.36505 0.00000 11.52924 2.83386 MINI EXTERN> -111.57125 27.28084 0.00000 0.00000 0.00000 MINI CONSTR> 15.19377 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10687 ATOM PAIRS WERE FOUND FOR ATOM LIST 323 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -34.40570 5.41088 0.98645 0.00065 MINI INTERN> 4.74152 15.61180 0.00000 11.41814 2.91911 MINI EXTERN> -111.17076 26.88308 0.00000 0.00000 0.00000 MINI CONSTR> 15.19141 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -34.50617 0.10047 0.46100 0.00028 MINI INTERN> 4.71862 15.44045 0.00000 11.34446 2.95723 MINI EXTERN> -110.82625 26.66893 0.00000 0.00000 0.00000 MINI CONSTR> 15.19040 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10687 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -34.53819 0.03202 0.15128 0.00012 MINI INTERN> 4.63317 15.40757 0.00000 11.33697 2.94581 MINI EXTERN> -110.65397 26.60117 0.00000 0.00000 0.00000 MINI CONSTR> 15.19109 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -34.54776 0.00958 0.16799 0.00013 MINI INTERN> 4.62732 15.35902 0.00000 11.31532 2.94847 MINI EXTERN> -110.52264 26.53146 0.00000 0.00000 0.00000 MINI CONSTR> 15.19329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10687 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -34.55400 0.00624 0.18683 0.00013 MINI INTERN> 4.61798 15.33085 0.00000 11.30056 2.94869 MINI EXTERN> -110.43759 26.48950 0.00000 0.00000 0.00000 MINI CONSTR> 15.19601 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -34.56228 0.00828 0.05771 0.00006 MINI INTERN> 4.58463 15.32716 0.00000 11.29196 2.95114 MINI EXTERN> -110.37197 26.45588 0.00000 0.00000 0.00000 MINI CONSTR> 15.19892 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10687 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -34.56679 0.00450 0.04896 0.00006 MINI INTERN> 4.57725 15.31016 0.00000 11.28224 2.95102 MINI EXTERN> -110.32204 26.43231 0.00000 0.00000 0.00000 MINI CONSTR> 15.20227 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -34.57098 0.00419 0.07532 0.00006 MINI INTERN> 4.56476 15.29747 0.00000 11.27290 2.95132 MINI EXTERN> -110.27352 26.40949 0.00000 0.00000 0.00000 MINI CONSTR> 15.20661 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10687 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -34.57463 0.00365 0.06424 0.00006 MINI INTERN> 4.55971 15.28525 0.00000 11.26540 2.95090 MINI EXTERN> -110.24156 26.39509 0.00000 0.00000 0.00000 MINI CONSTR> 15.21058 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -34.57786 0.00323 0.07559 0.00006 MINI INTERN> 4.55265 15.27618 0.00000 11.25862 2.95069 MINI EXTERN> -110.21368 26.38271 0.00000 0.00000 0.00000 MINI CONSTR> 15.21498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -34.58076 0.00290 0.08824 0.00007 MINI INTERN> 4.54439 15.27028 0.00000 11.25222 2.95076 MINI EXTERN> -110.19139 26.37340 0.00000 0.00000 0.00000 MINI CONSTR> 15.21958 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -34.58372 0.00295 0.11326 0.00007 MINI INTERN> 4.54224 15.26011 0.00000 11.24642 2.94999 MINI EXTERN> -110.17142 26.36407 0.00000 0.00000 0.00000 MINI CONSTR> 15.22486 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -34.58677 0.00305 0.09402 0.00007 MINI INTERN> 4.53691 15.25548 0.00000 11.24092 2.94994 MINI EXTERN> -110.15861 26.35896 0.00000 0.00000 0.00000 MINI CONSTR> 15.22964 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -34.58931 0.00254 0.12879 0.00007 MINI INTERN> 4.54144 15.24420 0.00000 11.23426 2.94901 MINI EXTERN> -110.14793 26.35435 0.00000 0.00000 0.00000 MINI CONSTR> 15.23535 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -34.59187 0.00257 0.12422 0.00008 MINI INTERN> 4.54149 15.23779 0.00000 11.23017 2.94827 MINI EXTERN> -110.14083 26.35129 0.00000 0.00000 0.00000 MINI CONSTR> 15.23994 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -34.59465 0.00277 0.11128 0.00008 MINI INTERN> 4.53118 15.23769 0.00000 11.22751 2.94846 MINI EXTERN> -110.13188 26.34722 0.00000 0.00000 0.00000 MINI CONSTR> 15.24518 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -34.59810 0.00346 0.03692 0.00003 MINI INTERN> 4.54991 15.21890 0.00000 11.22284 2.94522 MINI EXTERN> -110.13076 26.34592 0.00000 0.00000 0.00000 MINI CONSTR> 15.24986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -34.59939 0.00129 0.12304 0.00009 MINI INTERN> 4.52812 15.23018 0.00000 11.21944 2.94770 MINI EXTERN> -110.12545 26.34504 0.00000 0.00000 0.00000 MINI CONSTR> 15.25557 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -34.60306 0.00367 0.04110 0.00004 MINI INTERN> 4.55014 15.20919 0.00000 11.21556 2.94397 MINI EXTERN> -110.12589 26.34347 0.00000 0.00000 0.00000 MINI CONSTR> 15.26050 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -34.60521 0.00215 0.03422 0.00004 MINI INTERN> 4.54742 15.20748 0.00000 11.21286 2.94381 MINI EXTERN> -110.12479 26.34288 0.00000 0.00000 0.00000 MINI CONSTR> 15.26513 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -34.60762 0.00240 0.03501 0.00004 MINI INTERN> 4.54721 15.20379 0.00000 11.20973 2.94327 MINI EXTERN> -110.12463 26.34246 0.00000 0.00000 0.00000 MINI CONSTR> 15.27055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -34.60986 0.00224 0.03493 0.00004 MINI INTERN> 4.54707 15.20063 0.00000 11.20685 2.94282 MINI EXTERN> -110.12532 26.34242 0.00000 0.00000 0.00000 MINI CONSTR> 15.27568 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -34.61208 0.00223 0.03543 0.00004 MINI INTERN> 4.54718 15.19753 0.00000 11.20405 2.94235 MINI EXTERN> -110.12666 26.34260 0.00000 0.00000 0.00000 MINI CONSTR> 15.28087 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -34.61440 0.00232 0.05653 0.00004 MINI INTERN> 4.55444 15.18952 0.00000 11.20045 2.94109 MINI EXTERN> -110.12992 26.34319 0.00000 0.00000 0.00000 MINI CONSTR> 15.28684 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -34.61661 0.00221 0.04723 0.00005 MINI INTERN> 4.55211 15.18854 0.00000 11.19816 2.94092 MINI EXTERN> -110.13182 26.34360 0.00000 0.00000 0.00000 MINI CONSTR> 15.29189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -34.61903 0.00242 0.04179 0.00005 MINI INTERN> 4.54979 15.18746 0.00000 11.19554 2.94076 MINI EXTERN> -110.13436 26.34417 0.00000 0.00000 0.00000 MINI CONSTR> 15.29762 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -34.62122 0.00219 0.05274 0.00005 MINI INTERN> 4.55486 15.18165 0.00000 11.19252 2.93985 MINI EXTERN> -110.13846 26.34505 0.00000 0.00000 0.00000 MINI CONSTR> 15.30329 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -34.62355 0.00233 0.05152 0.00005 MINI INTERN> 4.55212 15.18116 0.00000 11.19024 2.93966 MINI EXTERN> -110.14178 26.34603 0.00000 0.00000 0.00000 MINI CONSTR> 15.30901 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10686 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -34.62544 0.00189 0.07368 0.00005 MINI INTERN> 4.56022 15.17394 0.00000 11.18707 2.93858 MINI EXTERN> -110.14707 26.34730 0.00000 0.00000 0.00000 MINI CONSTR> 15.31450 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -34.62743 0.00198 0.08209 0.00006 MINI INTERN> 4.56033 15.17173 0.00000 11.18526 2.93808 MINI EXTERN> -110.15039 26.34774 0.00000 0.00000 0.00000 MINI CONSTR> 15.31983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -34.62945 0.00203 0.08134 0.00006 MINI INTERN> 4.56374 15.16780 0.00000 11.18269 2.93748 MINI EXTERN> -110.15519 26.34899 0.00000 0.00000 0.00000 MINI CONSTR> 15.32505 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -34.63136 0.00191 0.09560 0.00006 MINI INTERN> 4.56411 15.16670 0.00000 11.17970 2.93741 MINI EXTERN> -110.16069 26.35097 0.00000 0.00000 0.00000 MINI CONSTR> 15.33044 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -34.63348 0.00212 0.08317 0.00006 MINI INTERN> 4.56514 15.16382 0.00000 11.17819 2.93677 MINI EXTERN> -110.16426 26.35132 0.00000 0.00000 0.00000 MINI CONSTR> 15.33553 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -34.63520 0.00172 0.10716 0.00006 MINI INTERN> 4.56553 15.16299 0.00000 11.17517 2.93678 MINI EXTERN> -110.17025 26.35363 0.00000 0.00000 0.00000 MINI CONSTR> 15.34094 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -34.63725 0.00205 0.09612 0.00007 MINI INTERN> 4.56783 15.15978 0.00000 11.17323 2.93620 MINI EXTERN> -110.17478 26.35458 0.00000 0.00000 0.00000 MINI CONSTR> 15.34591 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -34.63985 0.00260 0.03099 0.00003 MINI INTERN> 4.53935 15.17793 0.00000 11.17309 2.93881 MINI EXTERN> -110.17554 26.35595 0.00000 0.00000 0.00000 MINI CONSTR> 15.35055 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -34.64067 0.00082 0.12163 0.00007 MINI INTERN> 4.56061 15.16318 0.00000 11.16909 2.93670 MINI EXTERN> -110.18417 26.35794 0.00000 0.00000 0.00000 MINI CONSTR> 15.35598 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -34.64243 0.00176 0.12729 0.00007 MINI INTERN> 4.56214 15.16107 0.00000 11.16699 2.93633 MINI EXTERN> -110.18928 26.35931 0.00000 0.00000 0.00000 MINI CONSTR> 15.36102 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -34.64550 0.00307 0.03447 0.00003 MINI INTERN> 4.53730 15.17597 0.00000 11.16711 2.93833 MINI EXTERN> -110.19016 26.36018 0.00000 0.00000 0.00000 MINI CONSTR> 15.36576 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -34.64628 0.00078 0.11490 0.00008 MINI INTERN> 4.57342 15.14954 0.00000 11.16386 2.93416 MINI EXTERN> -110.19859 26.36013 0.00000 0.00000 0.00000 MINI CONSTR> 15.37120 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -34.64925 0.00297 0.03879 0.00003 MINI INTERN> 4.53555 15.17503 0.00000 11.16328 2.93803 MINI EXTERN> -110.20020 26.36304 0.00000 0.00000 0.00000 MINI CONSTR> 15.37603 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -34.65090 0.00165 0.03037 0.00004 MINI INTERN> 4.53999 15.17098 0.00000 11.16134 2.93738 MINI EXTERN> -110.20522 26.36423 0.00000 0.00000 0.00000 MINI CONSTR> 15.38038 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -34.65278 0.00187 0.03152 0.00004 MINI INTERN> 4.53951 15.17037 0.00000 11.15933 2.93723 MINI EXTERN> -110.21059 26.36581 0.00000 0.00000 0.00000 MINI CONSTR> 15.38556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -34.65457 0.00180 0.03192 0.00004 MINI INTERN> 4.53911 15.16968 0.00000 11.15748 2.93706 MINI EXTERN> -110.21571 26.36726 0.00000 0.00000 0.00000 MINI CONSTR> 15.39054 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -34.65646 0.00188 0.02913 0.00004 MINI INTERN> 4.54145 15.16707 0.00000 11.15537 2.93660 MINI EXTERN> -110.22144 26.36876 0.00000 0.00000 0.00000 MINI CONSTR> 15.39573 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -34.65842 0.00196 0.05428 0.00004 MINI INTERN> 4.53064 15.17368 0.00000 11.15376 2.93746 MINI EXTERN> -110.22646 26.37069 0.00000 0.00000 0.00000 MINI CONSTR> 15.40183 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10683 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -34.66018 0.00177 0.04379 0.00004 MINI INTERN> 4.53396 15.17050 0.00000 11.15175 2.93694 MINI EXTERN> -110.23195 26.37212 0.00000 0.00000 0.00000 MINI CONSTR> 15.40650 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -34.66192 0.00174 0.04984 0.00004 MINI INTERN> 4.53283 15.17064 0.00000 11.14971 2.93693 MINI EXTERN> -110.23753 26.37393 0.00000 0.00000 0.00000 MINI CONSTR> 15.41157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -34.66361 0.00169 0.05178 0.00005 MINI INTERN> 4.53112 15.17099 0.00000 11.14804 2.93690 MINI EXTERN> -110.24250 26.37539 0.00000 0.00000 0.00000 MINI CONSTR> 15.41644 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -34.66539 0.00178 0.05472 0.00005 MINI INTERN> 4.53190 15.16936 0.00000 11.14634 2.93654 MINI EXTERN> -110.24778 26.37668 0.00000 0.00000 0.00000 MINI CONSTR> 15.42157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -34.66692 0.00153 0.06561 0.00005 MINI INTERN> 4.52591 15.17313 0.00000 11.14464 2.93706 MINI EXTERN> -110.25265 26.37856 0.00000 0.00000 0.00000 MINI CONSTR> 15.42642 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -34.66898 0.00206 0.04771 0.00005 MINI INTERN> 4.53581 15.16520 0.00000 11.14202 2.93587 MINI EXTERN> -110.25975 26.38020 0.00000 0.00000 0.00000 MINI CONSTR> 15.43167 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -34.67033 0.00135 0.07437 0.00005 MINI INTERN> 4.52735 15.17080 0.00000 11.14052 2.93664 MINI EXTERN> -110.26430 26.38210 0.00000 0.00000 0.00000 MINI CONSTR> 15.43655 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -34.67184 0.00151 0.08572 0.00006 MINI INTERN> 4.52998 15.16756 0.00000 11.13947 2.93592 MINI EXTERN> -110.26857 26.38256 0.00000 0.00000 0.00000 MINI CONSTR> 15.44125 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -34.67338 0.00154 0.08847 0.00006 MINI INTERN> 4.52978 15.16700 0.00000 11.13779 2.93577 MINI EXTERN> -110.27361 26.38401 0.00000 0.00000 0.00000 MINI CONSTR> 15.44587 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -34.67543 0.00205 0.02827 0.00002 MINI INTERN> 4.55174 15.15071 0.00000 11.13466 2.93346 MINI EXTERN> -110.28139 26.38542 0.00000 0.00000 0.00000 MINI CONSTR> 15.44997 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -34.67654 0.00111 0.08358 0.00006 MINI INTERN> 4.52189 15.17186 0.00000 11.13402 2.93652 MINI EXTERN> -110.28409 26.38808 0.00000 0.00000 0.00000 MINI CONSTR> 15.45519 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -34.67869 0.00215 0.02988 0.00003 MINI INTERN> 4.55339 15.14812 0.00000 11.13099 2.93296 MINI EXTERN> -110.29229 26.38856 0.00000 0.00000 0.00000 MINI CONSTR> 15.45959 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -34.67920 0.00051 0.11403 0.00007 MINI INTERN> 4.53647 15.15950 0.00000 11.13103 2.93434 MINI EXTERN> -110.29415 26.38943 0.00000 0.00000 0.00000 MINI CONSTR> 15.46417 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -34.68169 0.00249 0.03186 0.00003 MINI INTERN> 4.55483 15.14579 0.00000 11.12759 2.93250 MINI EXTERN> -110.30243 26.39150 0.00000 0.00000 0.00000 MINI CONSTR> 15.46854 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -34.68303 0.00134 0.02685 0.00003 MINI INTERN> 4.55153 15.14751 0.00000 11.12634 2.93269 MINI EXTERN> -110.30637 26.39283 0.00000 0.00000 0.00000 MINI CONSTR> 15.47243 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -34.68449 0.00146 0.02669 0.00003 MINI INTERN> 4.55128 15.14706 0.00000 11.12474 2.93257 MINI EXTERN> -110.31121 26.39429 0.00000 0.00000 0.00000 MINI CONSTR> 15.47678 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -34.68604 0.00155 0.04239 0.00003 MINI INTERN> 4.55689 15.14254 0.00000 11.12248 2.93188 MINI EXTERN> -110.31758 26.39601 0.00000 0.00000 0.00000 MINI CONSTR> 15.48175 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -34.68740 0.00136 0.03448 0.00003 MINI INTERN> 4.55301 15.14466 0.00000 11.12127 2.93212 MINI EXTERN> -110.32147 26.39734 0.00000 0.00000 0.00000 MINI CONSTR> 15.48567 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -34.68879 0.00138 0.03497 0.00003 MINI INTERN> 4.55215 15.14467 0.00000 11.11976 2.93207 MINI EXTERN> -110.32607 26.39878 0.00000 0.00000 0.00000 MINI CONSTR> 15.48986 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -34.69015 0.00136 0.03905 0.00004 MINI INTERN> 4.55184 15.14435 0.00000 11.11819 2.93197 MINI EXTERN> -110.33080 26.40025 0.00000 0.00000 0.00000 MINI CONSTR> 15.49406 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -34.69122 0.00107 0.06455 0.00004 MINI INTERN> 4.55263 15.14358 0.00000 11.11647 2.93186 MINI EXTERN> -110.33561 26.40184 0.00000 0.00000 0.00000 MINI CONSTR> 15.49800 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -34.69253 0.00132 0.06548 0.00004 MINI INTERN> 4.55241 15.14318 0.00000 11.11499 2.93175 MINI EXTERN> -110.34012 26.40321 0.00000 0.00000 0.00000 MINI CONSTR> 15.50205 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -34.69386 0.00132 0.06811 0.00004 MINI INTERN> 4.55250 15.14257 0.00000 11.11344 2.93160 MINI EXTERN> -110.34479 26.40464 0.00000 0.00000 0.00000 MINI CONSTR> 15.50619 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -34.69515 0.00129 0.07357 0.00004 MINI INTERN> 4.55277 15.14188 0.00000 11.11185 2.93146 MINI EXTERN> -110.34954 26.40609 0.00000 0.00000 0.00000 MINI CONSTR> 15.51035 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -34.69634 0.00120 0.08150 0.00004 MINI INTERN> 4.55313 15.14118 0.00000 11.11029 2.93131 MINI EXTERN> -110.35415 26.40753 0.00000 0.00000 0.00000 MINI CONSTR> 15.51436 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -34.69751 0.00116 0.07691 0.00004 MINI INTERN> 4.55303 15.14069 0.00000 11.10909 2.93119 MINI EXTERN> -110.35789 26.40863 0.00000 0.00000 0.00000 MINI CONSTR> 15.51777 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -34.69875 0.00125 0.08041 0.00005 MINI INTERN> 4.55333 15.13997 0.00000 11.10757 2.93103 MINI EXTERN> -110.36245 26.41002 0.00000 0.00000 0.00000 MINI CONSTR> 15.52178 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -34.70003 0.00127 0.08252 0.00005 MINI INTERN> 4.55359 15.13925 0.00000 11.10604 2.93087 MINI EXTERN> -110.36703 26.41142 0.00000 0.00000 0.00000 MINI CONSTR> 15.52583 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -34.70170 0.00168 0.02553 0.00002 MINI INTERN> 4.55134 15.13936 0.00000 11.10553 2.93068 MINI EXTERN> -110.36984 26.41179 0.00000 0.00000 0.00000 MINI CONSTR> 15.52944 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -34.70231 0.00061 0.08999 0.00005 MINI INTERN> 4.55420 15.13789 0.00000 11.10320 2.93058 MINI EXTERN> -110.37553 26.41403 0.00000 0.00000 0.00000 MINI CONSTR> 15.53331 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -34.70351 0.00119 0.09238 0.00005 MINI INTERN> 4.55447 15.13720 0.00000 11.10174 2.93043 MINI EXTERN> -110.37990 26.41537 0.00000 0.00000 0.00000 MINI CONSTR> 15.53717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -34.70471 0.00120 0.09574 0.00005 MINI INTERN> 4.55477 15.13650 0.00000 11.10024 2.93028 MINI EXTERN> -110.38439 26.41676 0.00000 0.00000 0.00000 MINI CONSTR> 15.54113 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -34.70589 0.00118 0.10078 0.00006 MINI INTERN> 4.55512 15.13579 0.00000 11.09871 2.93013 MINI EXTERN> -110.38892 26.41818 0.00000 0.00000 0.00000 MINI CONSTR> 15.54510 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -34.70783 0.00194 0.03278 0.00002 MINI INTERN> 4.55210 15.13604 0.00000 11.09848 2.92989 MINI EXTERN> -110.39138 26.41823 0.00000 0.00000 0.00000 MINI CONSTR> 15.54882 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -34.70884 0.00101 0.02421 0.00003 MINI INTERN> 4.55255 15.13537 0.00000 11.09719 2.92978 MINI EXTERN> -110.39505 26.41944 0.00000 0.00000 0.00000 MINI CONSTR> 15.55189 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -34.71004 0.00121 0.02404 0.00003 MINI INTERN> 4.55276 15.13469 0.00000 11.09576 2.92963 MINI EXTERN> -110.39935 26.42075 0.00000 0.00000 0.00000 MINI CONSTR> 15.55572 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 325 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -34.71127 0.00122 0.02414 0.00003 MINI INTERN> 4.55295 15.13401 0.00000 11.09432 2.92947 MINI EXTERN> -110.40371 26.42207 0.00000 0.00000 0.00000 MINI CONSTR> 15.55963 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -34.71248 0.00121 0.02490 0.00003 MINI INTERN> 4.55310 15.13334 0.00000 11.09290 2.92932 MINI EXTERN> -110.40801 26.42337 0.00000 0.00000 0.00000 MINI CONSTR> 15.56350 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -34.71359 0.00112 0.05046 0.00003 MINI INTERN> 4.55281 15.13286 0.00000 11.09173 2.92911 MINI EXTERN> -110.41210 26.42438 0.00000 0.00000 0.00000 MINI CONSTR> 15.56761 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -34.71477 0.00118 0.03077 0.00003 MINI INTERN> 4.55332 15.13210 0.00000 11.09024 2.92900 MINI EXTERN> -110.41619 26.42579 0.00000 0.00000 0.00000 MINI CONSTR> 15.57096 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -34.71595 0.00118 0.03152 0.00003 MINI INTERN> 4.55352 15.13142 0.00000 11.08884 2.92885 MINI EXTERN> -110.42045 26.42708 0.00000 0.00000 0.00000 MINI CONSTR> 15.57479 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -34.71712 0.00117 0.03519 0.00003 MINI INTERN> 4.55367 15.13076 0.00000 11.08746 2.92868 MINI EXTERN> -110.42466 26.42833 0.00000 0.00000 0.00000 MINI CONSTR> 15.57863 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -34.71804 0.00092 0.05951 0.00003 MINI INTERN> 4.55361 15.13027 0.00000 11.08640 2.92850 MINI EXTERN> -110.42831 26.42924 0.00000 0.00000 0.00000 MINI CONSTR> 15.58226 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -34.71916 0.00112 0.06018 0.00004 MINI INTERN> 4.55385 15.12960 0.00000 11.08505 2.92835 MINI EXTERN> -110.43239 26.43047 0.00000 0.00000 0.00000 MINI CONSTR> 15.58592 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -34.72029 0.00113 0.06234 0.00004 MINI INTERN> 4.55412 15.12888 0.00000 11.08368 2.92818 MINI EXTERN> -110.43656 26.43171 0.00000 0.00000 0.00000 MINI CONSTR> 15.58969 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -34.72140 0.00111 0.06684 0.00004 MINI INTERN> 4.55442 15.12815 0.00000 11.08234 2.92801 MINI EXTERN> -110.44071 26.43292 0.00000 0.00000 0.00000 MINI CONSTR> 15.59347 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -34.72244 0.00104 0.07373 0.00004 MINI INTERN> 4.55471 15.12746 0.00000 11.08105 2.92784 MINI EXTERN> -110.44472 26.43407 0.00000 0.00000 0.00000 MINI CONSTR> 15.59715 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -34.72344 0.00100 0.07003 0.00004 MINI INTERN> 4.55487 15.12693 0.00000 11.07982 2.92772 MINI EXTERN> -110.44827 26.43519 0.00000 0.00000 0.00000 MINI CONSTR> 15.60030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -34.72451 0.00107 0.07323 0.00004 MINI INTERN> 4.55521 15.12620 0.00000 11.07850 2.92755 MINI EXTERN> -110.45229 26.43636 0.00000 0.00000 0.00000 MINI CONSTR> 15.60395 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -34.72560 0.00109 0.07521 0.00004 MINI INTERN> 4.55564 15.12540 0.00000 11.07716 2.92738 MINI EXTERN> -110.45641 26.43758 0.00000 0.00000 0.00000 MINI CONSTR> 15.60765 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10681 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -34.72671 0.00111 0.07539 0.00005 MINI INTERN> 4.55607 15.12459 0.00000 11.07579 2.92722 MINI EXTERN> -110.46053 26.43882 0.00000 0.00000 0.00000 MINI CONSTR> 15.61133 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -34.72812 0.00141 0.02434 0.00002 MINI INTERN> 4.55581 15.12451 0.00000 11.07363 2.92730 MINI EXTERN> -110.46505 26.44112 0.00000 0.00000 0.00000 MINI CONSTR> 15.61456 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -34.72862 0.00050 0.08360 0.00005 MINI INTERN> 4.55676 15.12327 0.00000 11.07335 2.92691 MINI EXTERN> -110.46793 26.44096 0.00000 0.00000 0.00000 MINI CONSTR> 15.61806 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 -34.72862 0.00050 0.08360 0.00002 STPD INTERN> 4.55676 15.12327 0.00000 11.07335 2.92691 STPD EXTERN> -110.46793 26.44096 0.00000 0.00000 0.00000 STPD CONSTR> 15.61806 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 10680 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10680 ATOM PAIRS WERE FOUND FOR ATOM LIST 324 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -34.72863 0.00001 0.06865 0.00000 MINI INTERN> 4.55607 15.12445 0.00000 11.07192 2.92735 MINI EXTERN> -110.46884 26.44296 0.00000 0.00000 0.00000 MINI CONSTR> 15.61746 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -34.88168 0.15305 0.02679 0.01557 MINI INTERN> 4.62394 14.98124 0.00000 10.71247 2.89145 MINI EXTERN> -111.54651 26.79789 0.00000 0.00000 0.00000 MINI CONSTR> 16.65783 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -34.88677 0.00509 0.09221 0.00809 MINI INTERN> 4.60810 14.92248 0.00000 10.69885 2.87459 MINI EXTERN> -111.52615 26.86247 0.00000 0.00000 0.00000 MINI CONSTR> 16.67288 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -34.90666 0.01989 0.12644 0.03410 MINI INTERN> 4.55318 14.88217 0.00000 10.66676 2.86624 MINI EXTERN> -111.58388 26.98692 0.00000 0.00000 0.00000 MINI CONSTR> 16.72195 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -34.92988 0.02322 0.09362 0.02498 MINI INTERN> 4.57285 14.92332 0.00000 10.60856 2.87352 MINI EXTERN> -111.56421 26.87915 0.00000 0.00000 0.00000 MINI CONSTR> 16.77693 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -34.93974 0.00986 0.06840 0.01261 MINI INTERN> 4.58931 14.92622 0.00000 10.56829 2.87172 MINI EXTERN> -111.52348 26.83144 0.00000 0.00000 0.00000 MINI CONSTR> 16.79676 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -34.94636 0.00662 0.06156 0.01046 MINI INTERN> 4.62739 14.94957 0.00000 10.56404 2.87783 MINI EXTERN> -111.50719 26.73576 0.00000 0.00000 0.00000 MINI CONSTR> 16.80624 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -34.95273 0.00636 0.05712 0.01191 MINI INTERN> 4.61068 14.91625 0.00000 10.53860 2.87151 MINI EXTERN> -111.39175 26.68811 0.00000 0.00000 0.00000 MINI CONSTR> 16.81387 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -34.95936 0.00663 0.05795 0.01361 MINI INTERN> 4.57766 14.90074 0.00000 10.52013 2.85869 MINI EXTERN> -111.33754 26.69738 0.00000 0.00000 0.00000 MINI CONSTR> 16.82358 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -34.96399 0.00463 0.05095 0.00784 MINI INTERN> 4.59269 14.89950 0.00000 10.52146 2.86622 MINI EXTERN> -111.31533 26.63868 0.00000 0.00000 0.00000 MINI CONSTR> 16.83278 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -34.96873 0.00474 0.05146 0.00995 MINI INTERN> 4.57961 14.92121 0.00000 10.49935 2.85928 MINI EXTERN> -111.29543 26.62227 0.00000 0.00000 0.00000 MINI CONSTR> 16.84498 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -34.97389 0.00516 0.05672 0.01242 MINI INTERN> 4.59281 14.89136 0.00000 10.49687 2.85423 MINI EXTERN> -111.31214 26.64009 0.00000 0.00000 0.00000 MINI CONSTR> 16.86289 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -34.97827 0.00438 0.04846 0.00864 MINI INTERN> 4.59807 14.88752 0.00000 10.47626 2.87248 MINI EXTERN> -111.34494 26.65166 0.00000 0.00000 0.00000 MINI CONSTR> 16.88068 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -34.98189 0.00362 0.04207 0.00881 MINI INTERN> 4.58911 14.89439 0.00000 10.49388 2.88647 MINI EXTERN> -111.39832 26.65551 0.00000 0.00000 0.00000 MINI CONSTR> 16.89707 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -34.98483 0.00294 0.03937 0.00690 MINI INTERN> 4.59202 14.89399 0.00000 10.50674 2.87128 MINI EXTERN> -111.44054 26.68153 0.00000 0.00000 0.00000 MINI CONSTR> 16.91016 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -34.98727 0.00244 0.03997 0.00719 MINI INTERN> 4.59718 14.90972 0.00000 10.51877 2.87590 MINI EXTERN> -111.47155 26.66399 0.00000 0.00000 0.00000 MINI CONSTR> 16.91872 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -34.98945 0.00218 0.03220 0.00588 MINI INTERN> 4.59569 14.92540 0.00000 10.53225 2.87830 MINI EXTERN> -111.45737 26.61261 0.00000 0.00000 0.00000 MINI CONSTR> 16.92367 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -34.99110 0.00165 0.02957 0.00375 MINI INTERN> 4.58984 14.91441 0.00000 10.52809 2.87509 MINI EXTERN> -111.44252 26.61950 0.00000 0.00000 0.00000 MINI CONSTR> 16.92448 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -34.99254 0.00144 0.02854 0.00560 MINI INTERN> 4.59432 14.91467 0.00000 10.53539 2.87548 MINI EXTERN> -111.42789 26.59319 0.00000 0.00000 0.00000 MINI CONSTR> 16.92231 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -34.99384 0.00130 0.02357 0.00476 MINI INTERN> 4.59758 14.91343 0.00000 10.55212 2.87270 MINI EXTERN> -111.45698 26.60905 0.00000 0.00000 0.00000 MINI CONSTR> 16.91825 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -34.99498 0.00114 0.02301 0.00501 MINI INTERN> 4.59016 14.90680 0.00000 10.55859 2.87184 MINI EXTERN> -111.43949 26.60384 0.00000 0.00000 0.00000 MINI CONSTR> 16.91328 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 -34.99498 0.00114 0.02301 0.02000 CONJ INTERN> 4.59016 14.90680 0.00000 10.55859 2.87184 CONJ EXTERN> -111.43949 26.60384 0.00000 0.00000 0.00000 CONJ CONSTR> 16.91328 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "11400" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "600" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.55768E-01 ( PROT LYS 1 HT2 ) 0.55768E-01 ( PROT LYS 1 N ) 0.69710E-01 ( PROT LYS 1 HT3 ) 0.55768E-01 ( PROT LYS 1 CA ) 0.69710E-01 ( PROT LYS 1 CB ) 0.55768E-01 ( PROT LYS 1 CG ) 0.55768E-01 ( PROT LYS 1 CD ) 0.55768E-01 ( PROT LYS 1 CE ) 0.55768E-01 ( PROT LYS 1 NZ ) 0.55768E-01 ( PROT LYS 1 HZ1 ) 0.55768E-01 ( PROT LYS 1 HZ2 ) 0.55768E-01 ( PROT LYS 1 HZ3 ) 0.55768E-01 ( PROT LYS 1 C ) 0.69710E-01 ( PROT LYS 1 O ) 0.69710E-01 ( PROT MET 2 N ) 0.69710E-01 ( PROT MET 2 H ) 0.55768E-01 ( PROT MET 2 CA ) 0.69710E-01 ( PROT MET 2 CB ) 0.55768E-01 ( PROT MET 2 CG ) 0.55768E-01 ( PROT MET 2 SD ) 0.55768E-01 ( PROT MET 2 CE ) 0.55768E-01 ( PROT MET 2 C ) 0.69710E-01 ( PROT MET 2 O ) 0.69710E-01 ( PROT LYS 3 N ) 0.69710E-01 ( PROT LYS 3 H ) 0.55768E-01 ( PROT LYS 3 CA ) 0.69710E-01 ( PROT LYS 3 CB ) 0.55768E-01 ( PROT LYS 3 CG ) 0.55768E-01 ( PROT LYS 3 CD ) 0.55768E-01 ( PROT LYS 3 CE ) 0.55768E-01 ( PROT LYS 3 NZ ) 0.55768E-01 ( PROT LYS 3 HZ1 ) 0.55768E-01 ( PROT LYS 3 HZ2 ) 0.55768E-01 ( PROT LYS 3 HZ3 ) 0.55768E-01 ( PROT LYS 3 C ) 0.69710E-01 ( PROT LYS 3 O ) 0.69710E-01 ( PROT ALA 4 N ) 0.69710E-01 ( PROT ALA 4 H ) 0.55768E-01 ( PROT ALA 4 CA ) 0.69710E-01 ( PROT ALA 4 CB ) 0.55768E-01 ( PROT ALA 4 C ) 0.69710E-01 ( PROT ALA 4 O ) 0.69710E-01 ( PROT VAL 5 N ) 0.69710E-01 ( PROT VAL 5 H ) 0.55768E-01 ( PROT VAL 5 CA ) 0.69710E-01 ( PROT VAL 5 CB ) 0.55768E-01 ( PROT VAL 5 CG1 ) 0.55768E-01 ( PROT VAL 5 CG2 ) 0.55768E-01 ( PROT VAL 5 C ) 0.69710E-01 ( PROT VAL 5 O ) 0.69710E-01 ( PROT MET 6 N ) 0.69710E-01 ( PROT MET 6 H ) 0.55768E-01 ( PROT MET 6 CA ) 0.69710E-01 ( PROT MET 6 CB ) 0.55768E-01 ( PROT MET 6 CG ) 0.55768E-01 ( PROT MET 6 SD ) 0.55768E-01 ( PROT MET 6 CE ) 0.55768E-01 ( PROT MET 6 C ) 0.69710E-01 ( PROT MET 6 O ) 0.69710E-01 ( PROT ILE 7 N ) 0.69710E-01 ( PROT ILE 7 H ) 0.55768E-01 ( PROT ILE 7 CA ) 0.69710E-01 ( PROT ILE 7 CB ) 0.55768E-01 ( PROT ILE 7 CG2 ) 0.55768E-01 ( PROT ILE 7 CG1 ) 0.55768E-01 ( PROT ILE 7 CD ) 0.55768E-01 ( PROT ILE 7 C ) 0.69710E-01 ( PROT ILE 7 O ) 0.69710E-01 ( PROT GLY 8 N ) 0.69710E-01 ( PROT GLY 8 H ) 0.55768E-01 ( PROT GLY 8 CA ) 0.69710E-01 ( PROT GLY 8 C ) 0.69710E-01 ( PROT GLY 8 O ) 0.69710E-01 ( PROT ALA 9 N ) 0.69710E-01 ( PROT ALA 9 H ) 0.55768E-01 ( PROT ALA 9 CA ) 0.69710E-01 ( PROT ALA 9 CB ) 0.55768E-01 ( PROT ALA 9 C ) 0.69710E-01 ( PROT ALA 9 O ) 0.69710E-01 ( PROT CYS 10 N ) 0.69710E-01 ( PROT CYS 10 H ) 0.55768E-01 ( PROT CYS 10 CA ) 0.69710E-01 ( PROT CYS 10 CB ) 0.55768E-01 ( PROT CYS 10 SG ) 0.55768E-01 ( PROT CYS 10 C ) 0.69710E-01 ( PROT CYS 10 O ) 0.69710E-01 ( PROT PHE 11 N ) 0.69710E-01 ( PROT PHE 11 H ) 0.55768E-01 ( PROT PHE 11 CA ) 0.69710E-01 ( PROT PHE 11 CB ) 0.55768E-01 ( PROT PHE 11 CG ) 0.55768E-01 ( PROT PHE 11 CD1 ) 0.55768E-01 ( PROT PHE 11 CD2 ) 0.55768E-01 ( PROT PHE 11 CE1 ) 0.55768E-01 ( PROT PHE 11 CE2 ) 0.55768E-01 ( PROT PHE 11 CZ ) 0.55768E-01 ( PROT PHE 11 C ) 0.69710E-01 ( PROT PHE 11 O ) 0.69710E-01 ( PROT LEU 12 N ) 0.69710E-01 ( PROT LEU 12 H ) 0.55768E-01 ( PROT LEU 12 CA ) 0.69710E-01 ( PROT LEU 12 CB ) 0.55768E-01 ( PROT LEU 12 CG ) 0.55768E-01 ( PROT LEU 12 CD1 ) 0.55768E-01 ( PROT LEU 12 CD2 ) 0.55768E-01 ( PROT LEU 12 C ) 0.69710E-01 ( PROT LEU 12 O ) 0.69710E-01 ( PROT ILE 13 N ) 0.69710E-01 ( PROT ILE 13 H ) 0.55768E-01 ( PROT ILE 13 CA ) 0.69710E-01 ( PROT ILE 13 CB ) 0.55768E-01 ( PROT ILE 13 CG2 ) 0.55768E-01 ( PROT ILE 13 CG1 ) 0.55768E-01 ( PROT ILE 13 CD ) 0.55768E-01 ( PROT ILE 13 C ) 0.69710E-01 ( PROT ILE 13 O ) 0.69710E-01 ( PROT ASP 14 N ) 0.69710E-01 ( PROT ASP 14 H ) 0.55768E-01 ( PROT ASP 14 CA ) 0.69710E-01 ( PROT ASP 14 CB ) 0.55768E-01 ( PROT ASP 14 CG ) 0.55768E-01 ( PROT ASP 14 OD1 ) 0.55768E-01 ( PROT ASP 14 OD2 ) 0.55768E-01 ( PROT ASP 14 C ) 0.69710E-01 ( PROT ASP 14 O ) 0.69710E-01 ( PROT PHE 15 N ) 0.69710E-01 ( PROT PHE 15 H ) 0.55768E-01 ( PROT PHE 15 CA ) 0.69710E-01 ( PROT PHE 15 CB ) 0.55768E-01 ( PROT PHE 15 CG ) 0.55768E-01 ( PROT PHE 15 CD1 ) 0.55768E-01 ( PROT PHE 15 CD2 ) 0.55768E-01 ( PROT PHE 15 CE1 ) 0.55768E-01 ( PROT PHE 15 CE2 ) 0.55768E-01 ( PROT PHE 15 CZ ) 0.55768E-01 ( PROT PHE 15 C ) 0.69710E-01 ( PROT PHE 15 O ) 0.69710E-01 ( PROT MET 16 N ) 0.69710E-01 ( PROT MET 16 H ) 0.55768E-01 ( PROT MET 16 CA ) 0.69710E-01 ( PROT MET 16 CB ) 0.55768E-01 ( PROT MET 16 CG ) 0.55768E-01 ( PROT MET 16 SD ) 0.55768E-01 ( PROT MET 16 CE ) 0.55768E-01 ( PROT MET 16 C ) 0.69710E-01 ( PROT MET 16 O ) 0.69710E-01 ( PROT PHE 17 N ) 0.69710E-01 ( PROT PHE 17 H ) 0.55768E-01 ( PROT PHE 17 CA ) 0.69710E-01 ( PROT PHE 17 CB ) 0.55768E-01 ( PROT PHE 17 CG ) 0.55768E-01 ( PROT PHE 17 CD1 ) 0.55768E-01 ( PROT PHE 17 CD2 ) 0.55768E-01 ( PROT PHE 17 CE1 ) 0.55768E-01 ( PROT PHE 17 CE2 ) 0.55768E-01 ( PROT PHE 17 CZ ) 0.55768E-01 ( PROT PHE 17 C ) 0.69710E-01 ( PROT PHE 17 O ) 0.69710E-01 ( PROT PHE 18 N ) 0.69710E-01 ( PROT PHE 18 H ) 0.55768E-01 ( PROT PHE 18 CA ) 0.69710E-01 ( PROT PHE 18 CB ) 0.55768E-01 ( PROT PHE 18 CG ) 0.55768E-01 ( PROT PHE 18 CD1 ) 0.55768E-01 ( PROT PHE 18 CD2 ) 0.55768E-01 ( PROT PHE 18 CE1 ) 0.55768E-01 ( PROT PHE 18 CE2 ) 0.55768E-01 ( PROT PHE 18 CZ ) 0.55768E-01 ( PROT PHE 18 C ) 0.69710E-01 ( PROT PHE 18 O ) 0.69710E-01 ( PROT GLU 19 N ) 0.69710E-01 ( PROT GLU 19 H ) 0.55768E-01 ( PROT GLU 19 CA ) 0.69710E-01 ( PROT GLU 19 CB ) 0.55768E-01 ( PROT GLU 19 CG ) 0.55768E-01 ( PROT GLU 19 CD ) 0.55768E-01 ( PROT GLU 19 OE1 ) 0.55768E-01 ( PROT GLU 19 OE2 ) 0.55768E-01 ( PROT GLU 19 C ) 0.69710E-01 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.40415 5.25298 -8.66688 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.00689 0.00693 -0.00481 ROTATION MATRIX 0.999999 -0.000631 0.001132 0.000630 0.999999 0.001332 -0.001133 -0.001331 0.999998 AXIS OF ROTATION IS 0.716578 -0.609336 -0.339448 ANGLE IS 0.11 TOTAL SQUARE DIFF IS 184.1983 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 1.006021 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.0060" Parameter: A <- "1.0060" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.74527 5.28155 -8.80304 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.03043 -0.01713 0.00868 ROTATION MATRIX 0.999971 0.002358 -0.007212 -0.002385 0.999990 -0.003762 0.007203 0.003780 0.999967 AXIS OF ROTATION IS -0.445045 0.850633 0.279927 ANGLE IS 0.49 TOTAL SQUARE DIFF IS 10.9176 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.758030 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.0060" RDCMND substituted energy or value "?RMS" to " 0.7580" Parameter: A <- "1.0060 0.7580" CHARMM> CHARMM> !write the set of rms difference to output CHARMM> open unit 11 appe form name ../out/@output.rms Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.rms:: OPNLGU> Unit 11 opened for APPEND access to ../out/mini_helix_allh.rms CHARMM> write title unit 11 RDTITL> *11400 1.0060 0.7580 RDTITL> * CHARMM> close unit 11 VCLOSE: Closing unit 11 with status "KEEP" CHARMM> CHARMM> FORMAT (F8.2) CHARMM> ! keep track of the current restraint energy. CHARMM> set h ?HARM RDCMND substituted energy or value "?HARM" to " 16.91" Parameter: H <- "16.91" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -51.90827 16.91328 0.10922 ENER INTERN> 4.59016 14.90680 0.00000 10.55859 2.87184 ENER EXTERN> -111.43949 26.60384 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -51.91" Parameter: B <- "-51.91" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 26.60" Parameter: C <- "26.60" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -111.44" Parameter: C <- " -84.84" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -84.84" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.59" Parameter: D <- "4.59" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.91" Parameter: D <- " 19.50" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.56" Parameter: D <- " 30.06" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.87" Parameter: D <- " 32.93" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 32.93" 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= -51.91 GRMS= 0.11 ELEC= 26.60 VDW= -111.44 RDTITL> *EXTERNAL= -84.84 INTERNAL= 32.93 USER= 0.00 HARM= 16.91 RDTITL> *BOND= 4.59 ANGL= 14.91 DIHE= 10.56 IMPR= 2.87 UREY= 0.00 RDTITL> * CHARMM> close unit 12 VCLOSE: Closing unit 12 with status "KEEP" CHARMM> CHARMM> FORMAT CHARMM> !check if the coordinates are written now or later CHARMM> if 5 lt @4 goto mini Parameter: 4 -> "800" Comparing "600" and "800". IF test evaluated as true. Performing command CHARMM> CHARMM> !read the coordinate to the comp set CHARMM> open read unit 10 card name ../coor/@name.crd Parameter: NAME -> ""helix_allh"" VOPEN> Attempting to open::../coor/helix_allh.crd:: OPNLGU> Unit 10 opened for READONLY access to ../coor/helix_allh.crd CHARMM> read coor comp card unit 10 SPATIAL COORDINATES BEING READ FROM UNIT 10 TITLE> * TUBBY FROM HELIX.PDB TITLE> * DATE: 3/17/14 17:11:11 CREATED BY USER: ANNESC TITLE> * ** WARNING ** Coordinates were overwritten for 182 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 10680 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10657 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 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 -40.85789 -11.05037 0.04393 0.02000 MINI INTERN> 4.59016 14.90680 0.00000 10.55859 2.87184 MINI EXTERN> -111.43949 26.60384 0.00000 0.00000 0.00000 MINI CONSTR> 11.05037 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -36.65709 -4.20080 6.77762 0.00360 MINI INTERN> 8.67681 15.99653 0.00000 10.63501 2.82022 MINI EXTERN> -113.92501 27.77901 0.00000 0.00000 0.00000 MINI CONSTR> 11.36033 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 10 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10650 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 10 -40.90520 4.24811 0.27244 0.00065 MINI INTERN> 4.87415 15.39318 0.00000 10.63084 2.88621 MINI EXTERN> -113.38423 27.33706 0.00000 0.00000 0.00000 MINI CONSTR> 11.35759 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -40.92960 0.02440 0.44014 0.00028 MINI INTERN> 4.73918 15.25553 0.00000 10.59777 2.90383 MINI EXTERN> -112.92724 27.14589 0.00000 0.00000 0.00000 MINI CONSTR> 11.35544 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 20 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10650 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 20 -40.95808 0.02848 0.15662 0.00012 MINI INTERN> 4.79083 15.11997 0.00000 10.57522 2.88705 MINI EXTERN> -112.79551 27.10908 0.00000 0.00000 0.00000 MINI CONSTR> 11.35529 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -40.96422 0.00614 0.19117 0.00013 MINI INTERN> 4.77842 15.07480 0.00000 10.56337 2.88466 MINI EXTERN> -112.68502 27.06373 0.00000 0.00000 0.00000 MINI CONSTR> 11.35582 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 30 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10650 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 30 -40.96929 0.00507 0.17754 0.00013 MINI INTERN> 4.76572 15.04980 0.00000 10.55611 2.88347 MINI EXTERN> -112.61582 27.03476 0.00000 0.00000 0.00000 MINI CONSTR> 11.35668 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -40.97604 0.00675 0.06559 0.00006 MINI INTERN> 4.68637 15.08216 0.00000 10.55339 2.88950 MINI EXTERN> -112.54985 27.00450 0.00000 0.00000 0.00000 MINI CONSTR> 11.35790 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 40 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10650 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 40 -40.97912 0.00309 0.06427 0.00006 MINI INTERN> 4.68133 15.06353 0.00000 10.54667 2.88834 MINI EXTERN> -112.50523 26.98693 0.00000 0.00000 0.00000 MINI CONSTR> 11.35931 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -40.98146 0.00233 0.07972 0.00006 MINI INTERN> 4.66450 15.05795 0.00000 10.54185 2.88863 MINI EXTERN> -112.46709 26.97179 0.00000 0.00000 0.00000 MINI CONSTR> 11.36092 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 50 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10650 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 50 -40.98340 0.00195 0.10692 0.00006 MINI INTERN> 4.66752 15.04010 0.00000 10.53572 2.88704 MINI EXTERN> -112.43779 26.96128 0.00000 0.00000 0.00000 MINI CONSTR> 11.36272 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -40.98533 0.00193 0.10411 0.00006 MINI INTERN> 4.66519 15.02950 0.00000 10.53143 2.88626 MINI EXTERN> -112.41555 26.95340 0.00000 0.00000 0.00000 MINI CONSTR> 11.36444 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 60 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10650 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 60 -40.98736 0.00202 0.09036 0.00007 MINI INTERN> 4.64576 15.03219 0.00000 10.52860 2.88728 MINI EXTERN> -112.39223 26.94457 0.00000 0.00000 0.00000 MINI CONSTR> 11.36648 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -40.98972 0.00236 0.03096 0.00003 MINI INTERN> 4.67928 14.99456 0.00000 10.52290 2.88267 MINI EXTERN> -112.38105 26.94358 0.00000 0.00000 0.00000 MINI CONSTR> 11.36835 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 70 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10650 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 70 -40.99122 0.00150 0.02773 0.00003 MINI INTERN> 4.67577 14.98927 0.00000 10.51985 2.88220 MINI EXTERN> -112.36799 26.93939 0.00000 0.00000 0.00000 MINI CONSTR> 11.37030 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -40.99194 0.00073 0.10258 0.00007 MINI INTERN> 4.63441 15.01612 0.00000 10.51846 2.88582 MINI EXTERN> -112.35049 26.93088 0.00000 0.00000 0.00000 MINI CONSTR> 11.37287 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 80 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10651 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 80 -40.99439 0.00245 0.03834 0.00003 MINI INTERN> 4.67834 14.97124 0.00000 10.51293 2.88015 MINI EXTERN> -112.34570 26.93350 0.00000 0.00000 0.00000 MINI CONSTR> 11.37514 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -40.99576 0.00136 0.03291 0.00003 MINI INTERN> 4.67512 14.96817 0.00000 10.51061 2.87982 MINI EXTERN> -112.33807 26.93128 0.00000 0.00000 0.00000 MINI CONSTR> 11.37732 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 90 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10650 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 90 -40.99707 0.00131 0.02624 0.00003 MINI INTERN> 4.66998 14.96752 0.00000 10.50854 2.87981 MINI EXTERN> -112.33146 26.92903 0.00000 0.00000 0.00000 MINI CONSTR> 11.37952 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -40.99848 0.00141 0.04568 0.00004 MINI INTERN> 4.67971 14.95356 0.00000 10.50518 2.87799 MINI EXTERN> -112.32667 26.92940 0.00000 0.00000 0.00000 MINI CONSTR> 11.38235 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10649 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -40.99983 0.00135 0.03973 0.00004 MINI INTERN> 4.67424 14.95450 0.00000 10.50347 2.87801 MINI EXTERN> -112.32187 26.92705 0.00000 0.00000 0.00000 MINI CONSTR> 11.38478 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 105 -41.00097 0.00114 0.05203 0.00004 MINI INTERN> 4.68122 14.94505 0.00000 10.50088 2.87676 MINI EXTERN> -112.31978 26.92763 0.00000 0.00000 0.00000 MINI CONSTR> 11.38727 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 110 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10649 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 110 -41.00230 0.00133 0.04254 0.00004 MINI INTERN> 4.67609 14.94517 0.00000 10.49927 2.87672 MINI EXTERN> -112.31708 26.92778 0.00000 0.00000 0.00000 MINI CONSTR> 11.38975 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 115 -41.00340 0.00110 0.05640 0.00004 MINI INTERN> 4.68207 14.93778 0.00000 10.49698 2.87573 MINI EXTERN> -112.31617 26.92789 0.00000 0.00000 0.00000 MINI CONSTR> 11.39232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 120 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10648 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 120 -41.00447 0.00108 0.06957 0.00004 MINI INTERN> 4.68158 14.93515 0.00000 10.49550 2.87503 MINI EXTERN> -112.31469 26.92808 0.00000 0.00000 0.00000 MINI CONSTR> 11.39488 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 125 -41.00568 0.00121 0.05979 0.00004 MINI INTERN> 4.68330 14.93116 0.00000 10.49357 2.87466 MINI EXTERN> -112.31490 26.92922 0.00000 0.00000 0.00000 MINI CONSTR> 11.39731 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 130 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10648 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 130 -41.00669 0.00101 0.07759 0.00005 MINI INTERN> 4.68333 14.93046 0.00000 10.49217 2.87422 MINI EXTERN> -112.31433 26.92751 0.00000 0.00000 0.00000 MINI CONSTR> 11.39995 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 135 -41.00782 0.00113 0.07104 0.00005 MINI INTERN> 4.68296 14.92891 0.00000 10.49070 2.87400 MINI EXTERN> -112.31473 26.92802 0.00000 0.00000 0.00000 MINI CONSTR> 11.40232 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 140 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10648 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 140 -41.00898 0.00116 0.06741 0.00005 MINI INTERN> 4.68411 14.92518 0.00000 10.48891 2.87364 MINI EXTERN> -112.31599 26.93028 0.00000 0.00000 0.00000 MINI CONSTR> 11.40489 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 145 -41.01039 0.00140 0.02336 0.00002 MINI INTERN> 4.65664 14.94653 0.00000 10.48930 2.87644 MINI EXTERN> -112.31366 26.92720 0.00000 0.00000 0.00000 MINI CONSTR> 11.40717 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 150 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10647 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 150 -41.01087 0.00049 0.08898 0.00005 MINI INTERN> 4.67550 14.92903 0.00000 10.48650 2.87422 MINI EXTERN> -112.31751 26.93153 0.00000 0.00000 0.00000 MINI CONSTR> 11.40985 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 155 -41.01199 0.00112 0.08336 0.00006 MINI INTERN> 4.68548 14.91936 0.00000 10.48466 2.87265 MINI EXTERN> -112.31993 26.93337 0.00000 0.00000 0.00000 MINI CONSTR> 11.41242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 160 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10647 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 160 -41.01283 0.00083 0.09977 0.00006 MINI INTERN> 4.67990 14.92402 0.00000 10.48430 2.87259 MINI EXTERN> -112.31984 26.93136 0.00000 0.00000 0.00000 MINI CONSTR> 11.41485 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 165 -41.01460 0.00177 0.02708 0.00002 MINI INTERN> 4.65322 14.94437 0.00000 10.48427 2.87583 MINI EXTERN> -112.31924 26.92975 0.00000 0.00000 0.00000 MINI CONSTR> 11.41721 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 170 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10647 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 170 -41.01494 0.00034 0.09009 0.00006 MINI INTERN> 4.69318 14.91022 0.00000 10.48093 2.87060 MINI EXTERN> -112.32532 26.93563 0.00000 0.00000 0.00000 MINI CONSTR> 11.41983 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 175 -41.01665 0.00171 0.03019 0.00003 MINI INTERN> 4.65184 14.94364 0.00000 10.48193 2.87552 MINI EXTERN> -112.32308 26.93120 0.00000 0.00000 0.00000 MINI CONSTR> 11.42228 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 180 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10647 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 180 -41.01758 0.00093 0.02300 0.00003 MINI INTERN> 4.65625 14.93907 0.00000 10.48063 2.87482 MINI EXTERN> -112.32553 26.93271 0.00000 0.00000 0.00000 MINI CONSTR> 11.42447 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 185 -41.01865 0.00107 0.02148 0.00003 MINI INTERN> 4.65788 14.93685 0.00000 10.47930 2.87441 MINI EXTERN> -112.32817 26.93395 0.00000 0.00000 0.00000 MINI CONSTR> 11.42713 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 190 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10647 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 190 -41.01978 0.00113 0.02283 0.00003 MINI INTERN> 4.65697 14.93675 0.00000 10.47809 2.87428 MINI EXTERN> -112.33076 26.93491 0.00000 0.00000 0.00000 MINI CONSTR> 11.42998 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 195 -41.02080 0.00102 0.03975 0.00003 MINI INTERN> 4.64686 14.94464 0.00000 10.47737 2.87533 MINI EXTERN> -112.33254 26.93469 0.00000 0.00000 0.00000 MINI CONSTR> 11.43286 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10647 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -41.02186 0.00106 0.03157 0.00003 MINI INTERN> 4.65300 14.93906 0.00000 10.47587 2.87445 MINI EXTERN> -112.33597 26.93634 0.00000 0.00000 0.00000 MINI CONSTR> 11.43539 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 205 -41.02280 0.00095 0.03700 0.00003 MINI INTERN> 4.65140 14.93999 0.00000 10.47488 2.87450 MINI EXTERN> -112.33849 26.93701 0.00000 0.00000 0.00000 MINI CONSTR> 11.43791 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 210 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10645 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 210 -41.02367 0.00087 0.04814 0.00003 MINI INTERN> 4.64560 14.94454 0.00000 10.47417 2.87506 MINI EXTERN> -112.34056 26.93709 0.00000 0.00000 0.00000 MINI CONSTR> 11.44043 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 215 -41.02464 0.00097 0.04822 0.00004 MINI INTERN> 4.64345 14.94537 0.00000 10.47319 2.87511 MINI EXTERN> -112.34311 26.93837 0.00000 0.00000 0.00000 MINI CONSTR> 11.44298 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 220 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10645 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 220 -41.02571 0.00107 0.03975 0.00004 MINI INTERN> 4.64996 14.93965 0.00000 10.47173 2.87417 MINI EXTERN> -112.34684 26.94007 0.00000 0.00000 0.00000 MINI CONSTR> 11.44555 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 225 -41.02652 0.00081 0.05295 0.00004 MINI INTERN> 4.64384 14.94462 0.00000 10.47106 2.87481 MINI EXTERN> -112.34904 26.94015 0.00000 0.00000 0.00000 MINI CONSTR> 11.44804 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 230 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10645 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 230 -41.02744 0.00092 0.05735 0.00004 MINI INTERN> 4.64039 14.94665 0.00000 10.47019 2.87506 MINI EXTERN> -112.35164 26.94128 0.00000 0.00000 0.00000 MINI CONSTR> 11.45063 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 235 -41.02837 0.00093 0.06149 0.00004 MINI INTERN> 4.64056 14.94668 0.00000 10.46910 2.87493 MINI EXTERN> -112.35483 26.94198 0.00000 0.00000 0.00000 MINI CONSTR> 11.45321 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 240 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10644 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 240 -41.02931 0.00094 0.05966 0.00004 MINI INTERN> 4.64209 14.94430 0.00000 10.46807 2.87457 MINI EXTERN> -112.35783 26.94385 0.00000 0.00000 0.00000 MINI CONSTR> 11.45565 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 245 -41.03021 0.00090 0.06323 0.00004 MINI INTERN> 4.64465 14.94266 0.00000 10.46677 2.87416 MINI EXTERN> -112.36141 26.94481 0.00000 0.00000 0.00000 MINI CONSTR> 11.45815 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 250 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10644 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 250 -41.03114 0.00092 0.06059 0.00005 MINI INTERN> 4.63977 14.94606 0.00000 10.46619 2.87462 MINI EXTERN> -112.36377 26.94535 0.00000 0.00000 0.00000 MINI CONSTR> 11.46064 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 255 -41.03232 0.00119 0.02140 0.00002 MINI INTERN> 4.66755 14.92159 0.00000 10.46362 2.87098 MINI EXTERN> -112.36973 26.95077 0.00000 0.00000 0.00000 MINI CONSTR> 11.46290 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 260 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10644 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 260 -41.03280 0.00047 0.07421 0.00005 MINI INTERN> 4.63933 14.94529 0.00000 10.46440 2.87441 MINI EXTERN> -112.36967 26.94788 0.00000 0.00000 0.00000 MINI CONSTR> 11.46556 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 265 -41.03350 0.00070 0.08859 0.00005 MINI INTERN> 4.65357 14.93448 0.00000 10.46218 2.87260 MINI EXTERN> -112.37480 26.95059 0.00000 0.00000 0.00000 MINI CONSTR> 11.46788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 270 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10644 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 270 -41.03494 0.00144 0.02405 0.00002 MINI INTERN> 4.67031 14.91834 0.00000 10.46061 2.87027 MINI EXTERN> -112.37914 26.95458 0.00000 0.00000 0.00000 MINI CONSTR> 11.47009 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 275 -41.03526 0.00033 0.08020 0.00006 MINI INTERN> 4.63924 14.94588 0.00000 10.46122 2.87419 MINI EXTERN> -112.37922 26.95080 0.00000 0.00000 0.00000 MINI CONSTR> 11.47264 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 280 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10644 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 280 -41.03666 0.00140 0.02665 0.00002 MINI INTERN> 4.67246 14.91606 0.00000 10.45857 2.86977 MINI EXTERN> -112.38562 26.95719 0.00000 0.00000 0.00000 MINI CONSTR> 11.47490 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 285 -41.03745 0.00078 0.02106 0.00002 MINI INTERN> 4.66868 14.91900 0.00000 10.45799 2.87014 MINI EXTERN> -112.38790 26.95764 0.00000 0.00000 0.00000 MINI CONSTR> 11.47700 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 290 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10644 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 290 -41.03834 0.00089 0.02065 0.00003 MINI INTERN> 4.66830 14.91913 0.00000 10.45703 2.87007 MINI EXTERN> -112.39111 26.95877 0.00000 0.00000 0.00000 MINI CONSTR> 11.47948 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 295 -41.03922 0.00088 0.03262 0.00003 MINI INTERN> 4.67661 14.91177 0.00000 10.45551 2.86891 MINI EXTERN> -112.39551 26.96135 0.00000 0.00000 0.00000 MINI CONSTR> 11.48214 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10644 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -41.04002 0.00080 0.02156 0.00003 MINI INTERN> 4.66936 14.91769 0.00000 10.45517 2.86972 MINI EXTERN> -112.39739 26.96124 0.00000 0.00000 0.00000 MINI CONSTR> 11.48420 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 305 -41.04086 0.00085 0.03652 0.00003 MINI INTERN> 4.67915 14.90919 0.00000 10.45355 2.86837 MINI EXTERN> -112.40200 26.96401 0.00000 0.00000 0.00000 MINI CONSTR> 11.48686 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 310 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10644 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 310 -41.04169 0.00083 0.02073 0.00003 MINI INTERN> 4.66877 14.91772 0.00000 10.45337 2.86958 MINI EXTERN> -112.40358 26.96351 0.00000 0.00000 0.00000 MINI CONSTR> 11.48893 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 315 -41.04247 0.00077 0.04564 0.00003 MINI INTERN> 4.67822 14.90916 0.00000 10.45187 2.86827 MINI EXTERN> -112.40805 26.96647 0.00000 0.00000 0.00000 MINI CONSTR> 11.49159 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 320 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10643 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 320 -41.04325 0.00079 0.04639 0.00003 MINI INTERN> 4.67949 14.90785 0.00000 10.45093 2.86800 MINI EXTERN> -112.41120 26.96782 0.00000 0.00000 0.00000 MINI CONSTR> 11.49386 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 325 -41.04404 0.00079 0.04670 0.00003 MINI INTERN> 4.68223 14.90535 0.00000 10.44987 2.86755 MINI EXTERN> -112.41459 26.96939 0.00000 0.00000 0.00000 MINI CONSTR> 11.49615 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 330 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10643 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 330 -41.04483 0.00078 0.04851 0.00003 MINI INTERN> 4.68549 14.90291 0.00000 10.44870 2.86706 MINI EXTERN> -112.41819 26.97073 0.00000 0.00000 0.00000 MINI CONSTR> 11.49846 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 335 -41.04559 0.00076 0.05366 0.00004 MINI INTERN> 4.68371 14.90386 0.00000 10.44804 2.86720 MINI EXTERN> -112.42095 26.97178 0.00000 0.00000 0.00000 MINI CONSTR> 11.50078 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 340 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10643 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 340 -41.04635 0.00076 0.05450 0.00004 MINI INTERN> 4.68577 14.90198 0.00000 10.44706 2.86684 MINI EXTERN> -112.42421 26.97318 0.00000 0.00000 0.00000 MINI CONSTR> 11.50303 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 345 -41.04713 0.00078 0.05354 0.00004 MINI INTERN> 4.68902 14.89926 0.00000 10.44595 2.86633 MINI EXTERN> -112.42770 26.97470 0.00000 0.00000 0.00000 MINI CONSTR> 11.50530 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 350 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10643 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 350 -41.04795 0.00082 0.06035 0.00004 MINI INTERN> 4.69077 14.89772 0.00000 10.44474 2.86603 MINI EXTERN> -112.43150 26.97641 0.00000 0.00000 0.00000 MINI CONSTR> 11.50788 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 355 -41.04872 0.00077 0.06033 0.00004 MINI INTERN> 4.68541 14.90168 0.00000 10.44452 2.86655 MINI EXTERN> -112.43348 26.97653 0.00000 0.00000 0.00000 MINI CONSTR> 11.51007 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 360 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10643 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 360 -41.04952 0.00080 0.05702 0.00004 MINI INTERN> 4.68995 14.89825 0.00000 10.44311 2.86595 MINI EXTERN> -112.43743 26.97831 0.00000 0.00000 0.00000 MINI CONSTR> 11.51234 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 365 -41.05051 0.00099 0.01967 0.00002 MINI INTERN> 4.66384 14.92000 0.00000 10.44393 2.86913 MINI EXTERN> -112.43719 26.97539 0.00000 0.00000 0.00000 MINI CONSTR> 11.51438 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 370 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10643 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 370 -41.05086 0.00035 0.07377 0.00005 MINI INTERN> 4.68750 14.90058 0.00000 10.44145 2.86612 MINI EXTERN> -112.44329 26.98001 0.00000 0.00000 0.00000 MINI CONSTR> 11.51677 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 375 -41.05169 0.00083 0.06446 0.00005 MINI INTERN> 4.69494 14.89315 0.00000 10.44040 2.86504 MINI EXTERN> -112.44692 26.98263 0.00000 0.00000 0.00000 MINI CONSTR> 11.51907 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 380 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10643 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 380 -41.05238 0.00069 0.07977 0.00005 MINI INTERN> 4.68944 14.89869 0.00000 10.43972 2.86559 MINI EXTERN> -112.44963 26.98231 0.00000 0.00000 0.00000 MINI CONSTR> 11.52150 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 385 -41.05321 0.00083 0.06983 0.00005 MINI INTERN> 4.69859 14.88987 0.00000 10.43837 2.86439 MINI EXTERN> -112.45375 26.98551 0.00000 0.00000 0.00000 MINI CONSTR> 11.52381 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 390 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10642 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 390 -41.05397 0.00077 0.07631 0.00005 MINI INTERN> 4.69708 14.89069 0.00000 10.43778 2.86438 MINI EXTERN> -112.45660 26.98639 0.00000 0.00000 0.00000 MINI CONSTR> 11.52631 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 395 -41.05523 0.00126 0.02511 0.00002 MINI INTERN> 4.66098 14.92150 0.00000 10.43877 2.86894 MINI EXTERN> -112.45596 26.98207 0.00000 0.00000 0.00000 MINI CONSTR> 11.52847 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10642 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -41.05541 0.00018 0.07734 0.00006 MINI INTERN> 4.70063 14.88749 0.00000 10.43580 2.86380 MINI EXTERN> -112.46310 26.98922 0.00000 0.00000 0.00000 MINI CONSTR> 11.53074 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 405 -41.05672 0.00131 0.03088 0.00002 MINI INTERN> 4.65894 14.92286 0.00000 10.43724 2.86900 MINI EXTERN> -112.46182 26.98402 0.00000 0.00000 0.00000 MINI CONSTR> 11.53304 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 410 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10642 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 410 -41.05743 0.00070 0.02543 0.00003 MINI INTERN> 4.66141 14.92063 0.00000 10.43629 2.86861 MINI EXTERN> -112.46489 26.98545 0.00000 0.00000 0.00000 MINI CONSTR> 11.53507 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 415 -41.05814 0.00072 0.02826 0.00003 MINI INTERN> 4.66106 14.92092 0.00000 10.43540 2.86860 MINI EXTERN> -112.46798 26.98657 0.00000 0.00000 0.00000 MINI CONSTR> 11.53728 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 420 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10642 ATOM PAIRS WERE FOUND FOR ATOM LIST 316 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 420 -41.05884 0.00069 0.02916 0.00003 MINI INTERN> 4.66015 14.92154 0.00000 10.43467 2.86863 MINI EXTERN> -112.47073 26.98750 0.00000 0.00000 0.00000 MINI CONSTR> 11.53940 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 425 -41.05953 0.00070 0.03146 0.00003 MINI INTERN> 4.65862 14.92260 0.00000 10.43402 2.86871 MINI EXTERN> -112.47338 26.98833 0.00000 0.00000 0.00000 MINI CONSTR> 11.54157 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 430 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10642 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 430 -41.06023 0.00070 0.03382 0.00003 MINI INTERN> 4.65874 14.92253 0.00000 10.43309 2.86866 MINI EXTERN> -112.47649 26.98949 0.00000 0.00000 0.00000 MINI CONSTR> 11.54375 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 435 -41.06085 0.00062 0.04561 0.00003 MINI INTERN> 4.65606 14.92436 0.00000 10.43268 2.86883 MINI EXTERN> -112.47876 26.99007 0.00000 0.00000 0.00000 MINI CONSTR> 11.54590 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 440 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10641 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 440 -41.06151 0.00065 0.04878 0.00003 MINI INTERN> 4.65480 14.92531 0.00000 10.43198 2.86891 MINI EXTERN> -112.48143 26.99093 0.00000 0.00000 0.00000 MINI CONSTR> 11.54799 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 445 -41.06214 0.00063 0.05271 0.00003 MINI INTERN> 4.65468 14.92525 0.00000 10.43126 2.86884 MINI EXTERN> -112.48412 26.99193 0.00000 0.00000 0.00000 MINI CONSTR> 11.55003 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 450 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10641 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 450 -41.06285 0.00072 0.04490 0.00003 MINI INTERN> 4.65313 14.92683 0.00000 10.43033 2.86904 MINI EXTERN> -112.48708 26.99282 0.00000 0.00000 0.00000 MINI CONSTR> 11.55207 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 455 -41.06347 0.00062 0.06124 0.00004 MINI INTERN> 4.65455 14.92498 0.00000 10.42966 2.86870 MINI EXTERN> -112.48996 26.99420 0.00000 0.00000 0.00000 MINI CONSTR> 11.55439 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 460 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10641 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 460 -41.06410 0.00063 0.05986 0.00004 MINI INTERN> 4.65830 14.92157 0.00000 10.42877 2.86814 MINI EXTERN> -112.49285 26.99572 0.00000 0.00000 0.00000 MINI CONSTR> 11.55625 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 465 -41.06498 0.00088 0.01824 0.00002 MINI INTERN> 4.67492 14.90746 0.00000 10.42685 2.86600 MINI EXTERN> -112.49754 26.99927 0.00000 0.00000 0.00000 MINI CONSTR> 11.55806 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 470 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10640 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 470 -41.06535 0.00037 0.06308 0.00004 MINI INTERN> 4.65576 14.92353 0.00000 10.42742 2.86830 MINI EXTERN> -112.49798 26.99734 0.00000 0.00000 0.00000 MINI CONSTR> 11.56027 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 475 -41.06608 0.00072 0.05488 0.00004 MINI INTERN> 4.65011 14.92892 0.00000 10.42660 2.86905 MINI EXTERN> -112.50071 26.99757 0.00000 0.00000 0.00000 MINI CONSTR> 11.56239 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 480 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10640 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 480 -41.06699 0.00092 0.01956 0.00002 MINI INTERN> 4.67665 14.90558 0.00000 10.42438 2.86554 MINI EXTERN> -112.50620 27.00272 0.00000 0.00000 0.00000 MINI CONSTR> 11.56434 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 485 -41.06759 0.00059 0.01754 0.00002 MINI INTERN> 4.67505 14.90679 0.00000 10.42380 2.86567 MINI EXTERN> -112.50847 27.00340 0.00000 0.00000 0.00000 MINI CONSTR> 11.56616 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 490 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10640 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 490 -41.06788 0.00029 0.07085 0.00005 MINI INTERN> 4.65144 14.92668 0.00000 10.42458 2.86855 MINI EXTERN> -112.50863 27.00101 0.00000 0.00000 0.00000 MINI CONSTR> 11.56849 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 495 -41.06848 0.00060 0.07411 0.00005 MINI INTERN> 4.65371 14.92583 0.00000 10.42315 2.86836 MINI EXTERN> -112.51232 27.00225 0.00000 0.00000 0.00000 MINI CONSTR> 11.57054 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10640 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -41.06912 0.00064 0.07296 0.00005 MINI INTERN> 4.64658 14.93074 0.00000 10.42323 2.86907 MINI EXTERN> -112.51369 27.00235 0.00000 0.00000 0.00000 MINI CONSTR> 11.57260 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- STEEPD> Minimization exiting with number of steps limit ( 500) exceeded. STPD MIN: Cycle ENERgy Delta-E GRMS Step-size STPD INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers STPD EXTERN: VDWaals ELEC HBONds ASP USER STPD CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- STPD> 500 -41.06912 0.00064 0.07296 0.00002 STPD INTERN> 4.64658 14.93074 0.00000 10.42323 2.86907 STPD EXTERN> -112.51369 27.00235 0.00000 0.00000 0.00000 STPD CONSTR> 11.57260 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 10640 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10640 ATOM PAIRS WERE FOUND FOR ATOM LIST 317 GROUP PAIRS REQUIRED ATOM SEARCHES CONJUG> An energy minimization has been requested. NCGCYC = 100 NSTEP = 100 PCUT = 0.9999000 PRTMIN = 1 STEP = 0.0200000 TOLFUN = 0.0000000 TOLGRD = 0.0100000 TOLITR = 100 TOLSTP = 0.0000000 MINI MIN: Cycle ENERgy Delta-E GRMS Step-size MINI INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers MINI EXTERN: VDWaals ELEC HBONds ASP USER MINI CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- MINI> 0 -41.06922 0.00010 0.05455 0.00000 MINI INTERN> 4.69450 14.89018 0.00000 10.42035 2.86302 MINI EXTERN> -112.51878 27.00933 0.00000 0.00000 0.00000 MINI CONSTR> 11.57217 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 5 -41.17667 0.10745 0.03085 0.02503 MINI INTERN> 4.74721 14.84127 0.00000 10.18101 2.83634 MINI EXTERN> -113.39986 27.35493 0.00000 0.00000 0.00000 MINI CONSTR> 12.26242 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 10 -41.17946 0.00279 0.06693 0.00469 MINI INTERN> 4.72499 14.79835 0.00000 10.17529 2.82534 MINI EXTERN> -113.36927 27.39308 0.00000 0.00000 0.00000 MINI CONSTR> 12.27277 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 15 -41.19261 0.01315 0.11139 0.02695 MINI INTERN> 4.68122 14.74259 0.00000 10.16189 2.82130 MINI EXTERN> -113.40793 27.49334 0.00000 0.00000 0.00000 MINI CONSTR> 12.31499 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 20 -41.21308 0.02047 0.09619 0.03186 MINI INTERN> 4.70837 14.77411 0.00000 10.11767 2.83036 MINI EXTERN> -113.43453 27.41176 0.00000 0.00000 0.00000 MINI CONSTR> 12.37919 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 25 -41.22417 0.01110 0.07845 0.01671 MINI INTERN> 4.70982 14.79430 0.00000 10.08767 2.83213 MINI EXTERN> -113.41958 27.36014 0.00000 0.00000 0.00000 MINI CONSTR> 12.41135 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 30 -41.23292 0.00875 0.07321 0.01567 MINI INTERN> 4.75901 14.82008 0.00000 10.10105 2.83369 MINI EXTERN> -113.43246 27.25319 0.00000 0.00000 0.00000 MINI CONSTR> 12.43251 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 35 -41.24108 0.00816 0.05776 0.01614 MINI INTERN> 4.74318 14.80001 0.00000 10.07918 2.82720 MINI EXTERN> -113.32688 27.18701 0.00000 0.00000 0.00000 MINI CONSTR> 12.44923 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 40 -41.24820 0.00712 0.05817 0.01386 MINI INTERN> 4.70437 14.78778 0.00000 10.07402 2.81857 MINI EXTERN> -113.25945 27.16333 0.00000 0.00000 0.00000 MINI CONSTR> 12.46317 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 45 -41.25266 0.00446 0.04481 0.00756 MINI INTERN> 4.71429 14.76500 0.00000 10.08013 2.82332 MINI EXTERN> -113.22906 27.12097 0.00000 0.00000 0.00000 MINI CONSTR> 12.47269 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 50 -41.25660 0.00394 0.04804 0.00825 MINI INTERN> 4.70225 14.77702 0.00000 10.05658 2.82317 MINI EXTERN> -113.20330 27.10503 0.00000 0.00000 0.00000 MINI CONSTR> 12.48266 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 55 -41.26097 0.00437 0.05384 0.01320 MINI INTERN> 4.71348 14.76468 0.00000 10.06006 2.81893 MINI EXTERN> -113.21303 27.09767 0.00000 0.00000 0.00000 MINI CONSTR> 12.49725 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 60 -41.26541 0.00444 0.05150 0.01087 MINI INTERN> 4.71982 14.75140 0.00000 10.03538 2.82645 MINI EXTERN> -113.24768 27.13431 0.00000 0.00000 0.00000 MINI CONSTR> 12.51491 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 65 -41.26945 0.00404 0.04743 0.01031 MINI INTERN> 4.71092 14.74857 0.00000 10.04780 2.83889 MINI EXTERN> -113.29467 27.14531 0.00000 0.00000 0.00000 MINI CONSTR> 12.53372 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 70 -41.27332 0.00387 0.04035 0.00922 MINI INTERN> 4.71501 14.76521 0.00000 10.05709 2.83065 MINI EXTERN> -113.34471 27.15001 0.00000 0.00000 0.00000 MINI CONSTR> 12.55342 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 75 -41.27589 0.00256 0.04037 0.00882 MINI INTERN> 4.71565 14.78864 0.00000 10.06953 2.83518 MINI EXTERN> -113.40786 27.15579 0.00000 0.00000 0.00000 MINI CONSTR> 12.56718 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 80 -41.27809 0.00221 0.03129 0.00631 MINI INTERN> 4.72247 14.80849 0.00000 10.08155 2.83498 MINI EXTERN> -113.40792 27.10380 0.00000 0.00000 0.00000 MINI CONSTR> 12.57853 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 85 -41.27956 0.00147 0.02763 0.00353 MINI INTERN> 4.72047 14.79779 0.00000 10.07462 2.83352 MINI EXTERN> -113.38798 27.09701 0.00000 0.00000 0.00000 MINI CONSTR> 12.58501 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 90 -41.28075 0.00119 0.02437 0.00435 MINI INTERN> 4.72255 14.79320 0.00000 10.07634 2.83308 MINI EXTERN> -113.38728 27.09241 0.00000 0.00000 0.00000 MINI CONSTR> 12.58895 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 95 -41.28182 0.00107 0.02379 0.00499 MINI INTERN> 4.72218 14.79858 0.00000 10.08750 2.83236 MINI EXTERN> -113.41218 27.09888 0.00000 0.00000 0.00000 MINI CONSTR> 12.59086 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -41.28286 0.00104 0.02215 0.00437 MINI INTERN> 4.71482 14.79452 0.00000 10.09388 2.82954 MINI EXTERN> -113.39519 27.08812 0.00000 0.00000 0.00000 MINI CONSTR> 12.59145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CONJUG> Minimization exiting with number of steps limit ( 100) exceeded. CONJ MIN: Cycle ENERgy Delta-E GRMS Step-size CONJ INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers CONJ EXTERN: VDWaals ELEC HBONds ASP USER CONJ CONSTR: HARMonic CDIHedral CIC RESDistance NOE ---------- --------- --------- --------- --------- --------- CONJ> 100 -41.28286 0.00104 0.02215 0.02000 CONJ INTERN> 4.71482 14.79452 0.00000 10.09388 2.82954 CONJ EXTERN> -113.39519 27.08812 0.00000 0.00000 0.00000 CONJ CONSTR> 12.59145 0.00000 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> incr 1 by @8 Parameter: 8 -> "600" Parameter: 1 <- "12000" CHARMM> incr 5 by @8 Parameter: 8 -> "600" Parameter: 5 <- "1200" CHARMM> CHARMM> !{reduce the harmonic force constants} CHARMM> SCALar CONStraint MULTiply 0.65 CHARMM> ! check the magnitude of the harmonic force CHARMM> SCALar CONStraint SHOW ( PROT LYS 1 HT1 ) 0.36249E-01 ( PROT LYS 1 HT2 ) 0.36249E-01 ( PROT LYS 1 N ) 0.45311E-01 ( PROT LYS 1 HT3 ) 0.36249E-01 ( PROT LYS 1 CA ) 0.45311E-01 ( PROT LYS 1 CB ) 0.36249E-01 ( PROT LYS 1 CG ) 0.36249E-01 ( PROT LYS 1 CD ) 0.36249E-01 ( PROT LYS 1 CE ) 0.36249E-01 ( PROT LYS 1 NZ ) 0.36249E-01 ( PROT LYS 1 HZ1 ) 0.36249E-01 ( PROT LYS 1 HZ2 ) 0.36249E-01 ( PROT LYS 1 HZ3 ) 0.36249E-01 ( PROT LYS 1 C ) 0.45311E-01 ( PROT LYS 1 O ) 0.45311E-01 ( PROT MET 2 N ) 0.45311E-01 ( PROT MET 2 H ) 0.36249E-01 ( PROT MET 2 CA ) 0.45311E-01 ( PROT MET 2 CB ) 0.36249E-01 ( PROT MET 2 CG ) 0.36249E-01 ( PROT MET 2 SD ) 0.36249E-01 ( PROT MET 2 CE ) 0.36249E-01 ( PROT MET 2 C ) 0.45311E-01 ( PROT MET 2 O ) 0.45311E-01 ( PROT LYS 3 N ) 0.45311E-01 ( PROT LYS 3 H ) 0.36249E-01 ( PROT LYS 3 CA ) 0.45311E-01 ( PROT LYS 3 CB ) 0.36249E-01 ( PROT LYS 3 CG ) 0.36249E-01 ( PROT LYS 3 CD ) 0.36249E-01 ( PROT LYS 3 CE ) 0.36249E-01 ( PROT LYS 3 NZ ) 0.36249E-01 ( PROT LYS 3 HZ1 ) 0.36249E-01 ( PROT LYS 3 HZ2 ) 0.36249E-01 ( PROT LYS 3 HZ3 ) 0.36249E-01 ( PROT LYS 3 C ) 0.45311E-01 ( PROT LYS 3 O ) 0.45311E-01 ( PROT ALA 4 N ) 0.45311E-01 ( PROT ALA 4 H ) 0.36249E-01 ( PROT ALA 4 CA ) 0.45311E-01 ( PROT ALA 4 CB ) 0.36249E-01 ( PROT ALA 4 C ) 0.45311E-01 ( PROT ALA 4 O ) 0.45311E-01 ( PROT VAL 5 N ) 0.45311E-01 ( PROT VAL 5 H ) 0.36249E-01 ( PROT VAL 5 CA ) 0.45311E-01 ( PROT VAL 5 CB ) 0.36249E-01 ( PROT VAL 5 CG1 ) 0.36249E-01 ( PROT VAL 5 CG2 ) 0.36249E-01 ( PROT VAL 5 C ) 0.45311E-01 ( PROT VAL 5 O ) 0.45311E-01 ( PROT MET 6 N ) 0.45311E-01 ( PROT MET 6 H ) 0.36249E-01 ( PROT MET 6 CA ) 0.45311E-01 ( PROT MET 6 CB ) 0.36249E-01 ( PROT MET 6 CG ) 0.36249E-01 ( PROT MET 6 SD ) 0.36249E-01 ( PROT MET 6 CE ) 0.36249E-01 ( PROT MET 6 C ) 0.45311E-01 ( PROT MET 6 O ) 0.45311E-01 ( PROT ILE 7 N ) 0.45311E-01 ( PROT ILE 7 H ) 0.36249E-01 ( PROT ILE 7 CA ) 0.45311E-01 ( PROT ILE 7 CB ) 0.36249E-01 ( PROT ILE 7 CG2 ) 0.36249E-01 ( PROT ILE 7 CG1 ) 0.36249E-01 ( PROT ILE 7 CD ) 0.36249E-01 ( PROT ILE 7 C ) 0.45311E-01 ( PROT ILE 7 O ) 0.45311E-01 ( PROT GLY 8 N ) 0.45311E-01 ( PROT GLY 8 H ) 0.36249E-01 ( PROT GLY 8 CA ) 0.45311E-01 ( PROT GLY 8 C ) 0.45311E-01 ( PROT GLY 8 O ) 0.45311E-01 ( PROT ALA 9 N ) 0.45311E-01 ( PROT ALA 9 H ) 0.36249E-01 ( PROT ALA 9 CA ) 0.45311E-01 ( PROT ALA 9 CB ) 0.36249E-01 ( PROT ALA 9 C ) 0.45311E-01 ( PROT ALA 9 O ) 0.45311E-01 ( PROT CYS 10 N ) 0.45311E-01 ( PROT CYS 10 H ) 0.36249E-01 ( PROT CYS 10 CA ) 0.45311E-01 ( PROT CYS 10 CB ) 0.36249E-01 ( PROT CYS 10 SG ) 0.36249E-01 ( PROT CYS 10 C ) 0.45311E-01 ( PROT CYS 10 O ) 0.45311E-01 ( PROT PHE 11 N ) 0.45311E-01 ( PROT PHE 11 H ) 0.36249E-01 ( PROT PHE 11 CA ) 0.45311E-01 ( PROT PHE 11 CB ) 0.36249E-01 ( PROT PHE 11 CG ) 0.36249E-01 ( PROT PHE 11 CD1 ) 0.36249E-01 ( PROT PHE 11 CD2 ) 0.36249E-01 ( PROT PHE 11 CE1 ) 0.36249E-01 ( PROT PHE 11 CE2 ) 0.36249E-01 ( PROT PHE 11 CZ ) 0.36249E-01 ( PROT PHE 11 C ) 0.45311E-01 ( PROT PHE 11 O ) 0.45311E-01 ( PROT LEU 12 N ) 0.45311E-01 ( PROT LEU 12 H ) 0.36249E-01 ( PROT LEU 12 CA ) 0.45311E-01 ( PROT LEU 12 CB ) 0.36249E-01 ( PROT LEU 12 CG ) 0.36249E-01 ( PROT LEU 12 CD1 ) 0.36249E-01 ( PROT LEU 12 CD2 ) 0.36249E-01 ( PROT LEU 12 C ) 0.45311E-01 ( PROT LEU 12 O ) 0.45311E-01 ( PROT ILE 13 N ) 0.45311E-01 ( PROT ILE 13 H ) 0.36249E-01 ( PROT ILE 13 CA ) 0.45311E-01 ( PROT ILE 13 CB ) 0.36249E-01 ( PROT ILE 13 CG2 ) 0.36249E-01 ( PROT ILE 13 CG1 ) 0.36249E-01 ( PROT ILE 13 CD ) 0.36249E-01 ( PROT ILE 13 C ) 0.45311E-01 ( PROT ILE 13 O ) 0.45311E-01 ( PROT ASP 14 N ) 0.45311E-01 ( PROT ASP 14 H ) 0.36249E-01 ( PROT ASP 14 CA ) 0.45311E-01 ( PROT ASP 14 CB ) 0.36249E-01 ( PROT ASP 14 CG ) 0.36249E-01 ( PROT ASP 14 OD1 ) 0.36249E-01 ( PROT ASP 14 OD2 ) 0.36249E-01 ( PROT ASP 14 C ) 0.45311E-01 ( PROT ASP 14 O ) 0.45311E-01 ( PROT PHE 15 N ) 0.45311E-01 ( PROT PHE 15 H ) 0.36249E-01 ( PROT PHE 15 CA ) 0.45311E-01 ( PROT PHE 15 CB ) 0.36249E-01 ( PROT PHE 15 CG ) 0.36249E-01 ( PROT PHE 15 CD1 ) 0.36249E-01 ( PROT PHE 15 CD2 ) 0.36249E-01 ( PROT PHE 15 CE1 ) 0.36249E-01 ( PROT PHE 15 CE2 ) 0.36249E-01 ( PROT PHE 15 CZ ) 0.36249E-01 ( PROT PHE 15 C ) 0.45311E-01 ( PROT PHE 15 O ) 0.45311E-01 ( PROT MET 16 N ) 0.45311E-01 ( PROT MET 16 H ) 0.36249E-01 ( PROT MET 16 CA ) 0.45311E-01 ( PROT MET 16 CB ) 0.36249E-01 ( PROT MET 16 CG ) 0.36249E-01 ( PROT MET 16 SD ) 0.36249E-01 ( PROT MET 16 CE ) 0.36249E-01 ( PROT MET 16 C ) 0.45311E-01 ( PROT MET 16 O ) 0.45311E-01 ( PROT PHE 17 N ) 0.45311E-01 ( PROT PHE 17 H ) 0.36249E-01 ( PROT PHE 17 CA ) 0.45311E-01 ( PROT PHE 17 CB ) 0.36249E-01 ( PROT PHE 17 CG ) 0.36249E-01 ( PROT PHE 17 CD1 ) 0.36249E-01 ( PROT PHE 17 CD2 ) 0.36249E-01 ( PROT PHE 17 CE1 ) 0.36249E-01 ( PROT PHE 17 CE2 ) 0.36249E-01 ( PROT PHE 17 CZ ) 0.36249E-01 ( PROT PHE 17 C ) 0.45311E-01 ( PROT PHE 17 O ) 0.45311E-01 ( PROT PHE 18 N ) 0.45311E-01 ( PROT PHE 18 H ) 0.36249E-01 ( PROT PHE 18 CA ) 0.45311E-01 ( PROT PHE 18 CB ) 0.36249E-01 ( PROT PHE 18 CG ) 0.36249E-01 ( PROT PHE 18 CD1 ) 0.36249E-01 ( PROT PHE 18 CD2 ) 0.36249E-01 ( PROT PHE 18 CE1 ) 0.36249E-01 ( PROT PHE 18 CE2 ) 0.36249E-01 ( PROT PHE 18 CZ ) 0.36249E-01 ( PROT PHE 18 C ) 0.45311E-01 ( PROT PHE 18 O ) 0.45311E-01 ( PROT GLU 19 N ) 0.45311E-01 ( PROT GLU 19 H ) 0.36249E-01 ( PROT GLU 19 CA ) 0.45311E-01 ( PROT GLU 19 CB ) 0.36249E-01 ( PROT GLU 19 CG ) 0.36249E-01 ( PROT GLU 19 CD ) 0.36249E-01 ( PROT GLU 19 OE1 ) 0.36249E-01 ( PROT GLU 19 OE2 ) 0.36249E-01 ( PROT GLU 19 C ) 0.45311E-01 ( PROT GLU 19 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.40076 5.24979 -8.66520 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.01027 0.01013 -0.00649 ROTATION MATRIX 0.999996 -0.000191 0.002681 0.000189 0.999999 0.001092 -0.002682 -0.001092 0.999996 AXIS OF ROTATION IS 0.376362 -0.924155 -0.065486 ANGLE IS 0.17 TOTAL SQUARE DIFF IS 211.4456 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 1.077863 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.0779" Parameter: A <- "1.0779" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.75063 5.29412 -8.80682 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.03579 -0.02970 0.01245 ROTATION MATRIX 0.999921 -0.001289 -0.012481 0.001288 0.999999 -0.000052 0.012481 0.000036 0.999922 AXIS OF ROTATION IS -0.003484 0.994707 -0.102693 ANGLE IS 0.72 TOTAL SQUARE DIFF IS 12.2452 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 0.802799 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.0779" RDCMND substituted energy or value "?RMS" to " 0.8028" Parameter: A <- "1.0779 0.8028" 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 1.0779 0.8028 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 " 12.59" Parameter: H <- "12.59" CHARMM> ! get an energy w/out the restraints CHARMM> SKIPE HARM SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> GETE ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ---------- --------- --------- --------- --------- --------- ENER> 0 -53.87430 12.59145 0.07678 ENER INTERN> 4.71482 14.79452 0.00000 10.09388 2.82954 ENER EXTERN> -113.39519 27.08812 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> ! switch on restraints again CHARMM> SKIPE EXCL ALL SKIPE> The following energy terms will be computed : BOND ANGL UREY DIHE IMPR VDW ELEC HBON USER HARM CDIH CIC CDRO NOE SBOU IMNB IMEL IMHB EWKS EWSE EXTE RXNF ST2 IMST TSM QMEL QMVD ASP EHAR GEO MDIP PINT PRMS PANG SSBP BK4D SHEL RESD SHAP STRB OOPL PULL POLA DMC RGY EWEX EWQC EWUT PBEL PBNP MBDE MBEL STRS BNDB BNDT EBST MBST BBT SST GBEN HMCM ADUM HYDR GSBP FQPO GRVD GREL SASL CMAP ELRC OLAP UMBR PHEN CHARMM> !get total energy w/o restraints CHARMM> set b ?ENER RDCMND substituted energy or value "?ENER" to " -53.87" Parameter: B <- "-53.87" CHARMM> ! get EXTernal energy contributions. CHARMM> set c ?ELEC RDCMND substituted energy or value "?ELEC" to " 27.09" Parameter: C <- "27.09" CHARMM> incr c by ?VDW RDCMND substituted energy or value "?VDW" to " -113.40" Parameter: C <- " -86.31" CHARMM> incr c by ?USER RDCMND substituted energy or value "?USER" to " 0.00" Parameter: C <- " -86.31" CHARMM> ! get INTernal energy contributions. CHARMM> set d ?BOND RDCMND substituted energy or value "?BOND" to " 4.71" Parameter: D <- "4.71" CHARMM> incr d by ?ANGL RDCMND substituted energy or value "?ANGL" to " 14.79" Parameter: D <- " 19.50" CHARMM> incr d by ?DIHE RDCMND substituted energy or value "?DIHE" to " 10.09" Parameter: D <- " 29.59" CHARMM> incr d by ?IMPR RDCMND substituted energy or value "?IMPR" to " 2.83" Parameter: D <- " 32.42" CHARMM> incr d by ?UREY RDCMND substituted energy or value "?UREY" to " 0.00" Parameter: D <- " 32.42" CHARMM> !write out the resulting energy differences CHARMM> open unit 12 appe form name ../out/@output.enr Parameter: OUTPUT -> "MINI_"helix_allh"" VOPEN> Attempting to open::../out/mini_helix_allh.enr:: OPNLGU> Unit 12 opened for APPEND access to ../out/mini_helix_allh.enr CHARMM> write title unit 12 RDTITL> *STEP= 12000 ENER= -53.87 GRMS= 0.08 ELEC= 27.09 VDW= -113.40 RDTITL> *EXTERNAL= -86.31 INTERNAL= 32.42 USER= 0.00 HARM= 12.59 RDTITL> *BOND= 4.71 ANGL= 14.79 DIHE= 10.09 IMPR= 2.83 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= -53.87 GRMS= 0.08 ELEC= 27.09 VDW= -113.40 RDTITL> *EXTERNAL= -86.31 INTERNAL= 32.42 USER= 0.00 HARM= 12.59 RDTITL> *BOND= 4.71 ANGL= 14.79 DIHE= 10.09 IMPR= 2.83 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= -53.87 GRMS= 0.08 ELEC= 27.09 VDW= -113.40 RDTITL> *EXTERNAL= -86.31 INTERNAL= 32.42 USER= 0.00 HARM= 12.59 RDTITL> *BOND= 4.71 ANGL= 14.79 DIHE= 10.09 IMPR= 2.83 UREY= 0.00 RDTITL> *=========================================================== RDTITL> * RMS COORDINATE DEVIATIONS: RDTITL> * STEP PROT .OR. PEPT PROT PEPT WATER TRACE RDTITL> * 12000 1.0779 0.8028 RDTITL> *=========================================================== RDTITL> * HUMAN SCRAMBLASE 1 : ALL-ATOM TOPOLOGY/PARAMETERS RDTITL> * INITIAL COORDINATES: RDTITL> * Write CHARMM-pdb format CHARMM> CHARMM> CHARMM> set 5 0 ! reset coordinate dump counter Parameter: 5 <- "0" CHARMM> if 1 lt @3 goto mini Parameter: 3 -> "12000" Comparing "12000" and "12000". IF test evaluated as false. Skipping command CHARMM> CHARMM> ! now do a minimization without any constraint CHARMM> cons harm clear CHARMM> ! check that constraint==0 CHARMM> scalar cons show ( PROT LYS 1 HT1 ) 0.0000 ( PROT LYS 1 HT2 ) 0.0000 ( PROT LYS 1 N ) 0.0000 ( PROT LYS 1 HT3 ) 0.0000 ( PROT LYS 1 CA ) 0.0000 ( PROT LYS 1 CB ) 0.0000 ( PROT LYS 1 CG ) 0.0000 ( PROT LYS 1 CD ) 0.0000 ( PROT LYS 1 CE ) 0.0000 ( PROT LYS 1 NZ ) 0.0000 ( PROT LYS 1 HZ1 ) 0.0000 ( PROT LYS 1 HZ2 ) 0.0000 ( PROT LYS 1 HZ3 ) 0.0000 ( PROT LYS 1 C ) 0.0000 ( PROT LYS 1 O ) 0.0000 ( PROT MET 2 N ) 0.0000 ( PROT MET 2 H ) 0.0000 ( PROT MET 2 CA ) 0.0000 ( PROT MET 2 CB ) 0.0000 ( PROT MET 2 CG ) 0.0000 ( PROT MET 2 SD ) 0.0000 ( PROT MET 2 CE ) 0.0000 ( PROT MET 2 C ) 0.0000 ( PROT MET 2 O ) 0.0000 ( PROT LYS 3 N ) 0.0000 ( PROT LYS 3 H ) 0.0000 ( PROT LYS 3 CA ) 0.0000 ( PROT LYS 3 CB ) 0.0000 ( PROT LYS 3 CG ) 0.0000 ( PROT LYS 3 CD ) 0.0000 ( PROT LYS 3 CE ) 0.0000 ( PROT LYS 3 NZ ) 0.0000 ( PROT LYS 3 HZ1 ) 0.0000 ( PROT LYS 3 HZ2 ) 0.0000 ( PROT LYS 3 HZ3 ) 0.0000 ( PROT LYS 3 C ) 0.0000 ( PROT LYS 3 O ) 0.0000 ( PROT ALA 4 N ) 0.0000 ( PROT ALA 4 H ) 0.0000 ( PROT ALA 4 CA ) 0.0000 ( PROT ALA 4 CB ) 0.0000 ( PROT ALA 4 C ) 0.0000 ( PROT ALA 4 O ) 0.0000 ( PROT VAL 5 N ) 0.0000 ( PROT VAL 5 H ) 0.0000 ( PROT VAL 5 CA ) 0.0000 ( PROT VAL 5 CB ) 0.0000 ( PROT VAL 5 CG1 ) 0.0000 ( PROT VAL 5 CG2 ) 0.0000 ( PROT VAL 5 C ) 0.0000 ( PROT VAL 5 O ) 0.0000 ( PROT MET 6 N ) 0.0000 ( PROT MET 6 H ) 0.0000 ( PROT MET 6 CA ) 0.0000 ( PROT MET 6 CB ) 0.0000 ( PROT MET 6 CG ) 0.0000 ( PROT MET 6 SD ) 0.0000 ( PROT MET 6 CE ) 0.0000 ( PROT MET 6 C ) 0.0000 ( PROT MET 6 O ) 0.0000 ( PROT ILE 7 N ) 0.0000 ( PROT ILE 7 H ) 0.0000 ( PROT ILE 7 CA ) 0.0000 ( PROT ILE 7 CB ) 0.0000 ( PROT ILE 7 CG2 ) 0.0000 ( PROT ILE 7 CG1 ) 0.0000 ( PROT ILE 7 CD ) 0.0000 ( PROT ILE 7 C ) 0.0000 ( PROT ILE 7 O ) 0.0000 ( PROT GLY 8 N ) 0.0000 ( PROT GLY 8 H ) 0.0000 ( PROT GLY 8 CA ) 0.0000 ( PROT GLY 8 C ) 0.0000 ( PROT GLY 8 O ) 0.0000 ( PROT ALA 9 N ) 0.0000 ( PROT ALA 9 H ) 0.0000 ( PROT ALA 9 CA ) 0.0000 ( PROT ALA 9 CB ) 0.0000 ( PROT ALA 9 C ) 0.0000 ( PROT ALA 9 O ) 0.0000 ( PROT CYS 10 N ) 0.0000 ( PROT CYS 10 H ) 0.0000 ( PROT CYS 10 CA ) 0.0000 ( PROT CYS 10 CB ) 0.0000 ( PROT CYS 10 SG ) 0.0000 ( PROT CYS 10 C ) 0.0000 ( PROT CYS 10 O ) 0.0000 ( PROT PHE 11 N ) 0.0000 ( PROT PHE 11 H ) 0.0000 ( PROT PHE 11 CA ) 0.0000 ( PROT PHE 11 CB ) 0.0000 ( PROT PHE 11 CG ) 0.0000 ( PROT PHE 11 CD1 ) 0.0000 ( PROT PHE 11 CD2 ) 0.0000 ( PROT PHE 11 CE1 ) 0.0000 ( PROT PHE 11 CE2 ) 0.0000 ( PROT PHE 11 CZ ) 0.0000 ( PROT PHE 11 C ) 0.0000 ( PROT PHE 11 O ) 0.0000 ( PROT LEU 12 N ) 0.0000 ( PROT LEU 12 H ) 0.0000 ( PROT LEU 12 CA ) 0.0000 ( PROT LEU 12 CB ) 0.0000 ( PROT LEU 12 CG ) 0.0000 ( PROT LEU 12 CD1 ) 0.0000 ( PROT LEU 12 CD2 ) 0.0000 ( PROT LEU 12 C ) 0.0000 ( PROT LEU 12 O ) 0.0000 ( PROT ILE 13 N ) 0.0000 ( PROT ILE 13 H ) 0.0000 ( PROT ILE 13 CA ) 0.0000 ( PROT ILE 13 CB ) 0.0000 ( PROT ILE 13 CG2 ) 0.0000 ( PROT ILE 13 CG1 ) 0.0000 ( PROT ILE 13 CD ) 0.0000 ( PROT ILE 13 C ) 0.0000 ( PROT ILE 13 O ) 0.0000 ( PROT ASP 14 N ) 0.0000 ( PROT ASP 14 H ) 0.0000 ( PROT ASP 14 CA ) 0.0000 ( PROT ASP 14 CB ) 0.0000 ( PROT ASP 14 CG ) 0.0000 ( PROT ASP 14 OD1 ) 0.0000 ( PROT ASP 14 OD2 ) 0.0000 ( PROT ASP 14 C ) 0.0000 ( PROT ASP 14 O ) 0.0000 ( PROT PHE 15 N ) 0.0000 ( PROT PHE 15 H ) 0.0000 ( PROT PHE 15 CA ) 0.0000 ( PROT PHE 15 CB ) 0.0000 ( PROT PHE 15 CG ) 0.0000 ( PROT PHE 15 CD1 ) 0.0000 ( PROT PHE 15 CD2 ) 0.0000 ( PROT PHE 15 CE1 ) 0.0000 ( PROT PHE 15 CE2 ) 0.0000 ( PROT PHE 15 CZ ) 0.0000 ( PROT PHE 15 C ) 0.0000 ( PROT PHE 15 O ) 0.0000 ( PROT MET 16 N ) 0.0000 ( PROT MET 16 H ) 0.0000 ( PROT MET 16 CA ) 0.0000 ( PROT MET 16 CB ) 0.0000 ( PROT MET 16 CG ) 0.0000 ( PROT MET 16 SD ) 0.0000 ( PROT MET 16 CE ) 0.0000 ( PROT MET 16 C ) 0.0000 ( PROT MET 16 O ) 0.0000 ( PROT PHE 17 N ) 0.0000 ( PROT PHE 17 H ) 0.0000 ( PROT PHE 17 CA ) 0.0000 ( PROT PHE 17 CB ) 0.0000 ( PROT PHE 17 CG ) 0.0000 ( PROT PHE 17 CD1 ) 0.0000 ( PROT PHE 17 CD2 ) 0.0000 ( PROT PHE 17 CE1 ) 0.0000 ( PROT PHE 17 CE2 ) 0.0000 ( PROT PHE 17 CZ ) 0.0000 ( PROT PHE 17 C ) 0.0000 ( PROT PHE 17 O ) 0.0000 ( PROT PHE 18 N ) 0.0000 ( PROT PHE 18 H ) 0.0000 ( PROT PHE 18 CA ) 0.0000 ( PROT PHE 18 CB ) 0.0000 ( PROT PHE 18 CG ) 0.0000 ( PROT PHE 18 CD1 ) 0.0000 ( PROT PHE 18 CD2 ) 0.0000 ( PROT PHE 18 CE1 ) 0.0000 ( PROT PHE 18 CE2 ) 0.0000 ( PROT PHE 18 CZ ) 0.0000 ( PROT PHE 18 C ) 0.0000 ( PROT PHE 18 O ) 0.0000 ( PROT GLU 19 N ) 0.0000 ( PROT GLU 19 H ) 0.0000 ( PROT GLU 19 CA ) 0.0000 ( PROT GLU 19 CB ) 0.0000 ( PROT GLU 19 CG ) 0.0000 ( PROT GLU 19 CD ) 0.0000 ( PROT GLU 19 OE1 ) 0.0000 ( PROT GLU 19 OE2 ) 0.0000 ( PROT GLU 19 C ) 0.0000 ( PROT GLU 19 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 10640 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10612 ATOM PAIRS WERE FOUND FOR ATOM LIST 315 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 -53.87430 12.59145 0.07678 0.00000 MINI INTERN> 4.71482 14.79452 0.00000 10.09388 2.82954 MINI EXTERN> -113.39519 27.08812 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -56.25919 2.38488 0.18999 0.04205 MINI INTERN> 5.09022 14.79595 0.00000 9.93913 2.71899 MINI EXTERN> -117.40637 28.60290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10458 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -56.25919 2.38488 0.18999 0.00000 MINI INTERN> 5.09022 14.79595 0.00000 9.93913 2.71899 MINI EXTERN> -117.40637 28.60290 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -56.91950 0.66032 0.09784 0.02984 MINI INTERN> 5.04407 14.73497 0.00000 10.12420 2.76216 MINI EXTERN> -117.02428 27.43936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10496 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -56.91950 0.66032 0.09784 0.00000 MINI INTERN> 5.04407 14.73497 0.00000 10.12420 2.76216 MINI EXTERN> -117.02428 27.43936 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -57.19217 0.27267 0.12602 0.01704 MINI INTERN> 5.19633 14.66266 0.00000 10.34646 2.74743 MINI EXTERN> -118.10402 27.95896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10451 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -57.19217 0.27267 0.12602 0.00000 MINI INTERN> 5.19633 14.66266 0.00000 10.34646 2.74743 MINI EXTERN> -118.10402 27.95896 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -57.34202 0.14985 0.05584 0.01191 MINI INTERN> 5.12379 14.65855 0.00000 10.37347 2.76631 MINI EXTERN> -117.70770 27.44356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10478 ATOM PAIRS WERE FOUND FOR ATOM LIST 306 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -57.34202 0.14985 0.05584 0.00000 MINI INTERN> 5.12379 14.65855 0.00000 10.37347 2.76631 MINI EXTERN> -117.70770 27.44356 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -57.43497 0.09295 0.11806 0.01004 MINI INTERN> 5.22630 14.63296 0.00000 10.58230 2.76744 MINI EXTERN> -118.41499 27.77102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10451 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -57.43497 0.09295 0.11806 0.00000 MINI INTERN> 5.22630 14.63296 0.00000 10.58230 2.76744 MINI EXTERN> -118.41499 27.77102 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -57.49496 0.05999 0.03370 0.00744 MINI INTERN> 5.18235 14.62042 0.00000 10.56975 2.78681 MINI EXTERN> -118.13880 27.48451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10468 ATOM PAIRS WERE FOUND FOR ATOM LIST 307 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -57.49496 0.05999 0.03370 0.00000 MINI INTERN> 5.18235 14.62042 0.00000 10.56975 2.78681 MINI EXTERN> -118.13880 27.48451 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -57.53650 0.04154 0.08342 0.00849 MINI INTERN> 5.25206 14.60205 0.00000 10.72837 2.78387 MINI EXTERN> -118.59476 27.69191 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10459 ATOM PAIRS WERE FOUND FOR ATOM LIST 310 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -57.53650 0.04154 0.08342 0.00000 MINI INTERN> 5.25206 14.60205 0.00000 10.72837 2.78387 MINI EXTERN> -118.59476 27.69191 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -57.56676 0.03027 0.02246 0.00530 MINI INTERN> 5.21350 14.59815 0.00000 10.70448 2.80257 MINI EXTERN> -118.41520 27.52973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10469 ATOM PAIRS WERE FOUND FOR ATOM LIST 310 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -57.56676 0.03027 0.02246 0.00000 MINI INTERN> 5.21350 14.59815 0.00000 10.70448 2.80257 MINI EXTERN> -118.41520 27.52973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -57.58960 0.02284 0.06651 0.00588 MINI INTERN> 5.26073 14.57835 0.00000 10.82442 2.80226 MINI EXTERN> -118.73588 27.68053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10461 ATOM PAIRS WERE FOUND FOR ATOM LIST 312 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -57.58960 0.02284 0.06651 0.00000 MINI INTERN> 5.26073 14.57835 0.00000 10.82442 2.80226 MINI EXTERN> -118.73588 27.68053 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -57.60638 0.01678 0.01489 0.00340 MINI INTERN> 5.23115 14.57747 0.00000 10.80654 2.81428 MINI EXTERN> -118.61673 27.58090 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10467 ATOM PAIRS WERE FOUND FOR ATOM LIST 311 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -57.60638 0.01678 0.01489 0.00000 MINI INTERN> 5.23115 14.57747 0.00000 10.80654 2.81428 MINI EXTERN> -118.61673 27.58090 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -57.61853 0.01214 0.05217 0.00511 MINI INTERN> 5.26245 14.57114 0.00000 10.90021 2.81355 MINI EXTERN> -118.83807 27.67219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10461 ATOM PAIRS WERE FOUND FOR ATOM LIST 311 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -57.61853 0.01214 0.05217 0.00000 MINI INTERN> 5.26245 14.57114 0.00000 10.90021 2.81355 MINI EXTERN> -118.83807 27.67219 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -57.62724 0.00871 0.01052 0.00283 MINI INTERN> 5.24207 14.56895 0.00000 10.88264 2.81951 MINI EXTERN> -118.76014 27.61973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10464 ATOM PAIRS WERE FOUND FOR ATOM LIST 312 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -57.62724 0.00871 0.01052 0.00000 MINI INTERN> 5.24207 14.56895 0.00000 10.88264 2.81951 MINI EXTERN> -118.76014 27.61973 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -57.63359 0.00635 0.02820 0.00469 MINI INTERN> 5.26286 14.56032 0.00000 10.94744 2.81767 MINI EXTERN> -118.89977 27.67789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10465 ATOM PAIRS WERE FOUND FOR ATOM LIST 311 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -57.63359 0.00635 0.02820 0.00000 MINI INTERN> 5.26286 14.56032 0.00000 10.94744 2.81767 MINI EXTERN> -118.89977 27.67789 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -57.63847 0.00488 0.00843 0.00197 MINI INTERN> 5.25051 14.56190 0.00000 10.93109 2.82138 MINI EXTERN> -118.83911 27.63577 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10465 ATOM PAIRS WERE FOUND FOR ATOM LIST 311 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -57.63847 0.00488 0.00843 0.00000 MINI INTERN> 5.25051 14.56190 0.00000 10.93109 2.82138 MINI EXTERN> -118.83911 27.63577 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -57.64235 0.00388 0.02082 0.00392 MINI INTERN> 5.26561 14.55455 0.00000 10.97970 2.81941 MINI EXTERN> -118.93597 27.67434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10465 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -57.64235 0.00388 0.02082 0.00000 MINI INTERN> 5.26561 14.55455 0.00000 10.97970 2.81941 MINI EXTERN> -118.93597 27.67434 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -57.64557 0.00321 0.00917 0.00165 MINI INTERN> 5.25437 14.55750 0.00000 10.96493 2.82122 MINI EXTERN> -118.88829 27.64470 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10466 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -57.64557 0.00321 0.00917 0.00000 MINI INTERN> 5.25437 14.55750 0.00000 10.96493 2.82122 MINI EXTERN> -118.88829 27.64470 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -57.64827 0.00270 0.01521 0.00299 MINI INTERN> 5.26630 14.55156 0.00000 11.00283 2.81886 MINI EXTERN> -118.96214 27.67431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10467 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -57.64827 0.00270 0.01521 0.00000 MINI INTERN> 5.26630 14.55156 0.00000 11.00283 2.81886 MINI EXTERN> -118.96214 27.67431 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1800 -57.65050 0.00223 0.00675 0.00127 MINI INTERN> 5.25761 14.55673 0.00000 10.98790 2.81993 MINI EXTERN> -118.92188 27.64920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10467 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1800 -57.65050 0.00223 0.00675 0.00000 MINI INTERN> 5.25761 14.55673 0.00000 10.98790 2.81993 MINI EXTERN> -118.92188 27.64920 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1900 -57.65236 0.00186 0.01257 0.00254 MINI INTERN> 5.26680 14.55166 0.00000 11.01689 2.81777 MINI EXTERN> -118.97868 27.67318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10469 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1900 -57.65236 0.00186 0.01257 0.00000 MINI INTERN> 5.26680 14.55166 0.00000 11.01689 2.81777 MINI EXTERN> -118.97868 27.67318 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 2000 -57.65392 0.00156 0.00499 0.00117 MINI INTERN> 5.25987 14.55587 0.00000 11.00440 2.81837 MINI EXTERN> -118.94657 27.65414 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 -57.65392 0.00156 0.00499 0.02000 CONJ INTERN> 5.25987 14.55587 0.00000 11.00440 2.81837 CONJ EXTERN> -118.94657 27.65414 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 10469 atom pairs and 764 atom exclusions. There are 0 group pairs and 167 group exclusions. Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10469 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 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 -57.65392 0.00156 0.00499 0.00000 MINI INTERN> 5.25987 14.55587 0.00000 11.00440 2.81837 MINI EXTERN> -118.94657 27.65414 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 100 -57.65525 0.00133 0.01120 0.00217 MINI INTERN> 5.26736 14.55159 0.00000 11.02748 2.81645 MINI EXTERN> -118.99188 27.67375 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10469 ATOM PAIRS WERE FOUND FOR ATOM LIST 309 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 100 -57.65525 0.00133 0.01120 0.00000 MINI INTERN> 5.26736 14.55159 0.00000 11.02748 2.81645 MINI EXTERN> -118.99188 27.67375 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 200 -57.65639 0.00114 0.00491 0.00095 MINI INTERN> 5.26156 14.55583 0.00000 11.01693 2.81684 MINI EXTERN> -118.96521 27.65767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10469 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 200 -57.65639 0.00114 0.00491 0.00000 MINI INTERN> 5.26156 14.55583 0.00000 11.01693 2.81684 MINI EXTERN> -118.96521 27.65767 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 300 -57.65736 0.00098 0.01019 0.00188 MINI INTERN> 5.26763 14.55228 0.00000 11.03560 2.81521 MINI EXTERN> -119.00205 27.67396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10469 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 300 -57.65736 0.00098 0.01019 0.00000 MINI INTERN> 5.26763 14.55228 0.00000 11.03560 2.81521 MINI EXTERN> -119.00205 27.67396 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 400 -57.65820 0.00084 0.00369 0.00085 MINI INTERN> 5.26287 14.55597 0.00000 11.02693 2.81529 MINI EXTERN> -118.97956 27.66029 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10469 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 400 -57.65820 0.00084 0.00369 0.00000 MINI INTERN> 5.26287 14.55597 0.00000 11.02693 2.81529 MINI EXTERN> -118.97956 27.66029 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 500 -57.65894 0.00073 0.01058 0.00171 MINI INTERN> 5.26786 14.55296 0.00000 11.04226 2.81390 MINI EXTERN> -119.00986 27.67394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10468 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 500 -57.65894 0.00073 0.01058 0.00000 MINI INTERN> 5.26786 14.55296 0.00000 11.04226 2.81390 MINI EXTERN> -119.00986 27.67394 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 600 -57.65957 0.00063 0.00315 0.00074 MINI INTERN> 5.26383 14.55653 0.00000 11.03503 2.81386 MINI EXTERN> -118.99088 27.66205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10467 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 600 -57.65957 0.00063 0.00315 0.00000 MINI INTERN> 5.26383 14.55653 0.00000 11.03503 2.81386 MINI EXTERN> -118.99088 27.66205 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 700 -57.66014 0.00057 0.01834 0.00151 MINI INTERN> 5.27026 14.55272 0.00000 11.04743 2.81240 MINI EXTERN> -119.01653 27.67357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10468 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 700 -57.66014 0.00057 0.01834 0.00000 MINI INTERN> 5.27026 14.55272 0.00000 11.04743 2.81240 MINI EXTERN> -119.01653 27.67357 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 800 -57.66062 0.00048 0.00243 0.00066 MINI INTERN> 5.26465 14.55690 0.00000 11.04209 2.81258 MINI EXTERN> -119.00134 27.66450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 800 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10470 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 800 -57.66062 0.00048 0.00243 0.00000 MINI INTERN> 5.26465 14.55690 0.00000 11.04209 2.81258 MINI EXTERN> -119.00134 27.66450 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 900 -57.66103 0.00040 0.01463 0.00136 MINI INTERN> 5.26951 14.55428 0.00000 11.05199 2.81139 MINI EXTERN> -119.02168 27.67348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 900 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10471 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 900 -57.66103 0.00040 0.01463 0.00000 MINI INTERN> 5.26951 14.55428 0.00000 11.05199 2.81139 MINI EXTERN> -119.02168 27.67348 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1000 -57.66137 0.00034 0.00197 0.00055 MINI INTERN> 5.26562 14.55741 0.00000 11.04764 2.81145 MINI EXTERN> -119.00983 27.66634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1000 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10471 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1000 -57.66137 0.00034 0.00197 0.00000 MINI INTERN> 5.26562 14.55741 0.00000 11.04764 2.81145 MINI EXTERN> -119.00983 27.66634 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1100 -57.66168 0.00031 0.01432 0.00122 MINI INTERN> 5.27015 14.55601 0.00000 11.05587 2.81048 MINI EXTERN> -119.02646 27.67228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1100 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10471 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1100 -57.66168 0.00031 0.01432 0.00000 MINI INTERN> 5.27015 14.55601 0.00000 11.05587 2.81048 MINI EXTERN> -119.02646 27.67228 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1200 -57.66194 0.00026 0.00166 0.00054 MINI INTERN> 5.26621 14.55760 0.00000 11.05247 2.81043 MINI EXTERN> -119.01698 27.66833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1200 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10472 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1200 -57.66194 0.00026 0.00166 0.00000 MINI INTERN> 5.26621 14.55760 0.00000 11.05247 2.81043 MINI EXTERN> -119.01698 27.66833 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1300 -57.66215 0.00021 0.00798 0.00109 MINI INTERN> 5.26954 14.55723 0.00000 11.05890 2.80919 MINI EXTERN> -119.03006 27.67304 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1300 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10472 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1300 -57.66215 0.00021 0.00798 0.00000 MINI INTERN> 5.26954 14.55723 0.00000 11.05890 2.80919 MINI EXTERN> -119.03006 27.67304 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1400 -57.66233 0.00018 0.00150 0.00036 MINI INTERN> 5.26694 14.55796 0.00000 11.05607 2.80949 MINI EXTERN> -119.02206 27.66926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1400 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10472 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1400 -57.66233 0.00018 0.00150 0.00000 MINI INTERN> 5.26694 14.55796 0.00000 11.05607 2.80949 MINI EXTERN> -119.02206 27.66926 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1500 -57.66248 0.00016 0.00753 0.00099 MINI INTERN> 5.26951 14.55752 0.00000 11.06142 2.80855 MINI EXTERN> -119.03251 27.67303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1500 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10472 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1500 -57.66248 0.00016 0.00753 0.00000 MINI INTERN> 5.26951 14.55752 0.00000 11.06142 2.80855 MINI EXTERN> -119.03251 27.67303 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1600 -57.66261 0.00013 0.00171 0.00027 MINI INTERN> 5.26714 14.55853 0.00000 11.05922 2.80879 MINI EXTERN> -119.02669 27.67039 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1600 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10472 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1600 -57.66261 0.00013 0.00171 0.00000 MINI INTERN> 5.26714 14.55853 0.00000 11.05922 2.80879 MINI EXTERN> -119.02669 27.67039 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- MINI> 1700 -57.66272 0.00010 0.00340 0.00077 MINI INTERN> 5.26960 14.55786 0.00000 11.06342 2.80804 MINI EXTERN> -119.03522 27.67359 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- UPDECI: Nonbond update at step 1700 Generating nonbond list with Exclusion mode = 5 == PRIMARY == SPACE FOR 16381 ATOM PAIRS AND 0 GROUP PAIRS General atom nonbond list generation found: 10472 ATOM PAIRS WERE FOUND FOR ATOM LIST 308 GROUP PAIRS REQUIRED ATOM SEARCHES MINI> 1700 -57.66272 0.00010 0.00340 0.00000 MINI INTERN> 5.26960 14.55786 0.00000 11.06342 2.80804 MINI EXTERN> -119.03522 27.67359 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> 1799 -57.66281 0.00009 0.00093 0.02000 CONJ INTERN> 5.26774 14.55857 0.00000 11.06172 2.80823 CONJ EXTERN> -119.03023 27.67116 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> 182 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.37691 5.23065 -8.65501 CENTER OF REFERENCE COORDINATE SET 9.41104 5.25991 -8.67169 NET TRANSLATION OF ROTATED ATOMS 0.03412 0.02926 -0.01668 ROTATION MATRIX 0.999930 0.000822 0.011768 -0.000852 0.999996 0.002578 -0.011766 -0.002588 0.999927 AXIS OF ROTATION IS 0.213929 -0.974387 0.069314 ANGLE IS 0.69 TOTAL SQUARE DIFF IS 448.9736 DENOMINATOR IS 182.0000 THUS RMS DIFF IS 1.570633 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a ?RMS RDCMND substituted energy or value "?RMS" to " 1.5706" Parameter: A <- "1.5706" CHARMM> set a @a ?RMS Parameter: A -> "1.5706" RDCMND substituted energy or value "?RMS" to " 1.5706" Parameter: A <- "1.5706 1.5706" CHARMM> ! trace only CHARMM> coor orie rms sele ( trace ) end SELRPN> 19 atoms have been selected out of 182 CENTER OF ATOMS BEFORE TRANSLATION 9.75792 5.32337 -8.83706 CENTER OF REFERENCE COORDINATE SET 9.71484 5.26442 -8.79437 NET TRANSLATION OF ROTATED ATOMS -0.04308 -0.05895 0.04269 ROTATION MATRIX 0.999927 0.006169 -0.010435 -0.006253 0.999948 -0.008046 0.010385 0.008110 0.999913 AXIS OF ROTATION IS -0.554527 0.714633 0.426379 ANGLE IS 0.83 TOTAL SQUARE DIFF IS 21.4324 DENOMINATOR IS 19.0000 THUS RMS DIFF IS 1.062083 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS. CHARMM> set a @a ?RMS Parameter: A -> "1.5706 1.5706" RDCMND substituted energy or value "?RMS" to " 1.0621" Parameter: A <- "1.5706 1.5706 1.0621" 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 1.5706 1.5706 1.0621 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" $$$$$$ New timer profile $$$$$ List time 0.00 Other: 0.00 Electrostatic & VDW 7.75 Other: 0.00 Nonbond force 7.78 Other: 0.02 Bond energy 0.08 Other: 0.00 Angle energy 0.65 Other: 0.00 Dihedral energy 0.41 Other: 0.00 Restraints energy 0.00 Other: 0.00 INTRNL energy 1.17 Other: 0.04 Energy time 9.03 Other: 0.08 Total time 10.17 Other: 1.14 NORMAL TERMINATION BY NORMAL STOP MAXIMUM STACK SPACE USED IS 47522 STACK CURRENTLY IN USE IS 0 MOST SEVERE WARNING WAS AT LEVEL 2 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 0 MAXIMUM SPACE USED IS 28406 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 10.18 SECONDS CPU TIME: 0.00 SECONDS