MODELLER 6a, Dec 13, 2000 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2000 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M. A. Marti-Renom, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 viol 6.5 IP28 Date and time of compilation : 2000/04/29 20:19:04 Job starting time (YY/MM/DD HH:MM:SS): 2001/08/01 14:59:50.231 TOP_________> 115 828 SET ALNFILE = 'TvLDH-4mdhA.ali' TOP_________> 116 829 SET KNOWNS = '4mdhA' TOP_________> 117 830 SET SEQUENCE = 'TvLDH' TOP_________> 118 831 SET STARTING_MODEL = 1 TOP_________> 119 832 SET ENDING_MODEL = 5 TOP_________> 120 833 CALL ROUTINE = 'model' TOP_________> 121 379 CALL ROUTINE = 'getnames' TOP_________> 122 469 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 123 470 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 124 471 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 125 472 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 126 473 SET ROOT_NAME = SEQUENCE TOP_________> 127 474 RETURN TOP_________> 128 380 CALL ROUTINE = 'homcsr' TOP_________> 129 108 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 33379 32.597 0.032 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 4888751 4774.171 4.662 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali Read the alignment from file : TvLDH-4mdhA.ali Total number of alignment positions: 336 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdhA 333 1 4mdhA undefined 2 TvLDH 335 1 TvLDH TOP_________> 130 109 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./4mdhA.pdb check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND TOP_________> 131 110 CALL ROUTINE = GENERATE_METHOD TOP_________> 132 82 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali Dynamically allocated memory at amaxseq [B,kB,MB]: 4605483 4497.542 4.392 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali Read the alignment from file : TvLDH-4mdhA.ali Total number of alignment positions: 333 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdhA 333 1 4mdhA undefined TOP_________> 133 83 IF ARGUMENTS = INITIAL_MALIGN3D 0, OPERATION = 'NE', ; THEN = 'MALIGN3D FIT = off, GAP_PENALTIES_3D = 0 4' TOP_________> 134 84 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 4888751 4774.171 4.662 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali Read the alignment from file : TvLDH-4mdhA.ali Total number of alignment positions: 336 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdhA 333 1 4mdhA undefined 2 TvLDH 335 1 TvLDH TOP_________> 135 85 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib//top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL6a}/modlib/models.lib TOP_________> 136 86 READ_PARAMETERS FILE = PARLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib//par.lib Dynamically allocated memory at amattacns [B,kB,MB]: 4889147 4774.558 4.663 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib//par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 137 87 CALL ROUTINE = 'create_topology' TOP_________> 138 102 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF getf_______W> RTF restraint not found in the atoms list: residue type, indices: 6 335 atom names : C +N atom indices : 2603 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 6 335 atom names : C CA +N O atom indices : 2603 2602 0 2604 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 335 2604 2670 0 0 1136 patch_______> segment topology patched using RTF: 1 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 1 335 2604 2670 3623 4313 1136 iatmcls_286W> MODEL atom not classified: GLY:OT1 GLY iatmcls_286W> MODEL atom not classified: GLY:OT2 GLY patch_______> segment topology patched using RTF: 335 ; GLY ; CTER segments residues atoms bonds angles dihedrals impropers: 1 335 2605 2671 3625 4314 1137 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 335 2605 2671 3625 4314 1137 TOP_________> 139 103 CALL ROUTINE = 'default_patches' TOP_________> 140 464 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali Read the alignment from file : TvLDH-4mdhA.ali Total number of alignment positions: 336 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdhA 333 1 4mdhA undefined 2 TvLDH 335 1 TvLDH TOP_________> 141 465 PATCH_SS_TEMPLATES TOP_________> 142 466 RETURN TOP_________> 143 104 CALL ROUTINE = 'special_patches' TOP_________> 144 461 RETURN TOP_________> 145 105 RETURN TOP_________> 146 88 TRANSFER_XYZ CLUSTER_CUT = -1.0 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 2111 494 TOP_________> 147 89 BUILD_MODEL INITIALIZE_XYZ = OFF TOP_________> 148 90 WRITE_MODEL FILE = MODEL openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.ini wrpdb2__568_> Residues, atoms, selected atoms: 335 2605 2605 TOP_________> 149 91 RETURN TOP_________> 150 111 IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'EQ', THE; N ='GO_TO __SKIP_RSRS' TOP_________> 151 112 CALL ROUTINE = 'mkhomcsr' TOP_________> 152 117 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS; = OFF Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: stereo r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints: 2671 3625 4132 1121 Total number of restraints before, now : 0 11549 make_re_422_> Number of previous, current restraints : 0 11549 make_re_423_> Number of previous, current selected restraints: 0 11549 TOP_________> 153 118 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali openf5__224_> Open 11 OLD SEQUENTIAL TvLDH-4mdhA.ali Read the alignment from file : TvLDH-4mdhA.ali Total number of alignment positions: 336 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdhA 333 1 4mdhA undefined 2 TvLDH 335 1 TvLDH TOP_________> 154 119 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/mnch1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 4mdhA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 11549 11882 make_re_423_> Number of previous, current selected restraints: 11549 11882 TOP_________> 155 120 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINT; S = 5 TOP_________> 156 121 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RE; STRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: omega_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/omega.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/omega.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 4mdhA getdata_289_> Proteins (all/accepted): 1 1 omgdel__425W> Unselected all O C +N +CA dihedrals: 350 make_re_422_> Number of previous, current restraints : 11882 12216 make_re_423_> Number of previous, current selected restraints: 11882 11866 TOP_________> 157 122 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: chi1_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/chi1.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 4mdhA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 12216 12495 make_re_423_> Number of previous, current selected restraints: 11866 12145 TOP_________> 158 123 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: chi2_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/chi2.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 4mdhA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 12495 12709 make_re_423_> Number of previous, current selected restraints: 12145 12359 TOP_________> 159 124 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: chi3_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/chi3.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. getdata_643_> Protein accepted: 4mdhA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 12709 12793 make_re_423_> Number of previous, current selected restraints: 12359 12443 TOP_________> 160 125 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: chi4_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/chi4.mdt irddata_401_> USER SYMMETRY, SYMMETRY: 1 T SYMMETRIC = .T. ==> NALN*NALN/2 SYMMETRIC = .F. ==> NALN*NALN All protein pairs always generated. mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. getdata_643_> Protein accepted: 4mdhA getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 12793 12825 make_re_423_> Number of previous, current selected restraints: 12443 12475 TOP_________> 161 126 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINT; S = 5 TOP_________> 162 127 SET RES_TYPES = 'STD' TOP_________> 163 128 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE TOP_________> 164 129 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 165 130 SET RESTRAINT_GROUP = 9 TOP_________> 166 131 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 335 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 167 132 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 335 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 168 133 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 12825 20099 make_re_423_> Number of previous, current selected restraints: 12475 19749 TOP_________> 169 134 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DI; STANCE TOP_________> 170 135 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 171 136 SET RESTRAINT_GROUP = 10 TOP_________> 172 137 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : N Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 335 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 173 138 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : O Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 335 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 174 139 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 20099 27290 make_re_423_> Number of previous, current selected restraints: 19749 26940 TOP_________> 175 140 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_; DISTANCE TOP_________> 176 141 SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = OFF TOP_________> 177 142 SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5 TOP_________> 178 143 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 1264 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 10 : THR 10 2 12 : ALA --- 13 : ALA 2 3 15 : GLN --- 16 : ILE 2 4 18 : TYR --- 26 : SER 9 5 28 : GLU --- 30 : TYR 3 6 32 : ASP --- 65 : ALA 34 7 67 : PHE --- 93 : PRO 27 8 95 : GLN --- 111 : THR 17 9 113 : GLU --- 128 : ILE 16 10 130 : ASN --- 170 : LEU 41 11 172 : VAL --- 183 : TRP 12 12 185 : ASN --- 186 : HSD 2 13 188 : GLU --- 202 : GLU 15 14 204 : LYS --- 225 : ILE 22 15 227 : HSD --- 236 : ARG 10 16 238 : PHE --- 257 : PHE 20 17 259 : THR --- 261 : PRO 3 18 263 : GLU --- 267 : MET 5 19 269 : ILE --- 273 : GLU 5 20 275 : ASN --- 277 : TYR 3 21 279 : ILE --- 281 : PRO 3 22 283 : VAL --- 294 : GLU 12 23 296 : LYS --- 301 : GLU 6 24 303 : PHE --- 333 : GLN 31 TOP_________> 179 144 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : MNCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 1341 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 180 145 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 27290 30628 make_re_423_> Number of previous, current selected restraints: 26940 30278 TOP_________> 181 146 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_; DISTANCE TOP_________> 182 147 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 183 148 SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0 TOP_________> 184 149 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 1264 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 10 : THR 10 2 12 : ALA --- 13 : ALA 2 3 15 : GLN --- 16 : ILE 2 4 18 : TYR --- 26 : SER 9 5 28 : GLU --- 30 : TYR 3 6 32 : ASP --- 65 : ALA 34 7 67 : PHE --- 93 : PRO 27 8 95 : GLN --- 111 : THR 17 9 113 : GLU --- 128 : ILE 16 10 130 : ASN --- 170 : LEU 41 11 172 : VAL --- 183 : TRP 12 12 185 : ASN --- 186 : HSD 2 13 188 : GLU --- 202 : GLU 15 14 204 : LYS --- 225 : ILE 22 15 227 : HSD --- 236 : ARG 10 16 238 : PHE --- 257 : PHE 20 17 259 : THR --- 261 : PRO 3 18 263 : GLU --- 267 : MET 5 19 269 : ILE --- 273 : GLU 5 20 275 : ASN --- 277 : TYR 3 21 279 : ILE --- 281 : PRO 3 22 283 : VAL --- 294 : GLU 12 23 296 : LYS --- 301 : GLU 6 24 303 : PHE --- 333 : GLN 31 TOP_________> 185 150 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 1264 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 10 : THR 10 2 12 : ALA --- 13 : ALA 2 3 15 : GLN --- 16 : ILE 2 4 18 : TYR --- 26 : SER 9 5 28 : GLU --- 30 : TYR 3 6 32 : ASP --- 65 : ALA 34 7 67 : PHE --- 93 : PRO 27 8 95 : GLN --- 111 : THR 17 9 113 : GLU --- 128 : ILE 16 10 130 : ASN --- 170 : LEU 41 11 172 : VAL --- 183 : TRP 12 12 185 : ASN --- 186 : HSD 2 13 188 : GLU --- 202 : GLU 15 14 204 : LYS --- 225 : ILE 22 15 227 : HSD --- 236 : ARG 10 16 238 : PHE --- 257 : PHE 20 17 259 : THR --- 261 : PRO 3 18 263 : GLU --- 267 : MET 5 19 269 : ILE --- 273 : GLU 5 20 275 : ASN --- 277 : TYR 3 21 279 : ILE --- 281 : PRO 3 22 283 : VAL --- 294 : GLU 12 23 296 : LYS --- 301 : GLU 6 24 303 : PHE --- 333 : GLN 31 TOP_________> 186 151 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 30628 31616 make_re_423_> Number of previous, current selected restraints: 30278 31266 TOP_________> 187 152 CALL ROUTINE = 'hetatm_restraints' TOP_________> 188 161 SET RESTRAINT_TYPE = 'distance' TOP_________> 189 162 SET DISTANCE_RSR_MODEL = 7 TOP_________> 190 163 SET MAXIMAL_DISTANCE = 7.0 TOP_________> 191 164 SET ADD_RESTRAINTS = ON TOP_________> 192 165 SET RESTRAINT_GROUP = 27 TOP_________> 193 166 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 194 167 SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 195 168 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : ALL Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2605 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 196 169 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : HET Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 197 170 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 31616 31616 make_re_423_> Number of previous, current selected restraints: 31266 31266 TOP_________> 198 171 RETURN TOP_________> 199 153 CALL ROUTINE = 'blk_restraints' TOP_________> 200 174 SET RESTRAINT_TYPE = 'distance' TOP_________> 201 175 SET DISTANCE_RSR_MODEL = 7 TOP_________> 202 176 SET MAXIMAL_DISTANCE = 10.0 TOP_________> 203 177 SET ADD_RESTRAINTS = ON TOP_________> 204 178 SET RESTRAINT_GROUP = 27 TOP_________> 205 179 SET RESTRAINT_STDEV = 0.05 0.0 TOP_________> 206 180 SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = ON TOP_________> 207 181 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 208 182 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 209 183 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 31616 31616 make_re_423_> Number of previous, current selected restraints: 31266 31266 TOP_________> 210 184 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 211 185 SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 212 186 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : ALL Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 335 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 213 187 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'BLK' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 214 188 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 31616 31616 make_re_423_> Number of previous, current selected restraints: 31266 31266 TOP_________> 215 189 RETURN TOP_________> 216 154 CALL ROUTINE = 'special_restraints' TOP_________> 217 458 RETURN TOP_________> 218 155 CONDENSE_RESTRAINTS delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 31616 29227 TOP_________> 219 156 WRITE_RESTRAINTS FILE = CSRFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.rsr TOP_________> 220 157 SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = O; N TOP_________> 221 158 RETURN TOP_________> 222 113 LABEL __SKIP_RSRS TOP_________> 223 114 RETURN TOP_________> 224 381 IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'EQ', THEN = 'RE; TURN' TOP_________> 225 382 CALL ROUTINE = 'rd_restraints' TOP_________> 226 255 READ_RESTRAINTS FILE = CSRFILE, ADD_RESTRAINTS = 'off' openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.rsr openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.rsr rdcsr2__307_> Number of restraints read : 29227 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 Dynamically allocated memory at amprmcns [B,kB,MB]: 12267659 11980.136 11.699 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.rsr openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.rsr rdcsr2__307_> Number of restraints read : 29227 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 29227 29227 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 TOP_________> 227 256 RETURN TOP_________> 228 383 CALL ROUTINE = 'multiple_models' TOP_________> 229 192 DO ID2 = STARTING_MODEL ENDING_MODEL 1 TOP_________> 230 193 SET FINAL_MODEL = 'default' TOP_________> 231 194 CALL ROUTINE = 'single_model' TOP_________> 232 205 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 233 206 SET ID1 = 0 TOP_________> 234 207 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000001 TOP_________> 235 208 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 1 335 2605 rdatm___298_> Segment: 1 1 1 2605 iatmcls_286W> MODEL atom not classified: GLY:OT1 GLY iatmcls_286W> MODEL atom not classified: GLY:OT2 GLY TOP_________> 236 209 CALL ROUTINE = 'select_atoms' TOP_________> 237 267 PICK_ATOMS SELECTION_SEGMENT ='@:@' 'X:X', SELECTION_SEAR; CH ='segment', PICK_ATOMS_SET =1, RES_TYPES =; 'all', ATOM_TYPES ='all', SELECTION_FROM ='a; ll', SELECTION_STATUS ='initialize' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2605 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 238 268 RETURN TOP_________> 239 210 CALL ROUTINE = RAND_METHOD TOP_________> 240 251 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2605 2605 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 241 252 RETURN TOP_________> 242 211 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/sched.lib TOP_________> 243 212 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 244 213 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 245 214 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 246 215 CALL ROUTINE = 'single_model_pass' TOP_________> 247 231 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 248 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 249 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 14859 TOP_________> 250 234 OPTIMIZE Dynamically allocated memory at ampairs [B,kB,MB]: 12559411 12265.050 11.978 TOP_________> 251 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 252 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 253 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 254 238 END_DO TOP_________> 255 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 256 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 16750 TOP_________> 257 234 OPTIMIZE TOP_________> 258 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 259 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 260 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 261 238 END_DO TOP_________> 262 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 263 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 17877 TOP_________> 264 234 OPTIMIZE TOP_________> 265 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 266 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 267 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 268 238 END_DO TOP_________> 269 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 270 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 19159 TOP_________> 271 234 OPTIMIZE TOP_________> 272 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 273 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 274 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 275 238 END_DO TOP_________> 276 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 277 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 20430 TOP_________> 278 234 OPTIMIZE TOP_________> 279 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 280 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 281 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 282 238 END_DO TOP_________> 283 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 284 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 22377 TOP_________> 285 234 OPTIMIZE TOP_________> 286 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 287 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 288 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 289 238 END_DO TOP_________> 290 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 291 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 24926 TOP_________> 292 234 OPTIMIZE TOP_________> 293 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 294 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 295 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 296 238 END_DO TOP_________> 297 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 298 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 25982 TOP_________> 299 234 OPTIMIZE TOP_________> 300 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 301 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 302 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 303 238 END_DO TOP_________> 304 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 305 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 27227 TOP_________> 306 234 OPTIMIZE TOP_________> 307 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 308 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 309 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 310 238 END_DO TOP_________> 311 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 312 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 28585 TOP_________> 313 234 OPTIMIZE TOP_________> 314 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 315 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 316 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 317 238 END_DO TOP_________> 318 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 319 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 320 234 OPTIMIZE TOP_________> 321 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 322 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 323 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 324 238 END_DO TOP_________> 325 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 326 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 327 234 OPTIMIZE TOP_________> 328 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 329 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 330 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 331 238 END_DO TOP_________> 332 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 333 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 334 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 335 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 336 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 337 285 CALL ROUTINE = MD_LEVEL TOP_________> 338 365 SET UPDATE_DYNAMIC = 0.39 TOP_________> 339 366 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 340 367 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 341 368 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 342 369 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 343 370 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 344 371 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 345 372 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 346 373 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 347 374 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 348 375 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 349 376 RETURN TOP_________> 350 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 351 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 352 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 353 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 354 307 RETURN TOP_________> 355 240 LABEL __ABORT TOP_________> 356 241 SET ERROR_STATUS = 0 TOP_________> 357 242 RETURN TOP_________> 358 216 END_DO TOP_________> 359 217 IUPAC_MODEL iupac_m_486_> OE1/2 swapped: -172.7446 28 28 iupac_m_485_> OD1/2 swapped: 136.4345 32 32 iupac_m_485_> OD1/2 swapped: 111.6390 41 41 iupac_m_487_> NH1/2 swapped: 176.2752 48 48 iupac_m_486_> OE1/2 swapped: -166.8966 57 57 iupac_m_485_> OD1/2 swapped: 161.2742 72 72 iupac_m_483_> CD1/2 CE1/2 swapped: -96.3546 108 108 iupac_m_483_> CD1/2 CE1/2 swapped: 93.6456 114 114 iupac_m_486_> OE1/2 swapped: 179.1769 137 137 iupac_m_486_> OE1/2 swapped: -153.0032 149 149 iupac_m_486_> OE1/2 swapped: -161.0309 202 202 iupac_m_485_> OD1/2 swapped: 159.7334 219 219 iupac_m_487_> NH1/2 swapped: 179.7676 228 228 iupac_m_486_> OE1/2 swapped: -178.1287 234 234 iupac_m_487_> NH1/2 swapped: 179.2686 236 236 iupac_m_483_> CD1/2 CE1/2 swapped: -91.1092 257 257 iupac_m_483_> CD1/2 CE1/2 swapped: 91.4322 287 287 iupac_m_484W> Dihedral still outside +-90: -90.0670 iupac_m_486_> OE1/2 swapped: -147.3421 294 294 iupac_m_486_> OE1/2 swapped: -146.4656 325 325 TOP_________> 360 218 SET ID1 = 9999 TOP_________> 361 219 SET OUTPUT2 = OUTPUT TOP_________> 362 220 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 1 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2605 2605 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 29227 29227 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5729 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 500 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 12 12 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1731.7185 Symmetry term within energy : 0.0000 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 2671 0 0 0.005 0.005 19.03063 1.000 2 Bond angle potential : 3625 0 8 2.058 2.058 304.7895 1.000 3 Stereochemical cosine torsion poten: 1743 0 50 47.003 47.003 586.4141 1.000 4 Stereochemical improper torsion pot: 1121 0 0 1.311 1.311 45.12437 1.000 5 Soft-sphere overlap restraints : 5729 0 0 0.003 0.003 7.582759 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.000000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.000000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.000000 1.000 9 Distance restraints 1 (CA-CA) : 7274 0 0 0.127 0.127 88.03117 1.000 10 Distance restraints 2 (N-O) : 7191 0 4 0.208 0.208 210.8186 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 13 Mainchain Omega dihedral restraints: 334 0 4 4.500 4.500 78.95935 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 2 78.523 78.523 67.08160 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 3 77.710 77.710 76.32609 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 0 62.796 62.796 42.32730 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 82.273 82.273 21.64214 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.000000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.000000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3338 0 0 0.370 0.370 83.07842 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.000000 1.000 25 Phi/Psi pair of dihedral restraints: 333 14 25 24.797 34.140 13.89549 1.000 26 Distance restraints 4 (SDCH-SDCH) : 988 0 3 0.720 0.720 86.61671 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.000000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.000000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.000000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990001 # Heavy relative violation of each residue is written to: TvLDH.V99990001 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 9189 29L 30Y C N 209 211 -116.65 -63.50 81.06 11.20 -63.50 81.06 11.20 1 30Y 30Y N CA 211 212 17.80 -43.40 -43.40 2 9255 95Q 96V C N 716 718 -101.36 -125.40 70.66 2.81 -62.40 125.45 14.07 2 96V 96V N CA 718 719 76.85 143.30 -42.40 3 9256 96V 97R C N 723 725 -176.78 -125.20 125.71 4.76 -63.00 130.37 23.76 3 97R 97R N CA 725 726 -104.76 140.60 -41.10 4 9260 100L 101I C N 755 757 2.78 -97.30 112.87 7.25 -120.60 135.20 7.29 4 101I 101I N CA 757 758 75.01 127.20 130.30 5 9314 154L 155S C N 1172 1174 -135.69 -64.10 87.46 8.16 -64.10 87.46 8.16 5 155S 155S N CA 1174 1175 15.25 -35.00 -35.00 6 9379 219D 220T C N 1688 1690 -122.92 -63.20 70.59 12.17 -63.20 70.59 12.17 6 220T 220T N CA 1690 1691 -79.72 -42.10 -42.10 7 9395 235H 236R C N 1830 1832 -112.58 -125.20 46.01 1.91 -63.00 146.12 17.03 7 236R 236R N CA 1832 1833 96.35 140.60 -41.10 8 9396 236R 237G C N 1841 1843 137.10 82.20 66.37 2.61 -62.40 160.98 28.23 8 237G 237G N CA 1843 1844 -28.79 8.50 -41.20 9 9397 237G 238F C N 1845 1847 61.75 58.10 13.87 0.82 -63.20 140.30 25.17 9 238F 238F N CA 1847 1848 19.52 32.90 -44.30 10 9401 241A 242A C N 1874 1876 -92.29 -62.50 32.82 6.67 -62.50 32.82 6.67 10 242A 242A N CA 1876 1877 -54.66 -40.90 -40.90 11 9422 262G 263E C N 2027 2029 62.33 54.60 25.87 1.45 -63.60 138.65 23.77 11 263E 263E N CA 2029 2030 17.71 42.40 -40.30 12 9432 272P 273E C N 2098 2100 -45.43 -69.30 35.57 1.99 -63.60 157.48 22.01 12 273E 273E N CA 2100 2101 116.13 142.50 -40.30 13 9452 292D 293K C N 2248 2250 66.38 56.60 49.35 2.86 -62.90 132.95 22.84 13 293K 293K N CA 2250 2251 -9.77 38.60 -40.80 14 9493 333Q 334G C N 2595 2597 66.47 78.70 28.36 0.42 82.20 149.84 8.06 14 334G 334G N CA 2597 2598 -140.51 -166.10 8.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 18 37 128 177 284 265 351 397 432 445 << end of ENERGY. TOP_________> 363 221 SET OUTPUT = OUTPUT2 TOP_________> 364 222 CALL ROUTINE = 'user_after_single_model' TOP_________> 365 228 RETURN TOP_________> 366 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990001 wrpdb2__568_> Residues, atoms, selected atoms: 335 2605 2605 TOP_________> 367 224 SET FINAL_MODEL = FILE TOP_________> 368 225 RETURN TOP_________> 369 195 END_DO TOP_________> 370 193 SET FINAL_MODEL = 'default' TOP_________> 371 194 CALL ROUTINE = 'single_model' TOP_________> 372 205 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 373 206 SET ID1 = 0 TOP_________> 374 207 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000002 TOP_________> 375 208 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 1 335 2605 rdatm___298_> Segment: 1 1 1 2605 iatmcls_286W> MODEL atom not classified: GLY:OT1 GLY iatmcls_286W> MODEL atom not classified: GLY:OT2 GLY TOP_________> 376 209 CALL ROUTINE = 'select_atoms' TOP_________> 377 267 PICK_ATOMS SELECTION_SEGMENT ='@:@' 'X:X', SELECTION_SEAR; CH ='segment', PICK_ATOMS_SET =1, RES_TYPES =; 'all', ATOM_TYPES ='all', SELECTION_FROM ='a; ll', SELECTION_STATUS ='initialize' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2605 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 378 268 RETURN TOP_________> 379 210 CALL ROUTINE = RAND_METHOD TOP_________> 380 251 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2605 2605 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 381 252 RETURN TOP_________> 382 211 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/sched.lib TOP_________> 383 212 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 384 213 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 385 214 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 386 215 CALL ROUTINE = 'single_model_pass' TOP_________> 387 231 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 388 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 389 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 14859 TOP_________> 390 234 OPTIMIZE TOP_________> 391 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 392 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 393 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 394 238 END_DO TOP_________> 395 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 396 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 16750 TOP_________> 397 234 OPTIMIZE TOP_________> 398 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 399 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 400 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 401 238 END_DO TOP_________> 402 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 403 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 17877 TOP_________> 404 234 OPTIMIZE TOP_________> 405 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 406 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 407 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 408 238 END_DO TOP_________> 409 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 410 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 19159 TOP_________> 411 234 OPTIMIZE TOP_________> 412 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 413 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 414 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 415 238 END_DO TOP_________> 416 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 417 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 20430 TOP_________> 418 234 OPTIMIZE TOP_________> 419 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 420 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 421 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 422 238 END_DO TOP_________> 423 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 424 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 22377 TOP_________> 425 234 OPTIMIZE TOP_________> 426 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 427 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 428 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 429 238 END_DO TOP_________> 430 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 431 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 24926 TOP_________> 432 234 OPTIMIZE TOP_________> 433 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 434 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 435 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 436 238 END_DO TOP_________> 437 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 438 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 25982 TOP_________> 439 234 OPTIMIZE TOP_________> 440 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 441 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 442 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 443 238 END_DO TOP_________> 444 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 445 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 27227 TOP_________> 446 234 OPTIMIZE TOP_________> 447 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 448 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 449 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 450 238 END_DO TOP_________> 451 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 452 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 28585 TOP_________> 453 234 OPTIMIZE TOP_________> 454 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 455 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 456 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 457 238 END_DO TOP_________> 458 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 459 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 460 234 OPTIMIZE TOP_________> 461 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 462 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 463 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 464 238 END_DO TOP_________> 465 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 466 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 467 234 OPTIMIZE TOP_________> 468 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 469 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 470 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 471 238 END_DO TOP_________> 472 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 473 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 474 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 475 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 476 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 477 285 CALL ROUTINE = MD_LEVEL TOP_________> 478 365 SET UPDATE_DYNAMIC = 0.39 TOP_________> 479 366 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 480 367 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 481 368 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 482 369 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 483 370 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 484 371 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 485 372 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 486 373 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 487 374 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 488 375 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 489 376 RETURN TOP_________> 490 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 491 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 492 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 493 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 494 307 RETURN TOP_________> 495 240 LABEL __ABORT TOP_________> 496 241 SET ERROR_STATUS = 0 TOP_________> 497 242 RETURN TOP_________> 498 216 END_DO TOP_________> 499 217 IUPAC_MODEL iupac_m_483_> CD1/2 CE1/2 swapped: 92.1483 30 30 iupac_m_485_> OD1/2 swapped: 101.7254 41 41 iupac_m_486_> OE1/2 swapped: 145.7228 57 57 iupac_m_485_> OD1/2 swapped: 161.8264 72 72 iupac_m_485_> OD1/2 swapped: 127.6598 81 81 iupac_m_487_> NH1/2 swapped: -175.8180 97 97 iupac_m_483_> CD1/2 CE1/2 swapped: -94.3646 108 108 iupac_m_486_> OE1/2 swapped: -177.1621 137 137 iupac_m_486_> OE1/2 swapped: -94.2385 149 149 iupac_m_487_> NH1/2 swapped: -172.0152 161 161 iupac_m_485_> OD1/2 swapped: 160.1882 210 210 iupac_m_485_> OD1/2 swapped: -113.1525 219 219 iupac_m_483_> CD1/2 CE1/2 swapped: -93.7560 222 222 iupac_m_487_> NH1/2 swapped: 177.9144 236 236 iupac_m_486_> OE1/2 swapped: 176.7119 263 263 iupac_m_483_> CD1/2 CE1/2 swapped: 95.1413 287 287 iupac_m_485_> OD1/2 swapped: -179.8468 292 292 iupac_m_486_> OE1/2 swapped: 138.9665 301 301 iupac_m_485_> OD1/2 swapped: 114.7684 314 314 iupac_m_486_> OE1/2 swapped: 146.9326 325 325 TOP_________> 500 218 SET ID1 = 9999 TOP_________> 501 219 SET OUTPUT2 = OUTPUT TOP_________> 502 220 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 2 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2605 2605 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 29227 29227 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5597 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 500 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 12 12 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1853.6068 Symmetry term within energy : 0.0000 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 2671 0 0 0.005 0.005 18.41045 1.000 2 Bond angle potential : 3625 0 11 2.069 2.069 308.2456 1.000 3 Stereochemical cosine torsion poten: 1743 0 50 47.593 47.593 592.2783 1.000 4 Stereochemical improper torsion pot: 1121 0 0 1.311 1.311 45.02674 1.000 5 Soft-sphere overlap restraints : 5597 0 0 0.003 0.003 5.573920 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.000000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.000000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.000000 1.000 9 Distance restraints 1 (CA-CA) : 7274 0 0 0.140 0.140 105.1844 1.000 10 Distance restraints 2 (N-O) : 7191 0 10 0.214 0.214 243.9395 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 13 Mainchain Omega dihedral restraints: 334 1 6 4.858 4.858 92.15704 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 4 75.951 75.951 77.48052 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 3 72.704 72.704 65.24216 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 1 58.798 58.798 51.60448 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 85.215 85.215 21.26917 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.000000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.000000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3338 0 0 0.368 0.368 88.15936 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.000000 1.000 25 Phi/Psi pair of dihedral restraints: 333 17 31 25.590 37.667 38.67799 1.000 26 Distance restraints 4 (SDCH-SDCH) : 988 0 0 0.773 0.773 100.3562 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.000000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.000000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.000000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990002 # Heavy relative violation of each residue is written to: TvLDH.V99990002 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 9765 272P 272P CA C 2094 2098 -153.39 -180.00 26.61 5.32 -180.00 26.61 5.32 ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 9191 31G 32D C N 225 227 -79.05 -96.50 48.37 2.04 -63.30 110.22 12.73 1 32D 32D N CA 227 228 69.09 114.20 -40.00 2 9255 95Q 96V C N 716 718 -105.20 -125.40 70.70 2.94 -62.40 125.47 13.97 2 96V 96V N CA 718 719 75.55 143.30 -42.40 3 9256 96V 97R C N 723 725 -173.51 -63.00 123.30 22.43 -63.00 123.30 22.43 3 97R 97R N CA 725 726 -95.79 -41.10 -41.10 4 9260 100L 101I C N 755 757 -6.91 -97.30 102.41 6.63 -120.60 124.71 6.71 4 101I 101I N CA 757 758 79.06 127.20 130.30 5 9314 154L 155S C N 1172 1174 -137.78 -64.10 93.80 8.38 -64.10 93.80 8.38 5 155S 155S N CA 1174 1175 23.06 -35.00 -35.00 6 9379 219D 220T C N 1688 1690 -122.31 -63.20 69.86 12.04 -63.20 69.86 12.04 6 220T 220T N CA 1690 1691 -79.33 -42.10 -42.10 7 9387 227H 228R C N 1757 1759 -107.71 -63.00 82.96 9.39 -63.00 82.96 9.39 7 228R 228R N CA 1759 1760 28.78 -41.10 -41.10 8 9395 235H 236R C N 1830 1832 -111.47 -125.20 49.87 2.07 -63.00 142.27 16.57 8 236R 236R N CA 1832 1833 92.66 140.60 -41.10 9 9396 236R 237G C N 1841 1843 139.08 82.20 68.34 2.72 -62.40 158.96 27.89 9 237G 237G N CA 1843 1844 -29.37 8.50 -41.20 10 9397 237G 238F C N 1845 1847 63.34 58.10 15.39 0.83 -63.20 141.24 25.31 10 238F 238F N CA 1847 1848 18.43 32.90 -44.30 11 9401 241A 242A C N 1874 1876 -92.33 -62.50 33.14 6.74 -62.50 33.14 6.74 11 242A 242A N CA 1876 1877 -55.33 -40.90 -40.90 12 9422 262G 263E C N 2027 2029 68.30 54.60 33.20 1.71 -63.60 141.94 24.23 12 263E 263E N CA 2029 2030 12.15 42.40 -40.30 13 9433 273E 274G C N 2107 2109 -83.03 -62.40 25.40 3.75 82.20 168.87 12.41 13 274G 274G N CA 2109 2110 -26.38 -41.20 8.50 14 9452 292D 293K C N 2248 2250 52.12 56.60 18.72 1.69 -62.90 130.30 22.76 14 293K 293K N CA 2250 2251 20.42 38.60 -40.80 15 9453 293K 294E C N 2257 2259 -137.27 -63.60 87.90 11.24 -63.60 87.90 11.24 15 294E 294E N CA 2259 2260 7.64 -40.30 -40.30 16 9461 301E 302G C N 2320 2322 -85.85 -62.40 26.11 4.07 82.20 172.35 12.73 16 302G 302G N CA 2322 2323 -29.72 -41.20 8.50 17 9493 333Q 334G C N 2595 2597 -75.18 -80.20 9.52 0.23 82.20 -137.33 6.96 17 334G 334G N CA 2597 2598 166.01 174.10 8.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 17 36 119 188 275 244 330 367 426 430 << end of ENERGY. TOP_________> 503 221 SET OUTPUT = OUTPUT2 TOP_________> 504 222 CALL ROUTINE = 'user_after_single_model' TOP_________> 505 228 RETURN TOP_________> 506 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990002 wrpdb2__568_> Residues, atoms, selected atoms: 335 2605 2605 TOP_________> 507 224 SET FINAL_MODEL = FILE TOP_________> 508 225 RETURN TOP_________> 509 195 END_DO TOP_________> 510 193 SET FINAL_MODEL = 'default' TOP_________> 511 194 CALL ROUTINE = 'single_model' TOP_________> 512 205 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 513 206 SET ID1 = 0 TOP_________> 514 207 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000003 TOP_________> 515 208 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 1 335 2605 rdatm___298_> Segment: 1 1 1 2605 iatmcls_286W> MODEL atom not classified: GLY:OT1 GLY iatmcls_286W> MODEL atom not classified: GLY:OT2 GLY TOP_________> 516 209 CALL ROUTINE = 'select_atoms' TOP_________> 517 267 PICK_ATOMS SELECTION_SEGMENT ='@:@' 'X:X', SELECTION_SEAR; CH ='segment', PICK_ATOMS_SET =1, RES_TYPES =; 'all', ATOM_TYPES ='all', SELECTION_FROM ='a; ll', SELECTION_STATUS ='initialize' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2605 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 518 268 RETURN TOP_________> 519 210 CALL ROUTINE = RAND_METHOD TOP_________> 520 251 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2605 2605 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 521 252 RETURN TOP_________> 522 211 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/sched.lib TOP_________> 523 212 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 524 213 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 525 214 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 526 215 CALL ROUTINE = 'single_model_pass' TOP_________> 527 231 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 528 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 529 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 14859 TOP_________> 530 234 OPTIMIZE TOP_________> 531 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 532 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 533 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 534 238 END_DO TOP_________> 535 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 536 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 16750 TOP_________> 537 234 OPTIMIZE TOP_________> 538 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 539 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 540 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 541 238 END_DO TOP_________> 542 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 543 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 17877 TOP_________> 544 234 OPTIMIZE TOP_________> 545 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 546 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 547 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 548 238 END_DO TOP_________> 549 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 550 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 19159 TOP_________> 551 234 OPTIMIZE TOP_________> 552 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 553 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 554 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 555 238 END_DO TOP_________> 556 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 557 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 20430 TOP_________> 558 234 OPTIMIZE TOP_________> 559 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 560 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 561 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 562 238 END_DO TOP_________> 563 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 564 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 22377 TOP_________> 565 234 OPTIMIZE TOP_________> 566 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 567 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 568 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 569 238 END_DO TOP_________> 570 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 571 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 24926 TOP_________> 572 234 OPTIMIZE TOP_________> 573 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 574 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 575 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 576 238 END_DO TOP_________> 577 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 578 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 25982 TOP_________> 579 234 OPTIMIZE TOP_________> 580 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 581 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 582 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 583 238 END_DO TOP_________> 584 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 585 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 27227 TOP_________> 586 234 OPTIMIZE TOP_________> 587 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 588 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 589 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 590 238 END_DO TOP_________> 591 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 592 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 28585 TOP_________> 593 234 OPTIMIZE TOP_________> 594 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 595 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 596 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 597 238 END_DO TOP_________> 598 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 599 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 600 234 OPTIMIZE TOP_________> 601 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 602 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 603 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 604 238 END_DO TOP_________> 605 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 606 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 607 234 OPTIMIZE TOP_________> 608 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 609 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 610 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 611 238 END_DO TOP_________> 612 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 613 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 614 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 615 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 616 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 617 285 CALL ROUTINE = MD_LEVEL TOP_________> 618 365 SET UPDATE_DYNAMIC = 0.39 TOP_________> 619 366 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 620 367 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 621 368 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 622 369 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 623 370 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 624 371 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 625 372 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 626 373 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 627 374 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 628 375 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 629 376 RETURN TOP_________> 630 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 631 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 632 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 633 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 634 307 RETURN TOP_________> 635 240 LABEL __ABORT TOP_________> 636 241 SET ERROR_STATUS = 0 TOP_________> 637 242 RETURN TOP_________> 638 216 END_DO TOP_________> 639 217 IUPAC_MODEL iupac_m_487_> NH1/2 swapped: 178.6027 33 33 iupac_m_485_> OD1/2 swapped: 96.3878 41 41 iupac_m_487_> NH1/2 swapped: 179.6891 48 48 iupac_m_486_> OE1/2 swapped: 102.5122 55 55 iupac_m_483_> CD1/2 CE1/2 swapped: 94.4835 67 67 iupac_m_485_> OD1/2 swapped: 130.9297 72 72 iupac_m_483_> CD1/2 CE1/2 swapped: 93.3223 77 77 iupac_m_485_> OD1/2 swapped: 160.9267 79 79 iupac_m_485_> OD1/2 swapped: -175.5080 81 81 iupac_m_483_> CD1/2 CE1/2 swapped: -92.7159 108 108 iupac_m_485_> OD1/2 swapped: 118.5200 132 132 iupac_m_487_> NH1/2 swapped: -172.3539 161 161 iupac_m_486_> OE1/2 swapped: 134.7549 165 165 iupac_m_485_> OD1/2 swapped: -174.3558 173 173 iupac_m_485_> OD1/2 swapped: 152.8440 176 176 iupac_m_485_> OD1/2 swapped: -125.9348 210 210 iupac_m_485_> OD1/2 swapped: 120.4297 213 213 iupac_m_485_> OD1/2 swapped: 163.7306 219 219 iupac_m_487_> NH1/2 swapped: 178.5997 236 236 iupac_m_483_> CD1/2 CE1/2 swapped: -91.2211 257 257 iupac_m_486_> OE1/2 swapped: -178.8844 273 273 iupac_m_483_> CD1/2 CE1/2 swapped: -90.5458 277 277 iupac_m_483_> CD1/2 CE1/2 swapped: 95.3663 287 287 iupac_m_485_> OD1/2 swapped: 167.4218 292 292 iupac_m_486_> OE1/2 swapped: 91.8401 294 294 TOP_________> 640 218 SET ID1 = 9999 TOP_________> 641 219 SET OUTPUT2 = OUTPUT TOP_________> 642 220 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 3 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2605 2605 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 29227 29227 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5590 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 500 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 12 12 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1825.8625 Symmetry term within energy : 0.0000 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 2671 0 0 0.005 0.005 20.42986 1.000 2 Bond angle potential : 3625 0 6 2.060 2.060 304.2665 1.000 3 Stereochemical cosine torsion poten: 1743 0 49 47.255 47.255 588.8020 1.000 4 Stereochemical improper torsion pot: 1121 0 0 1.307 1.307 44.42130 1.000 5 Soft-sphere overlap restraints : 5590 0 0 0.003 0.003 6.513250 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.000000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.000000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.000000 1.000 9 Distance restraints 1 (CA-CA) : 7274 0 0 0.136 0.136 105.2024 1.000 10 Distance restraints 2 (N-O) : 7191 0 1 0.210 0.210 221.4510 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 13 Mainchain Omega dihedral restraints: 334 0 3 4.571 4.571 81.48785 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 2 69.945 69.945 71.12194 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 0 80.837 80.837 81.31107 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 0 68.913 68.913 55.50817 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 85.066 85.066 25.49672 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.000000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.000000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3338 0 0 0.364 0.364 84.53208 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.000000 1.000 25 Phi/Psi pair of dihedral restraints: 333 18 28 25.450 38.402 26.68476 1.000 26 Distance restraints 4 (SDCH-SDCH) : 988 0 4 0.813 0.813 108.6331 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.000000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.000000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.000000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990003 # Heavy relative violation of each residue is written to: TvLDH.V99990003 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 9161 1M 2S C N 7 9 61.85 56.90 13.48 0.55 -136.60 -154.30 11.20 1 2S 2S N CA 9 10 23.86 36.40 151.20 2 9189 29L 30Y C N 209 211 -114.50 -63.50 79.68 11.00 -63.50 79.68 11.00 2 30Y 30Y N CA 211 212 17.82 -43.40 -43.40 3 9191 31G 32D C N 225 227 -85.11 -96.50 47.74 2.01 -63.30 110.02 12.41 3 32D 32D N CA 227 228 67.84 114.20 -40.00 4 9252 92K 93P C N 696 698 -64.92 -58.70 24.13 1.55 -64.50 154.38 11.54 4 93P 93P N CA 698 699 -7.18 -30.50 147.20 5 9253 93P 94G C N 703 705 -70.55 -62.40 32.68 4.55 82.20 153.82 10.92 5 94G 94G N CA 705 706 -9.55 -41.20 8.50 6 9255 95Q 96V C N 716 718 -98.01 -125.40 68.88 2.61 -62.40 127.57 14.44 6 96V 96V N CA 718 719 80.11 143.30 -42.40 7 9256 96V 97R C N 723 725 176.70 -125.20 124.38 4.51 -63.00 138.35 25.22 7 97R 97R N CA 725 726 -109.43 140.60 -41.10 8 9260 100L 101I C N 755 757 -6.62 -97.30 103.80 6.84 -120.60 125.96 6.70 8 101I 101I N CA 757 758 76.70 127.20 130.30 9 9314 154L 155S C N 1172 1174 -134.81 -64.10 88.17 8.05 -64.10 88.17 8.05 9 155S 155S N CA 1174 1175 17.66 -35.00 -35.00 10 9379 219D 220T C N 1688 1690 -119.83 -63.20 75.12 12.85 -63.20 75.12 12.85 10 220T 220T N CA 1690 1691 -91.45 -42.10 -42.10 11 9387 227H 228R C N 1757 1759 -112.04 -63.00 89.32 10.12 -63.00 89.32 10.12 11 228R 228R N CA 1759 1760 33.55 -41.10 -41.10 12 9397 237G 238F C N 1845 1847 69.96 58.10 21.86 1.16 -63.20 145.58 25.97 12 238F 238F N CA 1847 1848 14.54 32.90 -44.30 13 9401 241A 242A C N 1874 1876 -92.32 -62.50 32.53 6.60 -62.50 32.53 6.60 13 242A 242A N CA 1876 1877 -53.88 -40.90 -40.90 14 9421 261P 262G C N 2023 2025 -59.26 -62.40 6.32 0.86 -80.20 140.79 6.60 14 262G 262G N CA 2025 2026 -46.68 -41.20 174.10 15 9422 262G 263E C N 2027 2029 -107.60 -63.60 85.71 9.90 -63.60 85.71 9.90 15 263E 263E N CA 2029 2030 33.26 -40.30 -40.30 16 9432 272P 273E C N 2098 2100 -41.98 -69.30 38.58 2.15 -63.60 157.06 22.15 16 273E 273E N CA 2100 2101 115.26 142.50 -40.30 17 9452 292D 293K C N 2248 2250 68.44 56.60 53.40 3.02 -62.90 134.15 22.95 17 293K 293K N CA 2250 2251 -13.47 38.60 -40.80 18 9493 333Q 334G C N 2595 2597 -80.56 -80.20 7.57 0.28 82.20 -122.35 7.20 18 334G 334G N CA 2597 2598 -178.34 174.10 8.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 13 38 98 171 265 258 328 392 407 437 << end of ENERGY. TOP_________> 643 221 SET OUTPUT = OUTPUT2 TOP_________> 644 222 CALL ROUTINE = 'user_after_single_model' TOP_________> 645 228 RETURN TOP_________> 646 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990003 wrpdb2__568_> Residues, atoms, selected atoms: 335 2605 2605 TOP_________> 647 224 SET FINAL_MODEL = FILE TOP_________> 648 225 RETURN TOP_________> 649 195 END_DO TOP_________> 650 193 SET FINAL_MODEL = 'default' TOP_________> 651 194 CALL ROUTINE = 'single_model' TOP_________> 652 205 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 653 206 SET ID1 = 0 TOP_________> 654 207 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000004 TOP_________> 655 208 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 1 335 2605 rdatm___298_> Segment: 1 1 1 2605 iatmcls_286W> MODEL atom not classified: GLY:OT1 GLY iatmcls_286W> MODEL atom not classified: GLY:OT2 GLY TOP_________> 656 209 CALL ROUTINE = 'select_atoms' TOP_________> 657 267 PICK_ATOMS SELECTION_SEGMENT ='@:@' 'X:X', SELECTION_SEAR; CH ='segment', PICK_ATOMS_SET =1, RES_TYPES =; 'all', ATOM_TYPES ='all', SELECTION_FROM ='a; ll', SELECTION_STATUS ='initialize' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2605 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 658 268 RETURN TOP_________> 659 210 CALL ROUTINE = RAND_METHOD TOP_________> 660 251 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2605 2605 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 661 252 RETURN TOP_________> 662 211 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/sched.lib TOP_________> 663 212 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 664 213 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 665 214 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 666 215 CALL ROUTINE = 'single_model_pass' TOP_________> 667 231 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 668 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 669 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 14859 TOP_________> 670 234 OPTIMIZE TOP_________> 671 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 672 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 673 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 674 238 END_DO TOP_________> 675 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 676 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 16750 TOP_________> 677 234 OPTIMIZE TOP_________> 678 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 679 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 680 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 681 238 END_DO TOP_________> 682 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 683 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 17877 TOP_________> 684 234 OPTIMIZE TOP_________> 685 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 686 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 687 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 688 238 END_DO TOP_________> 689 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 690 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 19159 TOP_________> 691 234 OPTIMIZE TOP_________> 692 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 693 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 694 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 695 238 END_DO TOP_________> 696 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 697 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 20430 TOP_________> 698 234 OPTIMIZE TOP_________> 699 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 700 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 701 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 702 238 END_DO TOP_________> 703 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 704 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 22377 TOP_________> 705 234 OPTIMIZE TOP_________> 706 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 707 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 708 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 709 238 END_DO TOP_________> 710 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 711 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 24926 TOP_________> 712 234 OPTIMIZE TOP_________> 713 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 714 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 715 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 716 238 END_DO TOP_________> 717 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 718 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 25982 TOP_________> 719 234 OPTIMIZE TOP_________> 720 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 721 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 722 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 723 238 END_DO TOP_________> 724 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 725 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 27227 TOP_________> 726 234 OPTIMIZE TOP_________> 727 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 728 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 729 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 730 238 END_DO TOP_________> 731 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 732 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 28585 TOP_________> 733 234 OPTIMIZE TOP_________> 734 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 735 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 736 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 737 238 END_DO TOP_________> 738 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 739 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 740 234 OPTIMIZE TOP_________> 741 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 742 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 743 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 744 238 END_DO TOP_________> 745 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 746 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 747 234 OPTIMIZE TOP_________> 748 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 749 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 750 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 751 238 END_DO TOP_________> 752 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 753 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 754 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 755 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 756 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 757 285 CALL ROUTINE = MD_LEVEL TOP_________> 758 365 SET UPDATE_DYNAMIC = 0.39 TOP_________> 759 366 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 760 367 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 761 368 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 762 369 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 763 370 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 764 371 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 765 372 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 766 373 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 767 374 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 768 375 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 769 376 RETURN TOP_________> 770 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 771 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 772 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 773 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 774 307 RETURN TOP_________> 775 240 LABEL __ABORT TOP_________> 776 241 SET ERROR_STATUS = 0 TOP_________> 777 242 RETURN TOP_________> 778 216 END_DO TOP_________> 779 217 IUPAC_MODEL iupac_m_485_> OD1/2 swapped: 162.0859 32 32 iupac_m_487_> NH1/2 swapped: 179.8198 48 48 iupac_m_483_> CD1/2 CE1/2 swapped: 101.3970 67 67 iupac_m_487_> NH1/2 swapped: -178.0893 97 97 iupac_m_483_> CD1/2 CE1/2 swapped: -98.7903 108 108 iupac_m_486_> OE1/2 swapped: 95.8718 149 149 iupac_m_485_> OD1/2 swapped: 161.2126 173 173 iupac_m_485_> OD1/2 swapped: 145.8635 176 176 iupac_m_486_> OE1/2 swapped: 104.8088 188 188 iupac_m_486_> OE1/2 swapped: -172.7047 202 202 iupac_m_485_> OD1/2 swapped: -163.5500 210 210 iupac_m_483_> CD1/2 CE1/2 swapped: -93.6490 222 222 iupac_m_485_> OD1/2 swapped: -170.3745 231 231 iupac_m_487_> NH1/2 swapped: -177.8392 236 236 iupac_m_483_> CD1/2 CE1/2 swapped: 116.4077 238 238 iupac_m_486_> OE1/2 swapped: -176.2099 273 273 iupac_m_483_> CD1/2 CE1/2 swapped: 93.0141 287 287 iupac_m_485_> OD1/2 swapped: -175.9673 292 292 iupac_m_485_> OD1/2 swapped: 128.6028 314 314 iupac_m_486_> OE1/2 swapped: 100.6176 323 323 TOP_________> 780 218 SET ID1 = 9999 TOP_________> 781 219 SET OUTPUT2 = OUTPUT TOP_________> 782 220 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 4 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2605 2605 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 29227 29227 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5667 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 500 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 12 12 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1757.6575 Symmetry term within energy : 0.0000 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 2671 0 0 0.005 0.005 18.09789 1.000 2 Bond angle potential : 3625 0 8 2.049 2.049 302.3854 1.000 3 Stereochemical cosine torsion poten: 1743 0 52 47.093 47.093 584.3799 1.000 4 Stereochemical improper torsion pot: 1121 0 0 1.287 1.287 43.79860 1.000 5 Soft-sphere overlap restraints : 5667 0 0 0.003 0.003 4.763434 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.000000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.000000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.000000 1.000 9 Distance restraints 1 (CA-CA) : 7274 0 0 0.131 0.131 97.02684 1.000 10 Distance restraints 2 (N-O) : 7191 0 6 0.207 0.207 228.8852 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 13 Mainchain Omega dihedral restraints: 334 0 2 4.334 4.334 73.15299 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 4 72.974 72.974 66.10152 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 3 74.987 74.987 79.59485 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 1 74.548 74.548 57.68858 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 71.561 71.561 17.12919 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.000000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.000000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3338 0 0 0.381 0.381 80.93723 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.000000 1.000 25 Phi/Psi pair of dihedral restraints: 333 17 27 25.409 38.891 27.15884 1.000 26 Distance restraints 4 (SDCH-SDCH) : 988 0 1 0.701 0.701 76.55672 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.000000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.000000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.000000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990004 # Heavy relative violation of each residue is written to: TvLDH.V99990004 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 9191 31G 32D C N 225 227 -75.35 -96.50 51.59 2.17 -63.30 107.82 12.62 1 32D 32D N CA 227 228 67.15 114.20 -40.00 2 9252 92K 93P C N 696 698 -62.25 -58.70 23.67 1.68 -64.50 154.31 11.40 2 93P 93P N CA 698 699 -7.10 -30.50 147.20 3 9253 93P 94G C N 703 705 -71.38 -62.40 35.64 4.96 82.20 154.33 10.87 3 94G 94G N CA 705 706 -6.71 -41.20 8.50 4 9255 95Q 96V C N 716 718 -100.18 -125.40 68.40 2.66 -62.40 127.83 14.40 4 96V 96V N CA 718 719 79.72 143.30 -42.40 5 9256 96V 97R C N 723 725 176.63 -63.00 133.29 24.23 -63.00 133.29 24.23 5 97R 97R N CA 725 726 -98.35 -41.10 -41.10 6 9314 154L 155S C N 1172 1174 -134.80 -64.10 87.45 8.05 -64.10 87.45 8.05 6 155S 155S N CA 1174 1175 16.48 -35.00 -35.00 7 9379 219D 220T C N 1688 1690 -126.08 -63.20 71.48 12.30 -63.20 71.48 12.30 7 220T 220T N CA 1690 1691 -76.09 -42.10 -42.10 8 9387 227H 228R C N 1757 1759 -110.10 -63.00 84.38 9.57 -63.00 84.38 9.57 8 228R 228R N CA 1759 1760 28.91 -41.10 -41.10 9 9395 235H 236R C N 1830 1832 -108.47 -125.20 40.11 1.51 -63.00 152.19 17.97 9 236R 236R N CA 1832 1833 104.14 140.60 -41.10 10 9396 236R 237G C N 1841 1843 134.74 82.20 61.72 2.56 -62.40 163.77 28.50 10 237G 237G N CA 1843 1844 -23.88 8.50 -41.20 11 9397 237G 238F C N 1845 1847 65.65 58.10 22.48 1.22 -63.20 140.51 25.04 11 238F 238F N CA 1847 1848 11.73 32.90 -44.30 12 9401 241A 242A C N 1874 1876 -91.79 -62.50 33.16 6.74 -62.50 33.16 6.74 12 242A 242A N CA 1876 1877 -56.43 -40.90 -40.90 13 9421 261P 262G C N 2023 2025 -62.09 -62.40 2.81 0.41 -80.20 143.06 6.55 13 262G 262G N CA 2025 2026 -44.00 -41.20 174.10 14 9432 272P 273E C N 2098 2100 -44.23 -69.30 36.13 2.02 -63.60 157.98 22.15 14 273E 273E N CA 2100 2101 116.48 142.50 -40.30 15 9452 292D 293K C N 2248 2250 59.43 56.60 5.47 0.28 -62.90 143.34 25.01 15 293K 293K N CA 2250 2251 33.92 38.60 -40.80 16 9453 293K 294E C N 2257 2259 52.47 54.60 22.90 1.60 -63.60 156.86 26.73 16 294E 294E N CA 2259 2260 65.20 42.40 -40.30 17 9493 333Q 334G C N 2595 2597 179.34 -167.20 13.98 0.20 82.20 -164.31 13.84 17 334G 334G N CA 2597 2598 178.38 174.60 8.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 12 37 104 174 251 268 351 397 424 429 << end of ENERGY. TOP_________> 783 221 SET OUTPUT = OUTPUT2 TOP_________> 784 222 CALL ROUTINE = 'user_after_single_model' TOP_________> 785 228 RETURN TOP_________> 786 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990004 wrpdb2__568_> Residues, atoms, selected atoms: 335 2605 2605 TOP_________> 787 224 SET FINAL_MODEL = FILE TOP_________> 788 225 RETURN TOP_________> 789 195 END_DO TOP_________> 790 193 SET FINAL_MODEL = 'default' TOP_________> 791 194 CALL ROUTINE = 'single_model' TOP_________> 792 205 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 793 206 SET ID1 = 0 TOP_________> 794 207 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000005 TOP_________> 795 208 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 1 335 2605 rdatm___298_> Segment: 1 1 1 2605 iatmcls_286W> MODEL atom not classified: GLY:OT1 GLY iatmcls_286W> MODEL atom not classified: GLY:OT2 GLY TOP_________> 796 209 CALL ROUTINE = 'select_atoms' TOP_________> 797 267 PICK_ATOMS SELECTION_SEGMENT ='@:@' 'X:X', SELECTION_SEAR; CH ='segment', PICK_ATOMS_SET =1, RES_TYPES =; 'all', ATOM_TYPES ='all', SELECTION_FROM ='a; ll', SELECTION_STATUS ='initialize' Number of atoms to choose from, total : 2605 2605 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2605 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : GLY 335 TOP_________> 798 268 RETURN TOP_________> 799 210 CALL ROUTINE = RAND_METHOD TOP_________> 800 251 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2605 2605 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 801 252 RETURN TOP_________> 802 211 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6a}/modlib/sched.lib TOP_________> 803 212 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 804 213 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 805 214 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 806 215 CALL ROUTINE = 'single_model_pass' TOP_________> 807 231 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 808 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 809 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 14859 TOP_________> 810 234 OPTIMIZE TOP_________> 811 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 812 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 813 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 814 238 END_DO TOP_________> 815 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 816 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 16750 TOP_________> 817 234 OPTIMIZE TOP_________> 818 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 819 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 820 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 821 238 END_DO TOP_________> 822 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 823 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 17877 TOP_________> 824 234 OPTIMIZE TOP_________> 825 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 826 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 827 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 828 238 END_DO TOP_________> 829 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 830 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 19159 TOP_________> 831 234 OPTIMIZE TOP_________> 832 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 833 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 834 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 835 238 END_DO TOP_________> 836 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 837 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 20430 TOP_________> 838 234 OPTIMIZE TOP_________> 839 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 840 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 841 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 842 238 END_DO TOP_________> 843 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 844 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 22377 TOP_________> 845 234 OPTIMIZE TOP_________> 846 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 847 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 848 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 849 238 END_DO TOP_________> 850 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 851 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 24926 TOP_________> 852 234 OPTIMIZE TOP_________> 853 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 854 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 855 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 856 238 END_DO TOP_________> 857 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 858 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 25982 TOP_________> 859 234 OPTIMIZE TOP_________> 860 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 861 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 862 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 863 238 END_DO TOP_________> 864 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 865 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 27227 TOP_________> 866 234 OPTIMIZE TOP_________> 867 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 868 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 869 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 870 238 END_DO TOP_________> 871 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 872 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 28585 TOP_________> 873 234 OPTIMIZE TOP_________> 874 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 875 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 876 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 877 238 END_DO TOP_________> 878 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 879 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 880 234 OPTIMIZE TOP_________> 881 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 882 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 883 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 884 238 END_DO TOP_________> 885 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 886 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2605 29227 TOP_________> 887 234 OPTIMIZE TOP_________> 888 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 889 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 890 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 891 238 END_DO TOP_________> 892 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 893 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 894 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 895 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 896 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 897 285 CALL ROUTINE = MD_LEVEL TOP_________> 898 365 SET UPDATE_DYNAMIC = 0.39 TOP_________> 899 366 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 900 367 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 901 368 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 902 369 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 903 370 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 904 371 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 905 372 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 906 373 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 907 374 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 908 375 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 909 376 RETURN TOP_________> 910 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 911 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 912 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 913 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 914 307 RETURN TOP_________> 915 240 LABEL __ABORT TOP_________> 916 241 SET ERROR_STATUS = 0 TOP_________> 917 242 RETURN TOP_________> 918 216 END_DO TOP_________> 919 217 IUPAC_MODEL iupac_m_483_> CD1/2 CE1/2 swapped: 98.1288 30 30 iupac_m_487_> NH1/2 swapped: -172.1927 33 33 iupac_m_485_> OD1/2 swapped: 114.3236 41 41 iupac_m_487_> NH1/2 swapped: -179.6273 48 48 iupac_m_485_> OD1/2 swapped: 149.8032 58 58 iupac_m_485_> OD1/2 swapped: 156.0887 79 79 iupac_m_483_> CD1/2 CE1/2 swapped: -98.1536 108 108 iupac_m_486_> OE1/2 swapped: 112.2429 137 137 iupac_m_485_> OD1/2 swapped: -156.6725 173 173 iupac_m_486_> OE1/2 swapped: -92.5878 188 188 iupac_m_485_> OD1/2 swapped: -99.8316 213 213 iupac_m_485_> OD1/2 swapped: 143.6692 219 219 iupac_m_483_> CD1/2 CE1/2 swapped: -92.5033 222 222 iupac_m_487_> NH1/2 swapped: 178.2179 228 228 iupac_m_486_> OE1/2 swapped: 159.9938 234 234 iupac_m_487_> NH1/2 swapped: -178.7061 236 236 iupac_m_483_> CD1/2 CE1/2 swapped: 94.3319 287 287 iupac_m_486_> OE1/2 swapped: -169.4744 294 294 iupac_m_486_> OE1/2 swapped: -173.3567 301 301 iupac_m_485_> OD1/2 swapped: 160.9221 314 314 iupac_m_483_> CD1/2 CE1/2 swapped: 94.1306 315 315 iupac_m_486_> OE1/2 swapped: 105.3971 317 317 TOP_________> 920 218 SET ID1 = 9999 TOP_________> 921 219 SET OUTPUT2 = OUTPUT TOP_________> 922 220 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 5 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2605 2605 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 29227 29227 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5578 Dynamic pairs routine : 2, NATM x NATM cell sorting Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390 LENNARD_JONES_SWITCH : 6.500 7.500 COULOMB_JONES_SWITCH : 6.500 7.500 RESIDUE_SPAN_RANGE : 0 500 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 12 12 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1751.3380 Symmetry term within energy : 0.0000 Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 2671 0 0 0.005 0.005 19.42588 1.000 2 Bond angle potential : 3625 0 8 2.063 2.063 304.8411 1.000 3 Stereochemical cosine torsion poten: 1743 0 42 46.752 46.752 577.2202 1.000 4 Stereochemical improper torsion pot: 1121 0 0 1.311 1.311 44.90687 1.000 5 Soft-sphere overlap restraints : 5578 0 0 0.003 0.003 7.167367 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.000000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.000000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.000000 1.000 9 Distance restraints 1 (CA-CA) : 7274 0 0 0.134 0.134 93.46404 1.000 10 Distance restraints 2 (N-O) : 7191 0 6 0.219 0.219 231.2827 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.000000 1.000 13 Mainchain Omega dihedral restraints: 334 0 4 4.518 4.518 79.58681 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 3 68.325 68.325 69.31210 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 1 73.240 73.240 60.46600 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 1 76.720 76.720 57.21798 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 70.214 70.214 17.49544 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.000000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.000000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3338 0 0 0.361 0.361 82.57217 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.000000 1.000 25 Phi/Psi pair of dihedral restraints: 333 13 25 23.165 35.595 24.06074 1.000 26 Distance restraints 4 (SDCH-SDCH) : 988 0 2 0.727 0.727 82.31818 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.000000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.000000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.000000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.000000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.000000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990005 # Heavy relative violation of each residue is written to: TvLDH.V99990005 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 9161 1M 2S C N 7 9 -63.25 -64.10 8.66 0.68 -136.60 -167.86 7.93 1 2S 2S N CA 9 10 -26.39 -35.00 151.20 2 9191 31G 32D C N 225 227 -76.25 -96.50 48.16 2.03 -63.30 111.26 13.00 2 32D 32D N CA 227 228 70.50 114.20 -40.00 3 9260 100L 101I C N 755 757 -4.42 -97.30 106.48 7.04 -120.60 128.62 6.82 3 101I 101I N CA 757 758 75.12 127.20 130.30 4 9314 154L 155S C N 1172 1174 -136.64 -64.10 91.12 8.26 -64.10 91.12 8.26 4 155S 155S N CA 1174 1175 20.15 -35.00 -35.00 5 9362 202E 203G C N 1549 1551 175.79 82.20 94.73 5.76 -62.40 126.76 20.96 5 203G 203G N CA 1551 1552 -6.14 8.50 -41.20 6 9379 219D 220T C N 1688 1690 -119.63 -63.20 70.79 12.17 -63.20 70.79 12.17 6 220T 220T N CA 1690 1691 -84.84 -42.10 -42.10 7 9397 237G 238F C N 1845 1847 70.54 58.10 23.41 1.23 -63.20 145.53 25.92 7 238F 238F N CA 1847 1848 13.07 32.90 -44.30 8 9401 241A 242A C N 1874 1876 -91.71 -62.50 32.53 6.61 -62.50 32.53 6.61 8 242A 242A N CA 1876 1877 -55.21 -40.90 -40.90 9 9422 262G 263E C N 2027 2029 64.35 54.60 27.87 1.49 -63.60 139.90 23.96 9 263E 263E N CA 2029 2030 16.29 42.40 -40.30 10 9432 272P 273E C N 2098 2100 -42.41 -69.30 36.92 2.06 -63.60 158.93 22.38 10 273E 273E N CA 2100 2101 117.20 142.50 -40.30 11 9453 293K 294E C N 2257 2259 -95.44 -69.30 30.31 1.77 -63.60 164.97 23.79 11 294E 294E N CA 2259 2260 157.83 142.50 -40.30 12 9454 294E 295G C N 2266 2268 -54.62 -62.40 31.70 5.14 82.20 138.13 9.89 12 295G 295G N CA 2268 2269 -10.47 -41.20 8.50 13 9493 333Q 334G C N 2595 2597 -151.27 -167.20 20.33 0.72 82.20 -141.02 16.07 13 334G 334G N CA 2597 2598 -172.77 174.60 8.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 12 38 121 181 250 260 316 432 400 420 << end of ENERGY. TOP_________> 923 221 SET OUTPUT = OUTPUT2 TOP_________> 924 222 CALL ROUTINE = 'user_after_single_model' TOP_________> 925 228 RETURN TOP_________> 926 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990005 wrpdb2__568_> Residues, atoms, selected atoms: 335 2605 2605 TOP_________> 927 224 SET FINAL_MODEL = FILE TOP_________> 928 225 RETURN TOP_________> 929 195 END_DO TOP_________> 930 196 IF ARGUMENTS = DO_LOOPS 1, OPERATION = 'NE', THEN = 'GO_T; O NO_LOOPS' TOP_________> 931 202 RETURN TOP_________> 932 384 IF ARGUMENTS = FINAL_MALIGN3D 1, OPERATION = 'NE', ; THEN = 'GO_TO NO_MALIGN3D' TOP_________> 933 394 RETURN Dynamically allocated memory at finish [B,kB,MB]: 12559411 12265.050 11.978 Starting time : 2001/08/01 14:59:50.231 Closing time : 2001/08/01 15:35:20.997 Total CPU time [seconds] : 0.00