MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, 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, Linux sprite 2.4.20-8 i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/10/01 16:26:53.834 TOP_________> 105 705 SET ALNFILE = '1.ali' TOP_________> 106 706 SET KNOWNS = '1jji' TOP_________> 107 707 SET SEQUENCE = 'P23872' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL 1.ali rdpir___376W> Not enough fields in the second line of the sequence entry: sequence Actual fields, should be: 1 10 (Fields are separated by a colon, :) Dynamically allocated memory at amaxbnd [B,kB,MB]: 6884385 6723.032 6.565 openf5__224_> Open 11 OLD SEQUENTIAL 1.ali rdpir___376W> Not enough fields in the second line of the sequence entry: sequence Actual fields, should be: 1 10 (Fields are separated by a colon, :) Read the alignment from file : 1.ali Total number of alignment positions: 323 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1jji 311 1 1jji carboxylesterase 2 P23872 319 1 TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1jji.atm 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 ---------------------------------------------- 216 1 206 210 G L 8.730 END OF TABLE check_a_344_> << END OF COMMAND TOP_________> 122 108 CALL ROUTINE = GENERATE_METHOD TOP_________> 123 77 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 11 OLD SEQUENTIAL 1.ali Dynamically allocated memory at amaxseq [B,kB,MB]: 6610261 6455.333 6.304 openf5__224_> Open 11 OLD SEQUENTIAL 1.ali Read the alignment from file : 1.ali Total number of alignment positions: 311 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1jji 311 1 1jji carboxylesterase TOP_________> 124 78 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 11 OLD SEQUENTIAL 1.ali openf5__224_> Open 11 OLD SEQUENTIAL 1.ali Read the alignment from file : 1.ali Total number of alignment positions: 311 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1jji 311 1 1jji carboxylesterase TOP_________> 125 79 IF ARGUMENTS = INITIAL_MALIGN3D 0, OPERATION = 'EQ', THEN; = 'GO_TO NO_INITIAL_MALIGN3D' TOP_________> 126 82 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 6884385 6723.032 6.565 openf5__224_> Open 11 OLD SEQUENTIAL 1.ali rdpir___376W> Not enough fields in the second line of the sequence entry: sequence Actual fields, should be: 1 10 (Fields are separated by a colon, :) openf5__224_> Open 11 OLD SEQUENTIAL 1.ali rdpir___376W> Not enough fields in the second line of the sequence entry: sequence Actual fields, should be: 1 10 (Fields are separated by a colon, :) Read the alignment from file : 1.ali Total number of alignment positions: 323 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1jji 311 1 1jji carboxylesterase 2 P23872 319 1 TOP_________> 127 83 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL6v2}/modlib/models.lib TOP_________> 128 84 READ_PARAMETERS FILE = PARLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//par.lib Dynamically allocated memory at amattacns [B,kB,MB]: 6884781 6723.419 6.566 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 129 85 CALL ROUTINE = 'create_topology' TOP_________> 130 100 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 319 atom names : C +N atom indices : 2533 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 319 atom names : C CA +N O atom indices : 2533 2528 0 2534 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 319 2534 2600 0 0 1126 patch_______> segment topology patched using RTF: 1 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 1 319 2534 2600 3537 4175 1126 iatmcls_286W> MODEL atom not classified: LEU:OT1 LEU iatmcls_286W> MODEL atom not classified: LEU:OT2 LEU patch_______> segment topology patched using RTF: 319 ; LEU ; CTER segments residues atoms bonds angles dihedrals impropers: 1 319 2535 2601 3539 4177 1127 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 319 2535 2601 3539 4177 1127 TOP_________> 131 101 CALL ROUTINE = 'default_patches' TOP_________> 132 504 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 11 OLD SEQUENTIAL 1.ali rdpir___376W> Not enough fields in the second line of the sequence entry: sequence Actual fields, should be: 1 10 (Fields are separated by a colon, :) openf5__224_> Open 11 OLD SEQUENTIAL 1.ali rdpir___376W> Not enough fields in the second line of the sequence entry: sequence Actual fields, should be: 1 10 (Fields are separated by a colon, :) Read the alignment from file : 1.ali Total number of alignment positions: 323 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1jji 311 1 1jji carboxylesterase 2 P23872 319 1 TOP_________> 133 505 PATCH_SS_TEMPLATES TOP_________> 134 506 RETURN TOP_________> 135 102 CALL ROUTINE = 'special_patches' TOP_________> 136 501 RETURN TOP_________> 137 103 RETURN TOP_________> 138 86 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: 1908 627 TOP_________> 139 87 BUILD_MODEL INITIALIZE_XYZ = OFF TOP_________> 140 88 WRITE_MODEL FILE = MODEL openf5__224_> Open 14 UNKNOWN SEQUENTIAL P23872.ini wrpdb2__568_> Residues, atoms, selected atoms: 319 2535 2535 TOP_________> 141 89 RETURN TOP_________> 142 109 IF ARGUMENTS = EXIT_STAGE 2, OPERATION = 'EQ', THEN = 'RE; TURN' TOP_________> 143 110 IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'EQ', THE; N ='GO_TO __SKIP_RSRS' TOP_________> 144 111 CALL ROUTINE = 'mkhomcsr' TOP_________> 145 116 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS; = OFF Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 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 : 2601 3539 4011 1108 Total number of restraints before, now : 0 11259 make_re_422_> Number of previous, current restraints : 0 11259 make_re_423_> Number of previous, current selected restraints: 0 11259 TOP_________> 146 117 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 11 OLD SEQUENTIAL 1.ali rdpir___376W> Not enough fields in the second line of the sequence entry: sequence Actual fields, should be: 1 10 (Fields are separated by a colon, :) openf5__224_> Open 11 OLD SEQUENTIAL 1.ali rdpir___376W> Not enough fields in the second line of the sequence entry: sequence Actual fields, should be: 1 10 (Fields are separated by a colon, :) Read the alignment from file : 1.ali Total number of alignment positions: 323 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1jji 311 1 1jji carboxylesterase 2 P23872 319 1 TOP_________> 147 118 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/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: 1jji getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 11259 11576 make_re_423_> Number of previous, current selected restraints: 11259 11576 TOP_________> 148 119 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINT; S = 5 TOP_________> 149 120 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RE; STRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: omega_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/omega.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/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: 1jji getdata_289_> Proteins (all/accepted): 1 1 omgdel__425W> Unselected all O C +N +CA dihedrals: 337 make_re_422_> Number of previous, current restraints : 11576 11894 make_re_423_> Number of previous, current selected restraints: 11576 11557 TOP_________> 150 121 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: chi1_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/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: 1jji getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 11894 12160 make_re_423_> Number of previous, current selected restraints: 11557 11823 TOP_________> 151 122 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: chi2_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/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: 1jji getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 12160 12374 make_re_423_> Number of previous, current selected restraints: 11823 12037 TOP_________> 152 123 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: chi3_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/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: 1jji getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 12374 12465 make_re_423_> Number of previous, current selected restraints: 12037 12128 TOP_________> 153 124 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: chi4_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/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: 1jji getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 12465 12491 make_re_423_> Number of previous, current selected restraints: 12128 12154 TOP_________> 154 125 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINT; S = 5 TOP_________> 155 126 SET RES_TYPES = 'STD' TOP_________> 156 127 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE TOP_________> 157 128 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 158 129 SET RESTRAINT_GROUP = 9 TOP_________> 159 130 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 319 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 319 : LEU 319 TOP_________> 160 131 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 319 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 319 : LEU 319 TOP_________> 161 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 12491 19365 make_re_423_> Number of previous, current selected restraints: 12154 19028 TOP_________> 162 133 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DI; STANCE TOP_________> 163 134 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 164 135 SET RESTRAINT_GROUP = 10 TOP_________> 165 136 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 319 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 319 : LEU 319 TOP_________> 166 137 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 319 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 319 : LEU 319 TOP_________> 167 138 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19365 26230 make_re_423_> Number of previous, current selected restraints: 19028 25893 TOP_________> 168 139 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_; DISTANCE TOP_________> 169 140 SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = OFF TOP_________> 170 141 SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5 TOP_________> 171 142 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 1258 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 34 : THR 34 2 36 : THR --- 53 : ALA 18 3 55 : ALA --- 69 : TYR 15 4 71 : GLN --- 91 : HSD 21 5 95 : PHE --- 97 : LEU 3 6 99 : ASN --- 119 : ILE 21 7 121 : ILE --- 159 : ILE 39 8 161 : PHE --- 162 : ALA 2 9 164 : ASP --- 166 : ALA 3 10 168 : ALA --- 185 : CYS 18 11 187 : LYS --- 189 : ALA 3 12 191 : VAL --- 195 : TYR 5 13 197 : LEU --- 198 : TYR 2 14 200 : LEU --- 209 : LEU 10 15 212 : VAL --- 214 : ASP 3 16 216 : LEU --- 257 : ALA 42 17 259 : ALA --- 288 : PRO 30 18 290 : THR --- 310 : ASP 21 19 312 : ALA --- 319 : LEU 8 TOP_________> 172 143 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 1277 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 319 : LEU 319 TOP_________> 173 144 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 26230 28974 make_re_423_> Number of previous, current selected restraints: 25893 28637 TOP_________> 174 145 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_; DISTANCE TOP_________> 175 146 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 176 147 SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0 TOP_________> 177 148 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 1258 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 34 : THR 34 2 36 : THR --- 53 : ALA 18 3 55 : ALA --- 69 : TYR 15 4 71 : GLN --- 91 : HSD 21 5 95 : PHE --- 97 : LEU 3 6 99 : ASN --- 119 : ILE 21 7 121 : ILE --- 159 : ILE 39 8 161 : PHE --- 162 : ALA 2 9 164 : ASP --- 166 : ALA 3 10 168 : ALA --- 185 : CYS 18 11 187 : LYS --- 189 : ALA 3 12 191 : VAL --- 195 : TYR 5 13 197 : LEU --- 198 : TYR 2 14 200 : LEU --- 209 : LEU 10 15 212 : VAL --- 214 : ASP 3 16 216 : LEU --- 257 : ALA 42 17 259 : ALA --- 288 : PRO 30 18 290 : THR --- 310 : ASP 21 19 312 : ALA --- 319 : LEU 8 TOP_________> 178 149 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 1258 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 34 : THR 34 2 36 : THR --- 53 : ALA 18 3 55 : ALA --- 69 : TYR 15 4 71 : GLN --- 91 : HSD 21 5 95 : PHE --- 97 : LEU 3 6 99 : ASN --- 119 : ILE 21 7 121 : ILE --- 159 : ILE 39 8 161 : PHE --- 162 : ALA 2 9 164 : ASP --- 166 : ALA 3 10 168 : ALA --- 185 : CYS 18 11 187 : LYS --- 189 : ALA 3 12 191 : VAL --- 195 : TYR 5 13 197 : LEU --- 198 : TYR 2 14 200 : LEU --- 209 : LEU 10 15 212 : VAL --- 214 : ASP 3 16 216 : LEU --- 257 : ALA 42 17 259 : ALA --- 288 : PRO 30 18 290 : THR --- 310 : ASP 21 19 312 : ALA --- 319 : LEU 8 TOP_________> 179 150 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 28974 29754 make_re_423_> Number of previous, current selected restraints: 28637 29417 TOP_________> 180 151 CALL ROUTINE = 'hetatm_restraints' TOP_________> 181 160 SET RESTRAINT_TYPE = 'distance' TOP_________> 182 161 SET DISTANCE_RSR_MODEL = 7 TOP_________> 183 162 SET MAXIMAL_DISTANCE = 7.0 TOP_________> 184 163 SET ADD_RESTRAINTS = ON TOP_________> 185 164 SET RESTRAINT_GROUP = 27 TOP_________> 186 165 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 187 166 SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 188 167 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 2535 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 319 : LEU 319 TOP_________> 189 168 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: 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_________> 190 169 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 29754 29754 make_re_423_> Number of previous, current selected restraints: 29417 29417 TOP_________> 191 170 RETURN TOP_________> 192 152 CALL ROUTINE = 'blk_restraints' TOP_________> 193 173 SET RESTRAINT_TYPE = 'distance' TOP_________> 194 174 SET DISTANCE_RSR_MODEL = 7 TOP_________> 195 175 SET MAXIMAL_DISTANCE = 10.0 TOP_________> 196 176 SET ADD_RESTRAINTS = ON TOP_________> 197 177 SET RESTRAINT_GROUP = 27 TOP_________> 198 178 SET RESTRAINT_STDEV = 0.05 0.0 TOP_________> 199 179 SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = ON TOP_________> 200 180 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: 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_________> 201 181 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: 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_________> 202 182 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 29754 29754 make_re_423_> Number of previous, current selected restraints: 29417 29417 TOP_________> 203 183 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 204 184 SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 205 185 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 319 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 319 : LEU 319 TOP_________> 206 186 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'BLK' Number of atoms to choose from, total : 2535 2535 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) : 1 319 1: 319: 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_________> 207 187 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 18099453 17675.250 17.261 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 29754 29754 make_re_423_> Number of previous, current selected restraints: 29417 29417 TOP_________> 208 188 DELETE_ALIGNMENT TOP_________> 209 189 RETURN Dynamically allocated memory at amaxseq [B,kB,MB]: 17825329 17407.550 17.000 TOP_________> 210 153 CALL ROUTINE = 'special_restraints' TOP_________> 211 498 RETURN TOP_________> 212 154 CONDENSE_RESTRAINTS delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 29754 27457 TOP_________> 213 155 WRITE_RESTRAINTS FILE = CSRFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL P23872.rsr TOP_________> 214 156 SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = O; N TOP_________> 215 157 RETURN TOP_________> 216 112 LABEL __SKIP_RSRS TOP_________> 217 113 RETURN TOP_________> 218 401 IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'GE', THEN = 'RE; TURN' TOP_________> 219 402 CALL ROUTINE = 'rd_restraints' TOP_________> 220 255 READ_RESTRAINTS FILE = CSRFILE, ADD_RESTRAINTS = 'off' openf5__224_> Open 11 OLD SEQUENTIAL P23872.rsr openf5__224_> Open 11 OLD SEQUENTIAL P23872.rsr rdcsr2__307_> Number of restraints read : 0 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 Dynamically allocated memory at amprmcns [B,kB,MB]: 17825329 17407.550 17.000 openf5__224_> Open 11 OLD SEQUENTIAL P23872.rsr openf5__224_> Open 11 OLD SEQUENTIAL P23872.rsr rdcsr2__307_> Number of restraints read : 0 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 27457 27457 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 TOP_________> 221 256 RETURN TOP_________> 222 403 CALL ROUTINE = 'multiple_models' TOP_________> 223 192 DO ID2 = STARTING_MODEL ENDING_MODEL 1 TOP_________> 224 193 SET FINAL_MODEL = 'default' TOP_________> 225 194 CALL ROUTINE = 'single_model' TOP_________> 226 205 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 227 206 SET ID1 = 0 TOP_________> 228 207 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL P23872.D00000001 TOP_________> 229 208 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL P23872.ini openf5__224_> Open 11 OLD SEQUENTIAL P23872.ini rdatm___297_> Segments, residues, atoms: 1 319 2535 rdatm___298_> Segment: 1 1 1 2535 iatmcls_286W> MODEL atom not classified: LEU:OT1 LEU iatmcls_286W> MODEL atom not classified: LEU:OT2 LEU TOP_________> 230 209 CALL ROUTINE = 'select_atoms' TOP_________> 231 267 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 : 2535 2535 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) : 1 319 1: 319: selatm__462_> Number of selected atoms : 2535 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 319 : LEU 319 TOP_________> 232 268 RETURN TOP_________> 233 210 CALL ROUTINE = RAND_METHOD TOP_________> 234 251 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2535 2535 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 235 252 RETURN TOP_________> 236 211 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib/sched.lib TOP_________> 237 212 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL P23872.sch TOP_________> 238 213 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 239 214 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 240 215 CALL ROUTINE = 'single_model_pass' TOP_________> 241 231 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 242 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 243 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 13888 TOP_________> 244 234 OPTIMIZE Dynamically allocated memory at ampairs [B,kB,MB]: 18179207 17753.132 17.337 TOP_________> 245 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 246 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 247 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 248 238 END_DO TOP_________> 249 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 250 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 15565 TOP_________> 251 234 OPTIMIZE TOP_________> 252 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 253 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 254 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 255 238 END_DO TOP_________> 256 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 257 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 16612 TOP_________> 258 234 OPTIMIZE TOP_________> 259 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 260 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 261 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 262 238 END_DO TOP_________> 263 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 264 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 17848 TOP_________> 265 234 OPTIMIZE TOP_________> 266 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 267 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 268 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 269 238 END_DO TOP_________> 270 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 271 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 19007 TOP_________> 272 234 OPTIMIZE TOP_________> 273 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 274 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 275 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 276 238 END_DO TOP_________> 277 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 278 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 20369 TOP_________> 279 234 OPTIMIZE TOP_________> 280 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 281 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 282 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 283 238 END_DO TOP_________> 284 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 285 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 22173 TOP_________> 286 234 OPTIMIZE TOP_________> 287 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 288 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 289 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 290 238 END_DO TOP_________> 291 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 292 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 24995 TOP_________> 293 234 OPTIMIZE TOP_________> 294 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 295 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 296 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 297 238 END_DO TOP_________> 298 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 299 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 26059 TOP_________> 300 234 OPTIMIZE TOP_________> 301 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 302 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 303 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 304 238 END_DO TOP_________> 305 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 306 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 26817 TOP_________> 307 234 OPTIMIZE TOP_________> 308 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 309 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 310 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 311 238 END_DO TOP_________> 312 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 313 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 27457 TOP_________> 314 234 OPTIMIZE TOP_________> 315 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 316 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 317 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 318 238 END_DO TOP_________> 319 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 320 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2535 27457 TOP_________> 321 234 OPTIMIZE TOP_________> 322 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 323 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 324 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 325 238 END_DO TOP_________> 326 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 327 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 328 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 329 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 330 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 331 285 CALL ROUTINE = MD_LEVEL TOP_________> 332 310 SET UPDATE_DYNAMIC = 0.39 TOP_________> 333 311 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 334 312 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 335 313 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 336 314 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 337 315 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 338 316 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 339 317 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 340 318 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 341 319 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 342 320 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 343 321 RETURN TOP_________> 344 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 345 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 346 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 347 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 348 307 RETURN TOP_________> 349 240 LABEL __ABORT TOP_________> 350 241 SET ERROR_STATUS = 0 TOP_________> 351 242 RETURN TOP_________> 352 216 END_DO TOP_________> 353 217 IUPAC_MODEL iupac_m_486_> OE1/2 swapped: -90.7040 16 16 iupac_m_485_> OD1/2 swapped: 154.9859 27 27 iupac_m_487_> NH1/2 swapped: 179.5240 41 41 iupac_m_487_> NH1/2 swapped: -179.5590 49 49 iupac_m_483_> CD1/2 CE1/2 swapped: -90.0540 50 50 iupac_m_486_> OE1/2 swapped: -93.9526 57 57 iupac_m_483_> CD1/2 CE1/2 swapped: 93.9997 69 69 iupac_m_485_> OD1/2 swapped: -179.4443 101 101 iupac_m_485_> OD1/2 swapped: 117.7212 104 104 iupac_m_487_> NH1/2 swapped: -178.2195 105 105 iupac_m_487_> NH1/2 swapped: 179.4968 108 108 iupac_m_487_> NH1/2 swapped: -178.8155 130 130 iupac_m_483_> CD1/2 CE1/2 swapped: -90.7069 152 152 iupac_m_487_> NH1/2 swapped: 171.1027 158 158 iupac_m_483_> CD1/2 CE1/2 swapped: 108.3700 161 161 iupac_m_487_> NH1/2 swapped: 178.8920 179 179 iupac_m_485_> OD1/2 swapped: 179.2239 180 180 iupac_m_485_> OD1/2 swapped: 126.8204 184 184 iupac_m_487_> NH1/2 swapped: 175.0220 201 201 iupac_m_485_> OD1/2 swapped: -154.7956 202 202 iupac_m_487_> NH1/2 swapped: 179.1858 207 207 iupac_m_485_> OD1/2 swapped: 175.4933 214 214 iupac_m_486_> OE1/2 swapped: 100.3633 225 225 iupac_m_486_> OE1/2 swapped: -169.5908 226 226 iupac_m_485_> OD1/2 swapped: 157.3650 232 232 iupac_m_486_> OE1/2 swapped: -141.6882 250 250 iupac_m_486_> OE1/2 swapped: 177.9400 260 260 iupac_m_486_> OE1/2 swapped: 96.5436 283 283 iupac_m_483_> CD1/2 CE1/2 swapped: 90.5251 284 284 iupac_m_486_> OE1/2 swapped: 156.7965 306 306 iupac_m_487_> NH1/2 swapped: -178.1033 309 309 TOP_________> 354 218 SET ID1 = 9999 TOP_________> 355 219 SET OUTPUT2 = OUTPUT TOP_________> 356 220 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 : 319 Number of all, selected real atoms : 2535 2535 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 27457 27457 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 5981 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 : 1737.5060 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 : 2601 0 0 0.005 0.005 19.357 1.000 2 Bond angle potential : 3539 0 6 2.066 2.066 292.88 1.000 3 Stereochemical cosine torsion poten: 1714 0 58 46.862 46.862 564.89 1.000 4 Stereochemical improper torsion pot: 1108 0 0 1.249 1.249 35.437 1.000 5 Soft-sphere overlap restraints : 5981 0 0 0.003 0.003 5.9640 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.00000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.00000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.00000 1.000 9 Distance restraints 1 (CA-CA) : 6874 0 2 0.269 0.269 161.17 1.000 10 Distance restraints 2 (N-O) : 6865 0 0 0.352 0.352 214.57 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.00000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.00000 1.000 13 Mainchain Omega dihedral restraints: 318 0 6 4.486 4.486 73.813 1.000 14 Sidechain Chi_1 dihedral restraints: 266 0 1 77.399 77.399 77.033 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 0 73.407 73.407 81.947 1.000 16 Sidechain Chi_3 dihedral restraints: 91 0 0 79.762 79.762 55.465 1.000 17 Sidechain Chi_4 dihedral restraints: 26 0 0 103.819 103.819 19.855 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.00000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.00000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 2744 0 0 0.358 0.358 35.012 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.00000 1.000 25 Phi/Psi pair of dihedral restraints: 317 23 39 29.199 48.243 58.949 1.000 26 Distance restraints 4 (SDCH-SDCH) : 780 0 0 0.737 0.737 41.161 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.00000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.00000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.00000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.00000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.00000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL P23872.V99990001 # Heavy relative violation of each residue is written to: P23872.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 8963 1M 2K C N 7 9 -66.43 -70.20 4.23 0.27 -62.90 179.32 23.10 1 2K 2K N CA 9 10 138.49 140.40 -40.80 2 8965 3P 4E C N 23 25 63.15 -69.30 132.72 10.35 -63.60 -149.08 24.49 2 4E 4E N CA 25 26 151.11 142.50 -40.30 3 8969 7L 8P C N 57 59 -68.02 -58.70 49.46 3.39 -64.50 129.18 9.83 3 8P 8P N CA 59 60 18.07 -30.50 147.20 4 8989 27D 28L C N 208 210 -69.73 -70.70 46.76 3.51 -63.50 136.19 18.56 4 28L 28L N CA 210 211 94.85 141.60 -41.20 5 8990 28L 29P C N 216 218 -49.47 -64.50 35.23 2.06 -58.70 146.12 12.83 5 29P 29P N CA 218 219 115.33 147.20 -30.50 6 9020 58M 59A C N 466 468 -49.87 -68.20 35.22 2.27 -62.50 156.63 26.31 6 59A 59A N CA 468 469 115.23 145.30 -40.90 7 9046 84P 85A C N 672 674 2.85 -68.20 104.21 6.56 -62.50 127.92 24.45 7 85A 85A N CA 674 675 69.07 145.30 -40.90 8 9126 164D 165S C N 1300 1302 72.86 56.90 161.82 9.00 -64.10 163.68 15.66 8 165S 165S N CA 1302 1303 -124.63 36.40 -35.00 9 9142 180D 181K C N 1414 1416 -41.65 -118.00 77.84 3.21 -62.90 166.29 20.52 9 181K 181K N CA 1416 1417 154.27 139.10 -40.80 10 9145 183I 184D C N 1440 1442 -61.28 -70.90 15.17 0.56 54.50 151.47 10.19 10 184D 184D N CA 1442 1443 138.57 150.30 40.90 11 9147 185C 186G C N 1454 1456 118.28 82.20 36.88 2.16 -62.40 -175.82 30.93 11 186G 186G N CA 1456 1457 0.84 8.50 -41.20 12 9164 202D 203S C N 1587 1589 -82.79 -72.40 19.08 0.87 -64.10 157.71 12.63 12 203S 203S N CA 1589 1590 168.40 152.40 -35.00 13 9166 204V 205T C N 1600 1602 -25.79 -124.80 99.19 5.10 -63.20 -176.56 26.02 13 205T 205T N CA 1602 1603 137.48 143.50 -42.10 14 9172 210G 211G C N 1649 1651 -63.24 -62.40 5.65 0.89 82.20 155.60 11.91 14 211G 211G N CA 1651 1652 -46.79 -41.20 8.50 15 9173 211G 212V C N 1653 1655 -99.15 -125.40 82.79 3.36 -62.40 113.31 12.66 15 212V 212V N CA 1655 1656 64.78 143.30 -42.40 16 9176 214D 215G C N 1682 1684 74.70 78.70 38.03 0.92 82.20 136.99 7.03 16 215G 215G N CA 1684 1685 -128.28 -166.10 8.50 17 9203 241C 242L C N 1905 1907 -27.55 -70.70 68.85 4.29 -63.50 134.06 20.82 17 242L 242L N CA 1907 1908 87.94 141.60 -41.20 18 9204 242L 243F C N 1913 1915 -24.23 -124.20 122.25 3.17 -63.20 123.56 19.74 18 243F 243F N CA 1915 1916 72.95 143.30 -44.30 19 9209 247L 248T C N 1956 1958 -115.31 -63.20 79.62 8.56 -63.20 79.62 8.56 19 248T 248T N CA 1958 1959 18.09 -42.10 -42.10 20 9211 249R 250E C N 1974 1976 57.20 54.60 10.74 0.64 -63.60 140.77 24.22 20 250E 250E N CA 1976 1977 31.97 42.40 -40.30 21 9239 277A 278H C N 2189 2191 -86.23 -63.20 77.54 8.52 -63.20 77.54 8.52 21 278H 278H N CA 2191 2192 31.73 -42.30 -42.30 22 9258 296H 297Y C N 2349 2351 -97.55 -98.40 77.92 8.29 -63.50 99.87 14.30 22 297Y 297Y N CA 2351 2352 50.49 128.40 -43.40 23 9279 317A 318Q C N 2516 2518 58.08 55.10 3.75 0.49 -63.80 147.39 26.77 23 318Q 318Q N CA 2518 2519 42.58 40.30 -40.30 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 24 35 142 238 298 244 330 426 442 435 << end of ENERGY. TOP_________> 357 221 SET OUTPUT = OUTPUT2 TOP_________> 358 222 CALL ROUTINE = 'user_after_single_model' TOP_________> 359 228 RETURN TOP_________> 360 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL P23872.B99990001 wrpdb2__568_> Residues, atoms, selected atoms: 319 2535 2535 TOP_________> 361 224 SET FINAL_MODEL = FILE TOP_________> 362 225 RETURN TOP_________> 363 195 END_DO TOP_________> 364 196 IF ARGUMENTS = DO_LOOPS 1, OPERATION = 'NE', THEN = 'GO_T; O NO_LOOPS' TOP_________> 365 202 RETURN TOP_________> 366 404 IF ARGUMENTS =FINAL_MALIGN3D 1, OPERATION ='NE', THEN ='G; O_TO NO_MALIGN3D' TOP_________> 367 411 RETURN Dynamically allocated memory at finish [B,kB,MB]: 18179207 17753.132 17.337 Starting time : 2003/10/01 16:26:53.834 Closing time : 2003/10/01 16:29:14.085 Total CPU time [seconds] : 122.85