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): 2003/10/02 14:37:39.140 TOP_________> 105 705 SET ALNFILE = '1b9k_34.ali' TOP_________> 106 706 SET KNOWNS = '1B9K' TOP_________> 107 707 SET SEQUENCE = '3310' 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 1b9k_34.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 6006229 5865.458 5.728 openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali Read the alignment from file : 1b9k_34.ali Total number of alignment positions: 263 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1B9K 237 1 1B9K 2 3310 251 1 3310 TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1B9K.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 ---------------------------------------------- 203 1 881 889 D S 10.187 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 1b9k_34.ali Dynamically allocated memory at amaxseq [B,kB,MB]: 5778587 5643.151 5.511 openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali Read the alignment from file : 1b9k_34.ali Total number of alignment positions: 237 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1B9K 237 1 1B9K TOP_________> 124 78 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali Read the alignment from file : 1b9k_34.ali Total number of alignment positions: 237 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1B9K 237 1 1B9K 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]: 6006229 5865.458 5.728 openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali Read the alignment from file : 1b9k_34.ali Total number of alignment positions: 263 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1B9K 237 1 1B9K 2 3310 251 1 3310 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]: 6006625 5865.845 5.728 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: 2 251 atom names : C +N atom indices : 1914 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 2 251 atom names : C CA +N O atom indices : 1914 1911 0 1915 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 251 1915 1947 0 0 791 patch_______> segment topology patched using RTF: 1 ; GLY ; GLYP segments residues atoms bonds angles dihedrals impropers: 1 251 1915 1947 2629 3099 791 iatmcls_286W> MODEL atom not classified: CYS:OT1 CYS iatmcls_286W> MODEL atom not classified: CYS:OT2 CYS patch_______> segment topology patched using RTF: 251 ; CYS ; CTER segments residues atoms bonds angles dihedrals impropers: 1 251 1916 1948 2631 3101 792 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 251 1916 1948 2631 3101 792 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 1b9k_34.ali openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali Read the alignment from file : 1b9k_34.ali Total number of alignment positions: 263 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1B9K 237 1 1B9K 2 3310 251 1 3310 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: 1305 611 TOP_________> 139 87 BUILD_MODEL INITIALIZE_XYZ = OFF TOP_________> 140 88 WRITE_MODEL FILE = MODEL openf5__224_> Open 14 UNKNOWN SEQUENTIAL 3310.ini wrpdb2__568_> Residues, atoms, selected atoms: 251 1916 1916 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]: 15288817 14930.490 14.581 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 : 1948 2631 2943 782 Total number of restraints before, now : 0 8304 make_re_422_> Number of previous, current restraints : 0 8304 make_re_423_> Number of previous, current selected restraints: 0 8304 TOP_________> 146 117 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali openf5__224_> Open 11 OLD SEQUENTIAL 1b9k_34.ali Read the alignment from file : 1b9k_34.ali Total number of alignment positions: 263 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1B9K 237 1 1B9K 2 3310 251 1 3310 TOP_________> 147 118 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 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. errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 1 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 5 178 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 1 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 6 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 70 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 137 GLN errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 178 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 1 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 6 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 70 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 137 GLN errdih__638_> Missing atoms in a dihedral, residue index, residue type: 7 178 GLU errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 6 ARG errdih__638_> Missing atoms in a dihedral, residue index, residue type: 8 70 LYS getdata_643_> Protein accepted: 1B9K getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 8304 8553 make_re_423_> Number of previous, current selected restraints: 8304 8553 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]: 15288817 14930.490 14.581 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: 1B9K getdata_289_> Proteins (all/accepted): 1 1 omgdel__425W> Unselected all O C +N +CA dihedrals: 260 make_re_422_> Number of previous, current restraints : 8553 8803 make_re_423_> Number of previous, current selected restraints: 8553 8543 TOP_________> 150 121 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 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: 1B9K getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 8803 9025 make_re_423_> Number of previous, current selected restraints: 8543 8765 TOP_________> 151 122 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 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: 1B9K getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 9025 9175 make_re_423_> Number of previous, current selected restraints: 8765 8915 TOP_________> 152 123 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 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: 1B9K getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 9175 9243 make_re_423_> Number of previous, current selected restraints: 8915 8983 TOP_________> 153 124 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 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: 1B9K getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 9243 9265 make_re_423_> Number of previous, current selected restraints: 8983 9005 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 : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 251 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : GLY --- 251 : CYS 251 TOP_________> 160 131 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 251 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : GLY --- 251 : CYS 251 TOP_________> 161 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 9265 13450 make_re_423_> Number of previous, current selected restraints: 9005 13190 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 : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 251 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : GLY --- 251 : CYS 251 TOP_________> 166 137 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' Number of atoms to choose from, total : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 251 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : GLY --- 251 : CYS 251 TOP_________> 167 138 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 13450 17778 make_re_423_> Number of previous, current selected restraints: 13190 17518 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 : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 911 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 2 : GLU --- 6 : ASN 5 2 8 : ALA --- 36 : ARG 29 3 38 : SER --- 60 : LYS 23 4 62 : MET --- 78 : GLN 17 5 80 : SER --- 84 : ASP 5 6 86 : VAL --- 94 : PRO 9 7 96 : VAL --- 116 : LYS 21 8 118 : THR --- 127 : GLU 10 9 129 : ALA --- 162 : SER 34 10 164 : ASP --- 173 : ASP 10 11 175 : ILE --- 210 : GLN 36 12 212 : HSD --- 220 : LYS 9 13 222 : GLU --- 228 : ASP 7 14 230 : LYS --- 251 : CYS 22 TOP_________> 172 143 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' Number of atoms to choose from, total : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 1005 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : GLY --- 251 : CYS 251 TOP_________> 173 144 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 17778 19542 make_re_423_> Number of previous, current selected restraints: 17518 19282 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 : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 911 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 2 : GLU --- 6 : ASN 5 2 8 : ALA --- 36 : ARG 29 3 38 : SER --- 60 : LYS 23 4 62 : MET --- 78 : GLN 17 5 80 : SER --- 84 : ASP 5 6 86 : VAL --- 94 : PRO 9 7 96 : VAL --- 116 : LYS 21 8 118 : THR --- 127 : GLU 10 9 129 : ALA --- 162 : SER 34 10 164 : ASP --- 173 : ASP 10 11 175 : ILE --- 210 : GLN 36 12 212 : HSD --- 220 : LYS 9 13 222 : GLU --- 228 : ASP 7 14 230 : LYS --- 251 : CYS 22 TOP_________> 178 149 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 911 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 2 : GLU --- 6 : ASN 5 2 8 : ALA --- 36 : ARG 29 3 38 : SER --- 60 : LYS 23 4 62 : MET --- 78 : GLN 17 5 80 : SER --- 84 : ASP 5 6 86 : VAL --- 94 : PRO 9 7 96 : VAL --- 116 : LYS 21 8 118 : THR --- 127 : GLU 10 9 129 : ALA --- 162 : SER 34 10 164 : ASP --- 173 : ASP 10 11 175 : ILE --- 210 : GLN 36 12 212 : HSD --- 220 : LYS 9 13 222 : GLU --- 228 : ASP 7 14 230 : LYS --- 251 : CYS 22 TOP_________> 179 150 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 15288817 14930.490 14.581 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19542 19796 make_re_423_> Number of previous, current selected restraints: 19282 19536 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 : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 1916 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : GLY --- 251 : CYS 251 TOP_________> 189 168 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 1916 1916 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) : 1 251 1: 251: 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]: 15288817 14930.490 14.581 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19796 19796 make_re_423_> Number of previous, current selected restraints: 19536 19536 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 : 1916 1916 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) : 1 251 1: 251: 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 : 1916 1916 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) : 1 251 1: 251: 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]: 15288817 14930.490 14.581 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19796 19796 make_re_423_> Number of previous, current selected restraints: 19536 19536 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 : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 251 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : GLY --- 251 : CYS 251 TOP_________> 206 186 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'BLK' Number of atoms to choose from, total : 1916 1916 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) : 1 251 1: 251: 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]: 15288817 14930.490 14.581 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19796 19796 make_re_423_> Number of previous, current selected restraints: 19536 19536 TOP_________> 208 188 DELETE_ALIGNMENT TOP_________> 209 189 RETURN Dynamically allocated memory at amaxseq [B,kB,MB]: 15061175 14708.180 14.363 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: 19796 18018 TOP_________> 213 155 WRITE_RESTRAINTS FILE = CSRFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL 3310.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 3310.rsr openf5__224_> Open 11 OLD SEQUENTIAL 3310.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]: 15061175 14708.180 14.363 openf5__224_> Open 11 OLD SEQUENTIAL 3310.rsr openf5__224_> Open 11 OLD SEQUENTIAL 3310.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: 18018 18018 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 3310.D00000001 TOP_________> 229 208 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL 3310.ini openf5__224_> Open 11 OLD SEQUENTIAL 3310.ini rdatm___297_> Segments, residues, atoms: 1 251 1916 rdatm___298_> Segment: 1 1 1 1916 iatmcls_286W> MODEL atom not classified: CYS:OT1 CYS iatmcls_286W> MODEL atom not classified: CYS:OT2 CYS 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 : 1916 1916 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) : 1 251 1: 251: selatm__462_> Number of selected atoms : 1916 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : GLY --- 251 : CYS 251 TOP_________> 232 268 RETURN TOP_________> 233 210 CALL ROUTINE = RAND_METHOD TOP_________> 234 251 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 1916 1916 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 3310.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; 1916 9911 TOP_________> 244 234 OPTIMIZE Dynamically allocated memory at ampairs [B,kB,MB]: 15299831 14941.241 14.591 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; 1916 10902 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; 1916 11372 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; 1916 11922 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; 1916 12817 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; 1916 13642 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; 1916 14991 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; 1916 16708 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; 1916 17404 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; 1916 17933 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; 1916 18018 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_________> 319 239 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 320 271 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 321 272 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 322 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 323 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 324 285 CALL ROUTINE = MD_LEVEL TOP_________> 325 310 SET UPDATE_DYNAMIC = 0.39 TOP_________> 326 311 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 327 312 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 328 313 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 329 314 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 330 315 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 331 316 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 332 317 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 333 318 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 334 319 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 335 320 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 336 321 RETURN TOP_________> 337 286 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 338 291 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 339 292 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 340 306 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 341 307 RETURN TOP_________> 342 240 LABEL __ABORT TOP_________> 343 241 SET ERROR_STATUS = 0 TOP_________> 344 242 RETURN TOP_________> 345 216 END_DO TOP_________> 346 217 IUPAC_MODEL iupac_m_486_> OE1/2 swapped: -97.6708 10 10 iupac_m_486_> OE1/2 swapped: 179.5062 17 17 iupac_m_483_> CD1/2 CE1/2 swapped: 93.8764 20 20 iupac_m_487_> NH1/2 swapped: 177.9744 54 54 iupac_m_485_> OD1/2 swapped: 131.8973 68 68 iupac_m_487_> NH1/2 swapped: -179.1923 73 73 iupac_m_487_> NH1/2 swapped: -179.5433 76 76 iupac_m_485_> OD1/2 swapped: 173.5156 126 126 iupac_m_485_> OD1/2 swapped: 165.9660 135 135 iupac_m_483_> CD1/2 CE1/2 swapped: 99.5869 136 136 iupac_m_487_> NH1/2 swapped: 178.9445 137 137 iupac_m_485_> OD1/2 swapped: 125.4918 164 164 iupac_m_487_> NH1/2 swapped: 179.1019 176 176 iupac_m_487_> NH1/2 swapped: 179.6568 197 197 iupac_m_485_> OD1/2 swapped: 158.7814 233 233 iupac_m_486_> OE1/2 swapped: -110.7084 242 242 TOP_________> 347 218 SET ID1 = 9999 TOP_________> 348 219 SET OUTPUT2 = OUTPUT TOP_________> 349 220 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 : 251 Number of all, selected real atoms : 1916 1916 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 18018 18018 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4192 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 : 0 300 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 11 11 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 1541.8760 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 : 1948 0 0 0.005 0.005 13.975 1.000 2 Bond angle potential : 2631 0 3 1.741 1.741 154.36 1.000 3 Stereochemical cosine torsion poten: 1165 0 54 53.965 53.965 538.38 1.000 4 Stereochemical improper torsion pot: 782 0 0 1.048 1.048 18.025 1.000 5 Soft-sphere overlap restraints : 4192 0 0 0.003 0.003 4.2573 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) : 4185 0 4 0.548 0.548 179.21 1.000 10 Distance restraints 2 (N-O) : 4328 0 5 0.567 0.567 231.26 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: 250 0 3 4.160 4.160 51.021 1.000 14 Sidechain Chi_1 dihedral restraints: 222 0 1 81.284 81.284 52.878 1.000 15 Sidechain Chi_2 dihedral restraints: 150 0 0 73.354 73.354 44.897 1.000 16 Sidechain Chi_3 dihedral restraints: 68 0 0 74.374 74.374 48.923 1.000 17 Sidechain Chi_4 dihedral restraints: 22 0 0 83.024 83.024 15.682 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) : 1764 0 0 0.492 0.492 30.261 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: 249 37 23 31.791 67.900 140.78 1.000 26 Distance restraints 4 (SDCH-SDCH) : 254 0 1 1.172 1.172 17.967 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 3310.V99990001 # Heavy relative violation of each residue is written to: 3310.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 6527 1G 2E C N 3 5 -68.55 -69.30 3.33 0.23 -63.60 179.62 23.68 1 2E 2E N CA 5 6 139.25 142.50 -40.30 2 6528 2E 3P C N 12 14 -60.75 -58.70 4.31 0.25 -64.50 173.95 12.78 2 3P 3P N CA 14 15 -26.71 -30.50 147.20 3 6530 4V 5Q C N 26 28 -117.82 -121.10 20.67 1.03 -63.80 168.48 27.65 3 5Q 5Q N CA 28 29 160.11 139.70 -40.30 4 6531 5Q 6N C N 35 37 -100.97 -119.90 19.18 0.87 -63.20 -177.22 25.00 4 6N 6N N CA 37 38 140.07 137.00 -41.10 5 6532 6N 7G C N 43 45 -154.42 -167.20 34.02 1.11 82.20 -177.44 13.88 5 7G 7G N CA 45 46 143.07 174.60 8.50 6 6533 7G 8A C N 47 49 67.52 -68.20 139.47 12.81 -62.50 -167.72 29.47 6 8A 8A N CA 49 50 177.45 145.30 -40.90 7 6545 19S 20Y C N 138 140 -106.35 -98.40 17.70 1.67 -63.50 161.77 23.64 7 20Y 20Y N CA 140 141 112.59 128.40 -43.40 8 6546 20Y 21S C N 150 152 -57.16 -64.10 21.48 1.32 -136.60 172.81 9.79 8 21S 21S N CA 152 153 -55.33 -35.00 151.20 9 6553 27S 28Y C N 200 202 -93.19 -98.40 79.52 8.47 -63.50 97.10 14.03 9 28Y 28Y N CA 202 203 49.05 128.40 -43.40 10 6566 40Q 41E C N 303 305 80.40 54.60 128.16 11.92 -63.60 -150.79 24.79 10 41E 41E N CA 305 306 167.93 42.40 -40.30 11 6568 42D 43S C N 320 322 -146.79 -136.60 94.87 5.01 -64.10 123.60 9.57 11 43S 43S N CA 322 323 56.87 151.20 -35.00 12 6593 67L 68D C N 505 507 -134.07 -63.30 81.70 10.41 -63.30 81.70 10.41 12 68D 68D N CA 507 508 0.83 -40.00 -40.00 13 6594 68D 69S C N 513 515 -73.28 -72.40 13.15 0.80 -64.10 174.53 12.13 13 69S 69S N CA 515 516 139.28 152.40 -35.00 14 6595 69S 70L C N 519 521 -97.32 -108.50 17.99 0.83 -63.50 163.15 20.96 14 70L 70L N CA 521 522 118.41 132.50 -41.20 15 6596 70L 71N C N 527 529 -142.49 -119.90 26.12 0.79 -63.20 -173.49 27.79 15 71N 71N N CA 529 530 150.09 137.00 -41.10 16 6597 71N 72A C N 535 537 -69.39 -68.20 25.05 2.06 -62.50 161.33 26.11 16 72A 72A N CA 537 538 120.28 145.30 -40.90 17 6598 72A 73R C N 540 542 -149.16 -125.20 29.30 0.86 -63.00 -177.02 30.55 17 73R 73R N CA 542 543 157.48 140.60 -41.10 18 6600 74M 75A C N 559 561 -75.24 -68.20 9.05 0.58 -62.50 168.59 28.27 18 75A 75A N CA 561 562 151.00 145.30 -40.90 19 6601 75A 76R C N 564 566 -105.02 -125.20 24.83 0.73 -63.00 172.43 20.80 19 76R 76R N CA 566 567 126.14 140.60 -41.10 20 6609 83H 84D C N 624 626 -84.88 -96.50 11.77 0.48 -63.30 157.58 18.24 20 84D 84D N CA 626 627 116.10 114.20 -40.00 21 6610 84D 85G C N 632 634 128.86 82.20 61.47 2.10 -62.40 169.02 29.79 21 85G 85G N CA 634 635 -31.52 8.50 -41.20 22 6617 91Q 92L C N 684 686 -146.70 -108.50 38.21 1.83 -70.70 76.64 7.26 22 92L 92L N CA 686 687 131.75 132.50 141.60 23 6653 127E 128G C N 960 962 59.09 78.70 38.82 0.59 82.20 142.98 8.08 23 128G 128G N CA 962 963 -132.59 -166.10 8.50 24 6654 128G 129A C N 964 966 -114.28 -134.00 60.20 2.84 55.40 177.44 16.21 24 129A 129A N CA 966 967 90.12 147.00 38.20 25 6670 144S 145Y C N 1095 1097 -101.18 -98.40 76.16 8.08 -63.50 102.85 14.64 25 145Y 145Y N CA 1097 1098 52.29 128.40 -43.40 26 6699 173D 174G C N 1315 1317 149.48 82.20 74.95 3.47 -62.40 149.05 25.90 26 174G 174G N CA 1317 1318 -24.53 8.50 -41.20 27 6723 197R 198V C N 1516 1518 -162.13 -125.40 47.57 1.27 -62.40 175.23 28.16 27 198V 198V N CA 1518 1519 173.52 143.30 -42.40 28 6724 198V 199D C N 1523 1525 -88.86 -70.90 34.57 1.17 -63.30 142.48 19.21 28 199D 199D N CA 1525 1526 179.83 150.30 -40.00 29 6736 210Q 211G C N 1614 1616 156.38 -167.20 54.42 2.08 -80.20 129.72 9.47 29 211G 211G N CA 1616 1617 134.16 174.60 174.10 30 6745 219K 220K C N 1683 1685 -85.20 -118.00 33.02 1.19 -62.90 177.47 21.92 30 220K 220K N CA 1685 1686 135.26 139.10 -40.80 31 6746 220K 221G C N 1692 1694 91.54 82.20 49.91 1.95 -62.40 153.94 27.53 31 221G 221G N CA 1694 1695 -40.53 8.50 -41.20 32 6763 237L 238S C N 1809 1811 -74.61 -72.40 19.06 1.05 -64.10 154.03 11.82 32 238S 238S N CA 1811 1812 171.33 152.40 -35.00 33 6764 238S 239N C N 1815 1817 74.70 55.90 90.27 5.03 -63.20 138.11 20.57 33 239N 239N N CA 1817 1818 -48.79 39.50 -41.10 34 6772 246A 247T C N 1879 1881 -109.84 -124.80 77.74 2.90 -63.20 118.84 12.81 34 247T 247T N CA 1881 1882 67.21 143.50 -42.10 35 6773 247T 248L C N 1886 1888 -148.59 -108.50 42.63 1.90 -63.50 -168.29 31.88 35 248L 248L N CA 1888 1889 147.00 132.50 -41.20 36 6774 248L 249A C N 1894 1896 174.44 -134.00 57.64 1.31 -62.50 -168.80 37.72 36 249A 249A N CA 1896 1897 172.77 147.00 -40.90 37 6775 249A 250K C N 1899 1901 -141.57 -118.00 28.53 0.96 -62.90 -178.10 28.33 37 250K 250K N CA 1901 1902 155.18 139.10 -40.80 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 1 24 32 126 155 216 184 222 236 277 320 << end of ENERGY. TOP_________> 350 221 SET OUTPUT = OUTPUT2 TOP_________> 351 222 CALL ROUTINE = 'user_after_single_model' TOP_________> 352 228 RETURN TOP_________> 353 223 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL 3310.B99990001 wrpdb2__568_> Residues, atoms, selected atoms: 251 1916 1916 TOP_________> 354 224 SET FINAL_MODEL = FILE TOP_________> 355 225 RETURN TOP_________> 356 195 END_DO TOP_________> 357 196 IF ARGUMENTS = DO_LOOPS 1, OPERATION = 'NE', THEN = 'GO_T; O NO_LOOPS' TOP_________> 358 202 RETURN TOP_________> 359 404 IF ARGUMENTS =FINAL_MALIGN3D 1, OPERATION ='NE', THEN ='G; O_TO NO_MALIGN3D' TOP_________> 360 411 RETURN Dynamically allocated memory at finish [B,kB,MB]: 15299831 14941.241 14.591 Starting time : 2003/10/02 14:37:39.140 Closing time : 2003/10/02 14:39:12.510 Total CPU time [seconds] : 84.43