MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA 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 synth.compbio.ucsf.edu 2.6.8-1.521smp i686 Date and time of compilation : 09/12/2004 21:24:59 Job starting time (YY/MM/DD HH:MM:SS): 2004/09/15 18:43:20.294 getprog_531W> ROUTINE redefined: special_restraints TOP_________> 108 746 SET ALNFILE = 'TvLDH-4mdh-1emd_ed.ali' TOP_________> 109 747 SET KNOWNS = '4mdh' '1emd_ed' TOP_________> 110 748 SET SEQUENCE = 'TvLDH' TOP_________> 111 749 SET STARTING_MODEL = 1 TOP_________> 112 750 SET ENDING_MODEL = 5 TOP_________> 113 751 SET HETATM_IO = ON TOP_________> 114 752 CALL ROUTINE = 'model' TOP_________> 115 419 CALL ROUTINE = 'getnames' TOP_________> 116 531 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 117 532 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 118 533 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 119 534 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 120 535 SET ROOT_NAME = SEQUENCE TOP_________> 121 536 RETURN TOP_________> 122 420 CALL ROUTINE = 'homcsr' TOP_________> 123 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 90849 88.720 0.087 openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 9652915 9426.675 9.206 openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali read_al_374_> Non-standard residue type,position,sequence: . 566 1 read_al_374_> Non-standard residue type,position,sequence: . 569 1 read_al_374_> Non-standard residue type,position,sequence: . 567 2 read_al_374_> Non-standard residue type,position,sequence: . 568 2 read_al_374_> Non-standard residue type,position,sequence: . 567 3 read_al_374_> Non-standard residue type,position,sequence: . 568 3 Read the alignment from file : TvLDH-4mdh-1emd_ed.ali Total number of alignment positions: 569 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdh 335 2 4mdh undefined 2 1emd_ed 239 2 1emd_ed undefined 3 TvLDH 335 2 TOP_________> 124 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 125 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./4mdh.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1emd_ed.pdb fndatmi_285W> Number of residues <> number of atoms; atom code: 335 333 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 239 237 CA check_ali___> Checking pairwise structural superpositions. Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- END OF TABLE check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND TOP_________> 126 118 CALL ROUTINE = GENERATE_METHOD TOP_________> 127 83 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali read_al_374_> Non-standard residue type,position,sequence: . 563 1 read_al_374_> Non-standard residue type,position,sequence: . 566 1 read_al_374_> Non-standard residue type,position,sequence: . 564 2 read_al_374_> Non-standard residue type,position,sequence: . 565 2 Read the alignment from file : TvLDH-4mdh-1emd_ed.ali Total number of alignment positions: 566 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdh 335 2 4mdh undefined 2 1emd_ed 239 2 1emd_ed undefined TOP_________> 128 84 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali read_al_374_> Non-standard residue type,position,sequence: . 563 1 read_al_374_> Non-standard residue type,position,sequence: . 566 1 read_al_374_> Non-standard residue type,position,sequence: . 564 2 read_al_374_> Non-standard residue type,position,sequence: . 565 2 Read the alignment from file : TvLDH-4mdh-1emd_ed.ali Total number of alignment positions: 566 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdh 335 2 4mdh undefined 2 1emd_ed 239 2 1emd_ed undefined TOP_________> 129 85 IF ARGUMENTS = INITIAL_MALIGN3D 0, OPERATION = 'EQ', THEN; = 'GO_TO NO_INITIAL_MALIGN3D' TOP_________> 130 88 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali read_al_374_> Non-standard residue type,position,sequence: . 566 1 read_al_374_> Non-standard residue type,position,sequence: . 569 1 read_al_374_> Non-standard residue type,position,sequence: . 567 2 read_al_374_> Non-standard residue type,position,sequence: . 568 2 read_al_374_> Non-standard residue type,position,sequence: . 567 3 read_al_374_> Non-standard residue type,position,sequence: . 568 3 Read the alignment from file : TvLDH-4mdh-1emd_ed.ali Total number of alignment positions: 569 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdh 335 2 4mdh undefined 2 1emd_ed 239 2 1emd_ed undefined 3 TvLDH 335 2 TOP_________> 131 89 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL7v7}/modlib/models.lib TOP_________> 132 90 READ_PARAMETERS FILE = PARLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//par.lib Dynamically allocated memory at amattacns [B,kB,MB]: 9653615 9427.358 9.206 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 133 91 CALL ROUTINE = 'create_topology' TOP_________> 134 106 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF getf_______W> RTF restraint not found in the atoms list: residue type, indices: 14 333 atom names : C +N atom indices : 2595 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 14 333 atom names : C CA +N O atom indices : 2595 2589 0 2596 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 333 2596 2662 0 0 1134 patch_______> segment topology patched using RTF: 1 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 1 333 2596 2662 3613 4302 1134 patch_______> segment topology patched using RTF: 333 ; GLN ; CTER segments residues atoms bonds angles dihedrals impropers: 1 333 2597 2663 3615 4304 1135 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 333 2597 2663 3615 4304 1135 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 335 2647 2663 3615 4304 1135 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 335 2647 2663 3615 4304 1135 TOP_________> 135 107 CALL ROUTINE = 'default_patches' TOP_________> 136 526 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali read_al_374_> Non-standard residue type,position,sequence: . 566 1 read_al_374_> Non-standard residue type,position,sequence: . 569 1 read_al_374_> Non-standard residue type,position,sequence: . 567 2 read_al_374_> Non-standard residue type,position,sequence: . 568 2 read_al_374_> Non-standard residue type,position,sequence: . 567 3 read_al_374_> Non-standard residue type,position,sequence: . 568 3 Read the alignment from file : TvLDH-4mdh-1emd_ed.ali Total number of alignment positions: 569 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdh 335 2 4mdh undefined 2 1emd_ed 239 2 1emd_ed undefined 3 TvLDH 335 2 TOP_________> 137 527 PATCH_SS_TEMPLATES fndatmi_285W> Number of residues <> number of atoms; atom code: 335 333 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 239 237 CA TOP_________> 138 528 RETURN TOP_________> 139 108 CALL ROUTINE = 'special_patches' TOP_________> 140 523 RETURN TOP_________> 141 109 RETURN TOP_________> 142 92 TRANSFER_XYZ CLUSTER_CUT = -1.0 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 2 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 2202 445 TOP_________> 143 93 BUILD_MODEL INITIALIZE_XYZ = OFF TOP_________> 144 94 WRITE_MODEL FILE = MODEL openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.ini wrpdb2__568_> Residues, atoms, selected atoms: 335 2647 2647 TOP_________> 145 95 RETURN TOP_________> 146 119 IF ARGUMENTS = EXIT_STAGE 2, OPERATION = 'EQ', THEN = 'RE; TURN' TOP_________> 147 120 IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'EQ', THE; N ='GO_TO __SKIP_RSRS' TOP_________> 148 121 CALL ROUTINE = 'mkhomcsr' TOP_________> 149 126 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS; = OFF Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 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 : 2663 3615 4123 1119 Total number of restraints before, now : 0 11520 make_re_422_> Number of previous, current restraints : 0 11520 make_re_423_> Number of previous, current selected restraints: 0 11520 TOP_________> 150 127 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali openf5__224_> Open 20 OLD SEQUENTIAL TvLDH-4mdh-1emd_ed.ali read_al_374_> Non-standard residue type,position,sequence: . 566 1 read_al_374_> Non-standard residue type,position,sequence: . 569 1 read_al_374_> Non-standard residue type,position,sequence: . 567 2 read_al_374_> Non-standard residue type,position,sequence: . 568 2 read_al_374_> Non-standard residue type,position,sequence: . 567 3 read_al_374_> Non-standard residue type,position,sequence: . 568 3 Read the alignment from file : TvLDH-4mdh-1emd_ed.ali Total number of alignment positions: 569 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 4mdh 335 2 4mdh undefined 2 1emd_ed 239 2 1emd_ed undefined 3 TvLDH 335 2 TOP_________> 151 128 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 1 332 SER errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 333 ALA errdih__638_> Missing atoms in a dihedral, residue index, residue type: 3 333 ALA errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 333 ALA errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 236 ASN errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 237 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 3 237 LYS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 237 LYS getdata_643_> Protein accepted: 4mdh getdata_643_> Protein accepted: 1emd_ed getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 11520 11851 make_re_423_> Number of previous, current selected restraints: 11520 11851 TOP_________> 152 129 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINT; S = 5 TOP_________> 153 130 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RE; STRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: omega_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/omega.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 4mdh getdata_643_> Protein accepted: 1emd_ed getdata_289_> Proteins (all/accepted): 2 2 delete__442E> One or more atoms absent from MODEL: O: 333: C: 333: N: 334: CA: 334: delete__442E> One or more atoms absent from MODEL: O: 334: C: 334: N: 335: CA: 335: omgdel__425W> Unselected all O C +N +CA dihedrals: 348 make_re_422_> Number of previous, current restraints : 11851 12183 make_re_423_> Number of previous, current selected restraints: 11851 11835 TOP_________> 154 131 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: chi1_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 4mdh getdata_643_> Protein accepted: 1emd_ed getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 12183 12462 make_re_423_> Number of previous, current selected restraints: 11835 12114 TOP_________> 155 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: chi2_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 4mdh getdata_643_> Protein accepted: 1emd_ed getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 12462 12676 make_re_423_> Number of previous, current selected restraints: 12114 12328 TOP_________> 156 133 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: chi3_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 4mdh getdata_643_> Protein accepted: 1emd_ed getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 12676 12760 make_re_423_> Number of previous, current selected restraints: 12328 12412 TOP_________> 157 134 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: chi4_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/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: 4mdh getdata_643_> Protein accepted: 1emd_ed getdata_289_> Proteins (all/accepted): 2 2 make_re_422_> Number of previous, current restraints : 12760 12792 make_re_423_> Number of previous, current selected restraints: 12412 12444 TOP_________> 158 135 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINT; S = 5 TOP_________> 159 136 SET RES_TYPES = 'STD' TOP_________> 160 137 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE TOP_________> 161 138 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 162 139 SET RESTRAINT_GROUP = 9 TOP_________> 163 140 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 333 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 333 : GLN 333 TOP_________> 164 141 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 333 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 333 : GLN 333 TOP_________> 165 142 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: distance iup2crm_280W> No TOPOLOGY_LIB in memory or assigning a BLK residue. Default CHARMM atom type assigned: AP --> C This message is written only for the first such atom. iup2crm_280W> No TOPOLOGY_LIB in memory or assigning a BLK residue. Default CHARMM atom type assigned: C1 --> CT2 This message is written only for the first such atom. make_re_422_> Number of previous, current restraints : 12792 19799 make_re_423_> Number of previous, current selected restraints: 12444 19451 TOP_________> 166 143 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DI; STANCE TOP_________> 167 144 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 168 145 SET RESTRAINT_GROUP = 10 TOP_________> 169 146 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : N Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 333 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 333 : GLN 333 TOP_________> 170 147 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : O Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 333 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 333 : GLN 333 TOP_________> 171 148 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19799 26818 make_re_423_> Number of previous, current selected restraints: 19451 26470 TOP_________> 172 149 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_; DISTANCE TOP_________> 173 150 SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = OFF TOP_________> 174 151 SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5 TOP_________> 175 152 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 1265 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 10 : THR 10 2 12 : ALA --- 13 : ALA 2 3 15 : GLN --- 16 : ILE 2 4 18 : TYR --- 26 : SER 9 5 28 : GLU --- 30 : TYR 3 6 32 : ASP --- 65 : ALA 34 7 67 : PHE --- 93 : PRO 27 8 95 : GLN --- 111 : THR 17 9 113 : GLU --- 128 : ILE 16 10 130 : ASN --- 170 : LEU 41 11 172 : VAL --- 183 : TRP 12 12 185 : ASN --- 186 : HIS 2 13 188 : GLU --- 202 : GLU 15 14 204 : LYS --- 225 : ILE 22 15 227 : HIS --- 236 : ARG 10 16 238 : PHE --- 257 : PHE 20 17 259 : THR --- 261 : PRO 3 18 263 : GLU --- 267 : MET 5 19 269 : ILE --- 273 : GLU 5 20 275 : ASN --- 277 : TYR 3 21 279 : ILE --- 281 : PRO 3 22 283 : VAL --- 294 : GLU 12 23 296 : LYS --- 301 : GLU 6 24 303 : PHE --- 333 : GLN 31 TOP_________> 176 153 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : MNCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 1332 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 333 : GLN 333 TOP_________> 177 154 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 26818 30234 make_re_423_> Number of previous, current selected restraints: 26470 29886 TOP_________> 178 155 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_; DISTANCE TOP_________> 179 156 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 180 157 SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0 TOP_________> 181 158 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 1265 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 10 : THR 10 2 12 : ALA --- 13 : ALA 2 3 15 : GLN --- 16 : ILE 2 4 18 : TYR --- 26 : SER 9 5 28 : GLU --- 30 : TYR 3 6 32 : ASP --- 65 : ALA 34 7 67 : PHE --- 93 : PRO 27 8 95 : GLN --- 111 : THR 17 9 113 : GLU --- 128 : ILE 16 10 130 : ASN --- 170 : LEU 41 11 172 : VAL --- 183 : TRP 12 12 185 : ASN --- 186 : HIS 2 13 188 : GLU --- 202 : GLU 15 14 204 : LYS --- 225 : ILE 22 15 227 : HIS --- 236 : ARG 10 16 238 : PHE --- 257 : PHE 20 17 259 : THR --- 261 : PRO 3 18 263 : GLU --- 267 : MET 5 19 269 : ILE --- 273 : GLU 5 20 275 : ASN --- 277 : TYR 3 21 279 : ILE --- 281 : PRO 3 22 283 : VAL --- 294 : GLU 12 23 296 : LYS --- 301 : GLU 6 24 303 : PHE --- 333 : GLN 31 TOP_________> 182 159 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : SDCH Residue types to be searched for (RES_TYPES) : STD Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 1265 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 10 : THR 10 2 12 : ALA --- 13 : ALA 2 3 15 : GLN --- 16 : ILE 2 4 18 : TYR --- 26 : SER 9 5 28 : GLU --- 30 : TYR 3 6 32 : ASP --- 65 : ALA 34 7 67 : PHE --- 93 : PRO 27 8 95 : GLN --- 111 : THR 17 9 113 : GLU --- 128 : ILE 16 10 130 : ASN --- 170 : LEU 41 11 172 : VAL --- 183 : TRP 12 12 185 : ASN --- 186 : HIS 2 13 188 : GLU --- 202 : GLU 15 14 204 : LYS --- 225 : ILE 22 15 227 : HIS --- 236 : ARG 10 16 238 : PHE --- 257 : PHE 20 17 259 : THR --- 261 : PRO 3 18 263 : GLU --- 267 : MET 5 19 269 : ILE --- 273 : GLU 5 20 275 : ASN --- 277 : TYR 3 21 279 : ILE --- 281 : PRO 3 22 283 : VAL --- 294 : GLU 12 23 296 : LYS --- 301 : GLU 6 24 303 : PHE --- 333 : GLN 31 TOP_________> 183 160 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 30234 31351 make_re_423_> Number of previous, current selected restraints: 29886 31003 TOP_________> 184 161 CALL ROUTINE = 'hetatm_restraints' TOP_________> 185 170 SET RESTRAINT_TYPE = 'distance' TOP_________> 186 171 SET DISTANCE_RSR_MODEL = 7 TOP_________> 187 172 SET MAXIMAL_DISTANCE = 7.0 TOP_________> 188 173 SET ADD_RESTRAINTS = ON TOP_________> 189 174 SET RESTRAINT_GROUP = 27 TOP_________> 190 175 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 191 176 SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 192 177 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : ALL Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2647 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : BLK 335 TOP_________> 193 178 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : HET Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 50 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 334 : BLK --- 335 : BLK 2 TOP_________> 194 179 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 31351 32850 make_re_423_> Number of previous, current selected restraints: 31003 32502 TOP_________> 195 180 RETURN TOP_________> 196 162 CALL ROUTINE = 'blk_restraints' TOP_________> 197 183 SET RESTRAINT_TYPE = 'distance' TOP_________> 198 184 SET DISTANCE_RSR_MODEL = 7 TOP_________> 199 185 SET MAXIMAL_DISTANCE = 10.0 TOP_________> 200 186 SET ADD_RESTRAINTS = ON TOP_________> 201 187 SET RESTRAINT_GROUP = 27 TOP_________> 202 188 SET RESTRAINT_STDEV = 0.05 0.0 TOP_________> 203 189 SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = ON TOP_________> 204 190 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 50 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 334 : BLK --- 335 : BLK 2 TOP_________> 205 191 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 50 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 334 : BLK --- 335 : BLK 2 TOP_________> 206 192 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 32850 34154 make_re_423_> Number of previous, current selected restraints: 32502 33806 TOP_________> 207 193 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 208 194 SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 209 195 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : CA Residue types to be searched for (RES_TYPES) : ALL Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 333 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 333 : GLN 333 TOP_________> 210 196 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'BLK' Number of atoms to choose from, total : 2647 2647 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : BLK Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 50 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 334 : BLK --- 335 : BLK 2 TOP_________> 211 197 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 29611967 28917.938 28.240 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 34154 34422 make_re_423_> Number of previous, current selected restraints: 33806 34074 TOP_________> 212 198 DELETE_ALIGNMENT TOP_________> 213 199 RETURN Dynamically allocated memory at amaxseq [B,kB,MB]: 28639719 27968.477 27.313 TOP_________> 214 163 CALL ROUTINE = 'special_restraints' TOP_________> 215 754 ADD_RESTRAINT ATOM_IDS = 'NH1:161' 'O1A:334', RES; TRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 28639869 27968.621 27.313 TOP_________> 216 755 ADD_RESTRAINT ATOM_IDS = 'NH2:161' 'O1B:334', RES; TRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 28639869 27968.621 27.313 TOP_________> 217 756 ADD_RESTRAINT ATOM_IDS = 'NE2:186' 'O2:334', REST; RAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 28639869 27968.621 27.313 TOP_________> 218 757 RETURN TOP_________> 219 164 CONDENSE_RESTRAINTS delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 34425 32046 TOP_________> 220 165 WRITE_RESTRAINTS FILE = CSRFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.rsr TOP_________> 221 166 SET RESIDUE_SPAN_RANGE = -999 -999, RESIDUE_SPAN_SIGN = O; N top_mod_451W> Requested schedule step not available: 0 SCHEDULE_STEP set to N_SCHEDULE. TOP_________> 222 167 RETURN TOP_________> 223 122 LABEL __SKIP_RSRS TOP_________> 224 123 RETURN TOP_________> 225 421 IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'GE', THEN = 'RE; TURN' TOP_________> 226 422 CALL ROUTINE = 'rd_restraints' TOP_________> 227 276 READ_RESTRAINTS FILE = CSRFILE, ADD_RESTRAINTS = 'off' openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.rsr openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.rsr rdcsr2__307_> Number of restraints read : 0 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 Dynamically allocated memory at amprmcns [B,kB,MB]: 28639869 27968.621 27.313 openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.rsr openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.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: 32046 32046 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 TOP_________> 228 277 RETURN TOP_________> 229 423 CALL ROUTINE = 'multiple_models' TOP_________> 230 202 DO ID2 = STARTING_MODEL ENDING_MODEL 1 TOP_________> 231 203 SET FINAL_MODEL = 'default' TOP_________> 232 204 CALL ROUTINE = 'single_model' TOP_________> 233 215 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 234 216 SET ID1 = 0 TOP_________> 235 217 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000001 TOP_________> 236 218 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 2 335 2647 rdatm___298_> Segment: 1 1 333 2597 rdatm___298_> Segment: 2 334 335 50 TOP_________> 237 219 CALL ROUTINE = 'select_atoms' TOP_________> 238 288 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 : 2647 2647 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2647 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : BLK 335 TOP_________> 239 289 RETURN TOP_________> 240 220 CALL ROUTINE = RAND_METHOD TOP_________> 241 272 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2647 2647 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 242 273 RETURN TOP_________> 243 221 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 244 222 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 245 223 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 246 224 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 247 225 CALL ROUTINE = 'single_model_pass' TOP_________> 248 252 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 249 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 250 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 17112 TOP_________> 251 255 OPTIMIZE Dynamically allocated memory at ampairs [B,kB,MB]: 27729243 27079.340 26.445 TOP_________> 252 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 253 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 254 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 255 259 END_DO TOP_________> 256 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 257 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 19019 TOP_________> 258 255 OPTIMIZE TOP_________> 259 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 260 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 261 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 262 259 END_DO TOP_________> 263 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 264 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 20133 TOP_________> 265 255 OPTIMIZE TOP_________> 266 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 267 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 268 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 269 259 END_DO TOP_________> 270 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 271 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 21411 TOP_________> 272 255 OPTIMIZE TOP_________> 273 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 274 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 275 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 276 259 END_DO TOP_________> 277 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 278 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 22706 TOP_________> 279 255 OPTIMIZE TOP_________> 280 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 281 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 282 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 283 259 END_DO TOP_________> 284 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 285 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 24624 TOP_________> 286 255 OPTIMIZE TOP_________> 287 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 288 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 289 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 290 259 END_DO TOP_________> 291 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 292 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 27113 TOP_________> 293 255 OPTIMIZE TOP_________> 294 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 295 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 296 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 297 259 END_DO TOP_________> 298 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 299 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 28185 TOP_________> 300 255 OPTIMIZE TOP_________> 301 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 302 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 303 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 304 259 END_DO TOP_________> 305 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 306 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 29455 TOP_________> 307 255 OPTIMIZE TOP_________> 308 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 309 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 310 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 311 259 END_DO TOP_________> 312 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 313 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 30615 TOP_________> 314 255 OPTIMIZE TOP_________> 315 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 316 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 317 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 318 259 END_DO TOP_________> 319 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 320 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 321 255 OPTIMIZE TOP_________> 322 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 323 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 324 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 325 259 END_DO TOP_________> 326 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 327 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 328 255 OPTIMIZE TOP_________> 329 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 330 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 331 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 332 259 END_DO TOP_________> 333 260 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 334 292 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 335 293 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 336 294 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 337 295 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 338 306 CALL ROUTINE = MD_LEVEL TOP_________> 339 330 SET UPDATE_DYNAMIC = 0.39 TOP_________> 340 331 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 341 332 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 342 333 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 343 334 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 344 335 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 345 336 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 346 337 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 347 338 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 348 339 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 349 340 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 350 341 RETURN TOP_________> 351 307 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 352 312 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 353 313 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 354 326 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 355 327 RETURN TOP_________> 356 261 LABEL __ABORT TOP_________> 357 262 SET ERROR_STATUS = 0 TOP_________> 358 263 RETURN TOP_________> 359 226 END_DO TOP_________> 360 227 IUPAC_MODEL iupac_m_487_> NH1/2 swapped: 179.8601 48 48 iupac_m_486_> OE1/2 will be swapped: 177.2265 57 57 iupac_m_483_> CD1/2 CE1/2 swapped: 93.7967 67 67 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 170.5218 72 72 iupac_m_485_> OD1/2 will be swapped: 112.4796 79 79 iupac_m_487_> NH1/2 swapped: 174.3354 97 97 iupac_m_483_> CD1/2 CE1/2 swapped: -90.4941 108 108 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 139.3012 132 132 iupac_m_487_> NH1/2 swapped: -176.5657 161 161 iupac_m_485_> OD1/2 will be swapped: -168.3417 173 173 iupac_m_485_> OD1/2 will be swapped: 128.9037 176 176 iupac_m_486_> OE1/2 will be swapped: 172.9485 188 188 iupac_m_483_> CD1/2 CE1/2 swapped: 91.0852 199 199 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 172.1801 210 210 iupac_m_485_> OD1/2 will be swapped: 139.0875 213 213 iupac_m_483_> CD1/2 CE1/2 swapped: 91.8984 216 216 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 179.3584 219 219 iupac_m_487_> NH1/2 swapped: -179.8644 228 228 iupac_m_485_> OD1/2 will be swapped: 169.6448 231 231 iupac_m_487_> NH1/2 swapped: -179.6725 236 236 iupac_m_483_> CD1/2 CE1/2 swapped: 97.6862 287 287 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -174.2900 294 294 iupac_m_486_> OE1/2 will be swapped: -179.6511 301 301 iupac_m_485_> OD1/2 will be swapped: 134.2094 319 319 TOP_________> 361 228 SET ID1 = 9999 TOP_________> 362 229 SET OUTPUT2 = OUTPUT TOP_________> 363 230 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'eq', THEN = 'GO_TO __ACCELRYS2' TOP_________> 364 231 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 1 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2647 2647 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 32046 32046 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 6430 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 : 10207.6025 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 : 2663 3 12 0.011 0.011 95.307 1.000 2 Bond angle potential : 3615 7 41 2.960 2.960 525.67 1.000 3 Stereochemical cosine torsion poten: 1744 0 42 46.591 46.591 580.02 1.000 4 Stereochemical improper torsion pot: 1119 2 6 1.842 1.842 81.102 1.000 5 Soft-sphere overlap restraints : 6430 2 8 0.008 0.008 53.664 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 7007 8 52 0.326 0.326 502.36 1.000 10 Distance restraints 2 (N-O) : 7019 3 32 0.334 0.334 480.47 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 332 1 3 4.866 4.866 91.933 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 6 74.854 74.854 80.736 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 9 82.685 82.685 103.35 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 0 83.089 83.089 59.444 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 99.073 99.073 25.220 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 3 1 1 0.587 0.587 30.533 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3416 0 1 0.454 0.454 142.93 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 331 16 34 26.537 32.104 54.658 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1117 0 0 0.885 0.885 128.66 1.000 27 Distance restraints 5 (X-Y) : 3071 257 427 0.556 0.556 7171.6 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990001 # Heavy relative violation of each residue is written to: TvLDH.V99990001 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 42396.5586 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 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 10744 9I 86V CA CA 60 649 8.70 6.99 1.71 4.51 6.99 1.71 4.51 2 11000 14G 86V CA CA 89 649 10.56 8.83 1.74 4.67 8.83 1.74 4.67 3 11001 14G 87A CA CA 89 656 9.58 7.89 1.69 4.75 7.89 1.69 4.75 4 11116 17G 86V CA CA 110 649 9.03 7.49 1.54 4.89 7.49 1.54 4.89 5 12713 90P 97R CA CA 675 726 13.56 8.68 4.88 5.01 8.68 4.88 5.01 6 12726 91L 96V CA CA 682 719 11.92 7.21 4.72 4.75 7.21 4.72 4.75 7 12727 91L 97R CA CA 682 726 12.62 6.81 5.81 8.28 6.81 5.81 8.28 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 19231 87A 11G N O 655 77 6.89 5.19 1.70 4.85 5.19 1.70 4.85 2 19322 91L 97R N O 681 735 11.30 7.26 4.04 4.73 7.26 4.04 4.73 3 20134 131P 89M N O 988 673 8.94 6.49 2.45 4.55 6.49 2.45 4.55 ------------------------------------------------------------------------------------------------- Feature 22 : Upper bound distance restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 32045 161R 334. NH2 O1B 1229 2600 4.52 3.50 1.02 10.17 3.50 1.02 10.17 ------------------------------------------------------------------------------------------------- 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 9172 31G 32D C N 225 227 -76.56 -96.50 53.96 2.27 -63.30 104.90 12.20 1 32D 32D N CA 227 228 64.06 114.20 -40.00 2 9226 85L 86V C N 646 648 -137.88 -125.40 98.82 5.20 -62.40 115.69 13.03 2 86V 86V N CA 648 649 45.27 143.30 -42.40 3 9231 90P 91L C N 679 681 168.94 -108.50 99.43 4.39 -70.70 128.96 9.98 3 91L 91L N CA 681 682 -172.08 132.50 141.60 4 9238 97R 98A C N 734 736 -93.34 -62.50 88.85 13.43 -62.50 88.85 13.43 4 98A 98A N CA 736 737 42.43 -40.90 -40.90 5 9295 154L 155S C N 1172 1174 -135.64 -64.10 89.51 8.14 -64.10 89.51 8.14 5 155S 155S N CA 1174 1175 18.81 -35.00 -35.00 6 9355 214H 215D C N 1642 1644 -79.18 -63.30 78.13 8.80 -63.30 78.13 8.80 6 215D 215D N CA 1644 1645 36.50 -40.00 -40.00 7 9359 218F 219D C N 1680 1682 -112.19 -63.30 67.98 11.34 -63.30 67.98 11.34 7 219D 219D N CA 1682 1683 -87.24 -40.00 -40.00 8 9367 226G 227H C N 1747 1749 -108.77 -63.20 79.65 8.53 -63.20 79.65 8.53 8 227H 227H N CA 1749 1750 23.03 -42.30 -42.30 9 9381 240S 241A C N 1869 1871 -91.76 -62.50 33.97 6.91 -62.50 33.97 6.91 9 241A 241A N CA 1871 1872 -58.14 -40.90 -40.90 10 9397 256L 257F C N 1989 1991 -113.16 -63.20 63.93 7.65 -63.20 63.93 7.65 10 257F 257F N CA 1991 1992 -4.41 -44.30 -44.30 11 9413 272P 273E C N 2098 2100 16.01 -63.60 103.80 17.76 -63.60 103.80 17.76 11 273E 273E N CA 2100 2101 26.31 -40.30 -40.30 12 9414 273E 274G C N 2107 2109 -76.56 -62.40 14.33 2.46 82.20 165.71 12.48 12 274G 274G N CA 2109 2110 -38.98 -41.20 8.50 13 9433 292D 293K C N 2248 2250 51.28 -62.90 147.48 18.60 -62.90 147.48 18.60 13 293K 293K N CA 2250 2251 -134.14 -40.80 -40.80 14 9434 293K 294E C N 2257 2259 -114.66 -117.80 29.38 1.42 -63.60 156.46 18.57 14 294E 294E N CA 2259 2260 107.59 136.80 -40.30 15 9469 328L 329N C N 2555 2557 -93.16 -63.20 70.86 7.67 -63.20 70.86 7.67 15 329N 329N N CA 2557 2558 23.11 -41.10 -41.10 16 9470 329N 330H C N 2563 2565 -112.95 -63.20 49.76 7.93 -63.20 49.76 7.93 16 330H 330H N CA 2565 2566 -43.11 -42.30 -42.30 ------------------------------------------------------------------------------------------------- Feature 27 : Distance restraints 5 (X-Y) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 28975 86V 335. N NO4 648 2633 6.90 5.81 1.09 5.43 5.81 1.09 5.43 2 28976 86V 335. N NC6 648 2647 9.33 6.77 2.56 12.82 6.77 2.56 12.82 3 28981 86V 335. CA NO2 649 2629 7.40 6.24 1.16 5.80 6.24 1.16 5.80 4 28985 86V 335. CA NO4 649 2633 5.46 4.55 0.91 4.54 4.55 0.91 4.54 5 28990 86V 335. CA NN1 649 2639 7.29 5.99 1.30 6.49 5.99 1.30 6.49 6 28991 86V 335. CA NC2 649 2640 8.30 7.00 1.30 6.51 7.00 1.30 6.51 7 28992 86V 335. CA NC5 649 2646 9.30 6.18 3.12 15.62 6.18 3.12 15.62 8 28993 86V 335. CA NC6 649 2647 7.91 5.55 2.36 11.79 5.55 2.36 11.79 9 28999 86V 335. CB NO2 650 2629 6.71 5.67 1.04 5.22 5.67 1.04 5.22 10 29006 86V 335. CB NC4 650 2645 9.19 6.79 2.40 12.01 6.79 2.40 12.01 11 29007 86V 335. CB NC5 650 2646 8.40 5.76 2.64 13.21 5.76 2.64 13.21 12 29008 86V 335. CB NC6 650 2647 7.03 5.37 1.66 8.29 5.37 1.66 8.29 13 29016 86V 335. C AC2 653 2623 8.36 6.95 1.41 7.05 6.95 1.41 7.05 14 29017 86V 335. C AN3 653 2624 7.77 6.63 1.14 5.71 6.63 1.14 5.71 15 29021 86V 335. C NO2 653 2629 6.62 5.54 1.08 5.39 5.54 1.08 5.39 16 29030 86V 335. C NN1 653 2639 7.26 6.28 0.98 4.88 6.28 0.98 4.88 17 29031 86V 335. C NC5 653 2646 9.05 6.82 2.23 11.16 6.82 2.23 11.16 18 29032 86V 335. C NC6 653 2647 7.68 5.95 1.73 8.66 5.95 1.73 8.66 19 29051 86V 335. O NO2 654 2629 5.47 4.35 1.13 5.63 4.35 1.13 5.63 20 29061 86V 335. O NC5 654 2646 8.05 6.49 1.56 7.78 6.49 1.56 7.78 21 29062 86V 335. O NC6 654 2647 6.71 5.54 1.16 5.82 5.54 1.16 5.82 22 29075 87A 335. N AN1 655 2622 7.36 6.24 1.12 5.60 6.24 1.12 5.60 23 29076 87A 335. N AC2 655 2623 7.44 5.90 1.53 7.66 5.90 1.53 7.66 24 29077 87A 335. N AN3 655 2624 6.88 5.71 1.18 5.89 5.71 1.18 5.89 25 29079 87A 335. N NO2 655 2629 7.44 6.52 0.92 4.62 6.52 0.92 4.62 26 29083 87A 335. N NO4 655 2633 6.20 5.20 1.00 5.02 5.20 1.00 5.02 27 29103 87A 335. CA AC2 656 2623 6.10 5.12 0.98 4.92 5.12 0.98 4.92 28 29131 87A 335. CB AC2 657 2623 4.94 3.85 1.09 5.45 3.85 1.09 5.45 29 29132 87A 335. CB AN3 657 2624 4.65 3.74 0.92 4.58 3.74 0.92 4.58 30 29221 88S 335. CA AO1 661 2605 7.31 6.22 1.09 5.46 6.22 1.09 5.46 31 29248 88S 335. C AO1 664 2605 6.64 5.04 1.60 7.98 5.04 1.60 7.98 32 29271 88S 335. C NO3 664 2635 5.15 4.23 0.92 4.62 4.23 0.92 4.62 33 29276 88S 335. O AO1 665 2605 5.44 3.96 1.48 7.39 3.96 1.48 7.39 34 29305 89M 335. N AO1 666 2605 7.63 5.55 2.08 10.42 5.55 2.08 10.42 35 29314 89M 335. N AC8 666 2617 7.01 6.09 0.92 4.60 6.09 0.92 4.60 36 29316 89M 335. N O3 666 2626 6.51 5.60 0.90 4.52 5.60 0.90 4.52 37 29322 89M 335. N NC3 666 2634 5.46 4.44 1.02 5.08 4.44 1.02 5.08 38 29323 89M 335. N NO3 666 2635 5.76 4.23 1.53 7.67 4.23 1.53 7.67 39 29325 89M 335. N NO2 666 2637 7.55 6.35 1.20 6.02 6.35 1.20 6.02 40 29328 89M 335. CA AO1 667 2605 7.69 5.02 2.67 13.34 5.02 2.67 13.34 41 29334 89M 335. CA O3 667 2626 6.40 5.23 1.17 5.84 5.23 1.17 5.84 42 29341 89M 335. CA NC3 667 2634 6.05 4.79 1.26 6.28 4.79 1.26 6.28 43 29342 89M 335. CA NO3 667 2635 6.61 4.80 1.81 9.06 4.80 1.81 9.06 44 29344 89M 335. CA NO2 667 2637 7.97 6.37 1.60 8.00 6.37 1.60 8.00 45 29345 89M 335. CB AO1 668 2605 9.03 6.11 2.92 14.61 6.11 2.92 14.61 46 29347 89M 335. CB O3 668 2626 7.68 6.62 1.06 5.28 6.62 1.06 5.28 47 29350 89M 335. CB NC3 668 2634 7.03 6.07 0.96 4.81 6.07 0.96 4.81 48 29351 89M 335. CB NO3 668 2635 7.51 5.85 1.66 8.31 5.85 1.66 8.31 49 29353 89M 335. C AO1 672 2605 7.55 5.34 2.21 11.07 5.34 2.21 11.07 50 29356 89M 335. C O3 672 2626 5.91 4.96 0.95 4.73 4.96 0.95 4.73 51 29364 89M 335. C NC3 672 2634 5.29 3.89 1.40 7.00 3.89 1.40 7.00 52 29365 89M 335. C NO3 672 2635 6.05 4.05 2.00 9.99 4.05 2.00 9.99 53 29367 89M 335. C NO2 672 2637 6.98 5.08 1.90 9.48 5.08 1.90 9.48 54 29370 89M 335. O AO1 673 2605 8.02 6.35 1.67 8.36 6.35 1.67 8.36 55 29379 89M 335. O NC3 673 2634 4.56 3.18 1.37 6.87 3.18 1.37 6.87 56 29380 89M 335. O NO3 673 2635 5.16 3.06 2.10 10.52 3.06 2.10 10.52 57 29382 89M 335. O NO2 673 2637 6.11 4.16 1.95 9.77 4.16 1.95 9.77 58 29386 90P 335. N AO1 674 2605 7.36 4.80 2.56 12.82 4.80 2.56 12.82 59 29390 90P 335. N O3 674 2626 5.61 4.36 1.25 6.24 4.36 1.25 6.24 60 29398 90P 335. N NC3 674 2634 5.95 4.37 1.58 7.90 4.37 1.58 7.90 61 29399 90P 335. N NO3 674 2635 6.93 4.87 2.06 10.32 4.87 2.06 10.32 62 29401 90P 335. N NO2 674 2637 7.44 5.28 2.17 10.83 5.28 2.17 10.83 63 29404 90P 335. CA AO1 675 2605 7.76 5.72 2.04 10.18 5.72 2.04 10.18 64 29414 90P 335. CA NC3 675 2634 6.13 4.51 1.63 8.13 4.51 1.63 8.13 65 29415 90P 335. CA NO3 675 2635 7.26 5.11 2.15 10.77 5.11 2.15 10.77 66 29416 90P 335. CA NC2 675 2636 5.90 4.96 0.94 4.68 4.96 0.94 4.68 67 29417 90P 335. CA NO2 675 2637 7.20 4.71 2.49 12.44 4.71 2.49 12.44 68 29420 90P 335. CB AO1 677 2605 7.30 5.33 1.97 9.83 5.33 1.97 9.83 69 29423 90P 335. CB O3 677 2626 5.31 4.38 0.93 4.66 4.38 0.93 4.66 70 29430 90P 335. CB NC3 677 2634 6.74 5.32 1.42 7.08 5.32 1.42 7.08 71 29431 90P 335. CB NO3 677 2635 8.01 6.20 1.81 9.06 6.20 1.81 9.06 72 29432 90P 335. CB NC2 677 2636 6.49 5.57 0.92 4.58 5.57 0.92 4.58 73 29433 90P 335. CB NO2 677 2637 7.72 5.46 2.26 11.29 5.46 2.26 11.29 74 29434 90P 335. C AO1 679 2605 9.16 6.93 2.23 11.16 6.93 2.23 11.16 75 29442 90P 335. C NO3 679 2635 7.50 5.99 1.51 7.53 5.99 1.51 7.53 76 29444 90P 335. C NO2 679 2637 7.21 5.46 1.75 8.75 5.46 1.75 8.75 77 29445 90P 335. O AO1 680 2605 9.54 6.95 2.59 12.95 6.95 2.59 12.95 78 29452 91L 335. N NC3 681 2634 6.95 6.01 0.94 4.70 6.01 0.94 4.70 79 29453 91L 335. N NO3 681 2635 7.97 6.29 1.69 8.43 6.29 1.69 8.43 80 29455 91L 335. N NO2 681 2637 7.18 5.23 1.95 9.73 5.23 1.95 9.73 81 29456 91L 335. CA NO2 682 2637 8.14 6.42 1.71 8.57 6.42 1.71 8.57 82 29457 91L 335. CB NO2 683 2637 7.95 6.36 1.60 7.99 6.36 1.60 7.99 83 29458 97R 335. CA NO2 726 2637 7.82 6.75 1.07 5.36 6.75 1.07 5.36 84 29459 97R 335. CB NO2 727 2637 7.69 6.52 1.17 5.85 6.52 1.17 5.85 85 29490 100L 335. CD2 NO2 754 2637 4.99 4.00 0.99 4.94 4.00 0.99 4.94 86 29579 107I 335. O AN1 805 2622 7.16 6.23 0.94 4.69 6.23 0.94 4.69 87 31794 86V 335. CA AN1 649 2622 9.78 8.41 1.37 6.83 8.41 1.37 6.83 88 31795 86V 335. CA AC2 649 2623 9.82 7.96 1.86 9.30 7.96 1.86 9.30 89 31796 86V 335. CA AN3 649 2624 9.24 7.78 1.45 7.27 7.78 1.45 7.27 90 31801 86V 335. CA NO2 649 2629 7.40 6.24 1.16 5.80 6.24 1.16 5.80 91 31805 86V 335. CA NO4 649 2633 5.46 4.55 0.91 4.54 4.55 0.91 4.54 92 31811 86V 335. CA NN1 649 2639 7.29 5.99 1.30 6.49 5.99 1.30 6.49 93 31812 86V 335. CA NC2 649 2640 8.30 7.00 1.30 6.51 7.00 1.30 6.51 94 31813 86V 335. CA NC3 649 2641 9.64 7.45 2.19 10.96 7.45 2.19 10.96 95 31814 86V 335. CA NC7 649 2642 10.82 8.72 2.10 10.50 8.72 2.10 10.50 96 31815 86V 335. CA NO7 649 2643 11.90 9.52 2.38 11.91 9.52 2.38 11.91 97 31816 86V 335. CA NN7 649 2644 10.69 9.01 1.67 8.37 9.01 1.67 8.37 98 31817 86V 335. CA NC4 649 2645 10.10 7.10 3.00 15.00 7.10 3.00 15.00 99 31818 86V 335. CA NC5 649 2646 9.30 6.18 3.12 15.62 6.18 3.12 15.62 100 31819 86V 335. CA NC6 649 2647 7.91 5.55 2.36 11.79 5.55 2.36 11.79 101 31839 87A 335. CA AC2 656 2623 6.10 5.12 0.98 4.92 5.12 0.98 4.92 102 31857 87A 335. CA NC3 656 2641 10.92 9.94 0.98 4.89 9.94 0.98 4.89 103 31858 87A 335. CA NC4 656 2645 11.08 9.88 1.20 6.00 9.88 1.20 6.00 104 31859 87A 335. CA NC5 656 2646 10.09 8.87 1.21 6.07 8.87 1.21 6.07 105 31860 87A 335. CA NC6 656 2647 8.81 7.81 1.00 5.01 7.81 1.00 5.01 106 31862 88S 335. CA AO1 661 2605 7.31 6.22 1.09 5.46 6.22 1.09 5.46 107 31902 89M 335. CA AO1 667 2605 7.69 5.02 2.67 13.34 5.02 2.67 13.34 108 31920 89M 335. CA O3 667 2626 6.40 5.23 1.17 5.84 5.23 1.17 5.84 109 31928 89M 335. CA NC3 667 2634 6.05 4.79 1.26 6.28 4.79 1.26 6.28 110 31929 89M 335. CA NO3 667 2635 6.61 4.80 1.81 9.06 4.80 1.81 9.06 111 31931 89M 335. CA NO2 667 2637 7.97 6.37 1.60 8.00 6.37 1.60 8.00 112 31937 90P 335. CA AO1 675 2605 7.76 5.72 2.04 10.18 5.72 2.04 10.18 113 31953 90P 335. CA NC3 675 2634 6.13 4.51 1.63 8.13 4.51 1.63 8.13 114 31954 90P 335. CA NO3 675 2635 7.26 5.11 2.15 10.77 5.11 2.15 10.77 115 31955 90P 335. CA NC2 675 2636 5.90 4.96 0.94 4.68 4.96 0.94 4.68 116 31956 90P 335. CA NO2 675 2637 7.20 4.71 2.49 12.44 4.71 2.49 12.44 117 31965 91L 335. CA AO1 682 2605 11.47 9.28 2.19 10.95 9.28 2.19 10.95 118 31974 91L 335. CA NO3 682 2635 9.00 7.49 1.51 7.54 7.49 1.51 7.54 119 31976 91L 335. CA NO2 682 2637 8.14 6.42 1.71 8.57 6.42 1.71 8.57 120 31984 97R 335. CA NO2 726 2637 7.82 6.75 1.07 5.36 6.75 1.07 5.36 121 32002 103S 335. CA AC8 772 2617 10.42 9.36 1.05 5.27 9.36 1.05 5.27 122 32009 104N 335. CA AC8 778 2617 9.19 8.27 0.92 4.60 8.27 0.92 4.60 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 2 24 72 187 218 339 298 365 463 457 497 << end of ENERGY. TOP_________> 365 232 GO_TO __ACCELRYS3 TOP_________> 366 242 SET OUTPUT = OUTPUT2 TOP_________> 367 243 CALL ROUTINE = 'user_after_single_model' TOP_________> 368 249 RETURN TOP_________> 369 244 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990001.pdb wrpdb2__568_> Residues, atoms, selected atoms: 335 2647 2647 TOP_________> 370 245 SET FINAL_MODEL = FILE TOP_________> 371 246 RETURN TOP_________> 372 205 END_DO TOP_________> 373 203 SET FINAL_MODEL = 'default' TOP_________> 374 204 CALL ROUTINE = 'single_model' TOP_________> 375 215 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 376 216 SET ID1 = 0 TOP_________> 377 217 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000002 TOP_________> 378 218 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 2 335 2647 rdatm___298_> Segment: 1 1 333 2597 rdatm___298_> Segment: 2 334 335 50 TOP_________> 379 219 CALL ROUTINE = 'select_atoms' TOP_________> 380 288 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 : 2647 2647 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2647 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : BLK 335 TOP_________> 381 289 RETURN TOP_________> 382 220 CALL ROUTINE = RAND_METHOD TOP_________> 383 272 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2647 2647 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 384 273 RETURN TOP_________> 385 221 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 386 222 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 387 223 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 388 224 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 389 225 CALL ROUTINE = 'single_model_pass' TOP_________> 390 252 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 391 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 392 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 17112 TOP_________> 393 255 OPTIMIZE TOP_________> 394 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 395 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 396 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 397 259 END_DO TOP_________> 398 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 399 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 19019 TOP_________> 400 255 OPTIMIZE TOP_________> 401 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 402 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 403 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 404 259 END_DO TOP_________> 405 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 406 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 20133 TOP_________> 407 255 OPTIMIZE TOP_________> 408 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 409 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 410 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 411 259 END_DO TOP_________> 412 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 413 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 21411 TOP_________> 414 255 OPTIMIZE TOP_________> 415 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 416 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 417 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 418 259 END_DO TOP_________> 419 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 420 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 22706 TOP_________> 421 255 OPTIMIZE TOP_________> 422 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 423 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 424 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 425 259 END_DO TOP_________> 426 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 427 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 24624 TOP_________> 428 255 OPTIMIZE TOP_________> 429 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 430 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 431 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 432 259 END_DO TOP_________> 433 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 434 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 27113 TOP_________> 435 255 OPTIMIZE TOP_________> 436 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 437 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 438 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 439 259 END_DO TOP_________> 440 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 441 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 28185 TOP_________> 442 255 OPTIMIZE TOP_________> 443 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 444 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 445 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 446 259 END_DO TOP_________> 447 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 448 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 29455 TOP_________> 449 255 OPTIMIZE TOP_________> 450 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 451 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 452 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 453 259 END_DO TOP_________> 454 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 455 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 30615 TOP_________> 456 255 OPTIMIZE TOP_________> 457 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 458 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 459 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 460 259 END_DO TOP_________> 461 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 462 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 463 255 OPTIMIZE TOP_________> 464 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 465 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 466 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 467 259 END_DO TOP_________> 468 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 469 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 470 255 OPTIMIZE TOP_________> 471 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 472 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 473 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 474 259 END_DO TOP_________> 475 260 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 476 292 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 477 293 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 478 294 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 479 295 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 480 306 CALL ROUTINE = MD_LEVEL TOP_________> 481 330 SET UPDATE_DYNAMIC = 0.39 TOP_________> 482 331 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 483 332 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 484 333 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 485 334 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 486 335 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 487 336 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 488 337 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 489 338 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 490 339 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 491 340 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 492 341 RETURN TOP_________> 493 307 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 494 312 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 495 313 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 496 326 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 497 327 RETURN TOP_________> 498 261 LABEL __ABORT TOP_________> 499 262 SET ERROR_STATUS = 0 TOP_________> 500 263 RETURN TOP_________> 501 226 END_DO TOP_________> 502 227 IUPAC_MODEL iupac_m_486_> OE1/2 will be swapped: -179.5344 28 28 iupac_m_485_> OD1/2 will be swapped: 166.6881 32 32 iupac_m_487_> NH1/2 swapped: -179.6004 33 33 iupac_m_485_> OD1/2 will be swapped: 94.0381 41 41 iupac_m_487_> NH1/2 swapped: -179.3915 48 48 iupac_m_483_> CD1/2 CE1/2 swapped: 98.3381 67 67 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 143.2452 79 79 iupac_m_485_> OD1/2 will be swapped: 120.4287 81 81 iupac_m_487_> NH1/2 swapped: -179.4429 97 97 iupac_m_483_> CD1/2 CE1/2 swapped: -92.9775 108 108 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 144.2384 132 132 iupac_m_486_> OE1/2 will be swapped: -179.3845 137 137 iupac_m_483_> CD1/2 CE1/2 swapped: 92.8938 151 151 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: 90.5383 163 163 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -90.1052 iupac_m_485_> OD1/2 will be swapped: 169.6369 173 173 iupac_m_485_> OD1/2 will be swapped: 112.7979 176 176 iupac_m_486_> OE1/2 will be swapped: 167.7424 188 188 iupac_m_485_> OD1/2 will be swapped: 169.6597 210 210 iupac_m_485_> OD1/2 will be swapped: 137.5996 213 213 iupac_m_483_> CD1/2 CE1/2 swapped: 93.6274 216 216 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: -178.2883 231 231 iupac_m_486_> OE1/2 will be swapped: -115.9469 263 263 iupac_m_483_> CD1/2 CE1/2 swapped: -93.1327 285 285 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: 96.2383 287 287 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: 96.6701 303 303 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: 177.9854 310 310 iupac_m_485_> OD1/2 will be swapped: -173.9433 319 319 TOP_________> 503 228 SET ID1 = 9999 TOP_________> 504 229 SET OUTPUT2 = OUTPUT TOP_________> 505 230 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'eq', THEN = 'GO_TO __ACCELRYS2' TOP_________> 506 231 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 2 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2647 2647 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 32046 32046 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 6220 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 : 2199.2202 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 : 2663 0 0 0.006 0.006 23.532 1.000 2 Bond angle potential : 3615 4 11 2.814 2.814 381.87 1.000 3 Stereochemical cosine torsion poten: 1744 0 44 46.715 46.715 576.86 1.000 4 Stereochemical improper torsion pot: 1119 0 1 1.332 1.332 45.489 1.000 5 Soft-sphere overlap restraints : 6220 0 0 0.003 0.003 5.6757 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 7007 0 0 0.151 0.151 125.15 1.000 10 Distance restraints 2 (N-O) : 7019 0 6 0.242 0.242 274.84 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 332 0 2 4.199 4.199 68.250 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 8 77.079 77.079 105.70 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 3 80.387 80.387 90.474 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 0 74.350 74.350 56.401 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 77.126 77.126 17.512 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 3 0 0 0.021 0.021 0.39429E-01 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3416 0 2 0.470 0.470 180.65 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 331 15 30 27.168 32.904 39.781 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1117 0 1 0.891 0.891 162.89 1.000 27 Distance restraints 5 (X-Y) : 3071 0 1 0.044 0.044 44.101 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990002 # Heavy relative violation of each residue is written to: TvLDH.V99990002 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 32438.8574 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 9170 29L 30Y C N 209 211 -111.53 -124.30 87.03 5.16 -63.50 106.55 19.25 1 30Y 30Y N CA 211 212 -138.51 135.40 -43.40 2 9171 30Y 31G C N 221 223 -134.54 -167.20 57.06 2.27 78.70 149.31 8.06 2 31G 31G N CA 223 224 -138.61 174.60 -166.10 3 9172 31G 32D C N 225 227 -78.27 -96.50 53.79 2.27 -63.30 104.67 12.08 3 32D 32D N CA 227 228 63.59 114.20 -40.00 4 9242 101I 102S C N 763 765 -84.65 -72.40 55.76 3.70 -64.10 134.58 8.74 4 102S 102S N CA 765 766 98.00 152.40 -35.00 5 9243 102S 103S C N 769 771 151.62 -64.10 149.36 19.95 -64.10 149.36 19.95 5 103S 103S N CA 771 772 -73.64 -35.00 -35.00 6 9295 154L 155S C N 1172 1174 -135.67 -64.10 88.97 8.15 -64.10 88.97 8.15 6 155S 155S N CA 1174 1175 17.86 -35.00 -35.00 7 9355 214H 215D C N 1642 1644 -79.08 -63.30 78.21 8.81 -63.30 78.21 8.81 7 215D 215D N CA 1644 1645 36.60 -40.00 -40.00 8 9359 218F 219D C N 1680 1682 -113.62 -63.30 66.70 11.21 -63.30 66.70 11.21 8 219D 219D N CA 1682 1683 -83.78 -40.00 -40.00 9 9367 226G 227H C N 1747 1749 -109.16 -63.20 79.74 8.55 -63.20 79.74 8.55 9 227H 227H N CA 1749 1750 22.86 -42.30 -42.30 10 9381 240S 241A C N 1869 1871 -97.17 -62.50 37.86 7.69 -62.50 37.86 7.69 10 241A 241A N CA 1871 1872 -56.11 -40.90 -40.90 11 9397 256L 257F C N 1989 1991 -115.04 -63.20 70.65 8.24 -63.20 70.65 8.24 11 257F 257F N CA 1991 1992 3.70 -44.30 -44.30 12 9413 272P 273E C N 2098 2100 -154.81 -63.60 103.69 13.69 -63.60 103.69 13.69 12 273E 273E N CA 2100 2101 9.01 -40.30 -40.30 13 9433 292D 293K C N 2248 2250 -20.79 -70.20 79.20 4.76 -62.90 126.51 18.94 13 293K 293K N CA 2250 2251 78.50 140.40 -40.80 14 9434 293K 294E C N 2257 2259 -176.15 -63.60 114.74 17.07 -63.60 114.74 17.07 14 294E 294E N CA 2259 2260 -17.98 -40.30 -40.30 15 9442 301E 302G C N 2320 2322 -79.02 -62.40 19.81 2.97 82.20 165.85 12.30 15 302G 302G N CA 2322 2323 -30.42 -41.20 8.50 report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 0 24 57 155 213 335 299 388 406 433 466 << end of ENERGY. TOP_________> 507 232 GO_TO __ACCELRYS3 TOP_________> 508 242 SET OUTPUT = OUTPUT2 TOP_________> 509 243 CALL ROUTINE = 'user_after_single_model' TOP_________> 510 249 RETURN TOP_________> 511 244 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990002.pdb wrpdb2__568_> Residues, atoms, selected atoms: 335 2647 2647 TOP_________> 512 245 SET FINAL_MODEL = FILE TOP_________> 513 246 RETURN TOP_________> 514 205 END_DO TOP_________> 515 203 SET FINAL_MODEL = 'default' TOP_________> 516 204 CALL ROUTINE = 'single_model' TOP_________> 517 215 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 518 216 SET ID1 = 0 TOP_________> 519 217 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000003 TOP_________> 520 218 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 2 335 2647 rdatm___298_> Segment: 1 1 333 2597 rdatm___298_> Segment: 2 334 335 50 TOP_________> 521 219 CALL ROUTINE = 'select_atoms' TOP_________> 522 288 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 : 2647 2647 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2647 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : BLK 335 TOP_________> 523 289 RETURN TOP_________> 524 220 CALL ROUTINE = RAND_METHOD TOP_________> 525 272 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2647 2647 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 526 273 RETURN TOP_________> 527 221 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 528 222 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 529 223 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 530 224 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 531 225 CALL ROUTINE = 'single_model_pass' TOP_________> 532 252 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 533 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 534 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 17112 TOP_________> 535 255 OPTIMIZE TOP_________> 536 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 537 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 538 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 539 259 END_DO TOP_________> 540 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 541 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 19019 TOP_________> 542 255 OPTIMIZE TOP_________> 543 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 544 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 545 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 546 259 END_DO TOP_________> 547 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 548 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 20133 TOP_________> 549 255 OPTIMIZE TOP_________> 550 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 551 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 552 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 553 259 END_DO TOP_________> 554 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 555 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 21411 TOP_________> 556 255 OPTIMIZE TOP_________> 557 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 558 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 559 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 560 259 END_DO TOP_________> 561 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 562 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 22706 TOP_________> 563 255 OPTIMIZE TOP_________> 564 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 565 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 566 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 567 259 END_DO TOP_________> 568 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 569 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 24624 TOP_________> 570 255 OPTIMIZE TOP_________> 571 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 572 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 573 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 574 259 END_DO TOP_________> 575 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 576 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 27113 TOP_________> 577 255 OPTIMIZE TOP_________> 578 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 579 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 580 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 581 259 END_DO TOP_________> 582 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 583 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 28185 TOP_________> 584 255 OPTIMIZE TOP_________> 585 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 586 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 587 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 588 259 END_DO TOP_________> 589 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 590 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 29455 TOP_________> 591 255 OPTIMIZE TOP_________> 592 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 593 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 594 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 595 259 END_DO TOP_________> 596 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 597 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 30615 TOP_________> 598 255 OPTIMIZE TOP_________> 599 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 600 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 601 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 602 259 END_DO TOP_________> 603 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 604 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 605 255 OPTIMIZE TOP_________> 606 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 607 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 608 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 609 259 END_DO TOP_________> 610 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 611 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 612 255 OPTIMIZE TOP_________> 613 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 614 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 615 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 616 259 END_DO TOP_________> 617 260 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 618 292 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 619 293 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 620 294 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 621 295 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 622 306 CALL ROUTINE = MD_LEVEL TOP_________> 623 330 SET UPDATE_DYNAMIC = 0.39 TOP_________> 624 331 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 625 332 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 626 333 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 627 334 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 628 335 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 629 336 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 630 337 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 631 338 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 632 339 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 633 340 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 634 341 RETURN TOP_________> 635 307 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 636 312 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 637 313 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 638 326 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 639 327 RETURN TOP_________> 640 261 LABEL __ABORT TOP_________> 641 262 SET ERROR_STATUS = 0 TOP_________> 642 263 RETURN TOP_________> 643 226 END_DO TOP_________> 644 227 IUPAC_MODEL iupac_m_487_> NH1/2 swapped: 179.4539 48 48 iupac_m_483_> CD1/2 CE1/2 swapped: 95.6429 67 67 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 170.3781 72 72 iupac_m_483_> CD1/2 CE1/2 swapped: 91.8527 77 77 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -97.3225 108 108 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 146.5155 132 132 iupac_m_486_> OE1/2 will be swapped: -173.4533 149 149 iupac_m_486_> OE1/2 will be swapped: 126.3232 165 165 iupac_m_485_> OD1/2 will be swapped: -156.6295 176 176 iupac_m_483_> CD1/2 CE1/2 swapped: 91.0008 199 199 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 174.5993 210 210 iupac_m_485_> OD1/2 will be swapped: -179.9657 219 219 iupac_m_487_> NH1/2 swapped: 177.9822 228 228 iupac_m_483_> CD1/2 CE1/2 swapped: 95.8045 287 287 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: 178.3048 294 294 iupac_m_483_> CD1/2 CE1/2 swapped: 95.2831 303 303 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 122.7919 314 314 iupac_m_485_> OD1/2 will be swapped: 175.0934 319 319 TOP_________> 645 228 SET ID1 = 9999 TOP_________> 646 229 SET OUTPUT2 = OUTPUT TOP_________> 647 230 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'eq', THEN = 'GO_TO __ACCELRYS2' TOP_________> 648 231 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 3 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2647 2647 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 32046 32046 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 6579 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 : 11194.3457 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 : 2663 0 7 0.009 0.009 63.872 1.000 2 Bond angle potential : 3615 1 23 2.416 2.416 412.00 1.000 3 Stereochemical cosine torsion poten: 1744 0 49 46.709 46.709 586.60 1.000 4 Stereochemical improper torsion pot: 1119 1 8 1.905 1.905 86.015 1.000 5 Soft-sphere overlap restraints : 6579 0 4 0.007 0.007 35.518 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 7007 2 25 0.292 0.292 371.32 1.000 10 Distance restraints 2 (N-O) : 7019 3 33 0.356 0.356 502.32 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 332 1 9 5.030 5.030 98.294 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 10 73.204 73.204 106.40 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 2 82.931 82.931 100.27 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 0 80.159 80.159 56.983 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 85.588 85.588 22.223 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 3 0 0 0.002 0.002 0.41309E-03 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3416 0 0 0.438 0.438 149.48 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 331 20 32 28.270 35.766 80.287 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1117 0 4 0.915 0.915 157.92 1.000 27 Distance restraints 5 (X-Y) : 3071 285 532 0.538 0.538 8364.8 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990003 # Heavy relative violation of each residue is written to: TvLDH.V99990003 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 44113.7500 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 9 : Distance restraints 1 (CA-CA) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 12713 90P 97R CA CA 675 726 13.42 8.68 4.74 4.87 8.68 4.74 4.87 2 12727 91L 97R CA CA 682 726 12.59 6.81 5.77 8.23 6.81 5.77 8.23 ------------------------------------------------------------------------------------------------- Feature 10 : Distance restraints 2 (N-O) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 19309 90P 97R N O 674 735 14.52 9.04 5.48 5.01 9.04 5.48 5.01 2 19322 91L 97R N O 681 735 13.81 7.26 6.55 7.67 7.26 6.55 7.67 3 19396 100L 97R N O 749 735 5.57 2.93 2.65 6.33 2.93 2.65 6.33 ------------------------------------------------------------------------------------------------- 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 9170 29L 30Y C N 209 211 -115.64 -63.50 80.45 11.11 -63.50 80.45 11.11 1 30Y 30Y N CA 211 212 17.87 -43.40 -43.40 2 9172 31G 32D C N 225 227 -83.41 -96.50 47.16 1.99 -63.30 110.73 12.58 2 32D 32D N CA 227 228 68.89 114.20 -40.00 3 9226 85L 86V C N 646 648 -122.57 -62.40 93.93 10.54 -62.40 93.93 10.54 3 86V 86V N CA 648 649 29.73 -42.40 -42.40 4 9231 90P 91L C N 679 681 174.18 -108.50 99.17 4.41 -70.70 126.73 9.49 4 91L 91L N CA 681 682 -165.40 132.50 141.60 5 9237 96V 97R C N 723 725 -78.23 -63.00 67.71 8.23 -63.00 67.71 8.23 5 97R 97R N CA 725 726 24.88 -41.10 -41.10 6 9238 97R 98A C N 734 736 -139.49 -62.50 78.79 15.72 -62.50 78.79 15.72 6 98A 98A N CA 736 737 -57.64 -40.90 -40.90 7 9241 100L 101I C N 755 757 -63.52 -97.30 34.60 1.69 -63.40 163.29 26.76 7 101I 101I N CA 757 758 119.69 127.20 -43.60 8 9242 101I 102S C N 763 765 178.43 -136.60 125.24 5.25 -64.10 130.53 17.36 8 102S 102S N CA 765 766 -91.92 151.20 -35.00 9 9295 154L 155S C N 1172 1174 -135.98 -64.10 89.63 8.18 -64.10 89.63 8.18 9 155S 155S N CA 1174 1175 18.54 -35.00 -35.00 10 9355 214H 215D C N 1642 1644 -77.66 -63.30 77.88 8.84 -63.30 77.88 8.84 10 215D 215D N CA 1644 1645 36.54 -40.00 -40.00 11 9359 218F 219D C N 1680 1682 -112.76 -63.30 67.34 11.27 -63.30 67.34 11.27 11 219D 219D N CA 1682 1683 -85.70 -40.00 -40.00 12 9367 226G 227H C N 1747 1749 -109.34 -63.20 79.39 8.52 -63.20 79.39 8.52 12 227H 227H N CA 1749 1750 22.30 -42.30 -42.30 13 9381 240S 241A C N 1869 1871 -96.72 -62.50 38.14 7.75 -62.50 38.14 7.75 13 241A 241A N CA 1871 1872 -57.72 -40.90 -40.90 14 9413 272P 273E C N 2098 2100 -155.42 -63.60 102.18 13.72 -63.60 102.18 13.72 14 273E 273E N CA 2100 2101 4.53 -40.30 -40.30 15 9421 280K 281P C N 2159 2161 -62.06 -58.70 24.09 2.27 -64.50 158.47 11.95 15 281P 281P N CA 2161 2162 -54.35 -30.50 147.20 16 9422 281P 282G C N 2166 2168 -64.64 -62.40 42.04 6.17 82.20 147.05 10.14 16 282G 282G N CA 2168 2169 0.78 -41.20 8.50 17 9433 292D 293K C N 2248 2250 -32.06 -70.20 65.18 3.94 -62.90 131.99 18.96 17 293K 293K N CA 2250 2251 87.54 140.40 -40.80 18 9434 293K 294E C N 2257 2259 -176.16 -63.60 114.80 17.07 -63.60 114.80 17.07 18 294E 294E N CA 2259 2260 -17.75 -40.30 -40.30 19 9441 300V 301E C N 2311 2313 -132.25 -117.80 148.77 7.71 -117.80 148.77 7.71 19 301E 301E N CA 2313 2314 -11.27 136.80 136.80 20 9442 301E 302G C N 2320 2322 -73.54 -62.40 15.40 2.18 82.20 160.56 11.94 20 302G 302G N CA 2322 2323 -30.56 -41.20 8.50 ------------------------------------------------------------------------------------------------- Feature 27 : Distance restraints 5 (X-Y) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 28975 86V 335. N NO4 648 2633 7.04 5.81 1.22 6.10 5.81 1.22 6.10 2 28976 86V 335. N NC6 648 2647 9.41 6.77 2.64 13.22 6.77 2.64 13.22 3 28981 86V 335. CA NO2 649 2629 7.64 6.24 1.40 6.98 6.24 1.40 6.98 4 28985 86V 335. CA NO4 649 2633 5.54 4.55 1.00 4.98 4.55 1.00 4.98 5 28990 86V 335. CA NN1 649 2639 7.25 5.99 1.26 6.29 5.99 1.26 6.29 6 28991 86V 335. CA NC2 649 2640 8.23 7.00 1.23 6.14 7.00 1.23 6.14 7 28992 86V 335. CA NC5 649 2646 9.32 6.18 3.15 15.74 6.18 3.15 15.74 8 28993 86V 335. CA NC6 649 2647 7.92 5.55 2.37 11.86 5.55 2.37 11.86 9 28999 86V 335. CB NO2 650 2629 6.91 5.67 1.24 6.22 5.67 1.24 6.22 10 29006 86V 335. CB NC4 650 2645 9.17 6.79 2.38 11.89 6.79 2.38 11.89 11 29007 86V 335. CB NC5 650 2646 8.41 5.76 2.66 13.28 5.76 2.66 13.28 12 29008 86V 335. CB NC6 650 2647 7.05 5.37 1.68 8.39 5.37 1.68 8.39 13 29021 86V 335. C NO2 653 2629 6.75 5.54 1.21 6.05 5.54 1.21 6.05 14 29025 86V 335. C NO4 653 2633 5.28 4.37 0.92 4.58 4.37 0.92 4.58 15 29030 86V 335. C NN1 653 2639 7.32 6.28 1.03 5.17 6.28 1.03 5.17 16 29031 86V 335. C NC5 653 2646 9.18 6.82 2.36 11.79 6.82 2.36 11.79 17 29032 86V 335. C NC6 653 2647 7.78 5.95 1.83 9.13 5.95 1.83 9.13 18 29051 86V 335. O NO2 654 2629 5.57 4.35 1.23 6.13 4.35 1.23 6.13 19 29061 86V 335. O NC5 654 2646 8.24 6.49 1.74 8.72 6.49 1.74 8.72 20 29062 86V 335. O NC6 654 2647 6.86 5.54 1.32 6.58 5.54 1.32 6.58 21 29079 87A 335. N NO2 655 2629 7.52 6.52 1.00 5.00 6.52 1.00 5.00 22 29083 87A 335. N NO4 655 2633 6.40 5.20 1.21 6.05 5.20 1.21 6.05 23 29221 88S 335. CA AO1 661 2605 7.28 6.22 1.06 5.29 6.22 1.06 5.29 24 29248 88S 335. C AO1 664 2605 6.63 5.04 1.59 7.96 5.04 1.59 7.96 25 29271 88S 335. C NO3 664 2635 5.15 4.23 0.92 4.61 4.23 0.92 4.61 26 29276 88S 335. O AO1 665 2605 5.44 3.96 1.48 7.40 3.96 1.48 7.40 27 29305 89M 335. N AO1 666 2605 7.65 5.55 2.10 10.52 5.55 2.10 10.52 28 29322 89M 335. N NC3 666 2634 5.49 4.44 1.05 5.23 4.44 1.05 5.23 29 29323 89M 335. N NO3 666 2635 5.76 4.23 1.52 7.62 4.23 1.52 7.62 30 29325 89M 335. N NO2 666 2637 7.59 6.35 1.24 6.19 6.35 1.24 6.19 31 29328 89M 335. CA AO1 667 2605 7.63 5.02 2.61 13.04 5.02 2.61 13.04 32 29334 89M 335. CA O3 667 2626 6.34 5.23 1.11 5.56 5.23 1.11 5.56 33 29341 89M 335. CA NC3 667 2634 6.10 4.79 1.31 6.55 4.79 1.31 6.55 34 29342 89M 335. CA NO3 667 2635 6.64 4.80 1.83 9.16 4.80 1.83 9.16 35 29344 89M 335. CA NO2 667 2637 8.04 6.37 1.67 8.35 6.37 1.67 8.35 36 29345 89M 335. CB AO1 668 2605 8.94 6.11 2.83 14.15 6.11 2.83 14.15 37 29347 89M 335. CB O3 668 2626 7.60 6.62 0.97 4.87 6.62 0.97 4.87 38 29350 89M 335. CB NC3 668 2634 7.13 6.07 1.06 5.30 6.07 1.06 5.30 39 29351 89M 335. CB NO3 668 2635 7.59 5.85 1.74 8.70 5.85 1.74 8.70 40 29353 89M 335. C AO1 672 2605 7.53 5.34 2.19 10.94 5.34 2.19 10.94 41 29356 89M 335. C O3 672 2626 5.90 4.96 0.94 4.68 4.96 0.94 4.68 42 29364 89M 335. C NC3 672 2634 5.30 3.89 1.40 7.01 3.89 1.40 7.01 43 29365 89M 335. C NO3 672 2635 6.00 4.05 1.94 9.72 4.05 1.94 9.72 44 29367 89M 335. C NO2 672 2637 7.00 5.08 1.92 9.60 5.08 1.92 9.60 45 29370 89M 335. O AO1 673 2605 7.97 6.35 1.62 8.10 6.35 1.62 8.10 46 29379 89M 335. O NC3 673 2634 4.53 3.18 1.34 6.71 3.18 1.34 6.71 47 29380 89M 335. O NO3 673 2635 5.07 3.06 2.01 10.04 3.06 2.01 10.04 48 29382 89M 335. O NO2 673 2637 6.13 4.16 1.97 9.84 4.16 1.97 9.84 49 29386 90P 335. N AO1 674 2605 7.35 4.80 2.55 12.77 4.80 2.55 12.77 50 29390 90P 335. N O3 674 2626 5.63 4.36 1.27 6.36 4.36 1.27 6.36 51 29398 90P 335. N NC3 674 2634 5.97 4.37 1.60 8.00 4.37 1.60 8.00 52 29399 90P 335. N NO3 674 2635 6.90 4.87 2.03 10.15 4.87 2.03 10.15 53 29401 90P 335. N NO2 674 2637 7.49 5.28 2.21 11.05 5.28 2.21 11.05 54 29404 90P 335. CA AO1 675 2605 7.74 5.72 2.01 10.06 5.72 2.01 10.06 55 29406 90P 335. CA O3 675 2626 5.78 4.88 0.91 4.53 4.88 0.91 4.53 56 29414 90P 335. CA NC3 675 2634 6.15 4.51 1.64 8.19 4.51 1.64 8.19 57 29415 90P 335. CA NO3 675 2635 7.22 5.11 2.12 10.58 5.11 2.12 10.58 58 29416 90P 335. CA NC2 675 2636 5.93 4.96 0.97 4.86 4.96 0.97 4.86 59 29417 90P 335. CA NO2 675 2637 7.24 4.71 2.53 12.67 4.71 2.53 12.67 60 29420 90P 335. CB AO1 677 2605 7.25 5.33 1.92 9.61 5.33 1.92 9.61 61 29423 90P 335. CB O3 677 2626 5.32 4.38 0.94 4.68 4.38 0.94 4.68 62 29430 90P 335. CB NC3 677 2634 6.73 5.32 1.40 7.02 5.32 1.40 7.02 63 29431 90P 335. CB NO3 677 2635 7.97 6.20 1.77 8.83 6.20 1.77 8.83 64 29432 90P 335. CB NC2 677 2636 6.48 5.57 0.91 4.54 5.57 0.91 4.54 65 29433 90P 335. CB NO2 677 2637 7.72 5.46 2.26 11.32 5.46 2.26 11.32 66 29434 90P 335. C AO1 679 2605 9.13 6.93 2.21 11.04 6.93 2.21 11.04 67 29442 90P 335. C NO3 679 2635 7.45 5.99 1.45 7.27 5.99 1.45 7.27 68 29444 90P 335. C NO2 679 2637 7.26 5.46 1.80 8.99 5.46 1.80 8.99 69 29445 90P 335. O AO1 680 2605 9.57 6.95 2.63 13.13 6.95 2.63 13.13 70 29452 91L 335. N NC3 681 2634 6.95 6.01 0.93 4.67 6.01 0.93 4.67 71 29453 91L 335. N NO3 681 2635 7.92 6.29 1.64 8.18 6.29 1.64 8.18 72 29455 91L 335. N NO2 681 2637 7.22 5.23 1.99 9.94 5.23 1.99 9.94 73 29456 91L 335. CA NO2 682 2637 8.21 6.42 1.78 8.92 6.42 1.78 8.92 74 29457 91L 335. CB NO2 683 2637 7.97 6.36 1.61 8.07 6.36 1.61 8.07 75 29458 97R 335. CA NO2 726 2637 7.75 6.75 1.00 4.99 6.75 1.00 4.99 76 29459 97R 335. CB NO2 727 2637 7.72 6.52 1.20 6.02 6.52 1.20 6.02 77 29473 97R 335. O NO2 735 2637 9.16 6.86 2.30 11.52 6.86 2.30 11.52 78 29474 100L 335. CA NO3 750 2635 7.80 6.82 0.98 4.88 6.82 0.98 4.88 79 29476 100L 335. CB NO3 751 2635 6.35 5.44 0.91 4.55 5.44 0.91 4.55 80 29482 100L 335. CG NO2 752 2637 6.22 5.18 1.04 5.20 5.18 1.04 5.20 81 29490 100L 335. CD2 NO2 754 2637 5.03 4.00 1.03 5.15 4.00 1.03 5.15 82 30514 335. 335. AP AC8 2604 2617 7.86 7.58 0.28 5.62 7.58 0.28 5.62 83 30515 335. 335. AP AN7 2604 2618 9.09 8.85 0.23 4.70 8.85 0.23 4.70 84 30544 335. 335. AO1 AC2 2605 2613 5.58 5.15 0.44 8.75 5.15 0.44 8.75 85 30545 335. 335. AO1 AO2 2605 2614 6.55 6.13 0.41 8.25 6.13 0.41 8.25 86 30548 335. 335. AO1 AC8 2605 2617 7.91 7.15 0.77 15.33 7.15 0.77 15.33 87 30549 335. 335. AO1 AN7 2605 2618 9.06 8.44 0.62 12.32 8.44 0.62 12.32 88 30801 335. 335. AO3 NO2 2612 2629 6.54 6.15 0.39 7.72 6.15 0.39 7.72 89 30805 335. 335. AO3 NO4 2612 2633 9.99 9.70 0.28 5.63 9.70 0.28 5.63 90 30808 335. 335. AC2 AO1 2613 2605 5.58 5.15 0.44 8.75 5.15 0.44 8.75 91 30839 335. 335. AO2 AO1 2614 2605 6.55 6.13 0.41 8.25 6.13 0.41 8.25 92 30926 335. 335. AC8 AP 2617 2604 7.86 7.58 0.28 5.62 7.58 0.28 5.62 93 30927 335. 335. AC8 AO1 2617 2605 7.91 7.15 0.77 15.33 7.15 0.77 15.33 94 30947 335. 335. AC8 O3 2617 2626 8.46 8.18 0.28 5.53 8.18 0.28 5.53 95 30956 335. 335. AN7 AP 2618 2604 9.09 8.85 0.23 4.70 8.85 0.23 4.70 96 30957 335. 335. AN7 AO1 2618 2605 9.06 8.44 0.62 12.32 8.44 0.62 12.32 97 31103 335. 335. AN3 NO2 2624 2629 9.88 9.25 0.63 12.56 9.25 0.63 12.56 98 31105 335. 335. AN3 NC5 2624 2631 9.77 9.51 0.27 5.31 9.51 0.27 5.31 99 31148 335. 335. O3 AC8 2626 2617 8.46 8.18 0.28 5.53 8.18 0.28 5.53 100 31244 335. 335. NO2 AO3 2629 2612 6.54 6.15 0.39 7.72 6.15 0.39 7.72 101 31251 335. 335. NO2 AN3 2629 2624 9.88 9.25 0.63 12.56 9.25 0.63 12.56 102 31326 335. 335. NC5 AN3 2631 2624 9.77 9.51 0.27 5.31 9.51 0.27 5.31 103 31396 335. 335. NO4 AO3 2633 2612 9.99 9.70 0.28 5.63 9.70 0.28 5.63 104 31801 86V 335. CA NO2 649 2629 7.64 6.24 1.40 6.98 6.24 1.40 6.98 105 31805 86V 335. CA NO4 649 2633 5.54 4.55 1.00 4.98 4.55 1.00 4.98 106 31811 86V 335. CA NN1 649 2639 7.25 5.99 1.26 6.29 5.99 1.26 6.29 107 31812 86V 335. CA NC2 649 2640 8.23 7.00 1.23 6.14 7.00 1.23 6.14 108 31813 86V 335. CA NC3 649 2641 9.57 7.45 2.12 10.61 7.45 2.12 10.61 109 31814 86V 335. CA NC7 649 2642 10.70 8.72 1.99 9.93 8.72 1.99 9.93 110 31815 86V 335. CA NO7 649 2643 11.79 9.52 2.27 11.35 9.52 2.27 11.35 111 31816 86V 335. CA NN7 649 2644 10.55 9.01 1.53 7.67 9.01 1.53 7.67 112 31817 86V 335. CA NC4 649 2645 10.08 7.10 2.98 14.90 7.10 2.98 14.90 113 31818 86V 335. CA NC5 649 2646 9.32 6.18 3.15 15.74 6.18 3.15 15.74 114 31819 86V 335. CA NC6 649 2647 7.92 5.55 2.37 11.86 5.55 2.37 11.86 115 31857 87A 335. CA NC3 656 2641 11.08 9.94 1.14 5.72 9.94 1.14 5.72 116 31858 87A 335. CA NC4 656 2645 11.29 9.88 1.42 7.08 9.88 1.42 7.08 117 31859 87A 335. CA NC5 656 2646 10.30 8.87 1.43 7.15 8.87 1.43 7.15 118 31860 87A 335. CA NC6 656 2647 8.95 7.81 1.15 5.73 7.81 1.15 5.73 119 31862 88S 335. CA AO1 661 2605 7.28 6.22 1.06 5.29 6.22 1.06 5.29 120 31902 89M 335. CA AO1 667 2605 7.63 5.02 2.61 13.04 5.02 2.61 13.04 121 31920 89M 335. CA O3 667 2626 6.34 5.23 1.11 5.56 5.23 1.11 5.56 122 31928 89M 335. CA NC3 667 2634 6.10 4.79 1.31 6.55 4.79 1.31 6.55 123 31929 89M 335. CA NO3 667 2635 6.64 4.80 1.83 9.16 4.80 1.83 9.16 124 31931 89M 335. CA NO2 667 2637 8.04 6.37 1.67 8.35 6.37 1.67 8.35 125 31937 90P 335. CA AO1 675 2605 7.74 5.72 2.01 10.06 5.72 2.01 10.06 126 31945 90P 335. CA O3 675 2626 5.78 4.88 0.91 4.53 4.88 0.91 4.53 127 31953 90P 335. CA NC3 675 2634 6.15 4.51 1.64 8.19 4.51 1.64 8.19 128 31954 90P 335. CA NO3 675 2635 7.22 5.11 2.12 10.58 5.11 2.12 10.58 129 31955 90P 335. CA NC2 675 2636 5.93 4.96 0.97 4.86 4.96 0.97 4.86 130 31956 90P 335. CA NO2 675 2637 7.24 4.71 2.53 12.67 4.71 2.53 12.67 131 31965 91L 335. CA AO1 682 2605 11.39 9.28 2.11 10.55 9.28 2.11 10.55 132 31974 91L 335. CA NO3 682 2635 8.96 7.49 1.47 7.34 7.49 1.47 7.34 133 31976 91L 335. CA NO2 682 2637 8.21 6.42 1.78 8.92 6.42 1.78 8.92 134 31984 97R 335. CA NO2 726 2637 7.75 6.75 1.00 4.99 6.75 1.00 4.99 135 31992 98A 335. CA NO2 737 2637 10.40 9.50 0.91 4.54 9.50 0.91 4.54 136 31996 100L 335. CA NO3 750 2635 7.80 6.82 0.98 4.88 6.82 0.98 4.88 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 25 75 208 243 348 281 384 420 464 474 << end of ENERGY. TOP_________> 649 232 GO_TO __ACCELRYS3 TOP_________> 650 242 SET OUTPUT = OUTPUT2 TOP_________> 651 243 CALL ROUTINE = 'user_after_single_model' TOP_________> 652 249 RETURN TOP_________> 653 244 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990003.pdb wrpdb2__568_> Residues, atoms, selected atoms: 335 2647 2647 TOP_________> 654 245 SET FINAL_MODEL = FILE TOP_________> 655 246 RETURN TOP_________> 656 205 END_DO TOP_________> 657 203 SET FINAL_MODEL = 'default' TOP_________> 658 204 CALL ROUTINE = 'single_model' TOP_________> 659 215 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 660 216 SET ID1 = 0 TOP_________> 661 217 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000004 TOP_________> 662 218 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 2 335 2647 rdatm___298_> Segment: 1 1 333 2597 rdatm___298_> Segment: 2 334 335 50 TOP_________> 663 219 CALL ROUTINE = 'select_atoms' TOP_________> 664 288 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 : 2647 2647 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2647 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : BLK 335 TOP_________> 665 289 RETURN TOP_________> 666 220 CALL ROUTINE = RAND_METHOD TOP_________> 667 272 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2647 2647 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 668 273 RETURN TOP_________> 669 221 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 670 222 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 671 223 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 672 224 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 673 225 CALL ROUTINE = 'single_model_pass' TOP_________> 674 252 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 675 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 676 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 17112 TOP_________> 677 255 OPTIMIZE TOP_________> 678 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 679 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 680 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 681 259 END_DO TOP_________> 682 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 683 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 19019 TOP_________> 684 255 OPTIMIZE TOP_________> 685 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 686 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 687 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 688 259 END_DO TOP_________> 689 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 690 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 20133 TOP_________> 691 255 OPTIMIZE TOP_________> 692 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 693 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 694 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 695 259 END_DO TOP_________> 696 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 697 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 21411 TOP_________> 698 255 OPTIMIZE TOP_________> 699 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 700 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 701 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 702 259 END_DO TOP_________> 703 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 704 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 22706 TOP_________> 705 255 OPTIMIZE TOP_________> 706 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 707 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 708 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 709 259 END_DO TOP_________> 710 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 711 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 24624 TOP_________> 712 255 OPTIMIZE TOP_________> 713 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 714 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 715 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 716 259 END_DO TOP_________> 717 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 718 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 27113 TOP_________> 719 255 OPTIMIZE TOP_________> 720 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 721 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 722 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 723 259 END_DO TOP_________> 724 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 725 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 28185 TOP_________> 726 255 OPTIMIZE TOP_________> 727 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 728 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 729 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 730 259 END_DO TOP_________> 731 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 732 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 29455 TOP_________> 733 255 OPTIMIZE TOP_________> 734 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 735 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 736 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 737 259 END_DO TOP_________> 738 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 739 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 30615 TOP_________> 740 255 OPTIMIZE TOP_________> 741 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 742 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 743 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 744 259 END_DO TOP_________> 745 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 746 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 747 255 OPTIMIZE TOP_________> 748 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 749 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 750 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 751 259 END_DO TOP_________> 752 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 753 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 754 255 OPTIMIZE TOP_________> 755 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 756 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 757 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 758 259 END_DO TOP_________> 759 260 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 760 292 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 761 293 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 762 294 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 763 295 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 764 306 CALL ROUTINE = MD_LEVEL TOP_________> 765 330 SET UPDATE_DYNAMIC = 0.39 TOP_________> 766 331 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 767 332 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 768 333 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 769 334 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 770 335 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 771 336 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 772 337 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 773 338 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 774 339 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 775 340 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 776 341 RETURN TOP_________> 777 307 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 778 312 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 779 313 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 780 326 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 781 327 RETURN TOP_________> 782 261 LABEL __ABORT TOP_________> 783 262 SET ERROR_STATUS = 0 TOP_________> 784 263 RETURN TOP_________> 785 226 END_DO TOP_________> 786 227 IUPAC_MODEL iupac_m_486_> OE1/2 will be swapped: -178.1326 3 3 iupac_m_485_> OD1/2 will be swapped: 161.0357 32 32 iupac_m_485_> OD1/2 will be swapped: 97.4230 41 41 iupac_m_486_> OE1/2 will be swapped: -164.8908 55 55 iupac_m_486_> OE1/2 will be swapped: 179.7944 57 57 iupac_m_483_> CD1/2 CE1/2 swapped: 98.5536 67 67 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 155.6108 72 72 iupac_m_485_> OD1/2 will be swapped: -124.2078 81 81 iupac_m_483_> CD1/2 CE1/2 swapped: -96.3525 108 108 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: 168.0574 113 113 iupac_m_485_> OD1/2 will be swapped: 173.1168 132 132 iupac_m_486_> OE1/2 will be swapped: 177.8745 137 137 iupac_m_486_> OE1/2 will be swapped: 172.1860 165 165 iupac_m_485_> OD1/2 will be swapped: 99.9554 173 173 iupac_m_486_> OE1/2 will be swapped: 171.5321 188 188 iupac_m_485_> OD1/2 will be swapped: 178.9919 219 219 iupac_m_487_> NH1/2 swapped: -179.7897 228 228 iupac_m_485_> OD1/2 will be swapped: -178.1393 231 231 iupac_m_486_> OE1/2 will be swapped: 175.7901 273 273 iupac_m_483_> CD1/2 CE1/2 swapped: 98.7407 287 287 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 174.8362 292 292 iupac_m_486_> OE1/2 will be swapped: 177.0972 294 294 iupac_m_486_> OE1/2 will be swapped: 178.5908 301 301 iupac_m_485_> OD1/2 will be swapped: 123.8749 314 314 iupac_m_485_> OD1/2 will be swapped: -175.0710 319 319 TOP_________> 787 228 SET ID1 = 9999 TOP_________> 788 229 SET OUTPUT2 = OUTPUT TOP_________> 789 230 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'eq', THEN = 'GO_TO __ACCELRYS2' TOP_________> 790 231 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 4 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2647 2647 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 32046 32046 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 6411 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 : 2187.2544 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 : 2663 0 0 0.005 0.005 22.331 1.000 2 Bond angle potential : 3615 4 10 2.840 2.840 386.73 1.000 3 Stereochemical cosine torsion poten: 1744 0 40 46.789 46.789 575.69 1.000 4 Stereochemical improper torsion pot: 1119 0 2 1.446 1.446 51.201 1.000 5 Soft-sphere overlap restraints : 6411 0 0 0.003 0.003 5.2368 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 7007 0 0 0.158 0.158 128.71 1.000 10 Distance restraints 2 (N-O) : 7019 1 9 0.250 0.250 304.93 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 332 0 0 4.275 4.275 70.748 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 7 83.418 83.418 107.59 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 5 82.623 82.623 98.776 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 0 82.041 82.041 56.580 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 88.720 88.720 24.344 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 3 0 0 0.006 0.006 0.37292E-02 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3416 0 0 0.444 0.444 139.01 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 331 14 25 26.219 34.804 19.164 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1117 0 4 0.855 0.855 139.18 1.000 27 Distance restraints 5 (X-Y) : 3071 0 3 0.050 0.050 57.017 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990004 # Heavy relative violation of each residue is written to: TvLDH.V99990004 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 33571.2149 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 9142 1M 2S C N 7 9 51.32 56.90 9.61 0.46 -136.60 -157.37 10.69 1 2S 2S N CA 9 10 44.22 36.40 151.20 2 9226 85L 86V C N 646 648 -106.11 -62.40 66.58 7.51 -62.40 66.58 7.51 2 86V 86V N CA 648 649 7.82 -42.40 -42.40 3 9284 143A 144K C N 1083 1085 -73.75 -118.00 59.34 2.95 -62.90 140.99 18.92 3 144K 144K N CA 1085 1086 178.63 139.10 -40.80 4 9285 144K 145N C N 1092 1094 72.83 -63.20 136.21 20.95 -63.20 136.21 20.95 4 145N 145N N CA 1094 1095 -33.99 -41.10 -41.10 5 9295 154L 155S C N 1172 1174 -134.17 -64.10 88.85 7.97 -64.10 88.85 7.97 5 155S 155S N CA 1174 1175 19.64 -35.00 -35.00 6 9316 175K 176D C N 1338 1340 -90.06 -63.30 66.64 7.10 -63.30 66.64 7.10 6 176D 176D N CA 1340 1341 21.03 -40.00 -40.00 7 9355 214H 215D C N 1642 1644 -78.32 -63.30 78.72 8.91 -63.30 78.72 8.91 7 215D 215D N CA 1644 1645 37.28 -40.00 -40.00 8 9359 218F 219D C N 1680 1682 -112.54 -63.30 68.18 11.38 -63.30 68.18 11.38 8 219D 219D N CA 1682 1683 -87.15 -40.00 -40.00 9 9367 226G 227H C N 1747 1749 -108.57 -63.20 78.70 8.44 -63.20 78.70 8.44 9 227H 227H N CA 1749 1750 22.00 -42.30 -42.30 10 9381 240S 241A C N 1869 1871 -92.53 -62.50 33.79 6.87 -62.50 33.79 6.87 10 241A 241A N CA 1871 1872 -56.40 -40.90 -40.90 11 9413 272P 273E C N 2098 2100 117.09 -63.60 179.99 27.81 -63.60 179.99 27.81 11 273E 273E N CA 2100 2101 -24.79 -40.30 -40.30 12 9432 291V 292D C N 2240 2242 -67.78 -63.30 8.66 1.35 -96.50 164.14 6.91 12 292D 292D N CA 2242 2243 -47.40 -40.00 114.20 13 9433 292D 293K C N 2248 2250 168.29 -118.00 76.36 2.60 -62.90 -154.47 34.21 13 293K 293K N CA 2250 2251 159.04 139.10 -40.80 14 9434 293K 294E C N 2257 2259 60.23 54.60 19.71 1.12 -63.60 139.30 23.94 14 294E 294E N CA 2259 2260 23.51 42.40 -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 29 60 178 226 356 292 352 477 469 465 << end of ENERGY. TOP_________> 791 232 GO_TO __ACCELRYS3 TOP_________> 792 242 SET OUTPUT = OUTPUT2 TOP_________> 793 243 CALL ROUTINE = 'user_after_single_model' TOP_________> 794 249 RETURN TOP_________> 795 244 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990004.pdb wrpdb2__568_> Residues, atoms, selected atoms: 335 2647 2647 TOP_________> 796 245 SET FINAL_MODEL = FILE TOP_________> 797 246 RETURN TOP_________> 798 205 END_DO TOP_________> 799 203 SET FINAL_MODEL = 'default' TOP_________> 800 204 CALL ROUTINE = 'single_model' TOP_________> 801 215 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 802 216 SET ID1 = 0 TOP_________> 803 217 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL TvLDH.D00000005 TOP_________> 804 218 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini openf5__224_> Open 11 OLD SEQUENTIAL TvLDH.ini rdatm___297_> Segments, residues, atoms: 2 335 2647 rdatm___298_> Segment: 1 1 333 2597 rdatm___298_> Segment: 2 334 335 50 TOP_________> 805 219 CALL ROUTINE = 'select_atoms' TOP_________> 806 288 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 : 2647 2647 Atom types to be searched for (ATOM_TYPES) : all Residue types to be searched for (RES_TYPES) : all Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): initialize SEGMENT search; residue range (2i5,2a5) : 1 335 1: 335: selatm__462_> Number of selected atoms : 2647 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 335 : BLK 335 TOP_________> 807 289 RETURN TOP_________> 808 220 CALL ROUTINE = RAND_METHOD TOP_________> 809 272 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2647 2647 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 810 273 RETURN TOP_________> 811 221 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 812 222 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.sch TOP_________> 813 223 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 814 224 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 815 225 CALL ROUTINE = 'single_model_pass' TOP_________> 816 252 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 817 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 818 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 17112 TOP_________> 819 255 OPTIMIZE TOP_________> 820 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 821 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 822 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 823 259 END_DO TOP_________> 824 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 825 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 19019 TOP_________> 826 255 OPTIMIZE TOP_________> 827 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 828 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 829 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 830 259 END_DO TOP_________> 831 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 832 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 20133 TOP_________> 833 255 OPTIMIZE TOP_________> 834 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 835 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 836 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 837 259 END_DO TOP_________> 838 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 839 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 21411 TOP_________> 840 255 OPTIMIZE TOP_________> 841 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 842 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 843 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 844 259 END_DO TOP_________> 845 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 846 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 22706 TOP_________> 847 255 OPTIMIZE TOP_________> 848 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 849 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 850 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 851 259 END_DO TOP_________> 852 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 853 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 24624 TOP_________> 854 255 OPTIMIZE TOP_________> 855 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 856 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 857 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 858 259 END_DO TOP_________> 859 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 860 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 27113 TOP_________> 861 255 OPTIMIZE TOP_________> 862 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 863 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 864 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 865 259 END_DO TOP_________> 866 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 867 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 28185 TOP_________> 868 255 OPTIMIZE TOP_________> 869 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 870 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 871 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 872 259 END_DO TOP_________> 873 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 874 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 29455 TOP_________> 875 255 OPTIMIZE TOP_________> 876 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 877 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 878 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 879 259 END_DO TOP_________> 880 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 881 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 30615 TOP_________> 882 255 OPTIMIZE TOP_________> 883 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 884 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 885 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 886 259 END_DO TOP_________> 887 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 888 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 889 255 OPTIMIZE TOP_________> 890 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 891 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 892 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 893 259 END_DO TOP_________> 894 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 895 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 2647 32046 TOP_________> 896 255 OPTIMIZE TOP_________> 897 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 898 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 899 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 900 259 END_DO TOP_________> 901 260 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 902 292 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 903 293 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 904 294 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 905 295 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 906 306 CALL ROUTINE = MD_LEVEL TOP_________> 907 330 SET UPDATE_DYNAMIC = 0.39 TOP_________> 908 331 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 909 332 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 910 333 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 911 334 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 912 335 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 913 336 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 914 337 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 915 338 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 916 339 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 917 340 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 918 341 RETURN TOP_________> 919 307 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 920 312 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 921 313 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 922 326 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 923 327 RETURN TOP_________> 924 261 LABEL __ABORT TOP_________> 925 262 SET ERROR_STATUS = 0 TOP_________> 926 263 RETURN TOP_________> 927 226 END_DO TOP_________> 928 227 IUPAC_MODEL iupac_m_483_> CD1/2 CE1/2 swapped: 90.0469 30 30 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 165.9407 32 32 iupac_m_487_> NH1/2 swapped: -179.5433 33 33 iupac_m_486_> OE1/2 will be swapped: 175.3443 57 57 iupac_m_483_> CD1/2 CE1/2 swapped: 96.0185 67 67 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: 169.5459 72 72 iupac_m_483_> CD1/2 CE1/2 swapped: -90.4736 108 108 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -170.3498 113 113 iupac_m_486_> OE1/2 will be swapped: -170.2455 149 149 iupac_m_487_> NH1/2 swapped: -175.1995 161 161 iupac_m_485_> OD1/2 will be swapped: -166.8819 173 173 iupac_m_485_> OD1/2 will be swapped: 125.0450 176 176 iupac_m_486_> OE1/2 will be swapped: -171.1482 202 202 iupac_m_485_> OD1/2 will be swapped: -179.9407 219 219 iupac_m_486_> OE1/2 will be swapped: 179.0954 234 234 iupac_m_486_> OE1/2 will be swapped: -157.7056 263 263 iupac_m_483_> CD1/2 CE1/2 swapped: -90.8241 285 285 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: 90.3300 iupac_m_483_> CD1/2 CE1/2 swapped: 90.0545 287 287 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_484W> Dihedral still outside +-90: -91.3368 iupac_m_485_> OD1/2 will be swapped: 126.4438 292 292 iupac_m_486_> OE1/2 will be swapped: 162.1395 311 311 iupac_m_485_> OD1/2 will be swapped: 123.9450 314 314 iupac_m_485_> OD1/2 will be swapped: 170.4717 319 319 iupac_m_483_> CD1/2 CE1/2 swapped: 90.3293 321 321 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -179.9344 325 325 TOP_________> 929 228 SET ID1 = 9999 TOP_________> 930 229 SET OUTPUT2 = OUTPUT TOP_________> 931 230 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'eq', THEN = 'GO_TO __ACCELRYS2' TOP_________> 932 231 ENERGY OUTPUT = 'LONG VIOLATIONS_PROFILE', FILE = 'defaul; t', FILE_ID = '.V', FILE_EXT = '' >> ENERGY; Differences between the model's features and restraints: ID1, ID2 : 9999 5 Number of all residues in MODEL : 335 Number of all, selected real atoms : 2647 2647 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 32046 32046 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 6284 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 : 5037.6807 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 : 2663 0 2 0.007 0.007 33.641 1.000 2 Bond angle potential : 3615 3 15 2.259 2.259 359.92 1.000 3 Stereochemical cosine torsion poten: 1744 0 42 47.069 47.069 587.17 1.000 4 Stereochemical improper torsion pot: 1119 0 3 1.545 1.545 57.663 1.000 5 Soft-sphere overlap restraints : 6284 0 1 0.004 0.004 12.097 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 7007 0 0 0.181 0.181 159.62 1.000 10 Distance restraints 2 (N-O) : 7019 0 8 0.267 0.267 322.56 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 332 0 3 4.464 4.464 77.202 1.000 14 Sidechain Chi_1 dihedral restraints: 279 0 8 74.097 74.097 104.83 1.000 15 Sidechain Chi_2 dihedral restraints: 214 0 5 78.393 78.393 95.689 1.000 16 Sidechain Chi_3 dihedral restraints: 84 0 0 70.297 70.297 51.987 1.000 17 Sidechain Chi_4 dihedral restraints: 32 0 0 89.507 89.507 21.369 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 3 1 1 0.620 0.620 33.986 1.000 23 Distance restraints 3 (SDCH-MNCH) : 3416 0 0 0.435 0.435 152.27 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 331 16 31 27.464 33.629 63.016 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1117 0 3 0.917 0.917 167.61 1.000 27 Distance restraints 5 (X-Y) : 3071 114 221 0.219 0.219 2737.0 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL TvLDH.V99990005 # Heavy relative violation of each residue is written to: TvLDH.V99990005 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 # The sum of all numbers in the file: 36952.8477 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 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 3777 107I 107I N CA 798 799 131.93 113.50 18.44 4.96 113.50 18.44 4.96 2 3779 107I 107I CA CB 799 800 131.27 111.00 20.27 4.75 111.00 20.27 4.75 ------------------------------------------------------------------------------------------------- Feature 22 : Upper bound distance restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 32045 161R 334. NH2 O1B 1229 2600 4.57 3.50 1.07 10.73 3.50 1.07 10.73 ------------------------------------------------------------------------------------------------- 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 9170 29L 30Y C N 209 211 -116.71 -63.50 79.01 10.94 -63.50 79.01 10.94 1 30Y 30Y N CA 211 212 15.00 -43.40 -43.40 2 9172 31G 32D C N 225 227 -86.68 -96.50 69.03 2.91 -63.30 88.99 9.81 2 32D 32D N CA 227 228 45.87 114.20 -40.00 3 9173 32D 33R C N 233 235 -74.44 -63.00 11.63 1.81 -125.20 -173.37 7.77 3 33R 33R N CA 235 236 -38.99 -41.10 140.60 4 9174 33R 34Q C N 244 246 69.09 -73.00 142.58 9.96 -73.00 142.58 9.96 4 34Q 34Q N CA 246 247 128.89 140.70 140.70 5 9226 85L 86V C N 646 648 -121.60 -62.40 84.65 9.72 -62.40 84.65 9.72 5 86V 86V N CA 648 649 18.10 -42.40 -42.40 6 9238 97R 98A C N 734 736 -85.99 -62.50 90.36 13.86 -62.50 90.36 13.86 6 98A 98A N CA 736 737 46.35 -40.90 -40.90 7 9239 98A 99D C N 739 741 -120.54 -63.30 62.82 8.40 -63.30 62.82 8.40 7 99D 99D N CA 741 742 -14.12 -40.00 -40.00 8 9295 154L 155S C N 1172 1174 -134.94 -64.10 88.83 8.06 -64.10 88.83 8.06 8 155S 155S N CA 1174 1175 18.59 -35.00 -35.00 9 9343 202E 203G C N 1549 1551 173.79 82.20 93.06 5.57 -62.40 128.18 21.32 9 203G 203G N CA 1551 1552 -8.01 8.50 -41.20 10 9355 214H 215D C N 1642 1644 -78.84 -96.50 78.55 3.31 -63.30 79.20 8.94 10 215D 215D N CA 1644 1645 37.66 114.20 -40.00 11 9359 218F 219D C N 1680 1682 -112.42 -63.30 67.77 11.32 -63.30 67.77 11.32 11 219D 219D N CA 1682 1683 -86.69 -40.00 -40.00 12 9367 226G 227H C N 1747 1749 -108.79 -63.20 79.89 8.56 -63.20 79.89 8.56 12 227H 227H N CA 1749 1750 23.30 -42.30 -42.30 13 9381 240S 241A C N 1869 1871 -92.41 -62.50 33.64 6.84 -62.50 33.64 6.84 13 241A 241A N CA 1871 1872 -56.30 -40.90 -40.90 14 9413 272P 273E C N 2098 2100 46.79 -69.30 137.84 12.47 -63.60 150.90 18.17 14 273E 273E N CA 2100 2101 -143.19 142.50 -40.30 15 9433 292D 293K C N 2248 2250 -83.73 -70.20 80.34 6.13 -62.90 104.11 12.53 15 293K 293K N CA 2250 2251 61.21 140.40 -40.80 16 9434 293K 294E C N 2257 2259 47.02 54.60 18.91 0.98 -63.60 149.13 25.42 16 294E 294E N CA 2259 2260 59.72 42.40 -40.30 ------------------------------------------------------------------------------------------------- Feature 27 : Distance restraints 5 (X-Y) List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 29016 86V 335. C AC2 653 2623 8.73 6.95 1.77 8.86 6.95 1.77 8.86 2 29017 86V 335. C AN3 653 2624 8.04 6.63 1.42 7.08 6.63 1.42 7.08 3 29046 86V 335. O AN3 654 2624 7.97 6.82 1.15 5.74 6.82 1.15 5.74 4 29075 87A 335. N AN1 655 2622 7.56 6.24 1.31 6.57 6.24 1.31 6.57 5 29076 87A 335. N AC2 655 2623 7.71 5.90 1.81 9.05 5.90 1.81 9.05 6 29077 87A 335. N AN3 655 2624 7.10 5.71 1.40 6.99 5.71 1.40 6.99 7 29102 87A 335. CA AN1 656 2622 6.34 5.41 0.93 4.66 5.41 0.93 4.66 8 29103 87A 335. CA AC2 656 2623 6.39 5.12 1.27 6.35 5.12 1.27 6.35 9 29104 87A 335. CA AN3 656 2624 5.77 4.74 1.03 5.13 4.74 1.03 5.13 10 29130 87A 335. CB AN1 657 2622 5.02 3.97 1.04 5.22 3.97 1.04 5.22 11 29131 87A 335. CB AC2 657 2623 5.27 3.85 1.43 7.13 3.85 1.43 7.13 12 29132 87A 335. CB AN3 657 2624 4.88 3.74 1.15 5.73 3.74 1.15 5.73 13 29258 88S 335. C AC8 664 2617 6.24 5.31 0.94 4.68 5.31 0.94 4.68 14 29314 89M 335. N AC8 666 2617 7.29 6.09 1.20 6.00 6.09 1.20 6.00 15 29315 89M 335. N AN7 666 2618 7.73 6.78 0.95 4.75 6.78 0.95 4.75 16 29333 89M 335. CA AC8 667 2617 8.36 7.00 1.36 6.78 7.00 1.36 6.78 17 29504 104N 335. OD1 AC8 781 2617 7.98 6.93 1.06 5.28 6.93 1.06 5.28 18 29552 107I 335. CG1 AN7 802 2618 5.04 4.09 0.95 4.77 4.09 0.95 4.77 19 29562 107I 335. CD1 AC8 803 2617 5.27 4.11 1.16 5.82 4.11 1.16 5.82 20 29563 107I 335. CD1 AN7 803 2618 4.88 3.72 1.16 5.80 3.72 1.16 5.80 21 30514 335. 335. AP AC8 2604 2617 7.87 7.58 0.29 5.82 7.58 0.29 5.82 22 30515 335. 335. AP AN7 2604 2618 9.10 8.85 0.25 4.95 8.85 0.25 4.95 23 30544 335. 335. AO1 AC2 2605 2613 5.57 5.15 0.43 8.58 5.15 0.43 8.58 24 30545 335. 335. AO1 AO2 2605 2614 6.55 6.13 0.41 8.22 6.13 0.41 8.22 25 30548 335. 335. AO1 AC8 2605 2617 7.91 7.15 0.76 15.28 7.15 0.76 15.28 26 30549 335. 335. AO1 AN7 2605 2618 9.06 8.44 0.61 12.26 8.44 0.61 12.26 27 30692 335. 335. AC4 AN3 2609 2624 5.03 4.78 0.24 4.83 4.78 0.24 4.83 28 30801 335. 335. AO3 NO2 2612 2629 6.51 6.15 0.36 7.26 6.15 0.36 7.26 29 30805 335. 335. AO3 NO4 2612 2633 9.95 9.70 0.25 4.97 9.70 0.25 4.97 30 30808 335. 335. AC2 AO1 2613 2605 5.57 5.15 0.43 8.58 5.15 0.43 8.58 31 30839 335. 335. AO2 AO1 2614 2605 6.55 6.13 0.41 8.22 6.13 0.41 8.22 32 30926 335. 335. AC8 AP 2617 2604 7.87 7.58 0.29 5.82 7.58 0.29 5.82 33 30927 335. 335. AC8 AO1 2617 2605 7.91 7.15 0.76 15.28 7.15 0.76 15.28 34 30947 335. 335. AC8 O3 2617 2626 8.45 8.18 0.27 5.49 8.18 0.27 5.49 35 30955 335. 335. AC8 NO3 2617 2635 9.41 9.11 0.30 6.03 9.11 0.30 6.03 36 30956 335. 335. AN7 AP 2618 2604 9.10 8.85 0.25 4.95 8.85 0.25 4.95 37 30957 335. 335. AN7 AO1 2618 2605 9.06 8.44 0.61 12.26 8.44 0.61 12.26 38 31085 335. 335. AN3 AC4 2624 2609 5.03 4.78 0.24 4.83 4.78 0.24 4.83 39 31103 335. 335. AN3 NO2 2624 2629 9.88 9.25 0.63 12.52 9.25 0.63 12.52 40 31105 335. 335. AN3 NC5 2624 2631 9.77 9.51 0.26 5.28 9.51 0.26 5.28 41 31148 335. 335. O3 AC8 2626 2617 8.45 8.18 0.27 5.49 8.18 0.27 5.49 42 31244 335. 335. NO2 AO3 2629 2612 6.51 6.15 0.36 7.26 6.15 0.36 7.26 43 31251 335. 335. NO2 AN3 2629 2624 9.88 9.25 0.63 12.52 9.25 0.63 12.52 44 31326 335. 335. NC5 AN3 2631 2624 9.77 9.51 0.26 5.28 9.51 0.26 5.28 45 31396 335. 335. NO4 AO3 2633 2612 9.95 9.70 0.25 4.97 9.70 0.25 4.97 46 31470 335. 335. NO3 AC8 2635 2617 9.41 9.11 0.30 6.03 9.11 0.30 6.03 47 31794 86V 335. CA AN1 649 2622 10.04 8.41 1.62 8.12 8.41 1.62 8.12 48 31795 86V 335. CA AC2 649 2623 10.16 7.96 2.21 11.04 7.96 2.21 11.04 49 31796 86V 335. CA AN3 649 2624 9.50 7.78 1.71 8.56 7.78 1.71 8.56 50 31838 87A 335. CA AN1 656 2622 6.34 5.41 0.93 4.66 5.41 0.93 4.66 51 31839 87A 335. CA AC2 656 2623 6.39 5.12 1.27 6.35 5.12 1.27 6.35 52 31840 87A 335. CA AN3 656 2624 5.77 4.74 1.03 5.13 4.74 1.03 5.13 53 31914 89M 335. CA AC8 667 2617 8.36 7.00 1.36 6.78 7.00 1.36 6.78 54 31915 89M 335. CA AN7 667 2618 8.90 7.83 1.07 5.37 7.83 1.07 5.37 55 32009 104N 335. CA AC8 778 2617 9.39 8.27 1.13 5.64 8.27 1.13 5.64 56 32010 104N 335. CA AN7 778 2618 8.98 7.98 1.00 4.99 7.98 1.00 4.99 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 22 51 178 234 315 304 351 437 457 461 << end of ENERGY. TOP_________> 933 232 GO_TO __ACCELRYS3 TOP_________> 934 242 SET OUTPUT = OUTPUT2 TOP_________> 935 243 CALL ROUTINE = 'user_after_single_model' TOP_________> 936 249 RETURN TOP_________> 937 244 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL TvLDH.B99990005.pdb wrpdb2__568_> Residues, atoms, selected atoms: 335 2647 2647 TOP_________> 938 245 SET FINAL_MODEL = FILE TOP_________> 939 246 RETURN TOP_________> 940 205 END_DO TOP_________> 941 206 IF ARGUMENTS = DO_LOOPS 1, OPERATION = 'NE', THEN = 'GO_T; O NO_LOOPS' TOP_________> 942 212 RETURN TOP_________> 943 424 IF ARGUMENTS =FINAL_MALIGN3D 1, OPERATION ='NE', THEN ='G; O_TO NO_MALIGN3D' TOP_________> 944 434 RETURN Dynamically allocated memory at finish [B,kB,MB]: 27729243 27079.340 26.445 Starting time : 2004/09/15 18:43:20.294 Closing time : 2004/09/15 18:53:04.393 Total CPU time [seconds] : 583.73