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): 2004/09/16 11:43:57.047 TOP_________> 109 749 SET ALNFILE ='cpCN-V.ali' TOP_________> 110 750 SET KNOWNS ='2ezm' TOP_________> 111 751 SET SEQUENCE = 'cpCN-V' TOP_________> 112 752 SET STARTING_MODEL = 1 TOP_________> 113 753 SET ENDING_MODEL = 1 TOP_________> 114 754 CALL ROUTINE = 'model' TOP_________> 115 419 CALL ROUTINE = 'getnames' TOP_________> 116 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 117 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 118 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 119 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 120 538 SET ROOT_NAME = SEQUENCE TOP_________> 121 539 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]: 84067 82.097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 2114659 2065.097 2.017 openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali Read the alignment from file : cpCN-V.ali Total number of alignment positions: 102 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ezm 101 1 2ezm 2 cpCN-V 101 1 cpCN-V 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 ./2ezm.pdb check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE check_a_344_> << END OF COMMAND TOP_________> 126 118 CALL ROUTINE = GENERATE_METHOD TOP_________> 127 83 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali Read the alignment from file : cpCN-V.ali Total number of alignment positions: 101 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ezm 101 1 2ezm TOP_________> 128 84 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali Read the alignment from file : cpCN-V.ali Total number of alignment positions: 101 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ezm 101 1 2ezm 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 cpCN-V.ali openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali Read the alignment from file : cpCN-V.ali Total number of alignment positions: 102 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ezm 101 1 2ezm 2 cpCN-V 101 1 cpCN-V 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]: 2115209 2065.634 2.017 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: 4 101 atom names : C +N atom indices : 769 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 4 101 atom names : C CA +N O atom indices : 769 763 0 770 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 101 770 779 0 0 323 patch_______> segment topology patched using RTF: 1 ; LEU ; NTER segments residues atoms bonds angles dihedrals impropers: 1 101 770 779 1054 1228 323 patch_______> segment topology patched using RTF: 101 ; GLU ; CTER segments residues atoms bonds angles dihedrals impropers: 1 101 771 780 1056 1230 324 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 101 771 780 1056 1230 324 TOP_________> 135 107 CALL ROUTINE = 'default_patches' TOP_________> 136 529 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali Read the alignment from file : cpCN-V.ali Total number of alignment positions: 102 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ezm 101 1 2ezm 2 cpCN-V 101 1 cpCN-V TOP_________> 137 530 PATCH_SS_TEMPLATES patch_______> segment topology patched using RTF: 8 23 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 101 771 781 1058 1233 324 patch_______> segment topology patched using RTF: 59 73 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 101 771 782 1060 1236 324 patch_s_522_> Number of disulfides patched in MODEL: 2 TOP_________> 138 531 RETURN TOP_________> 139 108 CALL ROUTINE = 'special_patches' TOP_________> 140 526 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: 1 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 643 128 TOP_________> 143 93 BUILD_MODEL INITIALIZE_XYZ = OFF TOP_________> 144 94 WRITE_MODEL FILE = MODEL openf5__224_> Open 14 UNKNOWN SEQUENTIAL cpCN-V.ini wrpdb2__568_> Residues, atoms, selected atoms: 101 771 771 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]: 7247321 7077.462 6.912 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 : 782 1060 1152 323 Total number of restraints before, now : 0 3317 make_re_422_> Number of previous, current restraints : 0 3317 make_re_423_> Number of previous, current selected restraints: 0 3317 TOP_________> 150 127 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali openf5__224_> Open 20 OLD SEQUENTIAL cpCN-V.ali Read the alignment from file : cpCN-V.ali Total number of alignment positions: 102 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2ezm 101 1 2ezm 2 cpCN-V 101 1 cpCN-V TOP_________> 151 128 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 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. getdata_643_> Protein accepted: 2ezm getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 3317 3416 make_re_423_> Number of previous, current selected restraints: 3317 3416 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]: 7247321 7077.462 6.912 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: 2ezm getdata_289_> Proteins (all/accepted): 1 1 omgdel__425W> Unselected all O C +N +CA dihedrals: 101 make_re_422_> Number of previous, current restraints : 3416 3516 make_re_423_> Number of previous, current selected restraints: 3416 3415 TOP_________> 154 131 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 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: 2ezm getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 3516 3604 make_re_423_> Number of previous, current selected restraints: 3415 3503 TOP_________> 155 132 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 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: 2ezm getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 3604 3662 make_re_423_> Number of previous, current selected restraints: 3503 3561 TOP_________> 156 133 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 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: 2ezm getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 3662 3683 make_re_423_> Number of previous, current selected restraints: 3561 3582 TOP_________> 157 134 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 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: 2ezm getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 3683 3691 make_re_423_> Number of previous, current selected restraints: 3582 3590 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 : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 101 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 101 : GLU 101 TOP_________> 164 141 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 101 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 101 : GLU 101 TOP_________> 165 142 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 3691 5348 make_re_423_> Number of previous, current selected restraints: 3590 5247 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 : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 101 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 101 : GLU 101 TOP_________> 170 147 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' Number of atoms to choose from, total : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 101 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 101 : GLU 101 TOP_________> 171 148 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 5348 7154 make_re_423_> Number of previous, current selected restraints: 5247 7053 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 : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 367 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 1 : LEU 1 2 3 : LYS --- 14 : ALA 12 3 16 : SER --- 45 : ASP 30 4 47 : THR --- 65 : GLN 19 5 67 : SER --- 77 : ASN 11 6 80 : TYR --- 95 : ASP 16 7 97 : SER --- 101 : GLU 5 TOP_________> 176 153 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' Number of atoms to choose from, total : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 404 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 101 : GLU 101 TOP_________> 177 154 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 7154 8268 make_re_423_> Number of previous, current selected restraints: 7053 8167 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 : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 367 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 1 : LEU 1 2 3 : LYS --- 14 : ALA 12 3 16 : SER --- 45 : ASP 30 4 47 : THR --- 65 : GLN 19 5 67 : SER --- 77 : ASN 11 6 80 : TYR --- 95 : ASP 16 7 97 : SER --- 101 : GLU 5 TOP_________> 182 159 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 367 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 1 : LEU 1 2 3 : LYS --- 14 : ALA 12 3 16 : SER --- 45 : ASP 30 4 47 : THR --- 65 : GLN 19 5 67 : SER --- 77 : ASN 11 6 80 : TYR --- 95 : ASP 16 7 97 : SER --- 101 : GLU 5 TOP_________> 183 160 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 8268 8623 make_re_423_> Number of previous, current selected restraints: 8167 8522 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 : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 771 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 101 : GLU 101 TOP_________> 193 178 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 194 179 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 8623 8623 make_re_423_> Number of previous, current selected restraints: 8522 8522 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 : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 205 191 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 206 192 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 8623 8623 make_re_423_> Number of previous, current selected restraints: 8522 8522 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 : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 101 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 101 : GLU 101 TOP_________> 210 196 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'BLK' Number of atoms to choose from, total : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 211 197 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 7247321 7077.462 6.912 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 8623 8623 make_re_423_> Number of previous, current selected restraints: 8522 8522 TOP_________> 212 198 DELETE_ALIGNMENT TOP_________> 213 199 RETURN Dynamically allocated memory at amaxseq [B,kB,MB]: 7117821 6950.997 6.788 TOP_________> 214 163 CALL ROUTINE = 'special_restraints' TOP_________> 215 523 RETURN TOP_________> 216 164 CONDENSE_RESTRAINTS delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 8623 7942 TOP_________> 217 165 WRITE_RESTRAINTS FILE = CSRFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL cpCN-V.rsr TOP_________> 218 166 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_________> 219 167 RETURN TOP_________> 220 122 LABEL __SKIP_RSRS TOP_________> 221 123 RETURN TOP_________> 222 421 IF ARGUMENTS = EXIT_STAGE 1, OPERATION = 'GE', THEN = 'RE; TURN' TOP_________> 223 422 CALL ROUTINE = 'rd_restraints' TOP_________> 224 276 READ_RESTRAINTS FILE = CSRFILE, ADD_RESTRAINTS = 'off' openf5__224_> Open 11 OLD SEQUENTIAL cpCN-V.rsr openf5__224_> Open 11 OLD SEQUENTIAL cpCN-V.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]: 7117821 6950.997 6.788 openf5__224_> Open 11 OLD SEQUENTIAL cpCN-V.rsr openf5__224_> Open 11 OLD SEQUENTIAL cpCN-V.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: 7942 7942 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 TOP_________> 225 277 RETURN TOP_________> 226 423 CALL ROUTINE = 'multiple_models' TOP_________> 227 202 DO ID2 = STARTING_MODEL ENDING_MODEL 1 TOP_________> 228 203 SET FINAL_MODEL = 'default' TOP_________> 229 204 CALL ROUTINE = 'single_model' TOP_________> 230 215 SET MAX_ITERATIONS = MAX_VAR_ITERATIONS TOP_________> 231 216 SET ID1 = 0 TOP_________> 232 217 SWITCH_TRACE FILE = 'default', FILE_EXT = '', FILE_ID = '; .D' openf5__224_> Open 18 UNKNOWN SEQUENTIAL cpCN-V.D00000001 TOP_________> 233 218 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL cpCN-V.ini openf5__224_> Open 11 OLD SEQUENTIAL cpCN-V.ini rdatm___297_> Segments, residues, atoms: 1 101 771 rdatm___298_> Segment: 1 1 101 771 TOP_________> 234 219 CALL ROUTINE = 'select_atoms' TOP_________> 235 288 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 : 771 771 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) : 1 101 1: 101: selatm__462_> Number of selected atoms : 771 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : LEU --- 101 : GLU 101 TOP_________> 236 289 RETURN TOP_________> 237 220 CALL ROUTINE = RAND_METHOD TOP_________> 238 272 RANDOMIZE_XYZ randomi_498_> Atoms,selected atoms,random_seed,amplitude: 771 771 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. TOP_________> 239 273 RETURN TOP_________> 240 221 MAKE_SCHEDULE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib/sched.lib TOP_________> 241 222 WRITE_SCHEDULE FILE = SCHFILE openf5__224_> Open 14 UNKNOWN SEQUENTIAL cpCN-V.sch TOP_________> 242 223 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = PDB_E; XT', FILE_ID = '.B' TOP_________> 243 224 DO IREPEAT = 1 REPEAT_OPTIMIZATION 1 TOP_________> 244 225 CALL ROUTINE = 'single_model_pass' TOP_________> 245 252 DO SCHEDULE_STEP = 1 N_SCHEDULE 1 TOP_________> 246 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 247 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 4433 TOP_________> 248 255 OPTIMIZE Dynamically allocated memory at ampairs [B,kB,MB]: 7229183 7059.749 6.894 TOP_________> 249 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 250 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 251 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 252 259 END_DO TOP_________> 253 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 254 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 4922 TOP_________> 255 255 OPTIMIZE TOP_________> 256 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 257 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 258 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 259 259 END_DO TOP_________> 260 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 261 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 5179 TOP_________> 262 255 OPTIMIZE TOP_________> 263 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 264 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 265 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 266 259 END_DO TOP_________> 267 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 268 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 5528 TOP_________> 269 255 OPTIMIZE TOP_________> 270 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 271 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 272 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 273 259 END_DO TOP_________> 274 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 275 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 6290 TOP_________> 276 255 OPTIMIZE TOP_________> 277 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 278 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 279 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 280 259 END_DO TOP_________> 281 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 282 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 6647 TOP_________> 283 255 OPTIMIZE TOP_________> 284 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 285 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 286 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 287 259 END_DO TOP_________> 288 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 289 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 7095 TOP_________> 290 255 OPTIMIZE TOP_________> 291 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 292 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 293 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 294 259 END_DO TOP_________> 295 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 296 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 7637 TOP_________> 297 255 OPTIMIZE TOP_________> 298 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 299 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 300 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 301 259 END_DO TOP_________> 302 253 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 303 254 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 771 7942 TOP_________> 304 255 OPTIMIZE TOP_________> 305 256 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 306 257 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 307 258 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 308 259 END_DO TOP_________> 309 260 CALL ROUTINE = 'refine', SCHEDULE_STEP = N_SCHEDULE TOP_________> 310 292 STRING_IF STRING_ARGUMENTS = MD_LEVEL 'none', OPERATION =; 'EQ', THEN = RETURN TOP_________> 311 293 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'NE', THEN = 'WRITE_MODEL FILE = TO_BE_REFIN; ED.TMP' TOP_________> 312 294 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 313 295 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 314 306 CALL ROUTINE = MD_LEVEL TOP_________> 315 330 SET UPDATE_DYNAMIC = 0.39 TOP_________> 316 331 SET CAP_ATOM_SHIFT = UPDATE_DYNAMIC, MD_TIME_STEP = 4.0 TOP_________> 317 332 SET MAX_ITERATIONS = 50, EQUILIBRATE = 10, OPTIMIZATION_M; ETHOD = 3 TOP_________> 318 333 OPTIMIZE TEMPERATURE = 150.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = ON TOP_________> 319 334 OPTIMIZE TEMPERATURE = 400.0, MD_RETURN = 'FINAL', INIT_V; ELOCITIES = OFF TOP_________> 320 335 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 321 336 SET EQUILIBRATE = 100, MAX_ITERATIONS = 300 TOP_________> 322 337 OPTIMIZE TEMPERATURE =1000.0, MD_RETURN = 'FINAL' TOP_________> 323 338 OPTIMIZE TEMPERATURE = 800.0, MD_RETURN = 'FINAL' TOP_________> 324 339 OPTIMIZE TEMPERATURE = 500.0, MD_RETURN = 'FINAL' TOP_________> 325 340 OPTIMIZE TEMPERATURE = 300.0, MD_RETURN = 'FINAL' TOP_________> 326 341 RETURN TOP_________> 327 307 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __AFTER_MD' TOP_________> 328 312 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 200 TOP_________> 329 313 STRING_IF STRING_ARGUMENTS = FIT_IN_REFINE 'NO_FIT', OPER; ATION = 'INDEX', THEN = 'GO_TO __NO_FIT' TOP_________> 330 326 SET MAX_ITERATIONS = MAX_ITERATIONS_STORE TOP_________> 331 327 RETURN TOP_________> 332 261 LABEL __ABORT TOP_________> 333 262 SET ERROR_STATUS = 0 TOP_________> 334 263 RETURN TOP_________> 335 226 END_DO TOP_________> 336 227 IUPAC_MODEL iupac_m_486_> OE1/2 will be swapped: 134.4274 6 6 iupac_m_487_> NH1/2 swapped: -177.9062 9 9 iupac_m_486_> OE1/2 will be swapped: 112.2765 18 18 iupac_m_487_> NH1/2 swapped: -176.6574 26 26 iupac_m_485_> OD1/2 will be swapped: 112.4210 39 39 iupac_m_487_> NH1/2 swapped: -171.3461 75 75 iupac_m_486_> OE1/2 will be swapped: -110.1372 101 101 TOP_________> 337 228 SET ID1 = 9999 TOP_________> 338 229 SET OUTPUT2 = OUTPUT TOP_________> 339 230 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'eq', THEN = 'GO_TO __ACCELRYS2' TOP_________> 340 231 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 : 101 Number of all, selected real atoms : 771 771 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 7942 7942 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 1432 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 : 0 120 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SCHEDULE_STEP, N_SCHEDULE : 9 9 SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 692.8268 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 : 780 0 1 0.008 0.008 16.168 1.000 2 Bond angle potential : 1056 0 6 1.936 1.936 80.309 1.000 3 Stereochemical cosine torsion poten: 469 0 28 54.628 54.628 229.03 1.000 4 Stereochemical improper torsion pot: 323 0 0 1.132 1.132 9.1304 1.000 5 Soft-sphere overlap restraints : 1432 0 0 0.003 0.003 1.5661 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) : 1657 0 0 0.310 0.310 77.223 1.000 10 Distance restraints 2 (N-O) : 1806 0 0 0.311 0.311 84.215 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: 100 0 4 4.639 4.639 25.375 1.000 14 Sidechain Chi_1 dihedral restraints: 88 0 1 69.925 69.925 28.595 1.000 15 Sidechain Chi_2 dihedral restraints: 58 0 0 55.245 55.245 19.634 1.000 16 Sidechain Chi_3 dihedral restraints: 21 0 0 79.576 79.576 16.875 1.000 17 Sidechain Chi_4 dihedral restraints: 8 0 0 75.585 75.585 5.2312 1.000 18 Disulfide distance restraints : 2 0 0 0.013 0.013 0.60021E-01 1.000 19 Disulfide angle restraints : 4 0 0 1.058 1.058 0.98860E-01 1.000 20 Disulfide dihedral angle restraints: 2 0 0 43.372 43.372 2.9588 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 1114 0 0 0.408 0.408 19.749 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: 99 1 9 29.942 32.068 55.544 1.000 26 Distance restraints 4 (SDCH-SDCH) : 355 0 0 0.702 0.702 21.061 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 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 cpCN-V.V99990001 # Heavy relative violation of each residue is written to: cpCN-V.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: 8522.1826 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 2688 52P 53S C N 402 404 177.16 56.90 121.07 13.52 56.90 121.07 13.52 1 53S 53S N CA 404 405 22.48 36.40 36.40 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 6 9 46 43 62 72 84 84 80 104 << end of ENERGY. TOP_________> 341 232 GO_TO __ACCELRYS3 TOP_________> 342 242 SET OUTPUT = OUTPUT2 TOP_________> 343 243 CALL ROUTINE = 'user_after_single_model' TOP_________> 344 249 RETURN TOP_________> 345 244 WRITE_MODEL FILE = FINAL_MODEL, FILE_ID = '.B', FILE_EXT ; = PDB_EXT openf5__224_> Open 14 UNKNOWN SEQUENTIAL cpCN-V.B99990001.pdb wrpdb2__568_> Residues, atoms, selected atoms: 101 771 771 TOP_________> 346 245 SET FINAL_MODEL = FILE TOP_________> 347 246 RETURN TOP_________> 348 205 END_DO TOP_________> 349 206 IF ARGUMENTS = DO_LOOPS 1, OPERATION = 'NE', THEN = 'GO_T; O NO_LOOPS' TOP_________> 350 212 RETURN TOP_________> 351 424 IF ARGUMENTS =FINAL_MALIGN3D 1, OPERATION ='NE', THEN ='G; O_TO NO_MALIGN3D' TOP_________> 352 434 RETURN Dynamically allocated memory at finish [B,kB,MB]: 7229183 7059.749 6.894 Starting time : 2004/09/16 11:43:57.047 Closing time : 2004/09/16 11:44:19.212 Total CPU time [seconds] : 22.01