Checked out license feature: modeler [for 152:54072:13:UNIVERSITY OF MISSISSIPPI] (1 copy) MODELLER 6v1, 17 Jan 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 yogesh 6.5 IP30 Date and time of compilation : 01/24/2002 16:28:15 Job starting time (YY/MM/DD HH:MM:SS): 2004/07/14 08:04:49.856 getprog_531W> ROUTINE redefined: special_patches getprog_531W> ROUTINE redefined: default_patches getprog_531W> ROUTINE redefined: special_restraints TOP_________> 108 734 SET ALNFILE = 'trial01.pir' TOP_________> 109 735 SET KNOWNS = 'P_1L9H' TOP_________> 110 736 SET MD_LEVEL = 'refine_3' TOP_________> 111 737 SET SEQUENCE = 'AT1' TOP_________> 112 738 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 113 739 SET OUTPUT_DIRECTORY = './' TOP_________> 114 740 SET PDB_EXT = '.pdb' TOP_________> 115 741 SET ALIGNMENT_FORMAT = 'PIR' TOP_________> 116 742 SET STARTING_MODEL = 1 TOP_________> 117 743 SET ENDING_MODEL = 1 TOP_________> 118 744 SET DEVIATION = 4.000000 TOP_________> 119 745 SET FINAL_MALIGN3D = 1 TOP_________> 120 746 CALL ROUTINE = 'model' TOP_________> 121 400 CALL ROUTINE = 'getnames' TOP_________> 122 518 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 123 519 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 124 520 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 125 521 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 126 522 SET ROOT_NAME = SEQUENCE TOP_________> 127 523 RETURN TOP_________> 128 401 CALL ROUTINE = 'homcsr' TOP_________> 129 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir Dynamically allocated memory at amaxbnd [B,kB,MB]: 9138721 8924.532 8.715 openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir read_al_374_> Non-standard residue type,position,sequence: / 237 1 read_al_374_> Non-standard residue type,position,sequence: / 336 1 Read the alignment from file : trial01.pir Total number of alignment positions: 368 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 P_1L9H 340 3 P_1L9H unknown 2 AT1 359 1 AT1 unknown TOP_________> 130 107 WRITE_ALIGNMENT openf5__224_> Open 14 UNKNOWN SEQUENTIAL ./trial01.pir TOP_________> 131 108 READ_ALIGNMENT openf5__224_> Open 11 OLD SEQUENTIAL ./trial01.pir openf5__224_> Open 11 OLD SEQUENTIAL ./trial01.pir read_al_374_> Non-standard residue type,position,sequence: / 237 1 read_al_374_> Non-standard residue type,position,sequence: / 336 1 Read the alignment from file : ./trial01.pir Total number of alignment positions: 368 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 P_1L9H 340 3 P_1L9H unknown 2 AT1 359 1 AT1 unknown TOP_________> 132 109 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./P_1L9H.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_________> 133 110 CALL ROUTINE = GENERATE_METHOD TOP_________> 134 77 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir Dynamically allocated memory at amaxseq [B,kB,MB]: 8227037 8034.216 7.846 openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir read_al_374_> Non-standard residue type,position,sequence: / 236 1 read_al_374_> Non-standard residue type,position,sequence: / 327 1 Read the alignment from file : trial01.pir Total number of alignment positions: 342 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 P_1L9H 340 3 P_1L9H unknown TOP_________> 135 78 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir read_al_374_> Non-standard residue type,position,sequence: / 236 1 read_al_374_> Non-standard residue type,position,sequence: / 327 1 Read the alignment from file : trial01.pir Total number of alignment positions: 342 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 P_1L9H 340 3 P_1L9H unknown TOP_________> 136 79 IF ARGUMENTS = INITIAL_MALIGN3D 0, OPERATION = 'EQ', THEN; = 'GO_TO NO_INITIAL_MALIGN3D' TOP_________> 137 80 MALIGN3D FIT = OFF, GAP_PENALTIES_3D = 0 4 malign3_327W> Only one structure; nothing done. TOP_________> 138 81 LABEL NO_INITIAL_MALIGN3D TOP_________> 139 82 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 8447121 8249.142 8.056 openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir read_al_374_> Non-standard residue type,position,sequence: / 237 1 read_al_374_> Non-standard residue type,position,sequence: / 336 1 Read the alignment from file : trial01.pir Total number of alignment positions: 368 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 P_1L9H 340 3 P_1L9H unknown 2 AT1 359 1 AT1 unknown TOP_________> 140 83 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib//top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL6v1}/lib/models.lib TOP_________> 141 84 READ_PARAMETERS FILE = PARLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib//par.lib Dynamically allocated memory at amattacns [B,kB,MB]: 8575021 8374.044 8.178 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib//par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 142 85 CALL ROUTINE = 'create_topology' TOP_________> 143 100 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF getf_______W> RTF restraint not found in the atoms list: residue type, indices: 4 359 atom names : C +N atom indices : 2895 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 4 359 atom names : C CA +N O atom indices : 2895 2889 0 2896 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 359 2896 2973 0 0 1305 patch_______> segment topology patched using RTF: 1 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 1 359 2896 2973 4039 4851 1305 patch_______> segment topology patched using RTF: 359 ; GLU ; CTER segments residues atoms bonds angles dihedrals impropers: 1 359 2897 2974 4041 4853 1306 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 359 2897 2974 4041 4853 1306 TOP_________> 144 101 CALL ROUTINE = 'default_patches' TOP_________> 145 753 RETURN TOP_________> 146 102 CALL ROUTINE = 'special_patches' TOP_________> 147 748 PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = 18 274 patch_______> segment topology patched using RTF: 18 274 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 359 2897 2975 4043 4856 1306 TOP_________> 148 749 PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = 101 180 patch_______> segment topology patched using RTF: 101 180 ; CYS CYS ; DISU segments residues atoms bonds angles dihedrals impropers: 1 359 2897 2976 4045 4859 1306 TOP_________> 149 750 RETURN TOP_________> 150 103 RETURN TOP_________> 151 86 TRANSFER_XYZ CLUSTER_CUT = -1.0 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transfering coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 1994 903 TOP_________> 152 87 BUILD_MODEL INITIALIZE_XYZ = OFF TOP_________> 153 88 WRITE_MODEL FILE = MODEL openf5__224_> Open 14 UNKNOWN SEQUENTIAL ./AT1.ini wrpdb2__568_> Residues, atoms, selected atoms: 359 2897 2897 TOP_________> 154 89 RETURN TOP_________> 155 111 IF ARGUMENTS = CREATE_RESTRAINTS 0, OPERATION = 'EQ', THE; N ='GO_TO __SKIP_RSRS' TOP_________> 156 112 CALL ROUTINE = 'mkhomcsr' TOP_________> 157 117 MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo', ADD_RESTRAINTS; = OFF Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 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: 2976 4045 4638 1289 Total number of restraints before, now : 0 12948 make_re_422_> Number of previous, current restraints : 0 12948 make_re_423_> Number of previous, current selected restraints: 0 12948 TOP_________> 158 118 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir openf5__224_> Open 11 OLD SEQUENTIAL trial01.pir read_al_374_> Non-standard residue type,position,sequence: / 237 1 read_al_374_> Non-standard residue type,position,sequence: / 336 1 Read the alignment from file : trial01.pir Total number of alignment positions: 368 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 P_1L9H 340 3 P_1L9H unknown 2 AT1 359 1 AT1 unknown TOP_________> 159 119 MAKE_RESTRAINTS RESTRAINT_TYPE = 'phi-psi_binormal', ADD_; RESTRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: phi-psi_binormal openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/mnch1.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/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: P_1L9H getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 12948 13305 make_re_423_> Number of previous, current selected restraints: 12948 13305 TOP_________> 160 120 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.3, SPLINE_MIN_POINT; S = 5 TOP_________> 161 121 MAKE_RESTRAINTS RESTRAINT_TYPE = 'omega_dihedral', ADD_RE; STRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: omega_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/omega.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/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: P_1L9H getdata_289_> Proteins (all/accepted): 1 1 omgdel__425W> Unselected all O C +N +CA dihedrals: 375 make_re_422_> Number of previous, current restraints : 13305 13663 make_re_423_> Number of previous, current selected restraints: 13305 13288 TOP_________> 162 122 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi1_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: chi1_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/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: P_1L9H getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 13663 13987 make_re_423_> Number of previous, current selected restraints: 13288 13612 TOP_________> 163 123 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi2_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: chi2_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/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: P_1L9H getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 13987 14235 make_re_423_> Number of previous, current selected restraints: 13612 13860 TOP_________> 164 124 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi3_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: chi3_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/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: P_1L9H getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 14235 14310 make_re_423_> Number of previous, current selected restraints: 13860 13935 TOP_________> 165 125 MAKE_RESTRAINTS RESTRAINT_TYPE = 'chi4_dihedral', ADD_RES; TRAINTS = ON Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: chi4_dihedral openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/mdt.ini openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/chi1234.bin initmdt_400_> Distance function type: 1 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/lib/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: P_1L9H getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 14310 14346 make_re_423_> Number of previous, current selected restraints: 13935 13971 TOP_________> 166 126 SET SPLINE_RANGE = 4.0, SPLINE_DX = 0.7, SPLINE_MIN_POINT; S = 5 TOP_________> 167 127 SET RES_TYPES = 'STD' TOP_________> 168 128 SET DISTANCE_RSR_MODEL = 5, MAXIMAL_DISTANCE = MAX_CA-CA_; DISTANCE TOP_________> 169 129 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 170 130 SET RESTRAINT_GROUP = 9 TOP_________> 171 131 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 359 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 359 : GLU 359 TOP_________> 172 132 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'CA' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 359 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 359 : GLU 359 TOP_________> 173 133 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 14346 21282 make_re_423_> Number of previous, current selected restraints: 13971 20907 TOP_________> 174 134 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_N-O_DI; STANCE TOP_________> 175 135 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 176 136 SET RESTRAINT_GROUP = 10 TOP_________> 177 137 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'N' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 359 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 359 : GLU 359 TOP_________> 178 138 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'O' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 359 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 359 : GLU 359 TOP_________> 179 139 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 21282 28340 make_re_423_> Number of previous, current selected restraints: 20907 27965 TOP_________> 180 140 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-MC_; DISTANCE TOP_________> 181 141 SET RESIDUE_SPAN_RANGE = 1 2, RESIDUE_SPAN_SIGN = OFF TOP_________> 182 142 SET RESTRAINT_GROUP = 23, RESTRAINT_STDEV = 0.5 1.5 TOP_________> 183 143 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 1460 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 9 : ASP 9 2 11 : ILE --- 21 : ALA 11 3 23 : ARG --- 41 : VAL 19 4 43 : ILE --- 44 : PHE 2 5 46 : ASN --- 96 : PHE 51 6 98 : ASN --- 156 : ALA 59 7 158 : LEU --- 193 : ILE 36 8 195 : LEU --- 195 : LEU 1 9 197 : LEU --- 202 : LEU 6 10 204 : PHE --- 268 : LEU 65 11 270 : ILE --- 302 : TYR 33 12 304 : PHE --- 305 : LEU 2 13 307 : LYS --- 359 : GLU 53 TOP_________> 184 144 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'MNCH' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 1437 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 359 : GLU 359 TOP_________> 185 145 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 28340 31091 make_re_423_> Number of previous, current selected restraints: 27965 30716 TOP_________> 186 146 SET DISTANCE_RSR_MODEL = 6, MAXIMAL_DISTANCE = MAX_SC-SC_; DISTANCE TOP_________> 187 147 SET RESIDUE_SPAN_RANGE = 2 99999, RESIDUE_SPAN_SIGN = ON TOP_________> 188 148 SET RESTRAINT_GROUP = 26, RESTRAINT_STDEV = 0.5 2.0 TOP_________> 189 149 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 1460 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 9 : ASP 9 2 11 : ILE --- 21 : ALA 11 3 23 : ARG --- 41 : VAL 19 4 43 : ILE --- 44 : PHE 2 5 46 : ASN --- 96 : PHE 51 6 98 : ASN --- 156 : ALA 59 7 158 : LEU --- 193 : ILE 36 8 195 : LEU --- 195 : LEU 1 9 197 : LEU --- 202 : LEU 6 10 204 : PHE --- 268 : LEU 65 11 270 : ILE --- 302 : TYR 33 12 304 : PHE --- 305 : LEU 2 13 307 : LYS --- 359 : GLU 53 TOP_________> 190 150 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'SDCH' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 1460 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 9 : ASP 9 2 11 : ILE --- 21 : ALA 11 3 23 : ARG --- 41 : VAL 19 4 43 : ILE --- 44 : PHE 2 5 46 : ASN --- 96 : PHE 51 6 98 : ASN --- 156 : ALA 59 7 158 : LEU --- 193 : ILE 36 8 195 : LEU --- 195 : LEU 1 9 197 : LEU --- 202 : LEU 6 10 204 : PHE --- 268 : LEU 65 11 270 : ILE --- 302 : TYR 33 12 304 : PHE --- 305 : LEU 2 13 307 : LYS --- 359 : GLU 53 TOP_________> 191 151 MAKE_RESTRAINTS RESTRAINT_TYPE = 'distance', ADD_RESTRAIN; TS = 'ON' Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 31091 31643 make_re_423_> Number of previous, current selected restraints: 30716 31268 TOP_________> 192 152 CALL ROUTINE = 'hetatm_restraints' TOP_________> 193 161 SET RESTRAINT_TYPE = 'distance' TOP_________> 194 162 SET DISTANCE_RSR_MODEL = 7 TOP_________> 195 163 SET MAXIMAL_DISTANCE = 7.0 TOP_________> 196 164 SET ADD_RESTRAINTS = ON TOP_________> 197 165 SET RESTRAINT_GROUP = 27 TOP_________> 198 166 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 199 167 SET RESIDUE_SPAN_RANGE = 0 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 200 168 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 2897 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 359 : GLU 359 TOP_________> 201 169 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 202 170 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 31643 31643 make_re_423_> Number of previous, current selected restraints: 31268 31268 TOP_________> 203 171 RETURN TOP_________> 204 153 CALL ROUTINE = 'blk_restraints' TOP_________> 205 174 SET RESTRAINT_TYPE = 'distance' TOP_________> 206 175 SET DISTANCE_RSR_MODEL = 7 TOP_________> 207 176 SET MAXIMAL_DISTANCE = 10.0 TOP_________> 208 177 SET ADD_RESTRAINTS = ON TOP_________> 209 178 SET RESTRAINT_GROUP = 27 TOP_________> 210 179 SET RESTRAINT_STDEV = 0.05 0.0 TOP_________> 211 180 SET RESIDUE_SPAN_RANGE = 0 0, RESIDUE_SPAN_SIGN = ON TOP_________> 212 181 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: 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_________> 213 182 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_T; YPES = 'BLK' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 0 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN TOP_________> 214 183 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 31643 31643 make_re_423_> Number of previous, current selected restraints: 31268 31268 TOP_________> 215 184 SET RESTRAINT_STDEV = 0.2 0.0 TOP_________> 216 185 SET RESIDUE_SPAN_RANGE = 1 99999, RESIDUE_SPAN_SIGN = OFF TOP_________> 217 186 PICK_ATOMS PICK_ATOMS_SET = 2, ATOM_TYPES = 'CA', RES_TY; PES = 'ALL' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: selatm__462_> Number of selected atoms : 359 List of segments of contiguous residues with at least one selected atom: SEGMENT RESNUM AA --- RESNUM AA LEN 1 1 : MET --- 359 : GLU 359 TOP_________> 218 187 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'BLK' Number of atoms to choose from, total : 2897 2897 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) : 1 359 1: 359: 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_________> 219 188 MAKE_RESTRAINTS Dynamically allocated memory at amprmcns [B,kB,MB]: 18695293 18257.121 17.829 make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 31643 31643 make_re_423_> Number of previous, current selected restraints: 31268 31268 TOP_________> 220 189 DELETE_ALIGNMENT TOP_________> 221 190 RETURN Dynamically allocated memory at amaxseq [B,kB,MB]: 18347705 17917.680 17.498 TOP_________> 222 154 CALL ROUTINE = 'special_restraints' TOP_________> 223 756 READ_RESTRAINTS FILE = 'Constraints_USER.rsr', ADD_RESTRA; INTS = ON openf5__224_> Open 11 OLD SEQUENTIAL Constraints_USER.rsr openf5__224_> Open 11 OLD SEQUENTIAL Constraints_USER.rsr rdcsr1__305E> Incorrect record identifier in restraint file; card: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 18347705 17917.680 17.498 Starting time : 2004/07/14 08:04:49.856 Closing time : 2004/07/14 08:05:49.690 Total CPU time [seconds] : 0.00