MODELLER 9v7, 2009/06/12, r6923 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2009 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, M. Topf, 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 pinje.bccs.uib.no 2.6.18-238.19.1.el5 x86_64 Date and time of compilation : 2009/06/12 12:00:40 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2011/09/01 18:03:31 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v7}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v7}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234072 3158.273 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234600 3158.789 3.085 openf___224_> Open ${MODINSTALL9v7}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283200 3206.250 3.131 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v7}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292440 3215.273 3.140 openf___224_> Open ${MODINSTALL9v7}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v7}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v7}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v7}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v7}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v7}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v7}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open $(LIB)/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${MODINSTALL9v7}/modlib/models.lib openf___224_> Open $(LIB)/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241396 4141.988 4.045 openf___224_> Open $(LIB)/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 openf___224_> Open protein_pept.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4396070 4293.037 4.192 read_pd_459W> Residue type HSD not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. read_mo_297_> Segments, residues, atoms: 1 150 1226 read_mo_298_> Segment: 1 1 L 150 L 1226 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4400940 4297.793 4.197 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4489582 4384.357 4.282 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4491092 4385.832 4.283 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4579734 4472.396 4.368 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4598062 4490.295 4.385 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 3 150 atom names : C +N atom indices : 1224 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 3 150 atom names : C CA +N O atom indices : 1224 1219 0 1225 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 150 1225 1231 0 0 530 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4648890 4539.932 4.434 patch_______> segment topology patched using RTF: 1 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 1 150 1225 1231 1658 1935 530 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4702266 4592.057 4.484 patch_______> segment topology patched using RTF: 150 ; ASP ; CTER segments residues atoms bonds angles dihedrals impropers: 1 150 1226 1232 1660 1937 531 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 150 1226 1232 1660 1937 531 transfe_506_> MODEL is an average of all templates. transfe_511_> Number of templates for coordinate transfer: 1 After transferring coordinates of the equivalent template atoms, there are defined, undefined atoms in MODEL: 1219 7 openf___224_> Open ${LIB}/atmcls-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 4636422 4527.756 4.422 openf___224_> Open ${LIB}/atmcls-mf.lib openf___224_> Open ${LIB}/dist-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 8454942 8256.779 8.063 openf___224_> Open ${LIB}/dist-mf.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 0 0 0 0 12561 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: HSE:N HSE iatmcls_286W> MODEL atom not classified: HSE:CA HSE iatmcls_286W> MODEL atom not classified: HSE:NE2 HSE iatmcls_286W> MODEL atom not classified: HSE:CD2 HSE iatmcls_286W> MODEL atom not classified: HSE:ND1 HSE iatmcls_286W> MODEL atom not classified: HSE:CG HSE iatmcls_286W> MODEL atom not classified: HSE:CE1 HSE iatmcls_286W> MODEL atom not classified: HSE:CB HSE iatmcls_286W> MODEL atom not classified: HSE:C HSE iatmcls_286W> MODEL atom not classified: HSE:O HSE iatmcls_286W> MODEL atom not classified: HSE:N HSE iatmcls_286W> MODEL atom not classified: HSE:CA HSE iatmcls_286W> MODEL atom not classified: HSE:NE2 HSE iatmcls_286W> MODEL atom not classified: HSE:CD2 HSE iatmcls_286W> MODEL atom not classified: HSE:ND1 HSE iatmcls_286W> MODEL atom not classified: HSE:CG HSE iatmcls_286W> MODEL atom not classified: HSE:CE1 HSE iatmcls_286W> MODEL atom not classified: HSE:CB HSE iatmcls_286W> MODEL atom not classified: HSE:C HSE iatmcls_286W> MODEL atom not classified: HSE:O HSE iatmcls_286W> MODEL atom not classified: HSE:N HSE iatmcls_286W> MODEL atom not classified: HSE:CA HSE iatmcls_286W> MODEL atom not classified: HSE:NE2 HSE iatmcls_286W> MODEL atom not classified: HSE:CD2 HSE iatmcls_286W> MODEL atom not classified: HSE:ND1 HSE iatmcls_286W> MODEL atom not classified: HSE:CG HSE iatmcls_286W> MODEL atom not classified: HSE:CE1 HSE iatmcls_286W> MODEL atom not classified: HSE:CB HSE iatmcls_286W> MODEL atom not classified: HSE:C HSE iatmcls_286W> MODEL atom not classified: HSE:O HSE iatmcls_286W> MODEL atom not classified: HSE:N HSE iatmcls_286W> MODEL atom not classified: HSE:CA HSE iatmcls_286W> MODEL atom not classified: HSE:NE2 HSE iatmcls_286W> MODEL atom not classified: HSE:CD2 HSE iatmcls_286W> MODEL atom not classified: HSE:ND1 HSE iatmcls_286W> MODEL atom not classified: HSE:CG HSE iatmcls_286W> MODEL atom not classified: HSE:CE1 HSE iatmcls_286W> MODEL atom not classified: HSE:CB HSE iatmcls_286W> MODEL atom not classified: HSE:C HSE iatmcls_286W> MODEL atom not classified: HSE:O HSE iatmcls_286W> MODEL atom not classified: HSE:N HSE iatmcls_286W> MODEL atom not classified: HSE:CA HSE iatmcls_286W> MODEL atom not classified: HSE:NE2 HSE iatmcls_286W> MODEL atom not classified: HSE:CD2 HSE iatmcls_286W> MODEL atom not classified: HSE:ND1 HSE iatmcls_286W> MODEL atom not classified: HSE:CG HSE iatmcls_286W> MODEL atom not classified: HSE:CE1 HSE iatmcls_286W> MODEL atom not classified: HSE:CB HSE iatmcls_286W> MODEL atom not classified: HSE:C HSE iatmcls_286W> MODEL atom not classified: HSE:O HSE iatmcls_286W> MODEL atom not classified: ASP:OXT ASP preppdf_453W> No fixed restraints selected; there may be some dynamic ones. preppdf_454W> Restraints file was probably not read; use restraints.append(). Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 8808150 8601.709 8.400 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 8979610 8769.150 8.564 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 9009034 8797.885 8.592 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 9067882 8855.354 8.648 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 9185578 8970.291 8.760 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 9420970 9200.166 8.985 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 9891754 9659.916 9.434 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 10833322 10579.416 10.331 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 150 Number of all, selected real atoms : 1226 1226 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 0 0 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 199364 Dynamic pairs routine : 1, NATM x NATM double loop 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 : 1 9999 NLOGN_USE : 15 CONTACT_SHELL : 15.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : -14443.6377 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 : 0 0 0 0.000 0.000 0.0000 0.000 2 Bond angle potential : 0 0 0 0.000 0.000 0.0000 0.000 3 Stereochemical cosine torsion poten: 0 0 0 0.000 0.000 0.0000 0.000 4 Stereochemical improper torsion pot: 0 0 0 0.000 0.000 0.0000 0.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 0.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 0.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 0.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 0.000 9 Distance restraints 1 (CA-CA) : 0 0 0 0.000 0.000 0.0000 0.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 0.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 0.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 0.000 13 Mainchain Omega dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 14 Sidechain Chi_1 dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 15 Sidechain Chi_2 dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 0.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 0.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 0.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 0.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 0.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 0.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 25 Phi/Psi pair of dihedral restraints: 0 0 0 0.000 0.000 0.0000 0.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 0.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 0.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 0.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 0.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 0.000 31 Non-bonded restraints : 183401 0 83 6.657 6.657 -14444. 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 0.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 0.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 0.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 0.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 0.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 0.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 0.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 0.000 do_prof_492W> Are you sure you want to calculate a normalized energy profile! openf___224_> Open protein_pept.profile # Energy of each residue is written to: protein_pept.profile # The profile IS normalized by the number of restraints. # The profiles are smoothed over a window of residues: 9 # The sum of all numbers in the file: -5.5202 << end of ENERGY. DOPE score : -14443.637695 Dynamically allocated memory at finish [B,KiB,MiB]: 10691122 10440.549 10.196 Starting time : 2011/09/01 18:03:31 Closing time : 2011/09/01 18:03:38 Total CPU time [seconds] : 6.13