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, WinXP build 2600 Service Pack 3, BIOINFO, uni, x86 Family 6 Model 13 Stepping 6 Date and time of compilation : 2009/06/12 12:31:26 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2010/04/13 23:40:21 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 1dxt.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4791684 4679.379 4.570 read_mo_297_> Segments, residues, atoms: 8 580 4572 read_mo_298_> Segment: 1 1 A 141 A 1069 read_mo_298_> Segment: 2 1 B 147 B 1131 read_mo_298_> Segment: 3 1 C 141 C 1069 read_mo_298_> Segment: 4 1 D 147 D 1131 read_mo_298_> Segment: 5 142 A 142 A 43 read_mo_298_> Segment: 6 148 B 148 B 43 read_mo_298_> Segment: 7 142 C 142 C 43 read_mo_298_> Segment: 8 148 D 148 D 43 relabel_387W> Model has multiple chains, and they do not all have a unique chain ID. Suggest you relabel them as A, B, C, etc. Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 4809024 4696.312 4.586 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 5146216 5025.602 4.908 mutate_mode_> Model residue 85 changed from ASP to TYR Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 5151596 5030.855 4.913 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 5488788 5360.145 5.235 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5505372 5376.340 5.250 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 15 141 atom names : C +N atom indices : 1071 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 15 141 atom names : C CA +N O atom indices : 1071 1063 0 1072 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 141 1072 1101 0 0 486 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5551832 5421.711 5.295 patch_______> segment topology patched using RTF: 1 ; VAL ; NTER segments residues atoms bonds angles dihedrals impropers: 1 141 1072 1101 1498 1782 486 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5596328 5465.164 5.337 patch_______> segment topology patched using RTF: 141 ; ARG ; CTER segments residues atoms bonds angles dihedrals impropers: 1 141 1073 1102 1500 1784 487 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 141 1073 1102 1500 1784 487 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5613728 5482.156 5.354 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 288 atom names : C +N atom indices : 2202 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 288 atom names : C CA +N O atom indices : 2202 2195 0 2203 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 288 2203 2262 1500 1784 993 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5662448 5529.734 5.400 patch_______> segment topology patched using RTF: 142 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 2 288 2203 2262 3076 3647 993 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5710104 5576.273 5.446 patch_______> segment topology patched using RTF: 288 ; HIS ; CTER segments residues atoms bonds angles dihedrals impropers: 2 288 2204 2263 3078 3649 994 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 2 288 2204 2263 3078 3649 994 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5726560 5592.344 5.461 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 15 429 atom names : C +N atom indices : 3271 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 15 429 atom names : C CA +N O atom indices : 3271 3263 0 3272 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 429 3272 3359 3078 3649 1473 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5772804 5637.504 5.505 patch_______> segment topology patched using RTF: 289 ; VAL ; NTER segments residues atoms bonds angles dihedrals impropers: 3 429 3272 3359 4569 5421 1473 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5839820 5702.949 5.569 patch_______> segment topology patched using RTF: 429 ; ARG ; CTER segments residues atoms bonds angles dihedrals impropers: 3 429 3273 3360 4571 5423 1474 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 3 429 3273 3360 4571 5423 1474 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5857220 5719.941 5.586 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 576 atom names : C +N atom indices : 4402 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 576 atom names : C CA +N O atom indices : 4402 4395 0 4403 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 576 4403 4520 4571 5423 1980 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5905940 5767.520 5.632 patch_______> segment topology patched using RTF: 430 ; MET ; NTER segments residues atoms bonds angles dihedrals impropers: 4 576 4403 4520 6147 7286 1980 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5937796 5798.629 5.663 patch_______> segment topology patched using RTF: 576 ; HIS ; CTER segments residues atoms bonds angles dihedrals impropers: 4 576 4404 4521 6149 7288 1981 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 4 576 4404 4521 6149 7288 1981 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5951364 5811.879 5.676 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 577 4447 4571 6149 7288 2027 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5954492 5814.934 5.679 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 5 577 4447 4571 6231 7422 2027 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 578 4490 4621 6231 7422 2073 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5957620 5817.988 5.682 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 6 578 4490 4621 6313 7556 2073 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 579 4533 4671 6313 7556 2119 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5960748 5821.043 5.685 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 7 579 4533 4671 6395 7690 2119 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 580 4576 4721 6395 7690 2165 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 5963876 5824.098 5.688 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 8 580 4576 4721 6477 7824 2165 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: 4570 6 openf___224_> Open 1dxt.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 6514164 6361.488 6.212 read_mo_297_> Segments, residues, atoms: 8 580 4572 read_mo_298_> Segment: 1 1 A 141 A 1069 read_mo_298_> Segment: 2 1 B 147 B 1131 read_mo_298_> Segment: 3 1 C 141 C 1069 read_mo_298_> Segment: 4 1 D 147 D 1131 read_mo_298_> Segment: 5 142 A 142 A 43 read_mo_298_> Segment: 6 148 B 148 B 43 read_mo_298_> Segment: 7 142 C 142 C 43 read_mo_298_> Segment: 8 148 D 148 D 43 relabel_387W> Model has multiple chains, and they do not all have a unique chain ID. Suggest you relabel them as A, B, C, etc. # ALGNMT CODE 1 1dxt 2 1dxt openf___224_> Open 1dxtTYR85.tmp wrpdb___568_> Residues, atoms, selected atoms: 580 4576 4576 openf___224_> Open 1dxtTYR85.tmp read_mo_297_> Segments, residues, atoms: 8 580 4576 read_mo_298_> Segment: 1 1 A 141 A 1073 read_mo_298_> Segment: 2 1 B 147 B 1131 read_mo_298_> Segment: 3 1 C 141 C 1069 read_mo_298_> Segment: 4 1 D 147 D 1131 read_mo_298_> Segment: 5 142 A 142 A 43 read_mo_298_> Segment: 6 148 B 148 B 43 read_mo_298_> Segment: 7 142 C 142 C 43 read_mo_298_> Segment: 8 148 D 148 D 43 relabel_387W> Model has multiple chains, and they do not all have a unique chain ID. Suggest you relabel them as A, B, C, etc. make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6620632 6465.461 6.314 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6628824 6473.461 6.322 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6645208 6489.461 6.337 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6677976 6521.461 6.369 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6710744 6553.461 6.400 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6776280 6617.461 6.462 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6809048 6649.461 6.494 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6874584 6713.461 6.556 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6907352 6745.461 6.587 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7038424 6873.461 6.712 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7103960 6937.461 6.775 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7169496 7001.461 6.837 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7300568 7129.461 6.962 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7562712 7385.461 7.212 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7693784 7513.461 7.337 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7824856 7641.461 7.462 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 8087000 7897.461 7.712 generat_607W> Cannot find params in params file: CHARMM atoms : NPH FE NP1 CPA IUPAC atoms : NA FE NB C1B Atom indices : 4406 4405 4407 4414 Residues : HEME HEME HEME HEME Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 8087560 7898.008 7.713 addprm__440W> Adding params (mean,force,period): 18.2062 10.0000 3 For atoms: NPH FE NP1 CPA generat_607W> Cannot find params in params file: CHARMM atoms : NP1 FE NP1 CPA IUPAC atoms : ND FE NB C1B Atom indices : 4409 4405 4407 4414 Residues : HEME HEME HEME HEME addprm__440W> Adding params (mean,force,period): 99.1895 10.0000 3 For atoms: NP1 FE NP1 CPA generat_607W> Cannot find params in params file: CHARMM atoms : FE NP1 CPA CPM IUPAC atoms : FE NB C1B CHB Atom indices : 4405 4407 4414 4427 Residues : HEME HEME HEME HEME addprm__440W> Adding params (mean,force,period): -15.2754 10.0000 3 For atoms: FE NP1 CPA CPM generat_607W> Cannot find params in params file: CHARMM atoms : FE NP1 CPA CPB IUPAC atoms : FE NB C1B C2B Atom indices : 4405 4407 4414 4415 Residues : HEME HEME HEME HEME addprm__440W> Adding params (mean,force,period): 166.1787 10.0000 3 For atoms: FE NP1 CPA CPB generat_607W> Cannot find params in params file: CHARMM atoms : CPA NP1 CPA CPM IUPAC atoms : C4B NB C1B CHB Atom indices : 4417 4407 4414 4427 Residues : HEME HEME HEME HEME addprm__440W> Adding params (mean,force,period): -179.1348 10.0000 3 For atoms: CPA NP1 CPA CPM generat_607W> Cannot find params in params file: CHARMM atoms : CPA NP1 CPA CPB IUPAC atoms : C4B NB C1B C2B Atom indices : 4417 4407 4414 4415 Residues : HEME HEME HEME HEME addprm__440W> Adding params (mean,force,period): 2.3195 10.0000 3 For atoms: CPA NP1 CPA CPB Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 8611848 8410.008 8.213 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 8873992 8666.008 8.463 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 4721 6477 7138 2137 Total number of restraints before, now : 0 20473 make_re_422_> Number of previous, current restraints : 0 20473 make_re_423_> Number of previous, current selected restraints: 0 20473 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 8874128 8666.141 8.463 openf___224_> Open ${MODINSTALL9v7}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v7}/modlib/mnch1.mdt errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 575 TYR errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 576 HIS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 3 576 HIS errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 576 HIS getdata_643_> Protein accepted: 1dxt getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 20473 21041 make_re_423_> Number of previous, current selected restraints: 20473 21041 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 8874144 8666.156 8.463 openf___224_> Open ${MODINSTALL9v7}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v7}/modlib/omega.mdt getdata_643_> Protein accepted: 1dxt getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 600 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 21041 21613 make_re_423_> Number of previous, current selected restraints: 21041 21013 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 8874144 8666.156 8.463 openf___224_> Open ${MODINSTALL9v7}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v7}/modlib/chi1.mdt getdata_643_> Protein accepted: 1dxt getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 9136288 8922.156 8.713 make_re_422_> Number of previous, current restraints : 21613 22077 make_re_423_> Number of previous, current selected restraints: 21013 21477 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 9136288 8922.156 8.713 openf___224_> Open ${MODINSTALL9v7}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v7}/modlib/chi2.mdt getdata_643_> Protein accepted: 1dxt getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 22077 22409 make_re_423_> Number of previous, current selected restraints: 21477 21809 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 9136288 8922.156 8.713 openf___224_> Open ${MODINSTALL9v7}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v7}/modlib/chi3.mdt getdata_643_> Protein accepted: 1dxt getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 22409 22533 make_re_423_> Number of previous, current selected restraints: 21809 21933 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 9136288 8922.156 8.713 openf___224_> Open ${MODINSTALL9v7}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v7}/modlib/chi4.mdt 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: 1dxt getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 22533 22589 make_re_423_> Number of previous, current selected restraints: 21933 21989 pick_re_612_> Number of MODEL atoms, selected restraints; 12 80 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 10454140 10209.121 9.970 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 10706000 10455.078 10.210 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 580 Number of all, selected real atoms : 4576 12 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 22589 80 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 54 Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 3677.4766 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 : 14 0 0 0.029 0.029 3.4854 1.000 2 Bond angle potential : 21 0 0 2.558 2.558 2.2837 1.000 3 Stereochemical cosine torsion poten: 27 0 0 50.914 50.914 4.6440 1.000 4 Stereochemical improper torsion pot: 11 0 0 2.331 2.331 1.5855 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 54 0 5 0.602 0.602 3667.8 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.280 0.280 0.18476E-02 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 16.953 16.953 0.79391 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 172.580 172.580 0.26285 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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 : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 5.447 5.447 -3.3447 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 629 1047 2.161 serious non-bonded atom clash: 631 1047 1.627 serious non-bonded atom clash: 650 4405 2.247 serious non-bonded atom clash: 1778 4448 2.197 serious non-bonded atom clash: 2850 4491 2.252 serious non-bonded atom clash: 3978 4534 2.101 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: 1 3 2 0 3 15 34 66 205 411 389 422 667 796 876 << end of ENERGY. randomi_498_> Atoms,selected atoms,random_seed,amplitude: 4576 12 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 580 Number of all, selected real atoms : 4576 12 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 22589 80 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 37 Dynamic pairs routine : 5, NATM_SEL 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 : 0 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F T F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 3.9861 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 : 14 0 0 0.006 0.006 0.14685 1.000 2 Bond angle potential : 21 0 0 2.881 2.881 2.8215 1.000 3 Stereochemical cosine torsion poten: 27 0 0 49.114 49.114 4.2815 1.000 4 Stereochemical improper torsion pot: 11 0 0 0.410 0.410 0.50198E-01 1.000 5 Soft-sphere overlap restraints : 0 0 0 0.000 0.000 0.0000 1.000 6 Lennard-Jones 6-12 potential : 37 0 0 0.358 0.358 -0.62638E-01 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) : 0 0 0 0.000 0.000 0.0000 1.000 10 Distance restraints 2 (N-O) : 0 0 0 0.000 0.000 0.0000 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: 2 0 0 0.034 0.034 0.27729E-04 1.000 14 Sidechain Chi_1 dihedral restraints: 1 0 0 121.907 121.907 0.43883 1.000 15 Sidechain Chi_2 dihedral restraints: 1 0 0 161.787 161.787 0.19986 1.000 16 Sidechain Chi_3 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 17 Sidechain Chi_4 dihedral restraints: 0 0 0 0.000 0.000 0.0000 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 : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 0 0 0 0.000 0.000 0.0000 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: 3 0 0 2.987 2.987 -3.8901 1.000 26 Distance restraints 4 (SDCH-SDCH) : 0 0 0 0.000 0.000 0.0000 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 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000 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. report______> Distribution of short non-bonded contacts: serious non-bonded atom clash: 650 4405 2.247 serious non-bonded atom clash: 1778 4448 2.197 serious non-bonded atom clash: 2850 4491 2.252 serious non-bonded atom clash: 3978 4534 2.101 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 2 2 0 2 14 34 66 204 409 389 424 665 798 870 << end of ENERGY. openf___224_> Open 1dxtTYR85.pdb wrpdb___568_> Residues, atoms, selected atoms: 580 4576 4576 Dynamically allocated memory at finish [B,KiB,MiB]: 10706000 10455.078 10.210 Starting time : 2010/04/13 23:40:21 Closing time : 2010/04/13 23:40:36 Total CPU time [seconds] : 14.84