MODELLER 9.16, 2016/01/07, r10745 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2016 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, 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 sunflower.rnet.missouri.edu 2.6.32-431.23.3.el6.x86_64 x86_64 Date and time of compilation : 2016/01/07 10:19:44 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/04/05 22:39:10 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v16}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v16}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191562 187.072 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192090 187.588 0.183 openf___224_> Open ${MODINSTALL9v16}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240690 235.049 0.230 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 ${MODINSTALL9v16}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253990 248.037 0.242 openf___224_> Open ${MODINSTALL9v16}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v16}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v16}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v16}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v16}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 265439 259.218 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266889 260.634 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269789 263.466 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 330673 322.923 0.315 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331093 323.333 0.316 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 331305 323.540 0.316 Read the alignment from file : alignment.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx 54 1 1fdx ferredoxin check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb5fd1.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 364830 356.279 0.348 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 364830 356.279 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365001 356.446 0.348 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 365851 357.276 0.349 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 367109 358.505 0.350 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369013 360.364 0.352 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 369013 360.364 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 369103 360.452 0.352 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 371959 363.241 0.355 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 371959 363.241 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 372094 363.373 0.355 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376378 367.557 0.359 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 376378 367.557 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 376576 367.750 0.359 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383002 374.025 0.365 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 383002 374.025 0.365 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 383299 374.315 0.366 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 392921 383.712 0.375 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 392921 383.712 0.375 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 393371 384.151 0.375 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 392975 383.765 0.375 check_ali___> Checking the sequence-structure alignment. Implied intrachain 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 openf___224_> Open ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 532227 519.753 0.508 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 533827 521.315 0.509 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 537807 525.202 0.513 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 539807 527.155 0.515 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 542807 530.085 0.518 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 547307 534.479 0.522 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 552879 539.921 0.527 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 555679 542.655 0.530 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 559879 546.757 0.534 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 566179 552.909 0.540 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 568951 555.616 0.543 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 570351 556.983 0.544 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 578672 565.109 0.552 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 616990 602.529 0.588 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 622414 607.826 0.594 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 0 0 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 638650 623.682 0.609 patch_______> segment topology patched using RTF: 1 ; ALA ; NTER segments residues atoms bonds angles dihedrals impropers: 1 54 372 378 518 628 150 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 656626 641.236 0.626 patch_______> segment topology patched using RTF: 54 ; ASP ; CTER segments residues atoms bonds angles dihedrals impropers: 1 54 373 379 520 630 151 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 54 373 379 520 630 151 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: 322 51 openf___224_> Open 1fdx.ini wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 openf___224_> Open my.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 527504 515.141 0.503 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 625784 611.117 0.597 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 625984 611.312 0.597 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 626284 611.605 0.597 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 626732 612.043 0.598 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 627404 612.699 0.598 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 628412 613.684 0.599 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 629924 615.160 0.601 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 632192 617.375 0.603 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 635596 620.699 0.606 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 640700 625.684 0.611 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 648356 633.160 0.618 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 659840 644.375 0.629 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 677068 661.199 0.646 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 709836 693.199 0.677 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 735676 718.434 0.702 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 768444 750.434 0.733 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 807204 788.285 0.770 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 839972 820.285 0.801 rdcsr2__307_> Number of restraints read : 3767 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 3767 3767 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open 1fdx.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 839992 820.305 0.801 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 373 373 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 373 2202 Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 947360 925.156 0.903 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2459 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2613 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2753 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3106 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1248916 1219.645 1.191 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3367 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3746 pick_re_612_> Number of MODEL atoms, selected restraints; 373 3767 iupac_m_485_> OD1/2 will be swapped: 172.6882 6 6 iupac_m_483_> CD1/2 CE1/2 swapped: 92.3308 28 28 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_485_> OD1/2 will be swapped: -164.4491 31 31 iupac_m_485_> OD1/2 will be swapped: 114.5546 33 33 iupac_m_485_> OD1/2 will be swapped: -140.5370 37 37 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 54 Number of all, selected real atoms : 373 373 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 3767 3767 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 642 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 99999 NLOGN_USE : 15 CONTACT_SHELL : 4.000 DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F SPHERE_STDV : 0.050 RADII_FACTOR : 0.820 Current energy : 277.1464 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 : 379 0 0 0.005 0.005 2.3548 1.000 2 Bond angle potential : 520 0 0 2.309 2.309 53.608 1.000 3 Stereochemical cosine torsion poten: 244 0 10 54.485 54.485 99.078 1.000 4 Stereochemical improper torsion pot: 146 0 0 1.211 1.211 4.4497 1.000 5 Soft-sphere overlap restraints : 642 0 0 0.002 0.002 0.27856 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) : 804 0 0 0.364 0.364 28.081 1.000 10 Distance restraints 2 (N-O) : 837 0 0 0.417 0.417 30.547 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: 53 0 0 4.659 4.659 13.568 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 0 70.182 70.182 5.9012 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 70.696 70.696 8.9557 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 33.195 33.195 3.1908 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 0.565 0.565 0.22497 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) : 553 0 0 0.473 0.473 13.127 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: 52 7 2 22.365 59.544 6.8346 1.000 26 Distance restraints 4 (SDCH-SDCH) : 100 0 0 0.830 0.830 6.9479 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 openf___224_> Open 1fdx.V99990001 # Heavy relative violation of each residue is written to: 1fdx.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: 4918.7715 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 1296 7S 8C C N 53 55 -73.05 -117.90 48.08 1.37 -63.00 165.19 19.48 1 8C 8C N CA 55 56 123.79 141.10 -41.10 2 1297 8C 9I C N 59 61 -109.38 -97.30 65.48 6.66 -63.40 115.96 17.76 2 9I 9I N CA 61 62 62.85 127.20 -43.60 3 1298 9I 10A C N 67 69 43.07 55.40 24.16 0.91 -62.50 145.32 29.13 3 10A 10A N CA 69 70 58.97 38.20 -40.90 4 1299 10A 11C C N 72 74 -66.04 -63.00 4.67 0.79 -117.90 -178.20 7.80 4 11C 11C N CA 74 75 -44.65 -41.10 141.10 5 1310 21N 22I C N 146 148 -110.60 -120.60 75.32 3.92 -63.40 109.91 16.79 5 22I 22I N CA 148 149 55.65 130.30 -43.60 6 1313 24Q 25G C N 171 173 104.47 78.70 45.24 0.75 82.20 149.88 8.38 6 25G 25G N CA 173 174 156.72 -166.10 8.50 7 1314 25G 26S C N 175 177 -64.55 -64.10 10.70 0.80 -136.60 178.31 10.05 7 26S 26S N CA 177 178 -45.70 -35.00 151.20 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 2 2 12 21 35 28 40 39 60 44 << end of ENERGY. openf___224_> Open 1fdx.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Summary of successfully produced models: Filename molpdf ---------------------------------------- 1fdx.B99990001.pdb 277.14639 Dynamically allocated memory at finish [B,KiB,MiB]: 1248916 1219.645 1.191 Starting time : 2016/04/05 22:39:10 Closing time : 2016/04/05 22:39:12 Total CPU time [seconds] : 2.20