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 22:38:35 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 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 763655 745.757 0.728 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 771847 753.757 0.736 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 788231 769.757 0.752 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 820999 801.757 0.783 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 379 520 616 146 Total number of restraints before, now : 0 1661 make_re_422_> Number of previous, current restraints : 0 1661 make_re_423_> Number of previous, current selected restraints: 0 1661 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 849822 829.904 0.810 openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v16}/modlib/mnch1.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1661 1713 make_re_423_> Number of previous, current selected restraints: 1661 1713 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 849838 829.920 0.810 openf___224_> Open ${MODINSTALL9v16}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v16}/modlib/omega.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 58 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 1713 1766 make_re_423_> Number of previous, current selected restraints: 1713 1708 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 849838 829.920 0.810 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi1.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1766 1809 make_re_423_> Number of previous, current selected restraints: 1708 1751 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 849838 829.920 0.810 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi2.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1809 1835 make_re_423_> Number of previous, current selected restraints: 1751 1777 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 849838 829.920 0.810 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/modlib/chi3.mdt getdata_643_> Protein accepted: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 882606 861.920 0.842 make_re_422_> Number of previous, current restraints : 1835 1844 make_re_423_> Number of previous, current selected restraints: 1777 1786 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 882606 861.920 0.842 openf___224_> Open ${MODINSTALL9v16}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v16}/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: 5fd1 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 1844 1845 make_re_423_> Number of previous, current selected restraints: 1786 1787 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 989994 966.791 0.944 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1022762 998.791 0.975 make_re_422_> Number of previous, current restraints : 1845 2194 make_re_423_> Number of previous, current selected restraints: 1787 2136 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1088298 1062.791 1.038 make_re_422_> Number of previous, current restraints : 2194 2324 make_re_423_> Number of previous, current selected restraints: 2136 2266 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 2324 2700 make_re_423_> Number of previous, current selected restraints: 2266 2642 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 2700 2762 make_re_423_> Number of previous, current selected restraints: 2642 2704 0 atoms in HETATM/BLK residues constrained to protein atoms within 2.30 angstroms and protein CA atoms within 10.00 angstroms make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 2762 2762 make_re_423_> Number of previous, current selected restraints: 2704 2704 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 2762 2762 make_re_423_> Number of previous, current selected restraints: 2704 2704 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 2762 2762 make_re_423_> Number of previous, current selected restraints: 2704 2704 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 2762 2762 make_re_423_> Number of previous, current selected restraints: 2704 2704 0 atoms in residues without defined topology constrained to be rigid bodies make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 2762 2762 make_re_423_> Number of previous, current selected restraints: 2704 2704 rmdupl__427_> 314 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 2762 2390 openf___224_> Open 1fdx.rsr openf___224_> Open 1fdx.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 994916 971.598 0.949 rdcsr2__307_> Number of restraints read : 2390 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 2390 2390 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]: 994936 971.617 0.949 read_mo_297_> Segments, residues, atoms: 1 54 373 read_mo_298_> Segment: 1 1 54 373 pick_re_612_> Number of MODEL atoms, selected restraints; 373 1966 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2096 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2136 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1296472 1266.086 1.236 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2379 pick_re_612_> Number of MODEL atoms, selected restraints; 373 2390 iupac_m_485_> OD1/2 will be swapped: 96.1780 6 6 iupac_m_486_> OE1/2 will be swapped: -165.5598 17 17 iupac_m_485_> OD1/2 will be swapped: 170.8304 31 31 >> 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 : 2390 2390 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 657 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 : 257.3471 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 2.8910 1.000 2 Bond angle potential : 520 0 0 2.414 2.414 57.579 1.000 3 Stereochemical cosine torsion poten: 244 0 12 54.497 54.497 102.72 1.000 4 Stereochemical improper torsion pot: 146 0 0 1.084 1.084 3.4731 1.000 5 Soft-sphere overlap restraints : 657 0 0 0.004 0.004 1.2489 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) : 349 0 0 0.288 0.288 11.439 1.000 10 Distance restraints 2 (N-O) : 130 0 0 0.440 0.440 13.193 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 1 4.887 4.887 14.930 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 1 66.980 66.980 11.932 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 0 70.642 70.642 8.5319 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 58.904 58.904 2.6766 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 3.268 3.268 0.23771 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) : 376 0 0 0.335 0.335 4.3227 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 6 5 31.199 61.690 21.182 1.000 26 Distance restraints 4 (SDCH-SDCH) : 62 0 0 0.359 0.359 0.98477 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.V99990002 # Heavy relative violation of each residue is written to: 1fdx.V99990002 # 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: 4055.5029 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 -51.11 -117.90 73.12 2.05 -63.00 152.91 19.50 1 8C 8C N CA 55 56 111.35 141.10 -41.10 2 1297 8C 9I C N 59 61 -105.96 -97.30 87.11 8.99 -63.40 94.28 14.38 2 9I 9I N CA 61 62 40.52 127.20 -43.60 3 1298 9I 10A C N 67 69 45.22 55.40 12.42 0.83 -62.50 137.97 27.88 3 10A 10A N CA 69 70 45.31 38.20 -40.90 4 1299 10A 11C C N 72 74 -65.11 -63.00 6.52 0.95 -117.90 179.57 7.72 4 11C 11C N CA 74 75 -47.27 -41.10 141.10 5 1310 21N 22I C N 146 148 -102.39 -120.60 64.33 3.01 -63.40 118.79 18.34 5 22I 22I N CA 148 149 68.60 130.30 -43.60 6 1313 24Q 25G C N 171 173 -96.82 -80.20 23.47 1.66 82.20 -127.07 8.11 6 25G 25G N CA 173 174 157.53 174.10 8.50 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 4 24 25 26 32 40 50 51 55 << end of ENERGY. >> Model assessment by GA341 potential Surface library : /home/tools/modeller-9.16//modlib/surf5.de Pair library : /home/tools/modeller-9.16//modlib/pair9.de Chain identifier : _ % sequence identity : 37.036999 Sequence length : 54 Compactness : 0.676732 Native energy (pair) : -43.474395 Native energy (surface) : -1.770786 Native energy (combined) : -4.148067 Z score (pair) : -4.783736 Z score (surface) : -4.554024 Z score (combined) : -6.741669 GA341 score : 1.000000 openf___224_> Open 1fdx.B99990002.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 >> Summary of successfully produced models: Filename molpdf GA341 score ------------------------------------------------------- 1fdx.B99990002.pdb 257.34711 1.00000 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1298454 1268.021 1.238 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1299904 1269.438 1.240 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1302804 1272.270 1.242 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1303224 1272.680 1.243 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 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1305188 1274.598 1.245 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1334784 1303.500 1.273 openf___224_> Open .tmp.ali openf___224_> Open .tmp.ali Read the alignment from file : .tmp.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx_9999 54 1 1fdx.B99990 compare_343_> >> BEGINNING OF COMMAND openf___224_> Open ../atom_files/pdb5fd1.ent Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1368309 1336.239 1.305 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1368309 1336.239 1.305 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1368480 1336.406 1.305 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1369330 1337.236 1.306 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1370588 1338.465 1.307 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1372492 1340.324 1.309 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1372492 1340.324 1.309 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1372582 1340.412 1.309 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1375438 1343.201 1.312 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1375438 1343.201 1.312 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1375573 1343.333 1.312 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1379857 1347.517 1.316 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1379857 1347.517 1.316 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1380055 1347.710 1.316 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1386481 1353.985 1.322 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1386481 1353.985 1.322 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1386778 1354.275 1.323 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1396400 1363.672 1.332 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1396400 1363.672 1.332 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1396850 1364.111 1.332 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1396454 1363.725 1.332 openf___224_> Open 1fdx.B99990002.pdb Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1396454 1363.725 1.332 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1396148 1363.426 1.331 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1396148 1363.426 1.331 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1396238 1363.514 1.332 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1396238 1363.514 1.332 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1396373 1363.646 1.332 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1396373 1363.646 1.332 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1396571 1363.839 1.332 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1396454 1363.725 1.332 COMPARISON OF SEVERAL 3D STRUCTURES: # ALGNMT CODE ATOM FILE 1 5fd1 ../atom_files/pdb5fd1.ent 2 1fdx_99990002 1fdx.B99990002.pdb Variability at a given position is calculated as: VAR = 1/Nij * sum_ij (feat_i - feat_j) sum runs over all pairs of proteins with residues present. >> Least-squares superposition (FIT) : T Atom types for superposition/RMS (FIT_ATOMS): CA Atom type for position average/variability (VARATOM): CA Position comparison (FIT_ATOMS): Cutoff for RMS calculation: 3.5000 Upper = RMS, Lower = numb equiv positions 5fd1 1fdx_999 5fd1 0.000 2.797 1fdx_999 8 0.000 Distance comparison (FIT_ATOMS): Cutoff for rms calculation: 3.5000 Upper = Distance RMS, Lower = numb equiv distances 5fd1 1fdx_999 5fd1 0.000 1.762 1fdx_999 744 0.000 >> Sequence comparison: Diag=numb res, Upper=numb equiv res, Lower = % seq ID 5fd11fdx_999 5fd1 106 9 1fdx_999 17 54 >> Dihedral angle comparison: Alph Cutoff for rms comparison: 60.0000 Upper = RMS Alph, Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 29.892 1fdx_999 19 0.000 >> Dihedral angle comparison: Phi Cutoff for rms comparison: 60.0000 Upper = RMS Phi , Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 23.811 1fdx_999 40 0.000 >> Dihedral angle comparison: Psi Cutoff for rms comparison: 15.0000 Upper = RMS Psi , Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 7.885 1fdx_999 15 0.000 >> Dihedral angle comparison: Omeg Cutoff for rms comparison: 60.0000 Upper = RMS Omeg, Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 9.068 1fdx_999 53 0.000 >> Dihedral angle comparison: chi1 Cutoff for rms comparison: 60.0000 Upper = RMS chi1, Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 21.243 1fdx_999 14 0.000 >> Dihedral angle comparison: chi2 Cutoff for rms comparison: 60.0000 Upper = RMS chi2, Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 17.672 1fdx_999 5 0.000 >> Dihedral angle comparison: chi3 Cutoff for rms comparison: 60.0000 Upper = RMS chi3, Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 44.407 1fdx_999 1 0.000 >> Dihedral angle comparison: chi4 Cutoff for rms comparison: 60.0000 Upper = RMS chi4, Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 0.000 1fdx_999 0 0.000 >> Dihedral angle comparison: chi5 Cutoff for rms comparison: 60.0000 Upper = RMS chi5, Lower = numb of equiv angles 5fd1 1fdx_999 5fd1 0.000 0.000 1fdx_999 0 0.000 >> Ramachandran mainchain class substitution prot 1 --> prot 2; class on vert --> class on horiz A P B L E U A 16 4 5 3 0 0 P 4 1 1 1 0 1 B 2 5 3 0 0 0 L 3 1 1 2 0 0 E 0 0 0 0 0 0 U 0 0 0 0 0 1 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT A 16 12 28 30.2 22.6 52.8 P 1 7 8 1.9 13.2 15.1 B 3 7 10 5.7 13.2 18.9 L 2 5 7 3.8 9.4 13.2 E 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 22 31 53 41.5 58.5 100.0 -------------------------------------------- U 1 0 1 1.9 0.0 1.9 >> Dihedral class substitution: Alph prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 1 0 0 0 2 0 7 16 1 3 0 13 14 1 4 0 0 0 1 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 1 0 1 1.9 0.0 1.9 2 7 17 24 13.2 32.1 45.3 3 14 14 28 26.4 26.4 52.8 -------------------------------------------- SUMS 22 31 53 41.5 58.5 100.0 -------------------------------------------- 4 1 0 1 1.9 0.0 1.9 >> Dihedral class substitution: Phi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 19 4 3 0 2 4 2 1 0 3 11 0 9 0 4 0 0 0 1 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 19 7 26 35.8 13.2 49.1 2 2 5 7 3.8 9.4 13.2 3 9 11 20 17.0 20.8 37.7 -------------------------------------------- SUMS 30 23 53 56.6 43.4 100.0 -------------------------------------------- 4 1 0 1 1.9 0.0 1.9 >> Dihedral class substitution: Psi prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 15 4 4 0 2 4 4 4 0 3 6 2 10 1 4 0 0 0 0 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 15 8 23 27.8 14.8 42.6 2 4 8 12 7.4 14.8 22.2 3 10 9 19 18.5 16.7 35.2 -------------------------------------------- SUMS 29 25 54 53.7 46.3 100.0 -------------------------------------------- 4 0 0 0 0.0 0.0 0.0 >> Dihedral class substitution: Omeg prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 53 0 0 1 2 0 0 0 0 3 0 0 0 0 4 0 0 0 0 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 53 1 54 98.1 1.9 100.0 2 0 0 0 0.0 0.0 0.0 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 53 1 54 98.1 1.9 100.0 -------------------------------------------- 4 0 0 0 0.0 0.0 0.0 >> Dihedral class substitution: chi1 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 5 5 8 6 2 2 8 5 3 3 4 2 0 1 4 2 1 1 1 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 5 19 24 10.2 38.8 49.0 2 8 10 18 16.3 20.4 36.7 3 0 7 7 0.0 14.3 14.3 -------------------------------------------- SUMS 13 36 49 26.5 73.5 100.0 -------------------------------------------- 4 1 4 5 1.9 7.4 9.3 >> Dihedral class substitution: chi2 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 7 1 2 10 2 4 1 0 6 3 0 0 0 1 4 7 4 0 11 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 7 13 20 21.9 40.6 62.5 2 1 10 11 3.1 31.2 34.4 3 0 1 1 0.0 3.1 3.1 -------------------------------------------- SUMS 8 24 32 25.0 75.0 100.0 -------------------------------------------- 4 11 11 22 20.4 20.4 40.7 >> Dihedral class substitution: chi3 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 1 2 0 8 2 0 0 0 2 3 0 0 0 0 4 4 2 0 35 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 1 10 11 7.7 76.9 84.6 2 0 2 2 0.0 15.4 15.4 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 1 12 13 7.7 92.3 100.0 -------------------------------------------- 4 35 6 41 64.8 11.1 75.9 >> Dihedral class substitution: chi4 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 0 0 0 2 2 0 0 0 0 3 0 0 0 0 4 1 0 0 51 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 0 2 2 0.0 100.0 100.0 2 0 0 0 0.0 0.0 0.0 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 0 2 2 0.0 100.0 100.0 -------------------------------------------- 4 51 1 52 94.4 1.9 96.3 >> Dihedral class substitution: chi5 prot 1 --> prot 2; class on vert --> class on horiz 1 2 3 4 1 0 0 0 0 2 0 0 0 0 3 0 0 0 0 4 0 0 0 54 Summary (% does not count undefined): CODE # ID # NID # TOT % ID % NID % TOT 1 0 0 0 0.0 0.0 0.0 2 0 0 0 0.0 0.0 0.0 3 0 0 0 0.0 0.0 0.0 -------------------------------------------- SUMS 0 0 0 0.0 0.0 0.0 -------------------------------------------- 4 54 0 54 100.0 0.0 100.0 compare_344_> << END OF COMMAND Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 1398434 1365.658 1.334 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1435228 1401.590 1.369 malign3_328_> Initial framework positions: 106 malign3_330_> Framework, Cycles, RMS_frw(i-1,i): 1 2 0.0000 Least-squares dynamic programming alignment: FIT_ATOMS atoms for alignment : CA Max dist from frw for equivalence : 6.0000 Gap introduction penalty : 0.0000 Gap extension penalty : 3.0000 Numb of residues in framework : 54 malign3_332_> Framework: 1 # Sequence alignment of the structurally conserved regions # [average distance and standard deviation are with respect # to the framework (i.e., average structure)] # # N av ds st dv 5fd1 1fdx_9 # =============================== 1 1.815 0.000 * A 1 A 1 2 1.389 0.000 F 2 Y 2 3 1.348 0.000 * V 3 V 3 4 1.097 0.000 V 4 I 4 5 1.423 0.000 T 5 N 5 6 1.697 0.000 * D 6 D 6 7 1.486 0.000 N 7 S 7 8 1.466 0.000 * C 8 C 8 9 4.003 0.000 * I 9 I 9 10 3.853 0.000 K 10 A 10 11 3.830 0.000 * C 11 C 11 12 3.385 0.000 K 12 G 12 13 3.420 0.000 Y 13 A 13 14 2.608 0.000 T 14 C 14 15 2.764 0.000 D 15 K 15 16 3.202 0.000 C 16 P 16 17 2.581 0.000 V 17 E 17 18 3.097 0.000 E 18 C 18 19 3.847 0.000 V 19 P 19 20 3.482 0.000 C 20 V 20 21 4.038 0.000 P 21 N 21 22 4.017 0.000 V 22 I 22 23 3.654 0.000 D 23 I 23 24 4.717 0.000 C 24 Q 24 25 4.653 0.000 F 25 G 25 26 5.096 0.000 Y 26 S 26 27 3.684 0.000 E 27 I 27 28 3.173 0.000 G 28 Y 28 29 4.265 0.000 P 29 A 29 30 5.520 0.000 N 30 I 30 31 4.984 0.000 F 31 D 31 32 4.864 0.000 L 32 A 32 33 4.539 0.000 V 33 D 33 34 3.355 0.000 I 34 S 34 35 1.198 0.000 H 35 C 35 36 2.489 0.000 P 36 I 36 37 3.490 0.000 * D 37 D 37 38 3.884 0.000 E 38 C 38 39 3.323 0.000 C 39 G 39 40 3.912 0.000 I 40 S 40 41 4.444 0.000 D 41 C 41 42 4.442 0.000 C 42 A 42 43 3.105 0.000 A 43 S 43 44 2.950 0.000 L 44 V 44 45 2.915 0.000 * C 45 C 45 46 4.084 0.000 E 46 P 46 47 4.164 0.000 P 47 V 47 48 3.349 0.000 E 48 G 48 49 2.640 0.000 C 49 A 49 50 4.399 0.000 * P 50 P 50 51 5.080 0.000 A 51 N 51 52 5.498 0.000 Q 52 P 52 53 5.276 0.000 A 53 E 53 54 5.378 0.000 I 54 D 54 # =============================== openf___224_> Open 5fd1_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 106 841 841 openf___224_> Open 1fdx.B99990002_fit.pdb wrpdb___568_> Residues, atoms, selected atoms: 54 373 373 Dynamically allocated memory at finish [B,KiB,MiB]: 1296472 1266.086 1.236 Starting time : 2016/04/05 22:38:35 Closing time : 2016/04/05 22:38:38 Total CPU time [seconds] : 1.25