MODELLER 9.17, 2016/07/02, r10881 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 champaign 3.10.0-327.el7.x86_64 x86_64 Date and time of compilation : 2016/07/01 22:20:55 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2016/07/31 17:32:00 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v17}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v17}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL9v17}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 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 ${MODINSTALL9v17}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL9v17}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v17}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v17}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v17}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v17}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v17}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v17}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open rpn11_human_yeast.aln Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 265487 259.265 0.253 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 266937 260.681 0.255 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 269837 263.513 0.257 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 275637 269.177 0.263 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 392693 383.489 0.375 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 393821 384.591 0.376 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 394953 385.696 0.377 Read the alignment from file : rpn11_human_yeast.aln Total number of alignment positions: 284 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 rpn11_yea 283 1 rpn11_yeast 2 rpn11_hum 284 1 check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open rpn11_yeast_midres.pdb Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481578 470.291 0.459 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 481578 470.291 0.459 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 481749 470.458 0.459 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 482599 471.288 0.460 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 483857 472.517 0.461 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 485761 474.376 0.463 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 485761 474.376 0.463 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 485851 474.464 0.463 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 488707 477.253 0.466 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 488707 477.253 0.466 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 488842 477.385 0.466 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 493126 481.568 0.470 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 493126 481.568 0.470 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 493324 481.762 0.470 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 499750 488.037 0.477 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 499750 488.037 0.477 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 500047 488.327 0.477 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 509669 497.724 0.486 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 509669 497.724 0.486 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 510119 498.163 0.486 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 524569 512.274 0.500 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 524569 512.274 0.500 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 525244 512.934 0.501 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 546902 534.084 0.522 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 546902 534.084 0.522 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 547910 535.068 0.523 Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 580414 566.811 0.554 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 579928 566.336 0.553 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]: 719180 702.324 0.686 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 720780 703.887 0.687 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 724760 707.773 0.691 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 726760 709.727 0.693 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 729760 712.656 0.696 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 734260 717.051 0.700 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 739832 722.492 0.706 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 742632 725.227 0.708 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 746832 729.328 0.712 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 753132 735.480 0.718 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 755904 738.188 0.721 Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 757304 739.555 0.722 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 801735 782.944 0.765 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1023019 999.042 0.976 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1056339 1031.581 1.007 mkilst______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 284 2239 2281 0 0 942 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1151263 1124.280 1.098 patch_______> segment topology patched using RTF: 1 ; THR ; NTER segments residues atoms bonds angles dihedrals impropers: 1 284 2239 2281 3082 3623 942 Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1243359 1214.218 1.186 patch_______> segment topology patched using RTF: 284 ; LYS ; CTER segments residues atoms bonds angles dihedrals impropers: 1 284 2240 2282 3084 3625 943 genseg______> segment topology constructed from sequence and RTF: segments residues atoms bonds angles dihedrals impropers: 1 284 2240 2282 3084 3625 943 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: 2031 209 openf___224_> Open rpn11_human_27-310.ini wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 make_re_417_> Restraint type to be calculated: stereo Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1350408 1318.758 1.288 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1358600 1326.758 1.296 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1374984 1342.758 1.311 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1407752 1374.758 1.343 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1440520 1406.758 1.374 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1506056 1470.758 1.436 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1538824 1502.758 1.468 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1571592 1534.758 1.499 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1637128 1598.758 1.561 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1768200 1726.758 1.686 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1833736 1790.758 1.749 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1899272 1854.758 1.811 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2030344 1982.758 1.936 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2292488 2238.758 2.186 r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF. Added bond,angle,dihedral,improper restraints : 2282 3084 3448 933 Total number of restraints before, now : 0 9747 make_re_422_> Number of previous, current restraints : 0 9747 make_re_423_> Number of previous, current selected restraints: 0 9747 make_re_417_> Restraint type to be calculated: phi-psi_binormal Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2455839 2398.280 2.342 openf___224_> Open ${MODINSTALL9v17}/modlib/mnch1.bin openf___224_> Open ${MODINSTALL9v17}/modlib/mnch1.mdt errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 6 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 9 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 121 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 130 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 136 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 142 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 162 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 166 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 178 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 224 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 232 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 269 ILE errdih__638_> Missing atoms in a dihedral, residue index, residue type: 6 282 ILE getdata_643_> Protein accepted: rpn11_yeast_23-306 getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2586927 2526.296 2.467 make_re_422_> Number of previous, current restraints : 9747 10029 make_re_423_> Number of previous, current selected restraints: 9747 10029 make_re_417_> Restraint type to be calculated: omega_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2586927 2526.296 2.467 openf___224_> Open ${MODINSTALL9v17}/modlib/omega.bin openf___224_> Open ${MODINSTALL9v17}/modlib/omega.mdt getdata_643_> Protein accepted: rpn11_yeast_23-306 getdata_289_> Proteins (all/accepted): 1 1 omgdel__425_> Unselected all O C +N +CA dihedrals: 293 (This is to avoid clashes between STEREO and OMEGA_DIHEDRAL restraints) make_re_422_> Number of previous, current restraints : 10029 10312 make_re_423_> Number of previous, current selected restraints: 10029 10019 make_re_417_> Restraint type to be calculated: chi1_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2586927 2526.296 2.467 openf___224_> Open ${MODINSTALL9v17}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v17}/modlib/chi1.mdt getdata_643_> Protein accepted: rpn11_yeast_23-306 getdata_289_> Proteins (all/accepted): 1 1 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2717999 2654.296 2.592 make_re_422_> Number of previous, current restraints : 10312 10562 make_re_423_> Number of previous, current selected restraints: 10019 10269 make_re_417_> Restraint type to be calculated: chi2_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2717999 2654.296 2.592 openf___224_> Open ${MODINSTALL9v17}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v17}/modlib/chi2.mdt getdata_643_> Protein accepted: rpn11_yeast_23-306 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 10562 10750 make_re_423_> Number of previous, current selected restraints: 10269 10457 make_re_417_> Restraint type to be calculated: chi3_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2717999 2654.296 2.592 openf___224_> Open ${MODINSTALL9v17}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v17}/modlib/chi3.mdt getdata_643_> Protein accepted: rpn11_yeast_23-306 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 10750 10840 make_re_423_> Number of previous, current selected restraints: 10457 10547 make_re_417_> Restraint type to be calculated: chi4_dihedral Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2717999 2654.296 2.592 openf___224_> Open ${MODINSTALL9v17}/modlib/chi1234.bin openf___224_> Open ${MODINSTALL9v17}/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: rpn11_yeast_23-306 getdata_289_> Proteins (all/accepted): 1 1 make_re_422_> Number of previous, current restraints : 10840 10869 make_re_423_> Number of previous, current selected restraints: 10547 10576 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 3363083 3284.261 3.207 iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. iup2crm_279W> IUPAC atom CD not found in topology library for residue type ILE, index 8. Possible reasons are a non-standard PDB file, or new residue/atom types. Compare the offending residue in the PDB file with its definition in the topology library. make_re_422_> Number of previous, current restraints : 10869 15305 make_re_423_> Number of previous, current selected restraints: 10576 15012 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3625227 3540.261 3.457 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3887371 3796.261 3.707 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4411659 4308.261 4.207 make_re_422_> Number of previous, current restraints : 15305 20018 make_re_423_> Number of previous, current selected restraints: 15012 19725 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 20018 23887 make_re_423_> Number of previous, current selected restraints: 19725 23594 make_re_417_> Restraint type to be calculated: DISTANCE Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4673803 4564.261 4.457 make_re_422_> Number of previous, current restraints : 23887 25183 make_re_423_> Number of previous, current selected restraints: 23594 24890 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 : 25183 25183 make_re_423_> Number of previous, current selected restraints: 24890 24890 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 25183 25183 make_re_423_> Number of previous, current selected restraints: 24890 24890 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 25183 25183 make_re_423_> Number of previous, current selected restraints: 24890 24890 make_re_417_> Restraint type to be calculated: DISTANCE make_re_422_> Number of previous, current restraints : 25183 25183 make_re_423_> Number of previous, current selected restraints: 24890 24890 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 : 25183 25183 make_re_423_> Number of previous, current selected restraints: 24890 24890 rmdupl__427_> 1756 redundant cosine dihedral restraints were unselected. condens_443_> Restraints marked for deletion were removed. Total number of restraints before, now: 25183 23134 openf___224_> Open rpn11_human_27-310.rsr openf___224_> Open rpn11_human_27-310.rsr Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4717700 4607.129 4.499 rdcsr2__307_> Number of restraints read : 23134 Number of excluded pairs read: 0 Number of pseudo atoms read : 0 rdcsrs__304_> Restraints in memory, selected restraints: 23134 23134 Explicitly excluded atom pairs in memory : 0 Pseudo atoms in memory : 0 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 4717724 4607.152 4.499 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 5064064 4945.375 4.829 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_487_> NH1/2 swapped: -177.0059 20 20 iupac_m_486_> OE1/2 will be swapped: 175.4728 34 34 iupac_m_485_> OD1/2 will be swapped: -178.5601 37 37 iupac_m_487_> NH1/2 swapped: 177.8049 42 42 iupac_m_485_> OD1/2 will be swapped: -166.4364 45 45 iupac_m_483_> CD1/2 CE1/2 swapped: 91.2696 65 65 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: 165.5751 71 71 iupac_m_487_> NH1/2 swapped: 173.9373 78 78 iupac_m_483_> CD1/2 CE1/2 swapped: -115.9773 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -99.4276 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: 159.0804 108 108 iupac_m_487_> NH1/2 swapped: -177.8427 113 113 iupac_m_485_> OD1/2 will be swapped: -132.0401 132 132 iupac_m_487_> NH1/2 swapped: 177.4945 135 135 iupac_m_486_> OE1/2 will be swapped: 139.9872 147 147 iupac_m_487_> NH1/2 swapped: -173.9746 149 149 iupac_m_487_> NH1/2 swapped: -179.5086 172 172 iupac_m_487_> NH1/2 swapped: -178.1081 182 182 iupac_m_486_> OE1/2 will be swapped: -172.4442 210 210 iupac_m_486_> OE1/2 will be swapped: -172.0485 224 224 iupac_m_483_> CD1/2 CE1/2 swapped: -90.9526 229 229 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: 137.0753 234 234 iupac_m_485_> OD1/2 will be swapped: 136.7079 237 237 iupac_m_486_> OE1/2 will be swapped: -173.3913 242 242 iupac_m_487_> NH1/2 swapped: 178.4140 256 256 iupac_m_486_> OE1/2 will be swapped: -123.0855 259 259 iupac_m_485_> OD1/2 will be swapped: -170.6388 263 263 iupac_m_485_> OD1/2 will be swapped: 131.9689 279 279 iupac_m_483_> CD1/2 CE1/2 swapped: 102.4787 283 283 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. openf___224_> Open ${LIB}/atmcls-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5064484 4945.785 4.830 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5064548 4945.848 4.830 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5064606 4945.904 4.830 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5064670 4945.967 4.830 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5064736 4946.031 4.830 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5064800 4946.094 4.830 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5064956 4946.246 4.830 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5065084 4946.371 4.830 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5065378 4946.658 4.831 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5065570 4946.846 4.831 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5066074 4947.338 4.831 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5066330 4947.588 4.832 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5067326 4948.561 4.833 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5067710 4948.936 4.833 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5068286 4949.498 4.833 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5070320 4951.484 4.835 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5071216 4952.359 4.836 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5075668 4956.707 4.841 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5077012 4958.020 4.842 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5086630 4967.412 4.851 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5088614 4969.350 4.853 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5109260 4989.512 4.873 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5112268 4992.449 4.875 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5158234 5037.338 4.919 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5162714 5041.713 4.924 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5263934 5140.561 5.020 openf___224_> Open ${LIB}/dist-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5264330 5140.947 5.020 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5265126 5141.725 5.021 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5265922 5142.502 5.022 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5267110 5143.662 5.023 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5267510 5144.053 5.023 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5268110 5144.639 5.024 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5269010 5145.518 5.025 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5270358 5146.834 5.026 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5270558 5147.029 5.026 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5272582 5149.006 5.028 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5272882 5149.299 5.029 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5275918 5152.264 5.032 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5276366 5152.701 5.032 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5280918 5157.146 5.036 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5281590 5157.803 5.037 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5288418 5164.471 5.043 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5289426 5165.455 5.044 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5299670 5175.459 5.054 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5300270 5176.045 5.055 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5300670 5176.436 5.055 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5302182 5177.912 5.057 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5317546 5192.916 5.071 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5318446 5193.795 5.072 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5319046 5194.381 5.073 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5321314 5196.596 5.075 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5344362 5219.104 5.097 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5345706 5220.416 5.098 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5346606 5221.295 5.099 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5350010 5224.619 5.102 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5384582 5258.381 5.135 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5386598 5260.350 5.137 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5387946 5261.666 5.138 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5393050 5266.650 5.143 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5444906 5317.291 5.193 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5447930 5320.244 5.196 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5449954 5322.221 5.197 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5457610 5329.697 5.205 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5535394 5405.658 5.279 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5539930 5410.088 5.283 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5542966 5413.053 5.286 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5554450 5424.268 5.297 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5671126 5538.209 5.408 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5677930 5544.854 5.415 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5682482 5549.299 5.419 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5699710 5566.123 5.436 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5874726 5737.037 5.603 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5884938 5747.010 5.612 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5891766 5753.678 5.619 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 5917606 5778.912 5.643 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6180130 6035.283 5.894 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6195442 6050.236 5.908 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6205686 6060.240 5.918 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6244446 6098.092 5.955 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6638230 6482.646 6.331 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6661198 6505.076 6.353 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6676562 6520.080 6.367 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 6734702 6576.857 6.423 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 7325378 7153.689 6.986 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 7359830 7187.334 7.019 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 7382878 7209.842 7.041 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 7470090 7295.010 7.124 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 8356106 8160.260 7.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 8407790 8210.732 8.018 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 8442362 8244.494 8.051 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 8573178 8372.244 8.176 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 9902202 9670.119 9.443 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: LYS:OXT LYS Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 10248734 10008.529 9.774 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 10356254 10113.529 9.876 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 10571294 10323.529 10.082 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 11001374 10743.529 10.492 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 11861534 11583.529 11.312 Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 13581854 13263.529 12.953 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 329371 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 : -25815.3086 << end of ENERGY. DOPE score : -25815.308594 openf___224_> Open ${LIB}/atmcls-mf.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13289502 12978.029 12.674 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13289566 12978.092 12.674 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13289624 12978.148 12.674 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13289688 12978.211 12.674 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13289754 12978.275 12.674 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13289818 12978.338 12.674 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13289974 12978.490 12.674 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13290102 12978.615 12.674 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13290396 12978.902 12.675 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13290588 12979.090 12.675 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13291092 12979.582 12.675 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13291348 12979.832 12.676 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13292344 12980.805 12.677 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13292728 12981.180 12.677 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13293304 12981.742 12.677 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13295338 12983.729 12.679 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13296234 12984.604 12.680 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13300686 12988.951 12.685 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13302030 12990.264 12.686 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13311648 12999.656 12.695 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13313632 13001.594 12.697 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13334278 13021.756 12.717 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13337286 13024.693 12.719 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13383252 13069.582 12.763 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13387732 13073.957 12.768 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13488952 13172.805 12.864 openf___224_> Open ${LIB}/dist-mfhr.lib Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13489348 13173.191 12.864 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13490144 13173.969 12.865 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13490940 13174.746 12.866 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13491340 13175.137 12.866 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13492528 13176.297 12.867 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13493128 13176.883 12.868 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13494028 13177.762 12.869 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13495376 13179.078 12.870 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13497400 13181.055 12.872 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13500436 13184.020 12.875 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13504988 13188.465 12.879 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13511816 13195.133 12.886 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13512016 13195.328 12.886 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13522260 13205.332 12.896 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13522560 13205.625 12.896 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13537924 13220.629 12.911 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13538372 13221.066 12.911 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13561420 13243.574 12.933 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13562092 13244.230 12.934 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13596664 13277.992 12.967 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13597672 13278.977 12.968 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13598272 13279.562 12.968 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13598672 13279.953 12.969 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13650528 13330.594 13.018 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13652040 13332.070 13.020 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13652940 13332.949 13.020 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13653540 13333.535 13.021 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13731324 13409.496 13.095 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13733592 13411.711 13.097 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13734936 13413.023 13.099 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13735836 13413.902 13.100 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13852512 13527.844 13.211 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13855916 13531.168 13.214 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13857932 13533.137 13.216 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 13859280 13534.453 13.217 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14034296 13705.367 13.384 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14039400 13710.352 13.389 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14042424 13713.305 13.392 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14044448 13715.281 13.394 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14306972 13971.652 13.644 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14314628 13979.129 13.651 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14319164 13983.559 13.656 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14322200 13986.523 13.659 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14715984 14371.078 14.034 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14727468 14382.293 14.045 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14734272 14388.938 14.052 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 14738824 14393.383 14.056 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 15329500 14970.215 14.619 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 15346728 14987.039 14.636 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 15356940 14997.012 14.646 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 15363768 15003.680 14.652 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 16249784 15868.930 15.497 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 16275624 15894.164 15.522 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 16290936 15909.117 15.536 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 16301180 15919.121 15.546 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 17630204 17216.996 16.813 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 17668964 17254.848 16.850 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 17691932 17277.277 16.872 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 17707296 17292.281 16.887 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 19700832 19239.094 18.788 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 19758972 19295.871 18.844 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 19793424 19329.516 18.876 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 19816472 19352.023 18.898 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 22806776 22272.242 21.750 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 22893988 22357.410 21.833 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 22945672 22407.883 21.883 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 22980244 22441.645 21.916 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 27465700 26821.973 26.193 Dynamically allocated memory at amaxgroup_restr [B,KiB,MiB]: 27596516 26949.723 26.318 read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 0 0 0 0 12561 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 329371 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 : -21590.1406 << end of ENERGY. DOPE-HR score : -21590.140625 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.094802 Native energy (pair) : -200.826666 Native energy (surface) : -3.033592 Native energy (combined) : -6.291552 Z score (pair) : -7.939805 Z score (surface) : -5.836674 Z score (combined) : -9.889744 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4551 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 : 1859.6807 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 : 2282 0 0 0.005 0.005 16.593 1.000 2 Bond angle potential : 3084 0 7 2.050 2.050 243.83 1.000 3 Stereochemical cosine torsion poten: 1399 0 36 46.597 46.597 498.10 1.000 4 Stereochemical improper torsion pot: 933 0 1 1.375 1.375 41.658 1.000 5 Soft-sphere overlap restraints : 4551 0 1 0.004 0.004 9.2003 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) : 4436 0 0 0.150 0.150 106.97 1.000 10 Distance restraints 2 (N-O) : 4713 2 11 0.224 0.224 262.86 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: 283 2 5 11.065 11.065 74.080 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 1 70.669 70.669 45.113 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 0 71.313 71.313 63.104 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 1 77.018 77.018 63.624 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 66.120 66.120 16.865 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) : 3869 0 0 0.453 0.453 149.16 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: 282 10 37 32.070 41.741 123.63 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 3 0.863 0.863 144.89 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 rpn11_human_27-310.V99990001 # Heavy relative violation of each residue is written to: rpn11_human_27-310.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: 26981.4160 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8152 172R 172R CA C 1309 1317 -155.50 -180.00 24.50 4.90 -180.00 24.50 4.90 2 8185 205L 205L CA C 1599 1604 -10.68 -179.18 168.50 39.16 -179.18 168.50 39.16 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -72.50 -68.20 4.40 0.34 -62.50 173.19 28.88 1 2A 2A N CA 8 9 146.20 145.30 -40.90 2 7793 95W 96L C N 731 733 -82.67 -63.50 63.04 7.89 -63.50 63.04 7.89 2 96L 96L N CA 733 734 18.86 -41.20 -41.20 3 7844 146H 147E C N 1114 1116 87.62 54.60 111.86 11.22 -63.60 -132.16 26.80 3 147E 147E N CA 1116 1117 149.27 42.40 -40.30 4 7855 157H 158L C N 1200 1202 111.30 -108.50 146.29 7.50 -108.50 146.29 7.50 4 158L 158L N CA 1202 1203 90.72 132.50 132.50 5 7891 193N 194L C N 1504 1506 65.37 -70.70 147.77 14.75 -108.50 -173.76 9.73 5 194L 194L N CA 1506 1507 -160.78 141.60 132.50 6 7892 194L 195H C N 1512 1514 -76.78 -67.60 122.18 9.12 -67.60 122.18 9.12 6 195H 195H N CA 1514 1515 -98.17 140.00 140.00 7 7894 196K 197K C N 1531 1533 -175.27 -62.90 116.20 17.51 56.60 137.46 13.07 7 197K 197K N CA 1533 1534 -11.19 -40.80 38.60 8 7903 205L 206Q C N 1604 1606 -157.10 -121.10 134.35 6.86 -121.10 134.35 6.86 8 206Q 206Q N CA 1606 1607 10.26 139.70 139.70 9 7977 279D 280T C N 2197 2199 -157.25 -63.20 111.52 13.44 55.90 148.44 15.54 9 280T 280T N CA 2199 2200 17.82 -42.10 39.50 10 7978 280T 281V C N 2204 2206 85.68 55.90 92.59 4.65 -125.40 -135.10 6.56 10 281V 281V N CA 2206 2207 -48.17 39.50 143.30 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 1 22 40 106 131 219 204 249 280 350 363 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990001.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_486_> OE1/2 will be swapped: -124.8373 34 34 iupac_m_487_> NH1/2 swapped: -177.3487 42 42 iupac_m_485_> OD1/2 will be swapped: -177.1943 45 45 iupac_m_485_> OD1/2 will be swapped: -148.7198 71 71 iupac_m_483_> CD1/2 CE1/2 swapped: -121.0888 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -90.1850 92 92 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -97.9578 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -169.5585 108 108 iupac_m_486_> OE1/2 will be swapped: -175.1368 112 112 iupac_m_487_> NH1/2 swapped: -174.0043 113 113 iupac_m_487_> NH1/2 swapped: 178.4718 135 135 iupac_m_487_> NH1/2 swapped: 179.1882 149 149 iupac_m_487_> NH1/2 swapped: 179.2964 172 172 iupac_m_483_> CD1/2 CE1/2 swapped: 91.7482 181 181 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: -178.6640 182 182 iupac_m_486_> OE1/2 will be swapped: 141.3013 201 201 iupac_m_486_> OE1/2 will be swapped: 102.6516 210 210 iupac_m_486_> OE1/2 will be swapped: -111.4654 236 236 iupac_m_485_> OD1/2 will be swapped: 177.3851 237 237 iupac_m_486_> OE1/2 will be swapped: 152.2477 242 242 iupac_m_487_> NH1/2 swapped: -178.0152 256 256 iupac_m_486_> OE1/2 will be swapped: 123.4658 259 259 iupac_m_486_> OE1/2 will be swapped: 175.1826 260 260 iupac_m_485_> OD1/2 will be swapped: -156.8278 263 263 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 331853 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 : -25594.7930 << end of ENERGY. DOPE score : -25594.792969 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 331853 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 : -21195.6113 << end of ENERGY. DOPE-HR score : -21195.611328 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.075686 Native energy (pair) : -166.711301 Native energy (surface) : -2.669987 Native energy (combined) : -4.509097 Z score (pair) : -6.480518 Z score (surface) : -5.625274 Z score (combined) : -7.630962 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4524 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 : 2002.7985 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 : 2282 0 0 0.005 0.005 19.675 1.000 2 Bond angle potential : 3084 1 5 2.144 2.144 264.14 1.000 3 Stereochemical cosine torsion poten: 1399 0 42 47.732 47.732 515.63 1.000 4 Stereochemical improper torsion pot: 933 0 0 1.448 1.448 44.763 1.000 5 Soft-sphere overlap restraints : 4524 0 1 0.004 0.004 9.3354 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) : 4436 0 0 0.165 0.165 130.49 1.000 10 Distance restraints 2 (N-O) : 4713 0 8 0.233 0.233 264.64 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: 283 2 4 14.207 14.207 70.952 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 4 72.418 72.418 67.992 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 1 69.896 69.896 80.437 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 1 69.194 69.194 71.990 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 83.172 83.172 21.421 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) : 3869 0 0 0.455 0.455 147.27 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: 282 9 38 33.081 43.267 144.25 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 2 0.874 0.874 149.82 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 rpn11_human_27-310.V99990002 # Heavy relative violation of each residue is written to: rpn11_human_27-310.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: 28691.2344 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 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4523 207D 208Y C N 1621 1623 147.05 120.00 27.05 6.15 120.00 27.05 6.15 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -32.40 -179.18 146.79 34.11 -179.18 146.79 34.11 2 8187 207D 207D CA C 1616 1621 -4.88 -179.18 174.30 40.51 -179.18 174.30 40.51 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -72.98 -68.20 17.32 1.23 -62.50 157.51 26.34 1 2A 2A N CA 8 9 161.95 145.30 -40.90 2 7793 95W 96L C N 731 733 -82.75 -63.50 62.44 7.80 -63.50 62.44 7.80 2 96L 96L N CA 733 734 18.20 -41.20 -41.20 3 7844 146H 147E C N 1114 1116 87.12 54.60 110.01 11.04 -63.60 -131.15 26.89 3 147E 147E N CA 1116 1117 147.49 42.40 -40.30 4 7855 157H 158L C N 1200 1202 109.84 -108.50 146.92 7.49 -108.50 146.92 7.49 4 158L 158L N CA 1202 1203 93.53 132.50 132.50 5 7870 172R 173H C N 1317 1319 -110.22 -63.20 52.19 8.96 -63.20 52.19 8.96 5 173H 173H N CA 1319 1320 -64.95 -42.30 -42.30 6 7891 193N 194L C N 1504 1506 56.42 -70.70 133.74 13.20 -108.50 172.52 8.86 6 194L 194L N CA 1506 1507 -176.85 141.60 132.50 7 7905 207D 208Y C N 1621 1623 -91.45 -63.50 47.33 6.53 -63.50 47.33 6.53 7 208Y 208Y N CA 1623 1624 -5.20 -43.40 -43.40 8 7938 240T 241P C N 1893 1895 -121.05 -64.50 58.88 5.24 -58.70 177.21 19.75 8 241P 241P N CA 1895 1896 163.62 147.20 -30.50 9 7980 282V 283F C N 2218 2220 63.67 58.10 30.59 3.12 -124.20 -170.05 9.56 9 283F 283F N CA 2220 2221 62.97 32.90 143.30 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 2 18 29 105 142 195 219 248 309 370 376 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990002.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_487_> NH1/2 swapped: -175.7444 20 20 iupac_m_485_> OD1/2 will be swapped: 149.8356 37 37 iupac_m_483_> CD1/2 CE1/2 swapped: -94.5879 39 39 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_487_> NH1/2 swapped: -180.0000 42 42 iupac_m_485_> OD1/2 will be swapped: -143.1450 45 45 iupac_m_485_> OD1/2 will be swapped: -158.7098 71 71 iupac_m_487_> NH1/2 swapped: 179.0900 78 78 iupac_m_486_> OE1/2 will be swapped: 167.4380 80 80 iupac_m_483_> CD1/2 CE1/2 swapped: -129.8771 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -103.6490 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -120.7113 108 108 iupac_m_486_> OE1/2 will be swapped: 117.9946 112 112 iupac_m_487_> NH1/2 swapped: -179.2978 113 113 iupac_m_487_> NH1/2 swapped: -171.1601 135 135 iupac_m_487_> NH1/2 swapped: -178.7537 149 149 iupac_m_487_> NH1/2 swapped: 178.7537 172 172 iupac_m_486_> OE1/2 will be swapped: 174.8292 185 185 iupac_m_486_> OE1/2 will be swapped: -104.8248 201 201 iupac_m_486_> OE1/2 will be swapped: 144.0279 210 210 iupac_m_483_> CD1/2 CE1/2 swapped: -116.8424 229 229 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: 157.7050 237 237 iupac_m_487_> NH1/2 swapped: 179.1189 256 256 iupac_m_486_> OE1/2 will be swapped: 165.2194 260 260 iupac_m_485_> OD1/2 will be swapped: 149.2772 263 263 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 330122 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 : -25719.8574 << end of ENERGY. DOPE score : -25719.857422 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 330122 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 : -21105.9023 << end of ENERGY. DOPE-HR score : -21105.902344 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.097726 Native energy (pair) : -173.458386 Native energy (surface) : -3.747429 Native energy (combined) : -4.944365 Z score (pair) : -6.638553 Z score (surface) : -5.903379 Z score (combined) : -7.987898 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4489 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 : 1905.0619 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 : 2282 0 0 0.005 0.005 17.515 1.000 2 Bond angle potential : 3084 0 5 2.074 2.074 248.45 1.000 3 Stereochemical cosine torsion poten: 1399 0 38 47.036 47.036 507.00 1.000 4 Stereochemical improper torsion pot: 933 0 1 1.454 1.454 46.918 1.000 5 Soft-sphere overlap restraints : 4489 0 0 0.004 0.004 8.3214 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) : 4436 0 0 0.159 0.159 122.41 1.000 10 Distance restraints 2 (N-O) : 4713 0 3 0.217 0.217 245.83 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: 283 2 4 11.134 11.134 68.258 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 2 65.213 65.213 45.732 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 2 71.995 71.995 76.841 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 1 79.907 79.907 67.175 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 86.070 86.070 17.264 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) : 3869 0 0 0.434 0.434 137.66 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: 282 11 39 31.851 40.719 147.08 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 3 0.874 0.874 148.61 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 rpn11_human_27-310.V99990003 # Heavy relative violation of each residue is written to: rpn11_human_27-310.V99990003 # 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: 27514.4082 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -8.23 -179.18 170.95 39.73 -179.18 170.95 39.73 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -105.45 -134.00 32.26 1.64 -62.50 162.83 28.96 1 2A 2A N CA 8 9 162.04 147.00 -40.90 2 7793 95W 96L C N 731 733 -82.48 -63.50 61.34 7.66 -63.50 61.34 7.66 2 96L 96L N CA 733 734 17.12 -41.20 -41.20 3 7844 146H 147E C N 1114 1116 88.64 54.60 111.71 11.29 -63.60 -131.12 26.94 3 147E 147E N CA 1116 1117 148.79 42.40 -40.30 4 7855 157H 158L C N 1200 1202 106.85 -108.50 150.13 7.66 -108.50 150.13 7.66 4 158L 158L N CA 1202 1203 92.29 132.50 132.50 5 7870 172R 173H C N 1317 1319 -112.49 -63.20 52.60 8.97 -63.20 52.60 8.97 5 173H 173H N CA 1319 1320 -60.65 -42.30 -42.30 6 7892 194L 195H C N 1512 1514 93.18 -125.60 155.99 4.15 -67.60 173.44 14.79 6 195H 195H N CA 1514 1515 -154.95 138.80 140.00 7 7894 196K 197K C N 1531 1533 -167.18 -62.90 107.19 16.30 56.60 146.75 13.84 7 197K 197K N CA 1533 1534 -16.00 -40.80 38.60 8 7903 205L 206Q C N 1604 1606 -152.17 -121.10 132.38 6.72 -121.10 132.38 6.72 8 206Q 206Q N CA 1606 1607 11.01 139.70 139.70 9 7905 207D 208Y C N 1621 1623 -102.79 -63.50 44.13 6.58 -63.50 44.13 6.58 9 208Y 208Y N CA 1623 1624 -23.32 -43.40 -43.40 10 7977 279D 280T C N 2197 2199 -172.13 -63.20 122.38 15.46 55.90 134.48 13.70 10 280T 280T N CA 2199 2200 13.67 -42.10 39.50 11 7980 282V 283F C N 2218 2220 62.33 58.10 30.79 3.00 -124.20 -169.02 9.59 11 283F 283F N CA 2220 2221 63.40 32.90 143.30 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 1 19 31 90 141 211 205 268 284 348 348 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990003.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_485_> OD1/2 will be swapped: 161.2847 37 37 iupac_m_487_> NH1/2 swapped: -178.7794 42 42 iupac_m_485_> OD1/2 will be swapped: -167.4396 45 45 iupac_m_485_> OD1/2 will be swapped: -171.8504 71 71 iupac_m_487_> NH1/2 swapped: 179.3265 78 78 iupac_m_483_> CD1/2 CE1/2 swapped: -112.9460 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -101.5473 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -160.2962 108 108 iupac_m_486_> OE1/2 will be swapped: -90.3313 112 112 iupac_m_487_> NH1/2 swapped: -175.5067 113 113 iupac_m_487_> NH1/2 swapped: 178.4472 182 182 iupac_m_486_> OE1/2 will be swapped: 174.1339 210 210 iupac_m_486_> OE1/2 will be swapped: 93.0598 221 221 iupac_m_486_> OE1/2 will be swapped: -153.4565 224 224 iupac_m_483_> CD1/2 CE1/2 swapped: -96.2945 229 229 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -90.1368 234 234 iupac_m_486_> OE1/2 will be swapped: 164.9533 236 236 iupac_m_486_> OE1/2 will be swapped: -170.9519 242 242 iupac_m_487_> NH1/2 swapped: -179.7046 256 256 iupac_m_486_> OE1/2 will be swapped: 176.6007 260 260 iupac_m_485_> OD1/2 will be swapped: 146.2425 279 279 iupac_m_483_> CD1/2 CE1/2 swapped: 104.6123 283 283 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 329612 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 : -25456.1875 << end of ENERGY. DOPE score : -25456.187500 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 329612 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 : -20643.1992 << end of ENERGY. DOPE-HR score : -20643.199219 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.113798 Native energy (pair) : -167.429159 Native energy (surface) : -3.125704 Native energy (combined) : -4.639786 Z score (pair) : -6.406080 Z score (surface) : -5.732825 Z score (combined) : -7.729534 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4543 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 : 1867.0762 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 : 2282 0 0 0.005 0.005 16.024 1.000 2 Bond angle potential : 3084 0 7 2.031 2.031 240.61 1.000 3 Stereochemical cosine torsion poten: 1399 0 42 47.241 47.241 505.23 1.000 4 Stereochemical improper torsion pot: 933 0 1 1.390 1.390 43.096 1.000 5 Soft-sphere overlap restraints : 4543 0 0 0.004 0.004 8.9877 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) : 4436 0 3 0.157 0.157 115.89 1.000 10 Distance restraints 2 (N-O) : 4713 0 7 0.221 0.221 249.35 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: 283 2 6 11.218 11.218 69.594 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 2 67.876 67.876 35.116 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 0 70.734 70.734 58.477 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 1 68.182 68.182 56.807 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 77.676 77.676 19.852 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) : 3869 0 0 0.410 0.410 120.20 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: 282 14 43 34.791 43.287 210.96 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 3 0.780 0.780 116.87 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 rpn11_human_27-310.V99990004 # Heavy relative violation of each residue is written to: rpn11_human_27-310.V99990004 # 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: 26433.1562 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -7.09 -179.18 172.09 40.00 -179.18 172.09 40.00 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -70.87 -68.20 14.67 1.09 -62.50 159.59 26.57 1 2A 2A N CA 8 9 159.73 145.30 -40.90 2 7773 75Q 76T C N 569 571 -67.37 -63.20 62.83 8.33 -63.20 62.83 8.33 2 76T 76T N CA 571 572 -104.79 -42.10 -42.10 3 7774 76T 77G C N 576 578 -88.65 -62.40 27.51 5.16 82.20 -179.59 13.71 3 77G 77G N CA 578 579 -49.43 -41.20 8.50 4 7793 95W 96L C N 731 733 -82.27 -63.50 62.31 7.80 -63.50 62.31 7.80 4 96L 96L N CA 733 734 18.21 -41.20 -41.20 5 7844 146H 147E C N 1114 1116 85.23 54.60 111.39 11.00 -63.60 -133.91 26.56 5 147E 147E N CA 1116 1117 149.49 42.40 -40.30 6 7855 157H 158L C N 1200 1202 121.09 -108.50 137.91 7.14 -108.50 137.91 7.14 6 158L 158L N CA 1202 1203 87.66 132.50 132.50 7 7870 172R 173H C N 1317 1319 -110.13 -63.20 52.31 8.98 -63.20 52.31 8.98 7 173H 173H N CA 1319 1320 -65.39 -42.30 -42.30 8 7891 193N 194L C N 1504 1506 56.47 -70.70 134.64 13.33 -108.50 173.38 8.94 8 194L 194L N CA 1506 1507 -174.16 141.60 132.50 9 7894 196K 197K C N 1531 1533 77.76 56.60 130.97 11.00 56.60 130.97 11.00 9 197K 197K N CA 1533 1534 167.85 38.60 38.60 10 7895 197K 198S C N 1540 1542 72.41 -64.10 138.59 18.37 -64.10 138.59 18.37 10 198S 198S N CA 1542 1543 -11.09 -35.00 -35.00 11 7903 205L 206Q C N 1604 1606 -153.45 -121.10 141.11 7.16 -121.10 141.11 7.16 11 206Q 206Q N CA 1606 1607 2.35 139.70 139.70 12 7905 207D 208Y C N 1621 1623 -106.58 -63.50 47.36 7.15 -63.50 47.36 7.15 12 208Y 208Y N CA 1623 1624 -23.72 -43.40 -43.40 13 7977 279D 280T C N 2197 2199 -165.82 -63.20 114.24 14.57 55.90 141.81 14.18 13 280T 280T N CA 2199 2200 8.09 -42.10 39.50 14 7980 282V 283F C N 2218 2220 91.64 58.10 87.52 10.65 -124.20 147.16 6.59 14 283F 283F N CA 2220 2221 113.74 32.90 143.30 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 22 41 129 125 208 211 246 317 328 367 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990004.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_485_> OD1/2 will be swapped: 171.6211 37 37 iupac_m_483_> CD1/2 CE1/2 swapped: -93.4165 39 39 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: -172.6540 45 45 iupac_m_486_> OE1/2 will be swapped: -176.7090 59 59 iupac_m_485_> OD1/2 will be swapped: 179.3251 71 71 iupac_m_483_> CD1/2 CE1/2 swapped: -132.1008 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -98.7890 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: 164.9862 108 108 iupac_m_487_> NH1/2 swapped: -178.8569 172 172 iupac_m_487_> NH1/2 swapped: -177.4695 182 182 iupac_m_486_> OE1/2 will be swapped: -151.3245 201 201 iupac_m_486_> OE1/2 will be swapped: -145.2772 216 216 iupac_m_486_> OE1/2 will be swapped: -120.3887 221 221 iupac_m_486_> OE1/2 will be swapped: 177.2425 236 236 iupac_m_486_> OE1/2 will be swapped: 147.5764 259 259 iupac_m_486_> OE1/2 will be swapped: 162.5181 260 260 iupac_m_485_> OD1/2 will be swapped: 168.6171 263 263 iupac_m_483_> CD1/2 CE1/2 swapped: 99.7351 283 283 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 329592 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 : -25791.0195 << end of ENERGY. DOPE score : -25791.019531 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 329592 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 : -21284.9297 << end of ENERGY. DOPE-HR score : -21284.929688 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.112897 Native energy (pair) : -177.403774 Native energy (surface) : -3.155811 Native energy (combined) : -4.935514 Z score (pair) : -6.877131 Z score (surface) : -5.739981 Z score (combined) : -8.068315 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4547 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 : 1874.2838 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 : 2282 0 0 0.005 0.005 17.223 1.000 2 Bond angle potential : 3084 0 6 2.053 2.053 245.06 1.000 3 Stereochemical cosine torsion poten: 1399 0 42 47.002 47.002 503.47 1.000 4 Stereochemical improper torsion pot: 933 0 1 1.418 1.418 44.869 1.000 5 Soft-sphere overlap restraints : 4547 0 2 0.004 0.004 9.5691 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) : 4436 0 1 0.156 0.156 116.86 1.000 10 Distance restraints 2 (N-O) : 4713 0 4 0.221 0.221 254.52 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: 283 2 6 11.177 11.177 75.901 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 2 68.811 68.811 49.247 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 2 76.541 76.541 73.723 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 0 67.149 67.149 59.811 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 73.975 73.975 17.470 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) : 3869 0 0 0.431 0.431 137.56 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: 282 13 39 29.669 43.833 141.89 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 1 0.808 0.808 127.11 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 rpn11_human_27-310.V99990005 # Heavy relative violation of each residue is written to: rpn11_human_27-310.V99990005 # 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: 27504.4902 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -9.32 -179.18 169.86 39.48 -179.18 169.86 39.48 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -75.80 -68.20 10.03 0.64 -62.50 167.79 28.17 1 2A 2A N CA 8 9 151.84 145.30 -40.90 2 7793 95W 96L C N 731 733 -82.52 -63.50 61.90 7.74 -63.50 61.90 7.74 2 96L 96L N CA 733 734 17.71 -41.20 -41.20 3 7824 126K 127G C N 962 964 -94.21 -62.40 34.58 6.53 82.20 -172.59 14.29 3 127G 127G N CA 964 965 -54.75 -41.20 8.50 4 7844 146H 147E C N 1114 1116 70.28 54.60 104.06 9.26 -63.60 -140.12 25.57 4 147E 147E N CA 1116 1117 145.27 42.40 -40.30 5 7855 157H 158L C N 1200 1202 105.29 -108.50 149.51 7.51 -108.50 149.51 7.51 5 158L 158L N CA 1202 1203 101.23 132.50 132.50 6 7870 172R 173H C N 1317 1319 -110.02 -63.20 49.89 8.50 -63.20 49.89 8.50 6 173H 173H N CA 1319 1320 -59.52 -42.30 -42.30 7 7890 192L 193N C N 1496 1498 -84.58 -119.90 90.83 3.24 -63.20 96.81 11.06 7 193N 193N N CA 1498 1499 53.32 137.00 -41.10 8 7891 193N 194L C N 1504 1506 -58.73 -63.50 19.21 2.44 -108.50 174.91 9.86 8 194L 194L N CA 1506 1507 -59.81 -41.20 132.50 9 7893 195H 196K C N 1522 1524 -55.31 -62.90 14.99 1.73 -118.00 178.54 9.22 9 196K 196K N CA 1524 1525 -53.73 -40.80 139.10 10 7903 205L 206Q C N 1604 1606 -153.07 -121.10 131.16 6.67 -121.10 131.16 6.67 10 206Q 206Q N CA 1606 1607 12.50 139.70 139.70 11 7977 279D 280T C N 2197 2199 -169.31 -124.80 121.24 6.46 55.90 135.08 14.75 11 280T 280T N CA 2199 2200 30.72 143.50 39.50 12 7979 281V 282V C N 2211 2213 -138.82 -125.40 67.54 2.99 -73.50 95.96 6.87 12 282V 282V N CA 2213 2214 -150.50 143.30 139.20 13 7980 282V 283F C N 2218 2220 62.38 58.10 31.68 3.08 -124.20 -169.43 9.56 13 283F 283F N CA 2220 2221 64.29 32.90 143.30 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 2 20 25 115 135 218 211 236 306 335 361 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990005.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_486_> OE1/2 will be swapped: 179.5310 3 3 iupac_m_486_> OE1/2 will be swapped: 168.9062 34 34 iupac_m_485_> OD1/2 will be swapped: -179.8991 37 37 iupac_m_487_> NH1/2 swapped: -178.2105 42 42 iupac_m_485_> OD1/2 will be swapped: -158.7815 45 45 iupac_m_485_> OD1/2 will be swapped: 160.6298 71 71 iupac_m_487_> NH1/2 swapped: 177.4080 78 78 iupac_m_486_> OE1/2 will be swapped: 117.3552 80 80 iupac_m_483_> CD1/2 CE1/2 swapped: -113.0095 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -91.1393 92 92 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -103.7258 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: 170.0991 112 112 iupac_m_487_> NH1/2 swapped: -172.7785 113 113 iupac_m_485_> OD1/2 will be swapped: -154.2877 132 132 iupac_m_487_> NH1/2 swapped: -179.1901 172 172 iupac_m_486_> OE1/2 will be swapped: 175.5543 216 216 iupac_m_486_> OE1/2 will be swapped: -136.5747 234 234 iupac_m_486_> OE1/2 will be swapped: 145.8033 235 235 iupac_m_487_> NH1/2 swapped: 177.4633 256 256 iupac_m_486_> OE1/2 will be swapped: 174.5518 260 260 iupac_m_485_> OD1/2 will be swapped: 156.4819 263 263 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 328882 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 : -25631.3047 << end of ENERGY. DOPE score : -25631.304688 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 328882 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 : -21117.1270 << end of ENERGY. DOPE-HR score : -21117.126953 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.090416 Native energy (pair) : -170.855990 Native energy (surface) : -1.707584 Native energy (combined) : -4.499911 Z score (pair) : -6.777772 Z score (surface) : -5.516857 Z score (combined) : -7.778704 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4456 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 : 1881.9801 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 : 2282 0 0 0.005 0.005 16.437 1.000 2 Bond angle potential : 3084 1 7 2.089 2.089 255.37 1.000 3 Stereochemical cosine torsion poten: 1399 0 39 47.235 47.235 503.16 1.000 4 Stereochemical improper torsion pot: 933 0 0 1.397 1.397 43.513 1.000 5 Soft-sphere overlap restraints : 4456 0 0 0.004 0.004 9.7031 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) : 4436 0 1 0.153 0.153 110.52 1.000 10 Distance restraints 2 (N-O) : 4713 0 3 0.216 0.216 236.48 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: 283 2 8 14.963 14.963 85.788 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 2 61.831 61.831 36.584 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 0 68.696 68.696 58.049 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 1 63.702 63.702 58.801 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 88.327 88.327 19.191 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) : 3869 0 0 0.422 0.422 129.49 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: 282 13 39 31.393 42.721 182.55 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 1 0.837 0.837 136.34 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 rpn11_human_27-310.V99990006 # Heavy relative violation of each residue is written to: rpn11_human_27-310.V99990006 # 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: 26242.3262 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 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4523 207D 208Y C N 1621 1623 144.93 120.00 24.93 5.67 120.00 24.93 5.67 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -18.29 -179.18 160.89 37.39 -179.18 160.89 37.39 2 8187 207D 207D CA C 1616 1621 -4.28 -179.18 174.90 40.65 -179.18 174.90 40.65 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -64.92 -68.20 11.02 1.00 -62.50 163.30 26.88 1 2A 2A N CA 8 9 155.82 145.30 -40.90 2 7773 75Q 76T C N 569 571 -67.45 -63.20 65.60 8.69 -63.20 65.60 8.69 2 76T 76T N CA 571 572 -107.56 -42.10 -42.10 3 7774 76T 77G C N 576 578 -92.20 -62.40 29.89 5.43 82.20 -177.99 13.71 3 77G 77G N CA 578 579 -43.57 -41.20 8.50 4 7793 95W 96L C N 731 733 -81.95 -63.50 65.53 8.24 -63.50 65.53 8.24 4 96L 96L N CA 733 734 21.68 -41.20 -41.20 5 7844 146H 147E C N 1114 1116 83.62 54.60 103.78 10.29 -63.60 -129.27 26.97 5 147E 147E N CA 1116 1117 142.04 42.40 -40.30 6 7855 157H 158L C N 1200 1202 113.46 -108.50 143.92 7.37 -108.50 143.92 7.37 6 158L 158L N CA 1202 1203 91.78 132.50 132.50 7 7870 172R 173H C N 1317 1319 -112.57 -63.20 52.52 8.95 -63.20 52.52 8.95 7 173H 173H N CA 1319 1320 -60.22 -42.30 -42.30 8 7890 192L 193N C N 1496 1498 -77.00 -63.20 89.74 10.51 -63.20 89.74 10.51 8 193N 193N N CA 1498 1499 47.57 -41.10 -41.10 9 7891 193N 194L C N 1504 1506 -59.29 -63.50 16.97 2.15 -108.50 176.84 9.96 9 194L 194L N CA 1506 1507 -57.64 -41.20 132.50 10 7894 196K 197K C N 1531 1533 -143.50 -62.90 86.96 12.46 56.60 166.59 16.85 10 197K 197K N CA 1533 1534 -8.17 -40.80 38.60 11 7905 207D 208Y C N 1621 1623 -92.70 -63.50 49.50 6.83 -63.50 49.50 6.83 11 208Y 208Y N CA 1623 1624 -3.43 -43.40 -43.40 12 7977 279D 280T C N 2197 2199 -161.55 -63.20 113.15 13.98 55.90 144.84 14.89 12 280T 280T N CA 2199 2200 13.84 -42.10 39.50 13 7980 282V 283F C N 2218 2220 94.06 58.10 85.85 10.72 -124.20 145.41 6.60 13 283F 283F N CA 2220 2221 110.86 32.90 143.30 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 1 20 36 107 142 198 197 261 294 333 338 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990006.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_486_> OE1/2 will be swapped: -115.4802 26 26 iupac_m_485_> OD1/2 will be swapped: 152.2474 37 37 iupac_m_485_> OD1/2 will be swapped: -169.2688 45 45 iupac_m_486_> OE1/2 will be swapped: 113.8792 80 80 iupac_m_483_> CD1/2 CE1/2 swapped: -112.9880 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -105.2705 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -92.5357 108 108 iupac_m_486_> OE1/2 will be swapped: -168.6313 112 112 iupac_m_486_> OE1/2 will be swapped: 141.4250 147 147 iupac_m_487_> NH1/2 swapped: -175.9847 172 172 iupac_m_487_> NH1/2 swapped: -178.7462 182 182 iupac_m_483_> CD1/2 CE1/2 swapped: -97.2169 229 229 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: 178.0792 234 234 iupac_m_486_> OE1/2 will be swapped: -126.8648 235 235 iupac_m_485_> OD1/2 will be swapped: 113.5639 237 237 iupac_m_487_> NH1/2 swapped: -179.4902 256 256 iupac_m_485_> OD1/2 will be swapped: 178.0629 263 263 iupac_m_485_> OD1/2 will be swapped: 146.1733 279 279 iupac_m_483_> CD1/2 CE1/2 swapped: -98.9179 283 283 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 331562 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 : -25428.0156 << end of ENERGY. DOPE score : -25428.015625 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 331562 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 : -20388.7148 << end of ENERGY. DOPE-HR score : -20388.714844 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.106483 Native energy (pair) : -198.985408 Native energy (surface) : -2.901856 Native energy (combined) : -5.438246 Z score (pair) : -7.007693 Z score (surface) : -5.721815 Z score (combined) : -7.967980 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4609 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 : 1887.2423 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 : 2282 0 0 0.005 0.005 15.849 1.000 2 Bond angle potential : 3084 1 10 2.111 2.111 257.74 1.000 3 Stereochemical cosine torsion poten: 1399 0 44 47.735 47.735 513.94 1.000 4 Stereochemical improper torsion pot: 933 0 0 1.376 1.376 41.956 1.000 5 Soft-sphere overlap restraints : 4609 0 0 0.004 0.004 9.6371 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) : 4436 0 0 0.156 0.156 112.15 1.000 10 Distance restraints 2 (N-O) : 4713 0 2 0.214 0.214 233.14 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: 283 2 5 14.886 14.886 74.875 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 2 71.115 71.115 44.848 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 1 62.923 62.923 56.399 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 1 70.622 70.622 62.308 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 73.951 73.951 19.828 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) : 3869 0 0 0.407 0.407 120.27 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: 282 12 40 31.716 43.187 191.22 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 0 0.831 0.831 133.08 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 rpn11_human_27-310.V99990007 # Heavy relative violation of each residue is written to: rpn11_human_27-310.V99990007 # 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: 27164.9473 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 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4523 207D 208Y C N 1621 1623 145.73 120.00 25.73 5.85 120.00 25.73 5.85 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -17.05 -179.18 162.13 37.68 -179.18 162.13 37.68 2 8187 207D 207D CA C 1616 1621 -4.77 -179.18 174.41 40.54 -179.18 174.41 40.54 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -130.66 -134.00 12.20 0.74 -62.50 174.26 32.21 1 2A 2A N CA 8 9 158.73 147.00 -40.90 2 7793 95W 96L C N 731 733 -81.77 -63.50 61.64 7.72 -63.50 61.64 7.72 2 96L 96L N CA 733 734 17.67 -41.20 -41.20 3 7844 146H 147E C N 1114 1116 88.71 54.60 114.40 11.50 -63.60 -133.16 26.74 3 147E 147E N CA 1116 1117 151.59 42.40 -40.30 4 7855 157H 158L C N 1200 1202 110.16 -108.50 144.83 7.30 -108.50 144.83 7.30 4 158L 158L N CA 1202 1203 100.90 132.50 132.50 5 7870 172R 173H C N 1317 1319 -112.46 -63.20 53.01 9.06 -63.20 53.01 9.06 5 173H 173H N CA 1319 1320 -61.89 -42.30 -42.30 6 7890 192L 193N C N 1496 1498 -82.01 -119.90 92.96 3.27 -63.20 95.09 10.95 6 193N 193N N CA 1498 1499 52.11 137.00 -41.10 7 7891 193N 194L C N 1504 1506 -59.99 -63.50 19.95 2.59 -108.50 173.57 9.78 7 194L 194L N CA 1506 1507 -60.85 -41.20 132.50 8 7893 195H 196K C N 1522 1524 30.86 -62.90 122.27 15.35 -118.00 -179.76 8.68 8 196K 196K N CA 1524 1525 -119.27 -40.80 139.10 9 7937 239M 240T C N 1886 1888 -81.50 -63.20 94.78 11.04 -63.20 94.78 11.04 9 240T 240T N CA 1888 1889 50.89 -42.10 -42.10 10 7938 240T 241P C N 1893 1895 23.44 -64.50 102.45 7.72 -58.70 149.69 18.85 10 241P 241P N CA 1895 1896 94.64 147.20 -30.50 11 7977 279D 280T C N 2197 2199 -164.51 -63.20 118.42 14.43 55.90 141.06 14.79 11 280T 280T N CA 2199 2200 19.20 -42.10 39.50 12 7978 280T 281V C N 2204 2206 85.25 55.90 89.25 4.46 -125.40 -132.27 6.68 12 281V 281V N CA 2206 2207 -44.78 39.50 143.30 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 26 31 113 145 214 230 241 305 335 392 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990007.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_485_> OD1/2 will be swapped: 159.0460 37 37 iupac_m_487_> NH1/2 swapped: 178.0963 42 42 iupac_m_485_> OD1/2 will be swapped: -166.7095 45 45 iupac_m_486_> OE1/2 will be swapped: 154.0601 59 59 iupac_m_483_> CD1/2 CE1/2 swapped: 90.4894 65 65 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: 167.6650 71 71 iupac_m_486_> OE1/2 will be swapped: 118.3647 80 80 iupac_m_483_> CD1/2 CE1/2 swapped: -106.9303 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -101.7019 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: 173.7738 112 112 iupac_m_487_> NH1/2 swapped: -178.7457 113 113 iupac_m_487_> NH1/2 swapped: 179.5836 172 172 iupac_m_487_> NH1/2 swapped: 179.8242 182 182 iupac_m_485_> OD1/2 will be swapped: -173.6886 207 207 iupac_m_486_> OE1/2 will be swapped: 119.1001 224 224 iupac_m_486_> OE1/2 will be swapped: 145.4685 234 234 iupac_m_486_> OE1/2 will be swapped: 175.6821 236 236 iupac_m_486_> OE1/2 will be swapped: 165.0865 260 260 iupac_m_485_> OD1/2 will be swapped: 168.8574 263 263 iupac_m_485_> OD1/2 will be swapped: 136.9671 279 279 >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 330721 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 : -25491.0234 << end of ENERGY. DOPE score : -25491.023438 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 330721 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 : -20628.7266 << end of ENERGY. DOPE-HR score : -20628.726562 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.100381 Native energy (pair) : -170.510963 Native energy (surface) : -3.651646 Native energy (combined) : -4.915718 Z score (pair) : -6.673081 Z score (surface) : -5.848419 Z score (combined) : -7.962662 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4612 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 : 1863.6370 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 : 2282 0 0 0.005 0.005 16.558 1.000 2 Bond angle potential : 3084 1 5 2.057 2.057 247.03 1.000 3 Stereochemical cosine torsion poten: 1399 0 39 47.285 47.285 506.21 1.000 4 Stereochemical improper torsion pot: 933 0 0 1.346 1.346 40.360 1.000 5 Soft-sphere overlap restraints : 4612 0 1 0.004 0.004 10.357 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) : 4436 0 0 0.154 0.154 111.31 1.000 10 Distance restraints 2 (N-O) : 4713 0 1 0.209 0.209 224.13 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: 283 2 6 15.123 15.123 75.011 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 1 71.593 71.593 50.578 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 0 72.853 72.853 61.018 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 1 70.265 70.265 60.523 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 83.337 83.337 18.245 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) : 3869 0 0 0.431 0.431 140.71 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: 282 10 43 33.058 43.147 154.77 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 2 0.864 0.864 146.84 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 rpn11_human_27-310.V99990008 # Heavy relative violation of each residue is written to: rpn11_human_27-310.V99990008 # 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: 27725.6719 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 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4523 207D 208Y C N 1621 1623 145.94 120.00 25.94 5.89 120.00 25.94 5.89 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -12.20 -179.18 166.98 38.81 -179.18 166.98 38.81 2 8187 207D 207D CA C 1616 1621 -4.00 -179.18 175.18 40.72 -179.18 175.18 40.72 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -148.00 -134.00 24.08 0.88 -62.50 174.84 33.22 1 2A 2A N CA 8 9 166.59 147.00 -40.90 2 7793 95W 96L C N 731 733 -82.19 -63.50 61.73 7.72 -63.50 61.73 7.72 2 96L 96L N CA 733 734 17.63 -41.20 -41.20 3 7844 146H 147E C N 1114 1116 89.59 54.60 116.42 11.73 -63.60 -133.93 26.70 3 147E 147E N CA 1116 1117 153.43 42.40 -40.30 4 7846 148P 149R C N 1130 1132 -70.44 -63.00 7.61 1.17 -72.10 178.63 13.78 4 149R 149R N CA 1132 1133 -39.48 -41.10 141.90 5 7847 149R 150Q C N 1141 1143 -100.25 -121.10 58.25 2.36 55.10 161.74 16.87 5 150Q 150Q N CA 1143 1144 85.30 139.70 40.30 6 7855 157H 158L C N 1200 1202 113.24 -108.50 143.91 7.36 -108.50 143.91 7.36 6 158L 158L N CA 1202 1203 92.59 132.50 132.50 7 7870 172R 173H C N 1317 1319 -111.99 -63.20 52.32 8.93 -63.20 52.32 8.93 7 173H 173H N CA 1319 1320 -61.18 -42.30 -42.30 8 7891 193N 194L C N 1504 1506 58.72 -70.70 141.40 14.14 -108.50 179.80 9.41 8 194L 194L N CA 1506 1507 -161.44 141.60 132.50 9 7977 279D 280T C N 2197 2199 -166.85 -63.20 116.74 14.71 55.90 140.06 14.21 9 280T 280T N CA 2199 2200 11.60 -42.10 39.50 10 7980 282V 283F C N 2218 2220 90.89 58.10 83.67 10.25 -124.20 148.71 6.76 10 283F 283F N CA 2220 2221 109.87 32.90 143.30 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 1 18 41 124 143 222 201 250 320 338 351 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990008.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_486_> OE1/2 will be swapped: -98.3933 26 26 iupac_m_485_> OD1/2 will be swapped: 174.6564 37 37 iupac_m_487_> NH1/2 swapped: -179.2016 42 42 iupac_m_485_> OD1/2 will be swapped: -163.6508 45 45 iupac_m_486_> OE1/2 will be swapped: -160.0585 59 59 iupac_m_485_> OD1/2 will be swapped: 131.4076 62 62 iupac_m_485_> OD1/2 will be swapped: 135.5869 71 71 iupac_m_483_> CD1/2 CE1/2 swapped: -121.2401 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -101.7014 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -152.1837 108 108 iupac_m_486_> OE1/2 will be swapped: 174.9147 112 112 iupac_m_487_> NH1/2 swapped: 176.8117 135 135 iupac_m_487_> NH1/2 swapped: -178.2849 172 172 iupac_m_486_> OE1/2 will be swapped: 101.3906 187 187 iupac_m_486_> OE1/2 will be swapped: -179.0085 210 210 iupac_m_486_> OE1/2 will be swapped: 175.0687 216 216 iupac_m_486_> OE1/2 will be swapped: -178.6280 234 234 iupac_m_486_> OE1/2 will be swapped: -172.6158 235 235 iupac_m_486_> OE1/2 will be swapped: 169.4204 236 236 iupac_m_485_> OD1/2 will be swapped: 172.9727 237 237 iupac_m_486_> OE1/2 will be swapped: 129.6479 259 259 iupac_m_485_> OD1/2 will be swapped: 165.8130 263 263 iupac_m_483_> CD1/2 CE1/2 swapped: 102.2140 283 283 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 331653 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 : -25642.0703 << end of ENERGY. DOPE score : -25642.070312 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 331653 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 : -20948.5879 << end of ENERGY. DOPE-HR score : -20948.587891 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.112132 Native energy (pair) : -175.357367 Native energy (surface) : -4.116358 Native energy (combined) : -5.071533 Z score (pair) : -6.640754 Z score (surface) : -5.784208 Z score (combined) : -7.824368 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4621 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 : 1845.2419 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 : 2282 0 0 0.005 0.005 15.953 1.000 2 Bond angle potential : 3084 0 7 2.003 2.003 233.66 1.000 3 Stereochemical cosine torsion poten: 1399 0 40 47.445 47.445 507.63 1.000 4 Stereochemical improper torsion pot: 933 0 1 1.344 1.344 41.916 1.000 5 Soft-sphere overlap restraints : 4621 0 1 0.004 0.004 8.8082 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) : 4436 0 3 0.166 0.166 126.80 1.000 10 Distance restraints 2 (N-O) : 4713 0 4 0.220 0.220 247.49 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: 283 1 6 10.957 10.957 71.146 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 1 68.137 68.137 36.952 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 0 73.728 73.728 68.868 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 0 80.279 80.279 61.925 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 74.352 74.352 17.853 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) : 3869 0 0 0.429 0.429 131.16 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: 282 15 40 30.896 42.700 147.64 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 3 0.810 0.810 127.44 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 rpn11_human_27-310.V99990009 # Heavy relative violation of each residue is written to: rpn11_human_27-310.V99990009 # 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: 26999.8672 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 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -11.96 -179.18 167.22 38.86 -179.18 167.22 38.86 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -78.48 -68.20 16.26 1.02 -62.50 161.99 27.36 1 2A 2A N CA 8 9 157.91 145.30 -40.90 2 7793 95W 96L C N 731 733 -82.39 -63.50 61.27 7.66 -63.50 61.27 7.66 2 96L 96L N CA 733 734 17.09 -41.20 -41.20 3 7835 137I 138N C N 1048 1050 -116.93 -63.20 62.12 7.65 -63.20 62.12 7.65 3 138N 138N N CA 1050 1051 -9.92 -41.10 -41.10 4 7844 146H 147E C N 1114 1116 85.16 54.60 114.00 11.20 -63.60 -136.00 26.35 4 147E 147E N CA 1116 1117 152.23 42.40 -40.30 5 7855 157H 158L C N 1200 1202 117.33 -108.50 139.48 7.13 -108.50 139.48 7.13 5 158L 158L N CA 1202 1203 94.39 132.50 132.50 6 7870 172R 173H C N 1317 1319 -112.74 -63.20 52.99 9.04 -63.20 52.99 9.04 6 173H 173H N CA 1319 1320 -61.09 -42.30 -42.30 7 7890 192L 193N C N 1496 1498 -73.98 -119.90 93.35 3.08 -63.20 97.42 11.62 7 193N 193N N CA 1498 1499 55.72 137.00 -41.10 8 7891 193N 194L C N 1504 1506 -61.23 -63.50 22.48 3.00 -108.50 170.61 9.61 8 194L 194L N CA 1506 1507 -63.57 -41.20 132.50 9 7893 195H 196K C N 1522 1524 60.06 -62.90 153.57 19.71 -118.00 -161.33 9.15 9 196K 196K N CA 1524 1525 -132.80 -40.80 139.10 10 7904 206Q 207D C N 1613 1615 -156.13 -96.50 60.83 2.50 -70.90 88.56 7.29 10 207D 207D N CA 1615 1616 126.24 114.20 150.30 11 7905 207D 208Y C N 1621 1623 -104.87 -63.50 45.37 6.86 -63.50 45.37 6.86 11 208Y 208Y N CA 1623 1624 -24.77 -43.40 -43.40 12 7977 279D 280T C N 2197 2199 -167.96 -63.20 124.08 14.97 55.90 136.97 14.62 12 280T 280T N CA 2199 2200 24.38 -42.10 39.50 13 7978 280T 281V C N 2204 2206 81.26 55.90 92.42 4.83 -125.40 -133.04 6.53 13 281V 281V N CA 2206 2207 -49.38 39.50 143.30 14 7979 281V 282V C N 2211 2213 -139.06 -125.40 61.64 2.69 -73.50 91.77 6.50 14 282V 282V N CA 2213 2214 -156.59 143.30 139.20 15 7980 282V 283F C N 2218 2220 62.77 58.10 29.80 2.96 -124.20 -168.96 9.62 15 283F 283F N CA 2220 2221 62.33 32.90 143.30 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 2 17 28 127 134 220 215 257 315 328 370 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990009.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 openf___224_> Open rpn11_human_27-310.ini Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 27596540 26949.746 26.318 read_mo_297_> Segments, residues, atoms: 1 284 2240 read_mo_298_> Segment: 1 1 284 2240 randomi_498_> Atoms,selected atoms,random_seed,amplitude: 2240 2240 1 4.0000 randomi_496_> Amplitude is > 0; randomization is done. pick_re_612_> Number of MODEL atoms, selected restraints; 2240 13659 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 15381 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 16351 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 17431 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 18267 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 19152 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 21030 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22197 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 22689 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 pick_re_612_> Number of MODEL atoms, selected restraints; 2240 23134 iupac_m_486_> OE1/2 will be swapped: -171.8879 3 3 iupac_m_486_> OE1/2 will be swapped: -138.1497 26 26 iupac_m_485_> OD1/2 will be swapped: -159.6368 45 45 iupac_m_485_> OD1/2 will be swapped: -150.6289 71 71 iupac_m_486_> OE1/2 will be swapped: 125.4650 80 80 iupac_m_483_> CD1/2 CE1/2 swapped: -139.1886 86 86 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_483_> CD1/2 CE1/2 swapped: -105.4659 107 107 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_486_> OE1/2 will be swapped: -142.7153 108 108 iupac_m_487_> NH1/2 swapped: -179.5612 113 113 iupac_m_487_> NH1/2 swapped: -177.0894 182 182 iupac_m_486_> OE1/2 will be swapped: 160.0035 185 185 iupac_m_486_> OE1/2 will be swapped: -124.3725 201 201 iupac_m_486_> OE1/2 will be swapped: 94.2465 242 242 iupac_m_487_> NH1/2 swapped: 179.0608 256 256 iupac_m_486_> OE1/2 will be swapped: 171.9268 259 259 iupac_m_486_> OE1/2 will be swapped: 152.2647 260 260 iupac_m_485_> OD1/2 will be swapped: 142.8555 263 263 iupac_m_485_> OD1/2 will be swapped: 139.8325 279 279 iupac_m_483_> CD1/2 CE1/2 swapped: -149.3689 283 283 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 330153 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 : -25561.0840 << end of ENERGY. DOPE score : -25561.083984 >> Model assessment by DOPE-HR potential iatmcls_286W> MODEL atom not classified: LYS:OXT LYS >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 330153 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 : -21061.1973 << end of ENERGY. DOPE-HR score : -21061.197266 >> Model assessment by GA341 potential Surface library : /usr/lib/modeller9.17/modlib/surf5.de Pair library : /usr/lib/modeller9.17/modlib/pair9.de Chain identifier : _ % sequence identity : 68.197998 Sequence length : 284 Compactness : 0.106998 Native energy (pair) : -182.321275 Native energy (surface) : -3.206923 Native energy (combined) : -4.998292 Z score (pair) : -6.582345 Z score (surface) : -5.751506 Z score (combined) : -7.725884 GA341 score : 1.000000 >> ENERGY; Differences between the model's features and restraints: Number of all residues in MODEL : 284 Number of all, selected real atoms : 2240 2240 Number of all, selected pseudo atoms : 0 0 Number of all static, selected restraints : 23134 23134 COVALENT_CYS : F NONBONDED_SEL_ATOMS : 1 Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4586 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 : 1937.0436 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 : 2282 0 0 0.005 0.005 18.318 1.000 2 Bond angle potential : 3084 2 7 2.142 2.142 263.57 1.000 3 Stereochemical cosine torsion poten: 1399 0 40 47.260 47.260 507.42 1.000 4 Stereochemical improper torsion pot: 933 0 0 1.387 1.387 42.940 1.000 5 Soft-sphere overlap restraints : 4586 0 1 0.004 0.004 10.922 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) : 4436 0 0 0.159 0.159 121.86 1.000 10 Distance restraints 2 (N-O) : 4713 0 2 0.214 0.214 242.37 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: 283 2 5 15.030 15.030 68.802 1.000 14 Sidechain Chi_1 dihedral restraints: 250 0 4 71.861 71.861 51.864 1.000 15 Sidechain Chi_2 dihedral restraints: 188 0 2 66.688 66.688 73.208 1.000 16 Sidechain Chi_3 dihedral restraints: 90 0 0 74.177 74.177 65.666 1.000 17 Sidechain Chi_4 dihedral restraints: 29 0 0 87.815 87.815 20.124 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) : 3869 0 0 0.441 0.441 140.66 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: 282 12 41 31.099 42.119 146.00 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1296 0 1 0.908 0.908 163.32 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 rpn11_human_27-310.V99990010 # Heavy relative violation of each residue is written to: rpn11_human_27-310.V99990010 # 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: 27956.8359 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 2 : Bond angle potential List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 4523 207D 208Y C N 1621 1623 144.30 120.00 24.30 5.52 120.00 24.30 5.52 2 5355 283F 284K C N 2229 2231 142.07 120.00 22.07 5.02 120.00 22.07 5.02 ------------------------------------------------------------------------------------------------- Feature 13 : Mainchain Omega dihedral restraints List of the RVIOL violations larger than : 4.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 8185 205L 205L CA C 1599 1604 -11.96 -179.18 167.22 38.86 -179.18 167.22 38.86 2 8187 207D 207D CA C 1616 1621 -4.99 -179.18 174.19 40.48 -179.18 174.19 40.48 ------------------------------------------------------------------------------------------------- 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 7699 1T 2A C N 6 8 -68.87 -68.20 8.41 0.65 -62.50 165.54 27.45 1 2A 2A N CA 8 9 153.68 145.30 -40.90 2 7793 95W 96L C N 731 733 -83.15 -63.50 61.55 7.67 -63.50 61.55 7.67 2 96L 96L N CA 733 734 17.13 -41.20 -41.20 3 7844 146H 147E C N 1114 1116 85.96 54.60 112.51 11.15 -63.60 -134.14 26.56 3 147E 147E N CA 1116 1117 150.45 42.40 -40.30 4 7855 157H 158L C N 1200 1202 113.28 -108.50 144.35 7.41 -108.50 144.35 7.41 4 158L 158L N CA 1202 1203 90.88 132.50 132.50 5 7870 172R 173H C N 1317 1319 -111.51 -63.20 51.35 8.75 -63.20 51.35 8.75 5 173H 173H N CA 1319 1320 -59.71 -42.30 -42.30 6 7891 193N 194L C N 1504 1506 52.03 -70.70 134.20 13.42 -108.50 172.59 9.03 6 194L 194L N CA 1506 1507 -164.12 141.60 132.50 7 7892 194L 195H C N 1512 1514 -70.15 -67.60 123.44 9.42 -67.60 123.44 9.42 7 195H 195H N CA 1514 1515 -96.59 140.00 140.00 8 7905 207D 208Y C N 1621 1623 -93.62 -63.50 48.89 6.74 -63.50 48.89 6.74 8 208Y 208Y N CA 1623 1624 -4.89 -43.40 -43.40 9 7975 277M 278L C N 2181 2183 -150.10 -108.50 53.72 2.98 -70.70 90.34 9.09 9 278L 278L N CA 2183 2184 98.51 132.50 141.60 10 7977 279D 280T C N 2197 2199 -157.86 -63.20 114.33 13.59 55.90 147.28 15.65 10 280T 280T N CA 2199 2200 22.02 -42.10 39.50 11 7978 280T 281V C N 2204 2206 85.22 55.90 93.75 4.74 -125.40 -135.82 6.51 11 281V 281V N CA 2206 2207 -49.55 39.50 143.30 12 7979 281V 282V C N 2211 2213 -141.03 -125.40 60.85 2.59 -73.50 92.29 6.50 12 282V 282V N CA 2213 2214 -157.89 143.30 139.20 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 2 20 35 120 137 205 219 266 294 344 378 << end of ENERGY. openf___224_> Open rpn11_human_27-310.B99990010.pdb wrpdb___568_> Residues, atoms, selected atoms: 284 2240 2240 >> Summary of successfully produced models: Filename molpdf DOPE score DOPE-HR score GA341 score ------------------------------------------------------------------------------------- rpn11_human_27-310.B99990001.pdb 1859.68066 -25815.30859 -21590.14062 1.00000 rpn11_human_27-310.B99990002.pdb 2002.79846 -25594.79297 -21195.61133 1.00000 rpn11_human_27-310.B99990003.pdb 1905.06189 -25719.85742 -21105.90234 1.00000 rpn11_human_27-310.B99990004.pdb 1867.07617 -25456.18750 -20643.19922 1.00000 rpn11_human_27-310.B99990005.pdb 1874.28381 -25791.01953 -21284.92969 1.00000 rpn11_human_27-310.B99990006.pdb 1881.98010 -25631.30469 -21117.12695 1.00000 rpn11_human_27-310.B99990007.pdb 1887.24231 -25428.01562 -20388.71484 1.00000 rpn11_human_27-310.B99990008.pdb 1863.63696 -25491.02344 -20628.72656 1.00000 rpn11_human_27-310.B99990009.pdb 1845.24194 -25642.07031 -20948.58789 1.00000 rpn11_human_27-310.B99990010.pdb 1937.04358 -25561.08398 -21061.19727 1.00000 Dynamically allocated memory at finish [B,KiB,MiB]: 27596516 26949.723 26.318 Starting time : 2016/07/31 17:32:00 Closing time : 2016/07/31 17:33:34 Total CPU time [seconds] : 93.77