Starting phenix.real_space_refine on Mon Dec 30 22:53:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tc0_25803/12_2024/7tc0_25803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tc0_25803/12_2024/7tc0_25803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tc0_25803/12_2024/7tc0_25803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tc0_25803/12_2024/7tc0_25803.map" model { file = "/net/cci-nas-00/data/ceres_data/7tc0_25803/12_2024/7tc0_25803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tc0_25803/12_2024/7tc0_25803.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8965 2.51 5 N 2289 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13809 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1781, 13636 Classifications: {'peptide': 1781} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 85, 'TRANS': 1693} Chain breaks: 13 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 285 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.50, per 1000 atoms: 0.62 Number of scatterers: 13809 At special positions: 0 Unit cell: (82.516, 98.514, 218.078, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2471 8.00 N 2289 7.00 C 8965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A1465 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1463 " - pdb=" SG CYS A1477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2502 " - " ASN A1637 " " NAG A2503 " - " ASN A 98 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.7 seconds 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 10 sheets defined 60.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 44 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.547A pdb=" N ARG A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 252 through 273 removed outlier: 4.061A pdb=" N GLU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.784A pdb=" N GLN A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 4.013A pdb=" N TYR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 371 through 380 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.466A pdb=" N PHE A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.729A pdb=" N MET A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 430 through 441 removed outlier: 4.085A pdb=" N ASP A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.861A pdb=" N PHE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.686A pdb=" N ALA A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 592 through 610 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 639 through 665 removed outlier: 4.371A pdb=" N PHE A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 677 through 707 removed outlier: 3.649A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 714 through 737 removed outlier: 3.799A pdb=" N VAL A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 742 through 767 removed outlier: 4.349A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Proline residue: A 760 - end of helix removed outlier: 3.608A pdb=" N ALA A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.840A pdb=" N VAL A 771 " --> pdb=" O ARG A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.649A pdb=" N ALA A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 846 removed outlier: 3.627A pdb=" N ALA A 844 " --> pdb=" O TRP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 948 Processing helix chain 'A' and resid 968 through 973 removed outlier: 3.584A pdb=" N GLN A 973 " --> pdb=" O SER A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1002 Processing helix chain 'A' and resid 1004 through 1020 removed outlier: 3.868A pdb=" N GLY A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1028 Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1046 through 1051 removed outlier: 6.705A pdb=" N GLY A1049 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A1050 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1051 " --> pdb=" O VAL A1048 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1051' Processing helix chain 'A' and resid 1064 through 1078 Processing helix chain 'A' and resid 1090 through 1098 removed outlier: 3.658A pdb=" N ALA A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1122 removed outlier: 3.862A pdb=" N LEU A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1191 removed outlier: 3.511A pdb=" N SER A1184 " --> pdb=" O VAL A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1228 removed outlier: 3.673A pdb=" N GLU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 3.735A pdb=" N ILE A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1342 removed outlier: 4.125A pdb=" N THR A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN A1326 " --> pdb=" O TRP A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1365 removed outlier: 4.098A pdb=" N VAL A1352 " --> pdb=" O PHE A1348 " (cutoff:3.500A) Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1380 through 1384 removed outlier: 3.551A pdb=" N MET A1383 " --> pdb=" O GLN A1380 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A1384 " --> pdb=" O PRO A1381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1380 through 1384' Processing helix chain 'A' and resid 1398 through 1409 Processing helix chain 'A' and resid 1442 through 1451 Processing helix chain 'A' and resid 1504 through 1522 Processing helix chain 'A' and resid 1550 through 1562 Processing helix chain 'A' and resid 1568 through 1583 Processing helix chain 'A' and resid 1600 through 1617 removed outlier: 3.753A pdb=" N SER A1604 " --> pdb=" O HIS A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1627 Processing helix chain 'A' and resid 1639 through 1649 Processing helix chain 'A' and resid 1650 through 1666 removed outlier: 4.696A pdb=" N LEU A1656 " --> pdb=" O SER A1652 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1657 " --> pdb=" O VAL A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 4.104A pdb=" N SER A1671 " --> pdb=" O PHE A1667 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A1681 " --> pdb=" O ILE A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1691 removed outlier: 4.226A pdb=" N SER A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1724 removed outlier: 3.563A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix removed outlier: 3.896A pdb=" N PHE A1724 " --> pdb=" O ILE A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1731 removed outlier: 3.724A pdb=" N SER A1731 " --> pdb=" O LYS A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1753 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1754 through 1758 Processing helix chain 'A' and resid 1765 through 1787 removed outlier: 3.945A pdb=" N VAL A1769 " --> pdb=" O THR A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1807 Processing helix chain 'A' and resid 1810 through 1836 Processing helix chain 'A' and resid 1850 through 1873 removed outlier: 3.710A pdb=" N GLN A1871 " --> pdb=" O THR A1867 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A1872 " --> pdb=" O VAL A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2014 removed outlier: 3.540A pdb=" N HIS A2006 " --> pdb=" O THR A2002 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A2007 " --> pdb=" O GLY A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2020 through 2032 Processing helix chain 'A' and resid 2034 through 2038 Processing helix chain 'A' and resid 2041 through 2045 Processing helix chain 'A' and resid 2046 through 2058 Processing helix chain 'A' and resid 2079 through 2092 removed outlier: 3.504A pdb=" N LEU A2083 " --> pdb=" O ALA A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2103 through 2111 removed outlier: 3.559A pdb=" N CYS A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2128 through 2135 Processing helix chain 'A' and resid 2152 through 2163 removed outlier: 3.779A pdb=" N GLN A2156 " --> pdb=" O LEU A2152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A2163 " --> pdb=" O PHE A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2201 removed outlier: 4.388A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A2200 " --> pdb=" O GLN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2223 removed outlier: 3.660A pdb=" N VAL A2216 " --> pdb=" O THR A2212 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A2223 " --> pdb=" O ASN A2219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.552A pdb=" N GLY A 616 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A1592 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 618 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE A1594 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN A 620 " --> pdb=" O PHE A1594 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A1388 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE A1535 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU A1537 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A1392 " --> pdb=" O LEU A1537 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL A1539 " --> pdb=" O SER A1392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 512 removed outlier: 6.485A pdb=" N LEU A 384 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE A 538 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 386 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 553 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 552 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE A1632 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR A 554 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 924 removed outlier: 3.504A pdb=" N VAL A 899 " --> pdb=" O PHE A 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA6, first strand: chain 'A' and resid 1101 through 1105 removed outlier: 6.035A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1195 through 1200 removed outlier: 5.945A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1942 through 1943 removed outlier: 6.537A pdb=" N ARG A2113 " --> pdb=" O GLY A1943 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1988 through 1991 removed outlier: 6.260A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP A2069 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS A1991 " --> pdb=" O ASP A2069 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A2066 " --> pdb=" O VAL A2098 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR A2100 " --> pdb=" O VAL A2066 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A2068 " --> pdb=" O THR A2100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2167 through 2172 removed outlier: 6.314A pdb=" N LEU A2168 " --> pdb=" O GLN A2179 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN A2179 " --> pdb=" O LEU A2168 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A2170 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A2175 " --> pdb=" O HIS A2172 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A2205 " --> pdb=" O ARG A2144 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4331 1.34 - 1.46: 3159 1.46 - 1.58: 6503 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14129 Sorted by residual: bond pdb=" C VAL A1737 " pdb=" N LEU A1738 " ideal model delta sigma weight residual 1.335 1.555 -0.221 1.27e-02 6.20e+03 3.02e+02 bond pdb=" C LEU A1738 " pdb=" N ALA A1739 " ideal model delta sigma weight residual 1.334 1.413 -0.079 1.33e-02 5.65e+03 3.52e+01 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C VAL A1712 " pdb=" N PRO A1713 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.82e+00 ... (remaining 14124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 19122 3.30 - 6.59: 86 6.59 - 9.89: 9 9.89 - 13.18: 1 13.18 - 16.48: 1 Bond angle restraints: 19219 Sorted by residual: angle pdb=" CA PRO A1713 " pdb=" N PRO A1713 " pdb=" CD PRO A1713 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" C SER A2127 " pdb=" CA SER A2127 " pdb=" CB SER A2127 " ideal model delta sigma weight residual 116.63 108.52 8.11 1.16e+00 7.43e-01 4.89e+01 angle pdb=" C VAL A1712 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " ideal model delta sigma weight residual 119.05 111.77 7.28 1.11e+00 8.12e-01 4.30e+01 angle pdb=" C VAL A1737 " pdb=" N LEU A1738 " pdb=" CA LEU A1738 " ideal model delta sigma weight residual 120.82 129.27 -8.45 1.50e+00 4.44e-01 3.18e+01 angle pdb=" CA VAL A1712 " pdb=" C VAL A1712 " pdb=" N PRO A1713 " ideal model delta sigma weight residual 120.83 117.41 3.42 6.10e-01 2.69e+00 3.15e+01 ... (remaining 19214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 8047 23.45 - 46.90: 412 46.90 - 70.35: 64 70.35 - 93.80: 30 93.80 - 117.25: 18 Dihedral angle restraints: 8571 sinusoidal: 3421 harmonic: 5150 Sorted by residual: dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1429 " pdb=" CB CYS A1429 " ideal model delta sinusoidal sigma weight residual -86.00 0.95 -86.95 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A1463 " pdb=" SG CYS A1463 " pdb=" SG CYS A1477 " pdb=" CB CYS A1477 " ideal model delta sinusoidal sigma weight residual -86.00 -8.54 -77.46 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" C PRO A1713 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " pdb=" CB PRO A1713 " ideal model delta harmonic sigma weight residual -120.70 -131.27 10.57 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 8568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2191 0.106 - 0.212: 40 0.212 - 0.318: 8 0.318 - 0.423: 2 0.423 - 0.529: 1 Chirality restraints: 2242 Sorted by residual: chirality pdb=" CA PRO A1713 " pdb=" N PRO A1713 " pdb=" C PRO A1713 " pdb=" CB PRO A1713 " both_signs ideal model delta sigma weight residual False 2.72 2.19 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C14 CLR A2504 " pdb=" C13 CLR A2504 " pdb=" C15 CLR A2504 " pdb=" C8 CLR A2504 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C14 CLR A2501 " pdb=" C13 CLR A2501 " pdb=" C15 CLR A2501 " pdb=" C8 CLR A2501 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2239 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1712 " 0.149 5.00e-02 4.00e+02 2.25e-01 8.09e+01 pdb=" N PRO A1713 " -0.389 5.00e-02 4.00e+02 pdb=" CA PRO A1713 " 0.124 5.00e-02 4.00e+02 pdb=" CD PRO A1713 " 0.117 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1738 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C LEU A1738 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A1738 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A1739 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1710 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TYR A1710 " -0.041 2.00e-02 2.50e+03 pdb=" O TYR A1710 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A1711 " 0.014 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 228 2.69 - 3.24: 13391 3.24 - 3.80: 21349 3.80 - 4.35: 26626 4.35 - 4.90: 44873 Nonbonded interactions: 106467 Sorted by model distance: nonbonded pdb=" OE2 GLU A2070 " pdb=" ND1 HIS A2102 " model vdw 2.141 3.120 nonbonded pdb=" OD2 ASP A1706 " pdb=" OH TYR A1754 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A1124 " pdb=" OE2 GLU A1246 " model vdw 2.252 3.040 nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A1083 " model vdw 2.278 3.040 nonbonded pdb=" O SER A2182 " pdb=" OG SER A2182 " model vdw 2.299 3.040 ... (remaining 106462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 35.230 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.221 14129 Z= 0.167 Angle : 0.594 16.477 19219 Z= 0.334 Chirality : 0.044 0.529 2242 Planarity : 0.006 0.225 2400 Dihedral : 15.733 117.246 5227 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.49 % Allowed : 9.87 % Favored : 87.64 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1753 helix: 0.11 (0.16), residues: 966 sheet: -1.33 (0.39), residues: 174 loop : -3.26 (0.21), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP A1705 HIS 0.001 0.000 HIS A 894 PHE 0.006 0.000 PHE A1449 TYR 0.007 0.000 TYR A1698 ARG 0.001 0.000 ARG A2173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8219 (m-80) cc_final: 0.7997 (t80) REVERT: A 99 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6198 (tmmt) REVERT: A 662 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 982 ASN cc_start: 0.7514 (p0) cc_final: 0.7311 (p0) REVERT: A 1128 LEU cc_start: 0.8084 (pt) cc_final: 0.7794 (pt) REVERT: A 1180 VAL cc_start: 0.9163 (m) cc_final: 0.8934 (t) REVERT: A 1245 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8209 (tt0) REVERT: A 1363 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 1656 LEU cc_start: 0.8922 (tt) cc_final: 0.8570 (mm) outliers start: 35 outliers final: 22 residues processed: 302 average time/residue: 0.2833 time to fit residues: 121.9260 Evaluate side-chains 212 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1537 LEU Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1713 PRO Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2073 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 chunk 139 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 283 GLN A 302 GLN A 452 GLN A 470 HIS A 820 ASN A 894 HIS A1600 HIS ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN A2179 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14129 Z= 0.300 Angle : 0.670 10.921 19219 Z= 0.332 Chirality : 0.046 0.227 2242 Planarity : 0.005 0.079 2400 Dihedral : 9.345 85.265 2238 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.91 % Allowed : 12.78 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1753 helix: 1.10 (0.17), residues: 979 sheet: -0.57 (0.42), residues: 163 loop : -2.68 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1747 HIS 0.013 0.002 HIS A 470 PHE 0.023 0.002 PHE A 725 TYR 0.024 0.002 TYR A1210 ARG 0.006 0.001 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 276 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8071 (tpp80) REVERT: A 601 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7314 (mt-10) REVERT: A 644 MET cc_start: 0.8274 (tpp) cc_final: 0.7858 (tpt) REVERT: A 662 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8038 (tm-30) REVERT: A 1015 MET cc_start: 0.7297 (mtt) cc_final: 0.7085 (ttm) REVERT: A 1180 VAL cc_start: 0.9141 (m) cc_final: 0.8906 (t) REVERT: A 1245 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8047 (tt0) REVERT: A 1357 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 1363 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8599 (m) REVERT: A 1380 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8319 (pt0) outliers start: 55 outliers final: 33 residues processed: 246 average time/residue: 0.2413 time to fit residues: 89.8530 Evaluate side-chains 216 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1558 MET Chi-restraints excluded: chain A residue 1720 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2170 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 174 optimal weight: 0.1980 chunk 144 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 894 HIS ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14129 Z= 0.168 Angle : 0.557 11.002 19219 Z= 0.273 Chirality : 0.042 0.211 2242 Planarity : 0.004 0.065 2400 Dihedral : 7.431 70.448 2222 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.98 % Allowed : 14.77 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1753 helix: 1.55 (0.17), residues: 979 sheet: -0.39 (0.42), residues: 163 loop : -2.37 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.019 0.001 PHE A1530 TYR 0.017 0.001 TYR A1210 ARG 0.005 0.000 ARG A2200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8934 (tt) REVERT: A 662 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 1128 LEU cc_start: 0.8053 (pt) cc_final: 0.7810 (tt) REVERT: A 1180 VAL cc_start: 0.9120 (m) cc_final: 0.8890 (t) REVERT: A 1245 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8033 (tt0) REVERT: A 1357 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.5948 (t80) REVERT: A 1552 ASN cc_start: 0.8520 (t0) cc_final: 0.8262 (m-40) REVERT: A 2131 LEU cc_start: 0.8668 (mt) cc_final: 0.8457 (mt) outliers start: 42 outliers final: 30 residues processed: 222 average time/residue: 0.2395 time to fit residues: 82.4098 Evaluate side-chains 208 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 172 optimal weight: 0.0970 chunk 154 optimal weight: 0.0020 chunk 46 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 894 HIS ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14129 Z= 0.169 Angle : 0.549 9.143 19219 Z= 0.271 Chirality : 0.041 0.161 2242 Planarity : 0.004 0.072 2400 Dihedral : 6.343 59.095 2220 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.41 % Allowed : 15.62 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1753 helix: 1.77 (0.17), residues: 979 sheet: -0.32 (0.41), residues: 166 loop : -2.23 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.016 0.001 PHE A1605 TYR 0.012 0.001 TYR A1210 ARG 0.010 0.000 ARG A2200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 181 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 662 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 1128 LEU cc_start: 0.8095 (pt) cc_final: 0.7783 (tt) REVERT: A 1180 VAL cc_start: 0.9114 (m) cc_final: 0.8883 (t) REVERT: A 1245 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8039 (tt0) REVERT: A 1357 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.5987 (t80) REVERT: A 1552 ASN cc_start: 0.8548 (t0) cc_final: 0.8320 (m-40) REVERT: A 2059 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8197 (pp) outliers start: 48 outliers final: 32 residues processed: 219 average time/residue: 0.2332 time to fit residues: 79.3725 Evaluate side-chains 206 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 894 HIS A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14129 Z= 0.181 Angle : 0.545 9.030 19219 Z= 0.271 Chirality : 0.041 0.168 2242 Planarity : 0.005 0.112 2400 Dihedral : 5.879 57.709 2220 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.48 % Allowed : 16.83 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1753 helix: 1.90 (0.17), residues: 981 sheet: -0.30 (0.40), residues: 166 loop : -2.23 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.024 0.001 PHE A 287 TYR 0.012 0.001 TYR A1206 ARG 0.009 0.000 ARG A2200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 662 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8145 (tt0) REVERT: A 672 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7873 (mmm160) REVERT: A 1180 VAL cc_start: 0.9101 (m) cc_final: 0.8881 (t) REVERT: A 1245 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8069 (tt0) REVERT: A 1357 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.5970 (t80) REVERT: A 2059 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8230 (pp) REVERT: A 2204 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8063 (mt-10) outliers start: 49 outliers final: 33 residues processed: 220 average time/residue: 0.2459 time to fit residues: 82.4599 Evaluate side-chains 209 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 172 optimal weight: 0.0040 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN A1552 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14129 Z= 0.208 Angle : 0.557 9.434 19219 Z= 0.278 Chirality : 0.042 0.188 2242 Planarity : 0.005 0.110 2400 Dihedral : 5.827 59.928 2219 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.34 % Allowed : 17.19 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1753 helix: 1.97 (0.17), residues: 981 sheet: -0.24 (0.40), residues: 166 loop : -2.17 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.017 0.001 PHE A1605 TYR 0.009 0.001 TYR A 924 ARG 0.010 0.000 ARG A2200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 662 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8162 (tt0) REVERT: A 672 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7882 (mmm160) REVERT: A 1180 VAL cc_start: 0.9101 (m) cc_final: 0.8882 (t) REVERT: A 1245 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8082 (tt0) REVERT: A 1693 VAL cc_start: 0.6560 (OUTLIER) cc_final: 0.6314 (t) REVERT: A 2059 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 2204 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8120 (mt-10) outliers start: 47 outliers final: 33 residues processed: 220 average time/residue: 0.2523 time to fit residues: 84.5920 Evaluate side-chains 206 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 104 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 ASN A2174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14129 Z= 0.275 Angle : 0.610 10.278 19219 Z= 0.304 Chirality : 0.044 0.182 2242 Planarity : 0.005 0.090 2400 Dihedral : 5.978 57.773 2218 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.05 % Allowed : 17.97 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1753 helix: 1.93 (0.17), residues: 982 sheet: -0.25 (0.40), residues: 172 loop : -2.17 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1705 HIS 0.006 0.001 HIS A1634 PHE 0.020 0.002 PHE A1605 TYR 0.014 0.001 TYR A1729 ARG 0.011 0.001 ARG A2200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 662 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8200 (tt0) REVERT: A 1180 VAL cc_start: 0.9092 (m) cc_final: 0.8878 (t) REVERT: A 1245 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8139 (tt0) REVERT: A 1380 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: A 1693 VAL cc_start: 0.6769 (OUTLIER) cc_final: 0.6517 (t) REVERT: A 1730 VAL cc_start: 0.8200 (m) cc_final: 0.7995 (t) REVERT: A 2059 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8235 (pp) REVERT: A 2204 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8150 (mt-10) outliers start: 43 outliers final: 35 residues processed: 206 average time/residue: 0.2501 time to fit residues: 78.1763 Evaluate side-chains 204 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 0.0670 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14129 Z= 0.160 Angle : 0.566 10.935 19219 Z= 0.279 Chirality : 0.041 0.174 2242 Planarity : 0.004 0.055 2400 Dihedral : 5.793 58.022 2218 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.12 % Allowed : 18.54 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1753 helix: 1.98 (0.17), residues: 984 sheet: -0.12 (0.41), residues: 172 loop : -2.09 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.014 0.001 PHE A1605 TYR 0.011 0.001 TYR A1698 ARG 0.006 0.000 ARG A2200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8739 (mm) REVERT: A 1180 VAL cc_start: 0.9076 (m) cc_final: 0.8867 (t) REVERT: A 1245 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8091 (tt0) REVERT: A 1380 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8084 (pt0) REVERT: A 1693 VAL cc_start: 0.6627 (OUTLIER) cc_final: 0.6376 (t) REVERT: A 2059 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8189 (pp) REVERT: A 2204 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8148 (mt-10) outliers start: 44 outliers final: 34 residues processed: 208 average time/residue: 0.2578 time to fit residues: 83.8496 Evaluate side-chains 200 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1753 MET Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 104 optimal weight: 0.1980 chunk 169 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14129 Z= 0.190 Angle : 0.581 11.750 19219 Z= 0.285 Chirality : 0.042 0.184 2242 Planarity : 0.004 0.050 2400 Dihedral : 5.743 56.513 2218 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.27 % Allowed : 18.82 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1753 helix: 2.01 (0.17), residues: 983 sheet: -0.10 (0.41), residues: 172 loop : -2.06 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.017 0.001 PHE A1835 TYR 0.010 0.001 TYR A1698 ARG 0.007 0.000 ARG A2189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1180 VAL cc_start: 0.9072 (m) cc_final: 0.8867 (t) REVERT: A 1245 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8128 (tt0) REVERT: A 1380 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: A 1693 VAL cc_start: 0.6702 (OUTLIER) cc_final: 0.6449 (t) REVERT: A 1999 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 2059 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8204 (pp) REVERT: A 2204 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8177 (mt-10) outliers start: 46 outliers final: 35 residues processed: 202 average time/residue: 0.2463 time to fit residues: 76.8575 Evaluate side-chains 199 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2100 THR Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 chunk 112 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 ASN A2174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14129 Z= 0.166 Angle : 0.581 11.974 19219 Z= 0.283 Chirality : 0.041 0.186 2242 Planarity : 0.004 0.050 2400 Dihedral : 5.678 56.308 2218 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.91 % Allowed : 19.18 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1753 helix: 2.05 (0.17), residues: 985 sheet: -0.04 (0.41), residues: 172 loop : -2.00 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.014 0.001 PHE A1605 TYR 0.010 0.001 TYR A1698 ARG 0.005 0.000 ARG A2173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8754 (mm) REVERT: A 1245 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8120 (tt0) REVERT: A 1380 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8143 (pt0) REVERT: A 1693 VAL cc_start: 0.6684 (OUTLIER) cc_final: 0.6434 (t) REVERT: A 1999 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7658 (mt-10) REVERT: A 2059 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 2204 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8150 (mt-10) outliers start: 41 outliers final: 37 residues processed: 198 average time/residue: 0.2553 time to fit residues: 77.8677 Evaluate side-chains 205 residues out of total 1559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2100 THR Chi-restraints excluded: chain A residue 2108 GLU Chi-restraints excluded: chain A residue 2174 ASN Chi-restraints excluded: chain A residue 2189 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 141 optimal weight: 0.0670 chunk 59 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.105030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072776 restraints weight = 26595.541| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.62 r_work: 0.2884 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14129 Z= 0.253 Angle : 0.624 11.852 19219 Z= 0.308 Chirality : 0.043 0.194 2242 Planarity : 0.004 0.050 2400 Dihedral : 5.831 55.922 2218 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.12 % Allowed : 19.46 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1753 helix: 2.02 (0.17), residues: 982 sheet: 0.04 (0.41), residues: 167 loop : -2.02 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1705 HIS 0.006 0.001 HIS A1634 PHE 0.019 0.002 PHE A1605 TYR 0.011 0.001 TYR A1729 ARG 0.012 0.001 ARG A2173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.95 seconds wall clock time: 57 minutes 41.84 seconds (3461.84 seconds total)