Starting phenix.real_space_refine on Tue Aug 26 18:34:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srh_40731/08_2025/8srh_40731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srh_40731/08_2025/8srh_40731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8srh_40731/08_2025/8srh_40731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srh_40731/08_2025/8srh_40731.map" model { file = "/net/cci-nas-00/data/ceres_data/8srh_40731/08_2025/8srh_40731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srh_40731/08_2025/8srh_40731.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.060 sd= 0.431 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 16 5.21 5 S 184 5.16 5 C 25560 2.51 5 N 6892 2.21 5 O 6800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39468 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9707 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 335} Link IDs: {'PTRANS': 55, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 1144 Unresolved non-hydrogen angles: 1415 Unresolved non-hydrogen dihedrals: 908 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 51, 'ASP:plan': 66, 'ARG:plan': 22, 'GLN:plan1': 19, 'ASN:plan1': 19, 'HIS:plan': 6, 'TYR:plan': 3, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 738 Chain: "B" Number of atoms: 9707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9707 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 335} Link IDs: {'PTRANS': 55, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 1144 Unresolved non-hydrogen angles: 1415 Unresolved non-hydrogen dihedrals: 908 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 51, 'ASP:plan': 66, 'ARG:plan': 22, 'GLN:plan1': 19, 'ASN:plan1': 19, 'HIS:plan': 6, 'TYR:plan': 3, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 738 Chain: "C" Number of atoms: 9707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9707 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 335} Link IDs: {'PTRANS': 55, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 1144 Unresolved non-hydrogen angles: 1415 Unresolved non-hydrogen dihedrals: 908 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 51, 'ASP:plan': 66, 'ARG:plan': 22, 'GLN:plan1': 19, 'ASN:plan1': 19, 'HIS:plan': 6, 'TYR:plan': 3, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 738 Chain: "D" Number of atoms: 9707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9707 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 335} Link IDs: {'PTRANS': 55, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 1144 Unresolved non-hydrogen angles: 1415 Unresolved non-hydrogen dihedrals: 908 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 51, 'ASP:plan': 66, 'ARG:plan': 22, 'GLN:plan1': 19, 'ASN:plan1': 19, 'HIS:plan': 6, 'TYR:plan': 3, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 738 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' MG': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' MG': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' MG': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' MG': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 10.07, per 1000 atoms: 0.26 Number of scatterers: 39468 At special positions: 0 Unit cell: (139.594, 139.594, 180.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 184 16.00 P 16 15.00 Mg 16 11.99 O 6800 8.00 N 6892 7.00 C 25560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 Simple disulfide: pdb=" SG CYS D 997 " - pdb=" SG CYS D1006 " 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=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10288 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 36 sheets defined 55.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 118 through 134 removed outlier: 3.755A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 removed outlier: 3.630A pdb=" N ASN A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 322 through 336 removed outlier: 3.800A pdb=" N ASP A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 removed outlier: 4.084A pdb=" N SER A 344 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.710A pdb=" N LEU A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.991A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 407 removed outlier: 3.696A pdb=" N SER A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 423 through 438 removed outlier: 3.644A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 457 removed outlier: 4.826A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 removed outlier: 3.543A pdb=" N VAL A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 513 through 521 removed outlier: 3.717A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.879A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.549A pdb=" N ARG A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 596 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA A 599 " --> pdb=" O ARG A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 641 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 651 through 679 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.613A pdb=" N LEU A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.625A pdb=" N VAL A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 800 Processing helix chain 'A' and resid 801 through 826 removed outlier: 3.508A pdb=" N ARG A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 856 Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 866 through 887 removed outlier: 3.786A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 3.656A pdb=" N LYS A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.558A pdb=" N ALA A 919 " --> pdb=" O ARG A 916 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 3.753A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 929 " --> pdb=" O GLY A 925 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.799A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1008 through 1012 removed outlier: 3.914A pdb=" N VAL A1011 " --> pdb=" O ARG A1008 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A1012 " --> pdb=" O GLU A1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1008 through 1012' Processing helix chain 'A' and resid 1013 through 1026 removed outlier: 3.704A pdb=" N LEU A1018 " --> pdb=" O VAL A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1046 Processing helix chain 'A' and resid 1047 through 1064 removed outlier: 4.014A pdb=" N LEU A1051 " --> pdb=" O ALA A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1088 removed outlier: 3.553A pdb=" N ALA A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1130 Processing helix chain 'A' and resid 1131 through 1168 removed outlier: 3.630A pdb=" N ALA A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1208 Processing helix chain 'A' and resid 1378 through 1390 Processing helix chain 'A' and resid 1404 through 1414 Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.677A pdb=" N ARG A1452 " --> pdb=" O ARG A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1490 removed outlier: 3.786A pdb=" N LEU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 134 removed outlier: 3.755A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 removed outlier: 3.630A pdb=" N ASN B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 272 through 286 Processing helix chain 'B' and resid 298 through 310 Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.800A pdb=" N ASP B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 removed outlier: 4.084A pdb=" N SER B 344 " --> pdb=" O ARG B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 358 removed outlier: 3.710A pdb=" N LEU B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.990A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 407 removed outlier: 3.696A pdb=" N SER B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 422 Processing helix chain 'B' and resid 423 through 438 removed outlier: 3.644A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 457 removed outlier: 4.826A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 removed outlier: 3.543A pdb=" N VAL B 463 " --> pdb=" O LYS B 459 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.717A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.879A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.548A pdb=" N ARG B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR B 596 " --> pdb=" O GLN B 592 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA B 599 " --> pdb=" O ARG B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 641 Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 651 through 679 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.613A pdb=" N LEU B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.625A pdb=" N VAL B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 800 Processing helix chain 'B' and resid 801 through 826 removed outlier: 3.508A pdb=" N ARG B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 856 Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 866 through 887 removed outlier: 3.786A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 3.655A pdb=" N LYS B 896 " --> pdb=" O ASN B 892 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 removed outlier: 3.558A pdb=" N ALA B 919 " --> pdb=" O ARG B 916 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 3.753A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 929 " --> pdb=" O GLY B 925 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.799A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.914A pdb=" N VAL B1011 " --> pdb=" O ARG B1008 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B1012 " --> pdb=" O GLU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1012' Processing helix chain 'B' and resid 1013 through 1026 removed outlier: 3.704A pdb=" N LEU B1018 " --> pdb=" O VAL B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1046 Processing helix chain 'B' and resid 1047 through 1064 removed outlier: 4.013A pdb=" N LEU B1051 " --> pdb=" O ALA B1047 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1088 removed outlier: 3.552A pdb=" N ALA B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1130 Processing helix chain 'B' and resid 1131 through 1168 removed outlier: 3.630A pdb=" N ALA B1168 " --> pdb=" O LEU B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1208 Processing helix chain 'B' and resid 1378 through 1390 Processing helix chain 'B' and resid 1404 through 1414 Processing helix chain 'B' and resid 1447 through 1452 removed outlier: 3.677A pdb=" N ARG B1452 " --> pdb=" O ARG B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1478 through 1490 removed outlier: 3.786A pdb=" N LEU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 134 removed outlier: 3.755A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 removed outlier: 3.630A pdb=" N ASN C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 200 Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 272 through 286 Processing helix chain 'C' and resid 298 through 310 Processing helix chain 'C' and resid 322 through 336 removed outlier: 3.800A pdb=" N ASP C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 345 removed outlier: 4.084A pdb=" N SER C 344 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 358 removed outlier: 3.710A pdb=" N LEU C 350 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.991A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 407 removed outlier: 3.695A pdb=" N SER C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 422 Processing helix chain 'C' and resid 423 through 438 removed outlier: 3.644A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 457 removed outlier: 4.826A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 467 removed outlier: 3.543A pdb=" N VAL C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 467 " --> pdb=" O VAL C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 Processing helix chain 'C' and resid 496 through 508 Processing helix chain 'C' and resid 513 through 521 removed outlier: 3.717A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.879A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.548A pdb=" N ARG C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR C 596 " --> pdb=" O GLN C 592 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA C 599 " --> pdb=" O ARG C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 641 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 651 through 679 Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.613A pdb=" N LEU C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 removed outlier: 3.625A pdb=" N VAL C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 800 Processing helix chain 'C' and resid 801 through 826 removed outlier: 3.508A pdb=" N ARG C 805 " --> pdb=" O ALA C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 856 Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 866 through 887 removed outlier: 3.786A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 3.656A pdb=" N LYS C 896 " --> pdb=" O ASN C 892 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 920 removed outlier: 3.558A pdb=" N ALA C 919 " --> pdb=" O ARG C 916 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 3.753A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 929 " --> pdb=" O GLY C 925 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.799A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1008 through 1012 removed outlier: 3.914A pdb=" N VAL C1011 " --> pdb=" O ARG C1008 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C1012 " --> pdb=" O GLU C1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1008 through 1012' Processing helix chain 'C' and resid 1013 through 1026 removed outlier: 3.704A pdb=" N LEU C1018 " --> pdb=" O VAL C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1046 Processing helix chain 'C' and resid 1047 through 1064 removed outlier: 4.014A pdb=" N LEU C1051 " --> pdb=" O ALA C1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1088 removed outlier: 3.553A pdb=" N ALA C1077 " --> pdb=" O PHE C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1130 Processing helix chain 'C' and resid 1131 through 1168 removed outlier: 3.630A pdb=" N ALA C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1208 Processing helix chain 'C' and resid 1378 through 1390 Processing helix chain 'C' and resid 1404 through 1414 Processing helix chain 'C' and resid 1447 through 1452 removed outlier: 3.677A pdb=" N ARG C1452 " --> pdb=" O ARG C1448 " (cutoff:3.500A) Processing helix chain 'C' and resid 1478 through 1490 removed outlier: 3.786A pdb=" N LEU C1482 " --> pdb=" O SER C1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.755A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.630A pdb=" N ASN D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 272 through 286 Processing helix chain 'D' and resid 298 through 310 Processing helix chain 'D' and resid 322 through 336 removed outlier: 3.800A pdb=" N ASP D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 removed outlier: 4.084A pdb=" N SER D 344 " --> pdb=" O ARG D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 358 removed outlier: 3.710A pdb=" N LEU D 350 " --> pdb=" O THR D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.991A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 407 removed outlier: 3.696A pdb=" N SER D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 422 Processing helix chain 'D' and resid 423 through 438 removed outlier: 3.644A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 457 removed outlier: 4.826A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 467 removed outlier: 3.543A pdb=" N VAL D 463 " --> pdb=" O LYS D 459 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 467 " --> pdb=" O VAL D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 476 Processing helix chain 'D' and resid 496 through 508 Processing helix chain 'D' and resid 513 through 521 removed outlier: 3.717A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 553 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.879A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.549A pdb=" N ARG D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 596 " --> pdb=" O GLN D 592 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA D 599 " --> pdb=" O ARG D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 641 Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 651 through 679 Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 699 through 708 Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.613A pdb=" N LEU D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 removed outlier: 3.625A pdb=" N VAL D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 800 Processing helix chain 'D' and resid 801 through 826 removed outlier: 3.508A pdb=" N ARG D 805 " --> pdb=" O ALA D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 856 Processing helix chain 'D' and resid 859 through 865 Processing helix chain 'D' and resid 866 through 887 removed outlier: 3.786A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 3.656A pdb=" N LYS D 896 " --> pdb=" O ASN D 892 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 removed outlier: 3.558A pdb=" N ALA D 919 " --> pdb=" O ARG D 916 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 3.753A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D 929 " --> pdb=" O GLY D 925 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.799A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1008 through 1012 removed outlier: 3.914A pdb=" N VAL D1011 " --> pdb=" O ARG D1008 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D1012 " --> pdb=" O GLU D1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1008 through 1012' Processing helix chain 'D' and resid 1013 through 1026 removed outlier: 3.704A pdb=" N LEU D1018 " --> pdb=" O VAL D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1046 Processing helix chain 'D' and resid 1047 through 1064 removed outlier: 4.014A pdb=" N LEU D1051 " --> pdb=" O ALA D1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1088 removed outlier: 3.553A pdb=" N ALA D1077 " --> pdb=" O PHE D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 Processing helix chain 'D' and resid 1131 through 1168 removed outlier: 3.630A pdb=" N ALA D1168 " --> pdb=" O LEU D1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 1203 through 1208 Processing helix chain 'D' and resid 1378 through 1390 Processing helix chain 'D' and resid 1404 through 1414 Processing helix chain 'D' and resid 1447 through 1452 removed outlier: 3.676A pdb=" N ARG D1452 " --> pdb=" O ARG D1448 " (cutoff:3.500A) Processing helix chain 'D' and resid 1478 through 1490 removed outlier: 3.787A pdb=" N LEU D1482 " --> pdb=" O SER D1478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 236 removed outlier: 3.662A pdb=" N LEU A 235 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 179 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 213 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 181 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL A 316 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A 292 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL A 318 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL A 294 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1200 removed outlier: 6.571A pdb=" N CYS B1439 " --> pdb=" O VAL B1419 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG B1421 " --> pdb=" O THR B1437 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR B1437 " --> pdb=" O ARG B1421 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR B1423 " --> pdb=" O VAL B1435 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL B1435 " --> pdb=" O TYR B1423 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP B1336 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 17.909A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.988A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.467A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.988A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.909A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1251 through 1252 removed outlier: 6.891A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA8, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 3.786A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.466A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.988A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.908A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.908A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.988A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1353 through 1360 current: chain 'A' and resid 1416 through 1423 Processing sheet with id=AB2, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB3, first strand: chain 'B' and resid 56 through 58 Processing sheet with id=AB4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB5, first strand: chain 'B' and resid 235 through 236 removed outlier: 3.662A pdb=" N LEU B 235 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 179 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 213 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR B 181 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL B 316 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 292 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL B 318 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 294 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1199 through 1200 removed outlier: 6.571A pdb=" N CYS C1439 " --> pdb=" O VAL C1419 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG C1421 " --> pdb=" O THR C1437 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR C1437 " --> pdb=" O ARG C1421 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR C1423 " --> pdb=" O VAL C1435 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL C1435 " --> pdb=" O TYR C1423 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP C1336 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 17.908A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.987A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.466A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.987A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.908A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1251 through 1252 removed outlier: 6.891A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AC1, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 3.786A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AC3, first strand: chain 'C' and resid 56 through 58 Processing sheet with id=AC4, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AC5, first strand: chain 'C' and resid 235 through 236 removed outlier: 3.662A pdb=" N LEU C 235 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 179 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE C 213 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR C 181 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL C 316 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR C 292 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL C 318 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL C 294 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1199 through 1200 removed outlier: 6.571A pdb=" N CYS D1439 " --> pdb=" O VAL D1419 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG D1421 " --> pdb=" O THR D1437 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR D1437 " --> pdb=" O ARG D1421 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TYR D1423 " --> pdb=" O VAL D1435 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL D1435 " --> pdb=" O TYR D1423 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP D1336 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 17.908A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.987A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.466A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.549A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.987A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.908A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 6.891A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AD1, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 3.787A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD3, first strand: chain 'D' and resid 56 through 58 Processing sheet with id=AD4, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD5, first strand: chain 'D' and resid 235 through 236 removed outlier: 3.662A pdb=" N LEU D 235 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL D 179 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE D 213 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR D 181 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL D 316 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR D 292 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL D 318 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL D 294 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 1251 through 1252 removed outlier: 6.891A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AD8, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 3.786A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1346 through 1347 2256 hydrogen bonds defined for protein. 6624 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: 8.92 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6088 1.32 - 1.44: 11217 1.44 - 1.57: 22771 1.57 - 1.69: 40 1.69 - 1.81: 328 Bond restraints: 40444 Sorted by residual: bond pdb=" C4 APR D6009 " pdb=" C5 APR D6009 " ideal model delta sigma weight residual 1.386 1.472 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C4 APR B1706 " pdb=" C5 APR B1706 " ideal model delta sigma weight residual 1.386 1.472 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C4 APR A1706 " pdb=" C5 APR A1706 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4 APR C1706 " pdb=" C5 APR C1706 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C ARG A1066 " pdb=" N PRO A1067 " ideal model delta sigma weight residual 1.334 1.369 -0.036 8.40e-03 1.42e+04 1.80e+01 ... (remaining 40439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 51691 2.35 - 4.69: 2916 4.69 - 7.04: 629 7.04 - 9.38: 164 9.38 - 11.73: 16 Bond angle restraints: 55416 Sorted by residual: angle pdb=" N PRO B 244 " pdb=" CA PRO B 244 " pdb=" C PRO B 244 " ideal model delta sigma weight residual 110.70 122.17 -11.47 1.22e+00 6.72e-01 8.85e+01 angle pdb=" N PRO C 244 " pdb=" CA PRO C 244 " pdb=" C PRO C 244 " ideal model delta sigma weight residual 110.70 122.16 -11.46 1.22e+00 6.72e-01 8.82e+01 angle pdb=" N PRO A 244 " pdb=" CA PRO A 244 " pdb=" C PRO A 244 " ideal model delta sigma weight residual 110.70 122.16 -11.46 1.22e+00 6.72e-01 8.82e+01 angle pdb=" N PRO D 244 " pdb=" CA PRO D 244 " pdb=" C PRO D 244 " ideal model delta sigma weight residual 110.70 122.16 -11.46 1.22e+00 6.72e-01 8.82e+01 angle pdb=" N VAL B 844 " pdb=" CA VAL B 844 " pdb=" C VAL B 844 " ideal model delta sigma weight residual 110.53 103.37 7.16 9.40e-01 1.13e+00 5.81e+01 ... (remaining 55411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 21823 15.88 - 31.76: 1905 31.76 - 47.64: 412 47.64 - 63.52: 164 63.52 - 79.40: 52 Dihedral angle restraints: 24356 sinusoidal: 8480 harmonic: 15876 Sorted by residual: dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N ALA B 597 " pdb=" CA ALA B 597 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA THR D 596 " pdb=" C THR D 596 " pdb=" N ALA D 597 " pdb=" CA ALA D 597 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N ALA C 597 " pdb=" CA ALA C 597 " ideal model delta harmonic sigma weight residual 180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 24353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 5273 0.074 - 0.147: 1027 0.147 - 0.221: 152 0.221 - 0.294: 76 0.294 - 0.368: 32 Chirality restraints: 6560 Sorted by residual: chirality pdb=" CB VAL B1027 " pdb=" CA VAL B1027 " pdb=" CG1 VAL B1027 " pdb=" CG2 VAL B1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CB VAL A1027 " pdb=" CA VAL A1027 " pdb=" CG1 VAL A1027 " pdb=" CG2 VAL A1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 6557 not shown) Planarity restraints: 6972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 672 " -0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C VAL B 672 " 0.085 2.00e-02 2.50e+03 pdb=" O VAL B 672 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU B 673 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 672 " 0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C VAL D 672 " -0.085 2.00e-02 2.50e+03 pdb=" O VAL D 672 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU D 673 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 672 " 0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C VAL A 672 " -0.085 2.00e-02 2.50e+03 pdb=" O VAL A 672 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU A 673 " 0.028 2.00e-02 2.50e+03 ... (remaining 6969 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2411 2.74 - 3.28: 35317 3.28 - 3.82: 63252 3.82 - 4.36: 76583 4.36 - 4.90: 129139 Nonbonded interactions: 306702 Sorted by model distance: nonbonded pdb="MG MG B1703 " pdb=" O1A APR B1706 " model vdw 2.198 2.170 nonbonded pdb="MG MG C1703 " pdb=" O1A APR C1706 " model vdw 2.198 2.170 nonbonded pdb="MG MG A1703 " pdb=" O1A APR A1706 " model vdw 2.198 2.170 nonbonded pdb="MG MG D6006 " pdb=" O1A APR D6009 " model vdw 2.198 2.170 nonbonded pdb="MG MG A1704 " pdb=" O1A APR A1706 " model vdw 2.217 2.170 ... (remaining 306697 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: 0.12 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 52 through 1494 or resid 1705)) selection = (chain 'B' and (resid 52 through 1494 or resid 1705)) selection = (chain 'C' and (resid 52 through 1494 or resid 1705)) selection = (chain 'D' and (resid 52 through 1494 or resid 6005)) } 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 group one per residue 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: 5.630 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 39.140 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.100 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 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 : 0.009 0.086 40448 Z= 0.485 Angle : 1.301 11.731 55424 Z= 0.763 Chirality : 0.067 0.368 6560 Planarity : 0.012 0.085 6972 Dihedral : 14.177 79.397 14056 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.36 % Allowed : 0.84 % Favored : 98.80 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.98 (0.08), residues: 5424 helix: -4.23 (0.04), residues: 2936 sheet: -0.71 (0.21), residues: 456 loop : -2.08 (0.12), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 100 TYR 0.030 0.004 TYR D 799 PHE 0.049 0.004 PHE C 795 TRP 0.020 0.002 TRP C 837 HIS 0.011 0.001 HIS B 903 Details of bonding type rmsd covalent geometry : bond 0.00921 (40444) covalent geometry : angle 1.30064 (55416) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.80544 ( 8) hydrogen bonds : bond 0.14845 ( 2244) hydrogen bonds : angle 7.85845 ( 6624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 650 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 ILE cc_start: 0.7565 (tp) cc_final: 0.7274 (tp) REVERT: A 594 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8074 (ttm170) REVERT: A 663 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7800 (tmtt) REVERT: A 697 LYS cc_start: 0.8356 (mmtm) cc_final: 0.8088 (mmmt) REVERT: A 860 ILE cc_start: 0.7706 (mm) cc_final: 0.7068 (pt) REVERT: A 920 LEU cc_start: 0.8954 (tp) cc_final: 0.8728 (tp) REVERT: A 934 MET cc_start: 0.7569 (mtt) cc_final: 0.7191 (mtp) REVERT: A 935 MET cc_start: 0.6396 (mtt) cc_final: 0.6090 (mtt) REVERT: A 937 ASP cc_start: 0.7614 (m-30) cc_final: 0.7406 (m-30) REVERT: A 1000 ASP cc_start: 0.6962 (m-30) cc_final: 0.6307 (t70) REVERT: A 1081 MET cc_start: 0.5481 (tmm) cc_final: 0.5017 (ttm) REVERT: A 1118 ASP cc_start: 0.7055 (m-30) cc_final: 0.6664 (t0) REVERT: A 1131 MET cc_start: 0.7843 (mmm) cc_final: 0.7258 (ttm) REVERT: A 1467 MET cc_start: 0.7991 (mtt) cc_final: 0.7704 (mtm) REVERT: B 591 ILE cc_start: 0.7571 (tp) cc_final: 0.7283 (tp) REVERT: B 594 ARG cc_start: 0.8274 (mtp-110) cc_final: 0.8067 (ttm170) REVERT: B 663 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7745 (tmtt) REVERT: B 697 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8095 (mmmt) REVERT: B 860 ILE cc_start: 0.7694 (mm) cc_final: 0.7051 (pt) REVERT: B 920 LEU cc_start: 0.8944 (tp) cc_final: 0.8718 (tp) REVERT: B 934 MET cc_start: 0.7548 (mtt) cc_final: 0.7192 (mtp) REVERT: B 935 MET cc_start: 0.6389 (mtt) cc_final: 0.6084 (mtt) REVERT: B 937 ASP cc_start: 0.7617 (m-30) cc_final: 0.7411 (m-30) REVERT: B 1000 ASP cc_start: 0.6962 (m-30) cc_final: 0.6310 (t70) REVERT: B 1081 MET cc_start: 0.5519 (tmm) cc_final: 0.5023 (ttm) REVERT: B 1118 ASP cc_start: 0.7037 (m-30) cc_final: 0.6638 (t0) REVERT: B 1131 MET cc_start: 0.7848 (mmm) cc_final: 0.7259 (ttm) REVERT: B 1467 MET cc_start: 0.8001 (mtt) cc_final: 0.7715 (mtm) REVERT: C 591 ILE cc_start: 0.7563 (tp) cc_final: 0.7276 (tp) REVERT: C 594 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.8075 (ttm170) REVERT: C 663 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7783 (tmtt) REVERT: C 697 LYS cc_start: 0.8358 (mmtm) cc_final: 0.8092 (mmmt) REVERT: C 860 ILE cc_start: 0.7715 (mm) cc_final: 0.7082 (pt) REVERT: C 920 LEU cc_start: 0.8955 (tp) cc_final: 0.8728 (tp) REVERT: C 934 MET cc_start: 0.7566 (mtt) cc_final: 0.7188 (mtp) REVERT: C 935 MET cc_start: 0.6397 (mtt) cc_final: 0.6089 (mtt) REVERT: C 1000 ASP cc_start: 0.6961 (m-30) cc_final: 0.6309 (t70) REVERT: C 1081 MET cc_start: 0.5518 (tmm) cc_final: 0.5023 (ttm) REVERT: C 1118 ASP cc_start: 0.7050 (m-30) cc_final: 0.6647 (t0) REVERT: C 1131 MET cc_start: 0.7844 (mmm) cc_final: 0.7257 (ttm) REVERT: C 1467 MET cc_start: 0.7987 (mtt) cc_final: 0.7703 (mtm) REVERT: D 591 ILE cc_start: 0.7564 (tp) cc_final: 0.7272 (tp) REVERT: D 594 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8074 (ttm170) REVERT: D 663 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7783 (tmtt) REVERT: D 697 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8089 (mmmt) REVERT: D 860 ILE cc_start: 0.7715 (mm) cc_final: 0.7081 (pt) REVERT: D 920 LEU cc_start: 0.8954 (tp) cc_final: 0.8733 (tp) REVERT: D 934 MET cc_start: 0.7566 (mtt) cc_final: 0.7187 (mtp) REVERT: D 935 MET cc_start: 0.6397 (mtt) cc_final: 0.6085 (mtt) REVERT: D 937 ASP cc_start: 0.7610 (m-30) cc_final: 0.7404 (m-30) REVERT: D 1000 ASP cc_start: 0.6957 (m-30) cc_final: 0.6306 (t70) REVERT: D 1081 MET cc_start: 0.5487 (tmm) cc_final: 0.5021 (ttm) REVERT: D 1118 ASP cc_start: 0.7050 (m-30) cc_final: 0.6649 (t0) REVERT: D 1131 MET cc_start: 0.7842 (mmm) cc_final: 0.7256 (ttm) REVERT: D 1467 MET cc_start: 0.7986 (mtt) cc_final: 0.7701 (mtm) outliers start: 12 outliers final: 4 residues processed: 662 average time/residue: 0.2593 time to fit residues: 275.8456 Evaluate side-chains 327 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 323 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 844 VAL Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain D residue 844 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 40.0000 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 0.2980 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 598 GLN A 689 HIS A 719 GLN A1026 ASN A1327 GLN B 417 GLN B 598 GLN B 689 HIS B 719 GLN B1026 ASN B1327 GLN C 417 GLN C 598 GLN C 689 HIS C 719 GLN C1026 ASN C1327 GLN D 417 GLN D 598 GLN D 689 HIS D 719 GLN D1026 ASN D1327 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093361 restraints weight = 103706.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093821 restraints weight = 92904.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094505 restraints weight = 67229.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094533 restraints weight = 49694.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.094633 restraints weight = 48375.747| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40448 Z= 0.142 Angle : 0.568 6.910 55424 Z= 0.302 Chirality : 0.040 0.153 6560 Planarity : 0.006 0.054 6972 Dihedral : 9.978 85.090 6976 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 6.51 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.10), residues: 5424 helix: -1.32 (0.08), residues: 2964 sheet: -0.47 (0.23), residues: 460 loop : -1.64 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 916 TYR 0.016 0.001 TYR B 138 PHE 0.023 0.001 PHE D 795 TRP 0.015 0.001 TRP B 842 HIS 0.003 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00308 (40444) covalent geometry : angle 0.56767 (55416) SS BOND : bond 0.00165 ( 4) SS BOND : angle 1.02277 ( 8) hydrogen bonds : bond 0.04326 ( 2244) hydrogen bonds : angle 4.57918 ( 6624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 343 time to evaluate : 1.554 Fit side-chains REVERT: A 860 ILE cc_start: 0.7663 (mm) cc_final: 0.6899 (pt) REVERT: A 876 ILE cc_start: 0.8128 (mt) cc_final: 0.7887 (mm) REVERT: A 935 MET cc_start: 0.6376 (mtt) cc_final: 0.6084 (mtt) REVERT: A 1081 MET cc_start: 0.6488 (tmm) cc_final: 0.6069 (ttm) REVERT: B 860 ILE cc_start: 0.7663 (mm) cc_final: 0.6899 (pt) REVERT: B 876 ILE cc_start: 0.8133 (mt) cc_final: 0.7899 (mm) REVERT: B 935 MET cc_start: 0.6379 (mtt) cc_final: 0.6080 (mtt) REVERT: B 1081 MET cc_start: 0.6496 (tmm) cc_final: 0.6076 (ttm) REVERT: C 860 ILE cc_start: 0.7678 (mm) cc_final: 0.6913 (pt) REVERT: C 876 ILE cc_start: 0.8114 (mt) cc_final: 0.7886 (mm) REVERT: C 1081 MET cc_start: 0.6489 (tmm) cc_final: 0.6068 (ttm) REVERT: D 860 ILE cc_start: 0.7684 (mm) cc_final: 0.6920 (pt) REVERT: D 876 ILE cc_start: 0.8128 (mt) cc_final: 0.7888 (mm) REVERT: D 935 MET cc_start: 0.6358 (mtt) cc_final: 0.6078 (mtt) REVERT: D 1081 MET cc_start: 0.6498 (tmm) cc_final: 0.6075 (ttm) outliers start: 49 outliers final: 24 residues processed: 377 average time/residue: 0.2298 time to fit residues: 146.1457 Evaluate side-chains 307 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 283 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1026 ASN Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 1026 ASN Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 1026 ASN Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 1026 ASN Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 399 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 504 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 366 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 116 optimal weight: 20.0000 chunk 540 optimal weight: 10.0000 chunk 390 optimal weight: 0.0980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 GLN A 660 HIS B 647 GLN B 660 HIS C 647 GLN C 660 HIS D 647 GLN D 660 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090680 restraints weight = 104170.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090772 restraints weight = 104207.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091552 restraints weight = 82606.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091556 restraints weight = 63466.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091697 restraints weight = 57317.915| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40448 Z= 0.150 Angle : 0.544 6.877 55424 Z= 0.282 Chirality : 0.041 0.147 6560 Planarity : 0.004 0.050 6972 Dihedral : 9.121 86.604 6972 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.63 % Allowed : 8.04 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.11), residues: 5424 helix: 0.31 (0.09), residues: 2960 sheet: -0.39 (0.23), residues: 436 loop : -1.33 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 913 TYR 0.011 0.001 TYR C 138 PHE 0.023 0.001 PHE C 795 TRP 0.011 0.001 TRP C 726 HIS 0.004 0.001 HIS C 601 Details of bonding type rmsd covalent geometry : bond 0.00335 (40444) covalent geometry : angle 0.54404 (55416) SS BOND : bond 0.00051 ( 4) SS BOND : angle 0.69128 ( 8) hydrogen bonds : bond 0.04039 ( 2244) hydrogen bonds : angle 4.03353 ( 6624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.8389 (tp) cc_final: 0.8171 (tp) REVERT: A 1081 MET cc_start: 0.6405 (tmm) cc_final: 0.6010 (ttm) REVERT: A 1467 MET cc_start: 0.7655 (mtt) cc_final: 0.7335 (mtm) REVERT: B 840 LEU cc_start: 0.8382 (tp) cc_final: 0.8155 (tp) REVERT: B 1081 MET cc_start: 0.6443 (tmm) cc_final: 0.6057 (ttm) REVERT: B 1467 MET cc_start: 0.7662 (mtt) cc_final: 0.7343 (mtm) REVERT: C 840 LEU cc_start: 0.8394 (tp) cc_final: 0.8170 (tp) REVERT: C 1081 MET cc_start: 0.6394 (tmm) cc_final: 0.6004 (ttm) REVERT: C 1467 MET cc_start: 0.7663 (mtt) cc_final: 0.7346 (mtm) REVERT: D 840 LEU cc_start: 0.8389 (tp) cc_final: 0.8163 (tp) REVERT: D 1081 MET cc_start: 0.6397 (tmm) cc_final: 0.5995 (ttm) REVERT: D 1467 MET cc_start: 0.7668 (mtt) cc_final: 0.7349 (mtm) outliers start: 54 outliers final: 32 residues processed: 342 average time/residue: 0.2185 time to fit residues: 128.4072 Evaluate side-chains 314 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 415 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 397 optimal weight: 7.9990 chunk 432 optimal weight: 8.9990 chunk 360 optimal weight: 0.9980 chunk 91 optimal weight: 0.0870 chunk 230 optimal weight: 0.9980 chunk 336 optimal weight: 0.0030 chunk 41 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 463 optimal weight: 0.9980 overall best weight: 0.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 GLN B 647 GLN C 647 GLN D 647 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093090 restraints weight = 105807.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092990 restraints weight = 116260.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093890 restraints weight = 88757.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093875 restraints weight = 69719.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094002 restraints weight = 62705.544| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 40448 Z= 0.098 Angle : 0.480 6.685 55424 Z= 0.247 Chirality : 0.039 0.159 6560 Planarity : 0.004 0.047 6972 Dihedral : 8.435 80.979 6972 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.17 % Allowed : 9.19 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.11), residues: 5424 helix: 1.28 (0.10), residues: 2936 sheet: -0.40 (0.23), residues: 440 loop : -1.12 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 969 TYR 0.010 0.001 TYR C 917 PHE 0.014 0.001 PHE D 795 TRP 0.009 0.001 TRP B 620 HIS 0.004 0.000 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00208 (40444) covalent geometry : angle 0.47986 (55416) SS BOND : bond 0.00061 ( 4) SS BOND : angle 0.37457 ( 8) hydrogen bonds : bond 0.03440 ( 2244) hydrogen bonds : angle 3.74085 ( 6624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.6926 (tmm) cc_final: 0.6559 (tmm) REVERT: A 1081 MET cc_start: 0.6307 (tmm) cc_final: 0.5882 (ttm) REVERT: A 1467 MET cc_start: 0.7547 (mtt) cc_final: 0.7275 (mtm) REVERT: B 129 MET cc_start: 0.6923 (tmm) cc_final: 0.6557 (tmm) REVERT: B 1081 MET cc_start: 0.6321 (tmm) cc_final: 0.5884 (ttm) REVERT: B 1467 MET cc_start: 0.7561 (mtt) cc_final: 0.7287 (mtm) REVERT: C 129 MET cc_start: 0.7000 (tmm) cc_final: 0.6755 (tmm) REVERT: C 1081 MET cc_start: 0.6304 (tmm) cc_final: 0.5878 (ttm) REVERT: C 1467 MET cc_start: 0.7587 (mtt) cc_final: 0.7297 (mtm) REVERT: D 129 MET cc_start: 0.6920 (tmm) cc_final: 0.6556 (tmm) REVERT: D 1081 MET cc_start: 0.6299 (tmm) cc_final: 0.5870 (ttm) REVERT: D 1467 MET cc_start: 0.7584 (mtt) cc_final: 0.7298 (mtm) outliers start: 39 outliers final: 23 residues processed: 307 average time/residue: 0.2055 time to fit residues: 111.8679 Evaluate side-chains 299 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 276 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 1013 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1013 MET Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 386 optimal weight: 0.9990 chunk 469 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 141 optimal weight: 0.4980 chunk 173 optimal weight: 6.9990 chunk 390 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 468 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 GLN B 647 GLN B1031 ASN C 647 GLN C1031 ASN D 647 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.108607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091703 restraints weight = 105842.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091432 restraints weight = 127372.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092101 restraints weight = 100554.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092327 restraints weight = 77342.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.092456 restraints weight = 69640.531| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40448 Z= 0.112 Angle : 0.483 6.685 55424 Z= 0.248 Chirality : 0.039 0.122 6560 Planarity : 0.004 0.047 6972 Dihedral : 7.954 75.599 6972 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.23 % Allowed : 10.51 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.11), residues: 5424 helix: 1.68 (0.10), residues: 2956 sheet: -0.32 (0.23), residues: 436 loop : -0.98 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 969 TYR 0.018 0.001 TYR C 917 PHE 0.016 0.001 PHE D 795 TRP 0.009 0.001 TRP A 726 HIS 0.003 0.001 HIS B 601 Details of bonding type rmsd covalent geometry : bond 0.00250 (40444) covalent geometry : angle 0.48273 (55416) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.43897 ( 8) hydrogen bonds : bond 0.03452 ( 2244) hydrogen bonds : angle 3.63711 ( 6624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.6929 (tmm) cc_final: 0.6567 (tmm) REVERT: A 1081 MET cc_start: 0.6214 (tmm) cc_final: 0.5815 (ttm) REVERT: A 1467 MET cc_start: 0.7593 (mtt) cc_final: 0.7310 (mtm) REVERT: B 129 MET cc_start: 0.6930 (tmm) cc_final: 0.6557 (tmm) REVERT: B 860 ILE cc_start: 0.7920 (mm) cc_final: 0.7143 (pt) REVERT: B 1081 MET cc_start: 0.6216 (tmm) cc_final: 0.5820 (ttm) REVERT: B 1467 MET cc_start: 0.7631 (mtt) cc_final: 0.7344 (mtm) REVERT: C 129 MET cc_start: 0.6958 (tmm) cc_final: 0.6678 (tmm) REVERT: C 1081 MET cc_start: 0.6219 (tmm) cc_final: 0.5824 (ttm) REVERT: C 1467 MET cc_start: 0.7615 (mtt) cc_final: 0.7331 (mtm) REVERT: D 129 MET cc_start: 0.6925 (tmm) cc_final: 0.6564 (tmm) REVERT: D 860 ILE cc_start: 0.7927 (mm) cc_final: 0.7158 (pt) REVERT: D 1081 MET cc_start: 0.6203 (tmm) cc_final: 0.5811 (ttm) REVERT: D 1467 MET cc_start: 0.7618 (mtt) cc_final: 0.7332 (mtm) outliers start: 41 outliers final: 20 residues processed: 305 average time/residue: 0.2046 time to fit residues: 110.1036 Evaluate side-chains 294 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 274 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 376 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 91 optimal weight: 0.0070 chunk 518 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 398 optimal weight: 9.9990 chunk 300 optimal weight: 0.0040 overall best weight: 1.7614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1031 ASN B1026 ASN C1026 ASN D1026 ASN D1031 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088692 restraints weight = 104958.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088789 restraints weight = 112180.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089454 restraints weight = 85214.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089823 restraints weight = 67649.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089909 restraints weight = 64309.039| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40448 Z= 0.149 Angle : 0.524 7.440 55424 Z= 0.270 Chirality : 0.040 0.127 6560 Planarity : 0.004 0.047 6972 Dihedral : 7.580 70.430 6972 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.63 % Allowed : 11.23 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.12), residues: 5424 helix: 1.79 (0.10), residues: 2964 sheet: -0.43 (0.23), residues: 428 loop : -0.88 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 916 TYR 0.020 0.002 TYR A 917 PHE 0.018 0.001 PHE A 604 TRP 0.011 0.001 TRP C 726 HIS 0.004 0.001 HIS C 601 Details of bonding type rmsd covalent geometry : bond 0.00338 (40444) covalent geometry : angle 0.52420 (55416) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.58918 ( 8) hydrogen bonds : bond 0.03854 ( 2244) hydrogen bonds : angle 3.72575 ( 6624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1081 MET cc_start: 0.6177 (tmm) cc_final: 0.5708 (ttm) REVERT: B 129 MET cc_start: 0.6937 (tmm) cc_final: 0.6595 (tmm) REVERT: B 860 ILE cc_start: 0.7957 (mm) cc_final: 0.7142 (pt) REVERT: B 1081 MET cc_start: 0.6196 (tmm) cc_final: 0.5666 (ttm) REVERT: C 129 MET cc_start: 0.7008 (tmm) cc_final: 0.6752 (tmm) REVERT: C 1081 MET cc_start: 0.6163 (tmm) cc_final: 0.5694 (ttm) REVERT: D 1081 MET cc_start: 0.6166 (tmm) cc_final: 0.5697 (ttm) outliers start: 54 outliers final: 29 residues processed: 305 average time/residue: 0.2040 time to fit residues: 109.4108 Evaluate side-chains 298 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 1027 VAL Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 440 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 406 optimal weight: 4.9990 chunk 502 optimal weight: 1.9990 chunk 462 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 510 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1026 ASN A1359 GLN C1359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.105952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089383 restraints weight = 104565.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089594 restraints weight = 108500.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.090147 restraints weight = 86449.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090285 restraints weight = 62930.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090377 restraints weight = 58957.620| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40448 Z= 0.129 Angle : 0.501 7.416 55424 Z= 0.258 Chirality : 0.039 0.125 6560 Planarity : 0.004 0.047 6972 Dihedral : 7.428 71.740 6972 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.23 % Allowed : 11.63 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.12), residues: 5424 helix: 1.98 (0.10), residues: 2968 sheet: -0.54 (0.23), residues: 428 loop : -0.76 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.011 0.001 TYR A 917 PHE 0.013 0.001 PHE C 604 TRP 0.009 0.001 TRP C 726 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00295 (40444) covalent geometry : angle 0.50053 (55416) SS BOND : bond 0.00065 ( 4) SS BOND : angle 0.51674 ( 8) hydrogen bonds : bond 0.03615 ( 2244) hydrogen bonds : angle 3.62994 ( 6624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 36 residues processed: 309 average time/residue: 0.2290 time to fit residues: 122.3212 Evaluate side-chains 302 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 1027 VAL Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 795 PHE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 54 optimal weight: 0.9980 chunk 470 optimal weight: 7.9990 chunk 420 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 342 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088371 restraints weight = 104619.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088702 restraints weight = 108330.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089211 restraints weight = 81927.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089294 restraints weight = 62593.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.089368 restraints weight = 59954.568| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40448 Z= 0.168 Angle : 0.539 7.213 55424 Z= 0.277 Chirality : 0.041 0.130 6560 Planarity : 0.004 0.054 6972 Dihedral : 7.435 71.216 6972 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.30 % Allowed : 12.05 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.12), residues: 5424 helix: 1.88 (0.10), residues: 2964 sheet: -0.65 (0.23), residues: 428 loop : -0.74 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 617 TYR 0.016 0.001 TYR C 917 PHE 0.016 0.001 PHE C 795 TRP 0.011 0.001 TRP B 726 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00388 (40444) covalent geometry : angle 0.53944 (55416) SS BOND : bond 0.00073 ( 4) SS BOND : angle 0.51689 ( 8) hydrogen bonds : bond 0.03987 ( 2244) hydrogen bonds : angle 3.77590 ( 6624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 39 residues processed: 307 average time/residue: 0.2103 time to fit residues: 114.2958 Evaluate side-chains 306 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 1027 VAL Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 795 PHE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 66 optimal weight: 0.8980 chunk 481 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 542 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 452 optimal weight: 9.9990 chunk 432 optimal weight: 7.9990 chunk 335 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088827 restraints weight = 103095.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089068 restraints weight = 101290.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089513 restraints weight = 84785.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089666 restraints weight = 64324.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.089746 restraints weight = 59366.344| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40448 Z= 0.139 Angle : 0.512 6.734 55424 Z= 0.264 Chirality : 0.040 0.128 6560 Planarity : 0.004 0.047 6972 Dihedral : 7.369 71.127 6972 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.69 % Allowed : 12.50 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.12), residues: 5424 helix: 1.98 (0.10), residues: 2964 sheet: -0.71 (0.23), residues: 428 loop : -0.74 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.013 0.001 TYR C 917 PHE 0.013 0.001 PHE B 604 TRP 0.011 0.001 TRP C 606 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00319 (40444) covalent geometry : angle 0.51234 (55416) SS BOND : bond 0.00028 ( 4) SS BOND : angle 0.47152 ( 8) hydrogen bonds : bond 0.03788 ( 2244) hydrogen bonds : angle 3.70322 ( 6624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 44 residues processed: 317 average time/residue: 0.2107 time to fit residues: 117.8897 Evaluate side-chains 309 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1027 VAL Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 518 LEU Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 795 PHE Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 391 optimal weight: 4.9990 chunk 346 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 469 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 347 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 289 optimal weight: 0.0010 chunk 357 optimal weight: 2.9990 chunk 281 optimal weight: 0.4980 chunk 152 optimal weight: 7.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.106564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089928 restraints weight = 102716.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090143 restraints weight = 100426.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.090724 restraints weight = 82038.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090873 restraints weight = 62771.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090950 restraints weight = 58174.615| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 40448 Z= 0.098 Angle : 0.475 6.746 55424 Z= 0.244 Chirality : 0.038 0.124 6560 Planarity : 0.004 0.047 6972 Dihedral : 7.175 71.878 6972 Min Nonbonded Distance : 1.397 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.23 % Allowed : 13.07 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.12), residues: 5424 helix: 2.19 (0.10), residues: 2964 sheet: -0.58 (0.24), residues: 400 loop : -0.66 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 112 TYR 0.010 0.001 TYR A 705 PHE 0.011 0.001 PHE A 604 TRP 0.012 0.001 TRP D 606 HIS 0.003 0.000 HIS D 715 Details of bonding type rmsd covalent geometry : bond 0.00211 (40444) covalent geometry : angle 0.47532 (55416) SS BOND : bond 0.00023 ( 4) SS BOND : angle 0.40295 ( 8) hydrogen bonds : bond 0.03356 ( 2244) hydrogen bonds : angle 3.54875 ( 6624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 33 residues processed: 306 average time/residue: 0.2239 time to fit residues: 120.7099 Evaluate side-chains 299 residues out of total 4660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 795 PHE Chi-restraints excluded: chain A residue 1027 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 687 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 795 PHE Chi-restraints excluded: chain B residue 1027 VAL Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1154 LEU Chi-restraints excluded: chain B residue 1281 VAL Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 687 MET Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1027 VAL Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1281 VAL Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 791 LEU Chi-restraints excluded: chain D residue 795 PHE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1281 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 56 optimal weight: 0.5980 chunk 297 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 484 optimal weight: 4.9990 chunk 487 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 499 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 overall best weight: 2.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1026 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.103762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.087397 restraints weight = 104522.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.087275 restraints weight = 113837.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087761 restraints weight = 95712.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087940 restraints weight = 75243.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088023 restraints weight = 69482.033| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40448 Z= 0.194 Angle : 0.573 8.273 55424 Z= 0.293 Chirality : 0.042 0.131 6560 Planarity : 0.004 0.048 6972 Dihedral : 7.382 72.815 6972 Min Nonbonded Distance : 1.203 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.45 % Allowed : 13.22 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.12), residues: 5424 helix: 1.90 (0.10), residues: 2964 sheet: -0.76 (0.23), residues: 428 loop : -0.76 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 916 TYR 0.014 0.002 TYR A1063 PHE 0.018 0.002 PHE B 795 TRP 0.014 0.002 TRP D1216 HIS 0.005 0.001 HIS C 618 Details of bonding type rmsd covalent geometry : bond 0.00457 (40444) covalent geometry : angle 0.57265 (55416) SS BOND : bond 0.00840 ( 4) SS BOND : angle 2.05657 ( 8) hydrogen bonds : bond 0.04114 ( 2244) hydrogen bonds : angle 3.81729 ( 6624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5132.58 seconds wall clock time: 90 minutes 10.76 seconds (5410.76 seconds total)