Starting phenix.real_space_refine on Sun Jun 15 14:48:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vi0_43245/06_2025/8vi0_43245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vi0_43245/06_2025/8vi0_43245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vi0_43245/06_2025/8vi0_43245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vi0_43245/06_2025/8vi0_43245.map" model { file = "/net/cci-nas-00/data/ceres_data/8vi0_43245/06_2025/8vi0_43245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vi0_43245/06_2025/8vi0_43245.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 11404 2.51 5 N 2911 2.21 5 O 3049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17454 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5798 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 684} Chain breaks: 2 Chain: "B" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5790 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 683} Chain breaks: 3 Chain: "D" Number of atoms: 5797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5797 Classifications: {'peptide': 724} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 684} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 10.33, per 1000 atoms: 0.59 Number of scatterers: 17454 At special positions: 0 Unit cell: (129.6, 135, 105.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3049 8.00 N 2911 7.00 C 11404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied BETA1-4 " BGC C 2 " - " BGC C 3 " " BGC E 2 " - " BGC E 3 " " BGC F 2 " - " BGC F 3 " BETA1-5 " BGC C 1 " - " BGC C 2 " " BGC E 1 " - " BGC E 2 " " BGC F 1 " - " BGC F 2 " Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 2.1 seconds 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 9 sheets defined 59.2% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 263 through 291 Proline residue: A 269 - end of helix removed outlier: 3.562A pdb=" N HIS A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 319 Processing helix chain 'A' and resid 320 through 323 removed outlier: 4.476A pdb=" N SER A 323 " --> pdb=" O PRO A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.563A pdb=" N LEU A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 376 removed outlier: 3.708A pdb=" N THR A 367 " --> pdb=" O PRO A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 394 through 419 removed outlier: 3.600A pdb=" N PHE A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 424 through 430 Processing helix chain 'A' and resid 443 through 469 Processing helix chain 'A' and resid 485 through 489 removed outlier: 4.692A pdb=" N ASN A 489 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 548 Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.724A pdb=" N PHE A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 582 removed outlier: 3.569A pdb=" N LYS A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.564A pdb=" N PHE A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 724 through 732 removed outlier: 3.732A pdb=" N LEU A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 777 through 789 removed outlier: 3.770A pdb=" N LEU A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 831 removed outlier: 3.770A pdb=" N ARG A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 857 Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 861 through 879 removed outlier: 3.505A pdb=" N LEU A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Proline residue: A 872 - end of helix Processing helix chain 'A' and resid 887 through 913 Processing helix chain 'A' and resid 915 through 947 removed outlier: 4.301A pdb=" N HIS A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU A 935 " --> pdb=" O ALA A 931 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 999 Processing helix chain 'A' and resid 1008 through 1023 removed outlier: 3.566A pdb=" N ALA A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.888A pdb=" N LEU A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1059 removed outlier: 3.566A pdb=" N LEU A1042 " --> pdb=" O PRO A1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 263 through 291 Proline residue: B 269 - end of helix removed outlier: 3.521A pdb=" N LEU B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 291 " --> pdb=" O TYR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 319 Processing helix chain 'B' and resid 320 through 323 removed outlier: 4.442A pdb=" N SER B 323 " --> pdb=" O PRO B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 323' Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.538A pdb=" N LEU B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 376 removed outlier: 3.692A pdb=" N THR B 367 " --> pdb=" O PRO B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 419 removed outlier: 3.582A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 424 through 430 Processing helix chain 'B' and resid 443 through 469 removed outlier: 3.561A pdb=" N GLU B 447 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 489 removed outlier: 4.695A pdb=" N ASN B 489 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 548 Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.808A pdb=" N PHE B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 582 removed outlier: 3.563A pdb=" N LYS B 582 " --> pdb=" O THR B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 612 through 618 Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 714 through 719 Processing helix chain 'B' and resid 724 through 732 removed outlier: 3.713A pdb=" N LEU B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 777 through 789 removed outlier: 3.750A pdb=" N LEU B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 789 " --> pdb=" O LYS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 831 removed outlier: 3.787A pdb=" N ARG B 814 " --> pdb=" O ASN B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'B' and resid 861 through 879 removed outlier: 3.648A pdb=" N LEU B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 887 through 913 Processing helix chain 'B' and resid 915 through 947 removed outlier: 4.301A pdb=" N HIS B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 935 " --> pdb=" O ALA B 931 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 999 Processing helix chain 'B' and resid 1008 through 1023 removed outlier: 3.515A pdb=" N ALA B1016 " --> pdb=" O ARG B1012 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS B1022 " --> pdb=" O TRP B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1032 removed outlier: 3.785A pdb=" N LEU B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1059 removed outlier: 3.557A pdb=" N LEU B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 269 - end of helix removed outlier: 3.571A pdb=" N HIS D 291 " --> pdb=" O TYR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 319 Processing helix chain 'D' and resid 320 through 323 removed outlier: 4.453A pdb=" N SER D 323 " --> pdb=" O PRO D 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 330 through 339 removed outlier: 3.599A pdb=" N LEU D 334 " --> pdb=" O TYR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 376 removed outlier: 3.674A pdb=" N THR D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 394 through 419 removed outlier: 3.634A pdb=" N PHE D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Proline residue: D 413 - end of helix Processing helix chain 'D' and resid 424 through 430 Processing helix chain 'D' and resid 443 through 469 removed outlier: 3.548A pdb=" N GLU D 447 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 removed outlier: 4.681A pdb=" N ASN D 489 " --> pdb=" O PRO D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 548 Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.742A pdb=" N PHE D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 582 removed outlier: 3.547A pdb=" N LYS D 582 " --> pdb=" O THR D 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 579 through 582' Processing helix chain 'D' and resid 606 through 612 removed outlier: 3.525A pdb=" N PHE D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 619 Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 714 through 719 Processing helix chain 'D' and resid 724 through 732 removed outlier: 3.731A pdb=" N LEU D 732 " --> pdb=" O ILE D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 777 through 789 removed outlier: 3.746A pdb=" N LEU D 781 " --> pdb=" O THR D 777 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS D 789 " --> pdb=" O LYS D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 831 removed outlier: 3.807A pdb=" N ARG D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 858 Processing helix chain 'D' and resid 861 through 879 removed outlier: 3.526A pdb=" N LEU D 865 " --> pdb=" O THR D 861 " (cutoff:3.500A) Proline residue: D 872 - end of helix Processing helix chain 'D' and resid 887 through 913 Processing helix chain 'D' and resid 915 through 947 removed outlier: 4.378A pdb=" N HIS D 934 " --> pdb=" O GLY D 930 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU D 935 " --> pdb=" O ALA D 931 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE D 936 " --> pdb=" O SER D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 999 Processing helix chain 'D' and resid 1008 through 1023 Processing helix chain 'D' and resid 1023 through 1032 removed outlier: 3.831A pdb=" N LEU D1027 " --> pdb=" O LEU D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1059 removed outlier: 3.643A pdb=" N LEU D1042 " --> pdb=" O PRO D1038 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 499 removed outlier: 7.652A pdb=" N VAL A 384 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N VAL A 518 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS A 386 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL A 520 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 388 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 350 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR A 387 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 352 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N SER A 389 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 354 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP A 351 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 556 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N PHE A 353 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS A 585 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 794 " --> pdb=" O CYS A 585 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL A 587 " --> pdb=" O VAL A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 561 through 562 removed outlier: 3.935A pdb=" N ARG A 592 " --> pdb=" O PHE A 803 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 261 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 499 removed outlier: 7.660A pdb=" N VAL B 384 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL B 518 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 386 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 520 " --> pdb=" O CYS B 386 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL B 388 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 350 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR B 387 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 352 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER B 389 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 354 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP B 351 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 585 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG B 792 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR B 586 " --> pdb=" O ARG B 792 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 561 through 562 removed outlier: 3.902A pdb=" N ARG B 592 " --> pdb=" O PHE B 803 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 257 through 261 Processing sheet with id=AA8, first strand: chain 'D' and resid 496 through 499 removed outlier: 7.630A pdb=" N VAL D 384 " --> pdb=" O ARG D 516 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N VAL D 518 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS D 386 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL D 520 " --> pdb=" O CYS D 386 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL D 388 " --> pdb=" O VAL D 520 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 350 " --> pdb=" O ALA D 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR D 387 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL D 352 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER D 389 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL D 354 " --> pdb=" O SER D 389 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP D 351 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS D 585 " --> pdb=" O ARG D 633 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL D 794 " --> pdb=" O CYS D 585 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL D 587 " --> pdb=" O VAL D 794 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 561 through 562 removed outlier: 3.921A pdb=" N ARG D 592 " --> pdb=" O PHE D 803 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2658 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: 5.36 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5419 1.35 - 1.46: 4538 1.46 - 1.58: 7856 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 17948 Sorted by residual: bond pdb=" CG1 ILE A 280 " pdb=" CD1 ILE A 280 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 bond pdb=" CB LYS B 740 " pdb=" CG LYS B 740 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CG LEU B 938 " pdb=" CD1 LEU B 938 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" CG LYS A 740 " pdb=" CD LYS A 740 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CB LYS A 740 " pdb=" CG LYS A 740 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.54e-01 ... (remaining 17943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 24189 2.33 - 4.66: 171 4.66 - 6.99: 27 6.99 - 9.32: 5 9.32 - 11.65: 3 Bond angle restraints: 24395 Sorted by residual: angle pdb=" CA LEU B 907 " pdb=" CB LEU B 907 " pdb=" CG LEU B 907 " ideal model delta sigma weight residual 116.30 127.95 -11.65 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CA LEU A 907 " pdb=" CB LEU A 907 " pdb=" CG LEU A 907 " ideal model delta sigma weight residual 116.30 127.74 -11.44 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CB LYS A 740 " pdb=" CG LYS A 740 " pdb=" CD LYS A 740 " ideal model delta sigma weight residual 111.30 118.77 -7.47 2.30e+00 1.89e-01 1.06e+01 angle pdb=" CB LYS B 740 " pdb=" CG LYS B 740 " pdb=" CD LYS B 740 " ideal model delta sigma weight residual 111.30 118.74 -7.44 2.30e+00 1.89e-01 1.05e+01 angle pdb=" CA LEU D 907 " pdb=" CB LEU D 907 " pdb=" CG LEU D 907 " ideal model delta sigma weight residual 116.30 127.21 -10.91 3.50e+00 8.16e-02 9.71e+00 ... (remaining 24390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9355 17.96 - 35.92: 957 35.92 - 53.88: 212 53.88 - 71.84: 47 71.84 - 89.80: 6 Dihedral angle restraints: 10577 sinusoidal: 4296 harmonic: 6281 Sorted by residual: dihedral pdb=" CB GLU A 827 " pdb=" CG GLU A 827 " pdb=" CD GLU A 827 " pdb=" OE1 GLU A 827 " ideal model delta sinusoidal sigma weight residual 0.00 89.80 -89.80 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 333 " pdb=" CD ARG A 333 " pdb=" NE ARG A 333 " pdb=" CZ ARG A 333 " ideal model delta sinusoidal sigma weight residual -180.00 -135.20 -44.80 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASP B 349 " pdb=" CB ASP B 349 " pdb=" CG ASP B 349 " pdb=" OD1 ASP B 349 " ideal model delta sinusoidal sigma weight residual -30.00 -85.82 55.82 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 10574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2124 0.048 - 0.096: 461 0.096 - 0.144: 94 0.144 - 0.192: 5 0.192 - 0.240: 2 Chirality restraints: 2686 Sorted by residual: chirality pdb=" CB ILE D 280 " pdb=" CA ILE D 280 " pdb=" CG1 ILE D 280 " pdb=" CG2 ILE D 280 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU D 907 " pdb=" CB LEU D 907 " pdb=" CD1 LEU D 907 " pdb=" CD2 LEU D 907 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LEU D 907 " pdb=" N LEU D 907 " pdb=" C LEU D 907 " pdb=" CB LEU D 907 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 2683 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 978 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 979 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 979 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 979 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 257 " -0.009 2.00e-02 2.50e+03 8.71e-03 1.90e+00 pdb=" CG TRP A 257 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 257 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 257 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 257 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 257 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 257 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 257 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 257 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 257 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 978 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO D 979 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 979 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 979 " -0.019 5.00e-02 4.00e+02 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 375 2.71 - 3.26: 17087 3.26 - 3.81: 28556 3.81 - 4.35: 35239 4.35 - 4.90: 59822 Nonbonded interactions: 141079 Sorted by model distance: nonbonded pdb=" OD1 ASN D 606 " pdb=" O6 BGC F 2 " model vdw 2.166 3.040 nonbonded pdb=" OE2 GLU B 456 " pdb=" OH TYR D 435 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLU B 426 " pdb=" OH TYR B 455 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU A 456 " pdb=" OH TYR B 435 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR A 435 " pdb=" OE2 GLU D 456 " model vdw 2.230 3.040 ... (remaining 141074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 249 through 853 or resid 855 through 864 or (resid 865 and \ (name N or name CA or name C or name O or name CB or name CG or name CD2)) or r \ esid 866 through 1059)) selection = (chain 'B' and (resid 249 through 864 or (resid 865 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD2)) or resid 866 through 1059)) selection = (chain 'D' and (resid 249 through 853 or resid 855 through 1059)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 38.670 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.002 0.048 17954 Z= 0.102 Angle : 0.500 11.646 24413 Z= 0.258 Chirality : 0.040 0.240 2686 Planarity : 0.004 0.035 3042 Dihedral : 15.046 89.805 6547 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.45 % Allowed : 13.82 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 2151 helix: 2.11 (0.16), residues: 1166 sheet: 1.58 (0.47), residues: 132 loop : -0.53 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 257 HIS 0.004 0.001 HIS B 917 PHE 0.009 0.001 PHE D 925 TYR 0.014 0.001 TYR D 270 ARG 0.009 0.000 ARG D 820 Details of bonding type rmsd link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 0.88019 ( 9) hydrogen bonds : bond 0.11516 ( 898) hydrogen bonds : angle 5.13382 ( 2658) glycosidic custom : bond 0.00191 ( 3) glycosidic custom : angle 0.75257 ( 9) covalent geometry : bond 0.00221 (17948) covalent geometry : angle 0.49922 (24395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TYR cc_start: 0.7564 (t80) cc_final: 0.7263 (t80) REVERT: A 840 TYR cc_start: 0.6787 (m-80) cc_final: 0.6498 (m-80) REVERT: A 922 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8055 (t0) REVERT: B 277 ARG cc_start: 0.7961 (ttt180) cc_final: 0.7531 (ttt-90) REVERT: B 506 VAL cc_start: 0.6366 (OUTLIER) cc_final: 0.6164 (p) REVERT: B 617 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 820 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.7926 (ttp80) REVERT: B 922 ASN cc_start: 0.8733 (t0) cc_final: 0.8353 (t0) REVERT: B 1018 TRP cc_start: 0.7806 (t60) cc_final: 0.7562 (t60) REVERT: D 275 VAL cc_start: 0.8183 (t) cc_final: 0.7851 (t) REVERT: D 491 ARG cc_start: 0.8528 (mtt90) cc_final: 0.8302 (ptp90) REVERT: D 528 TYR cc_start: 0.7716 (m-80) cc_final: 0.7401 (m-80) REVERT: D 895 MET cc_start: 0.6647 (mmp) cc_final: 0.6434 (mmp) outliers start: 27 outliers final: 15 residues processed: 294 average time/residue: 1.1052 time to fit residues: 373.7806 Evaluate side-chains 278 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 922 ASN Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 851 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 196 optimal weight: 0.0870 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 714 GLN B 817 GLN B 924 GLN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114509 restraints weight = 20821.290| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.32 r_work: 0.3192 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17954 Z= 0.127 Angle : 0.499 9.264 24413 Z= 0.254 Chirality : 0.042 0.177 2686 Planarity : 0.004 0.036 3042 Dihedral : 4.671 58.292 2506 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.36 % Allowed : 15.96 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.19), residues: 2151 helix: 2.19 (0.16), residues: 1174 sheet: 1.73 (0.47), residues: 130 loop : -0.66 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 257 HIS 0.003 0.001 HIS A 789 PHE 0.011 0.001 PHE B 637 TYR 0.016 0.001 TYR D 858 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd link_BETA1-4 : bond 0.00384 ( 3) link_BETA1-4 : angle 1.16883 ( 9) hydrogen bonds : bond 0.03880 ( 898) hydrogen bonds : angle 4.05923 ( 2658) glycosidic custom : bond 0.00133 ( 3) glycosidic custom : angle 0.86407 ( 9) covalent geometry : bond 0.00297 (17948) covalent geometry : angle 0.49813 (24395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 TRP cc_start: 0.7167 (p-90) cc_final: 0.6904 (p-90) REVERT: A 273 ILE cc_start: 0.8033 (tp) cc_final: 0.7774 (pp) REVERT: A 307 GLU cc_start: 0.6383 (mp0) cc_final: 0.6082 (mp0) REVERT: A 409 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8314 (mtt90) REVERT: A 426 GLU cc_start: 0.8563 (tp30) cc_final: 0.7741 (tp30) REVERT: A 840 TYR cc_start: 0.6723 (m-80) cc_final: 0.6223 (m-80) REVERT: B 506 VAL cc_start: 0.6597 (OUTLIER) cc_final: 0.6390 (p) REVERT: B 820 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7382 (ttp80) REVERT: B 880 LYS cc_start: 0.7089 (mmtm) cc_final: 0.6819 (mmmt) REVERT: B 936 PHE cc_start: 0.7438 (m-80) cc_final: 0.7146 (m-80) REVERT: D 426 GLU cc_start: 0.8496 (tp30) cc_final: 0.8249 (tp30) REVERT: D 491 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7184 (ptp90) REVERT: D 840 TYR cc_start: 0.6663 (m-80) cc_final: 0.6231 (m-80) REVERT: D 921 ARG cc_start: 0.8239 (mmt180) cc_final: 0.7881 (mmm-85) REVERT: D 938 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6754 (mp) outliers start: 44 outliers final: 13 residues processed: 300 average time/residue: 1.0148 time to fit residues: 350.2479 Evaluate side-chains 270 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 36 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN B 268 ASN B 917 HIS B 924 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109247 restraints weight = 20624.785| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.25 r_work: 0.3160 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17954 Z= 0.137 Angle : 0.503 11.926 24413 Z= 0.253 Chirality : 0.041 0.152 2686 Planarity : 0.004 0.036 3042 Dihedral : 4.060 52.443 2487 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.11 % Allowed : 16.76 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2151 helix: 2.12 (0.15), residues: 1179 sheet: 1.58 (0.48), residues: 131 loop : -0.69 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 257 HIS 0.004 0.001 HIS B 789 PHE 0.010 0.001 PHE D 925 TYR 0.016 0.001 TYR D 858 ARG 0.006 0.000 ARG B 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00324 ( 3) link_BETA1-4 : angle 1.01341 ( 9) hydrogen bonds : bond 0.03971 ( 898) hydrogen bonds : angle 3.97619 ( 2658) glycosidic custom : bond 0.00176 ( 3) glycosidic custom : angle 0.78521 ( 9) covalent geometry : bond 0.00331 (17948) covalent geometry : angle 0.50284 (24395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.6560 (mp0) cc_final: 0.6300 (mp0) REVERT: A 426 GLU cc_start: 0.8630 (tp30) cc_final: 0.7824 (tp30) REVERT: A 840 TYR cc_start: 0.6672 (m-80) cc_final: 0.6213 (m-80) REVERT: A 936 PHE cc_start: 0.7773 (m-80) cc_final: 0.7557 (m-80) REVERT: B 259 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7642 (mppt) REVERT: B 307 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: B 317 ASP cc_start: 0.8062 (t0) cc_final: 0.6987 (m-30) REVERT: B 335 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8414 (p) REVERT: B 491 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7533 (ptp-110) REVERT: B 528 TYR cc_start: 0.7673 (m-80) cc_final: 0.7032 (m-80) REVERT: B 820 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7443 (ttp80) REVERT: B 880 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6950 (mmmt) REVERT: B 921 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7215 (ttm110) REVERT: B 1020 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7161 (tp) REVERT: D 360 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7145 (mpm) REVERT: D 426 GLU cc_start: 0.8579 (tp30) cc_final: 0.8370 (tp30) REVERT: D 528 TYR cc_start: 0.7955 (m-80) cc_final: 0.7621 (m-80) REVERT: D 749 LYS cc_start: 0.7536 (tptp) cc_final: 0.6968 (mtpp) REVERT: D 808 PRO cc_start: 0.7766 (Cg_exo) cc_final: 0.7549 (Cg_endo) REVERT: D 840 TYR cc_start: 0.6635 (m-80) cc_final: 0.6227 (m-80) REVERT: D 860 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6300 (tp) REVERT: D 906 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6531 (mp) REVERT: D 936 PHE cc_start: 0.7832 (m-80) cc_final: 0.7568 (m-80) REVERT: D 938 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6885 (mp) outliers start: 58 outliers final: 26 residues processed: 310 average time/residue: 1.0104 time to fit residues: 360.1768 Evaluate side-chains 291 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1020 ILE Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 857 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110999 restraints weight = 20725.040| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.26 r_work: 0.3136 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17954 Z= 0.146 Angle : 0.503 8.038 24413 Z= 0.255 Chirality : 0.042 0.153 2686 Planarity : 0.004 0.036 3042 Dihedral : 4.051 54.527 2485 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.86 % Allowed : 17.41 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2151 helix: 2.25 (0.15), residues: 1152 sheet: 1.62 (0.49), residues: 131 loop : -0.81 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 919 HIS 0.004 0.001 HIS D 291 PHE 0.017 0.001 PHE B 637 TYR 0.016 0.001 TYR D 858 ARG 0.007 0.000 ARG A 820 Details of bonding type rmsd link_BETA1-4 : bond 0.00272 ( 3) link_BETA1-4 : angle 1.04633 ( 9) hydrogen bonds : bond 0.04021 ( 898) hydrogen bonds : angle 3.94206 ( 2658) glycosidic custom : bond 0.00194 ( 3) glycosidic custom : angle 0.80719 ( 9) covalent geometry : bond 0.00354 (17948) covalent geometry : angle 0.50232 (24395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 272 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7959 (t0) cc_final: 0.7046 (m-30) REVERT: A 920 TRP cc_start: 0.7356 (t-100) cc_final: 0.7110 (t-100) REVERT: A 933 SER cc_start: 0.8628 (m) cc_final: 0.8168 (p) REVERT: A 936 PHE cc_start: 0.7854 (m-80) cc_final: 0.7584 (m-80) REVERT: B 259 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7650 (mppt) REVERT: B 317 ASP cc_start: 0.8089 (t0) cc_final: 0.7047 (m-30) REVERT: B 335 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8374 (p) REVERT: B 360 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7889 (mpp) REVERT: B 426 GLU cc_start: 0.8648 (tp30) cc_final: 0.8029 (tp30) REVERT: B 820 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7447 (ttp80) REVERT: B 921 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7219 (ttm110) REVERT: D 349 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: D 426 GLU cc_start: 0.8619 (tp30) cc_final: 0.8356 (tp30) REVERT: D 528 TYR cc_start: 0.7956 (m-80) cc_final: 0.7588 (m-80) REVERT: D 740 LYS cc_start: 0.8093 (mppt) cc_final: 0.7817 (mmmt) REVERT: D 792 ARG cc_start: 0.7536 (mpt180) cc_final: 0.7107 (mpp-170) REVERT: D 808 PRO cc_start: 0.7839 (Cg_exo) cc_final: 0.7621 (Cg_endo) REVERT: D 860 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6426 (mt) REVERT: D 906 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6524 (mp) REVERT: D 938 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6992 (mp) outliers start: 72 outliers final: 37 residues processed: 313 average time/residue: 1.0833 time to fit residues: 389.2179 Evaluate side-chains 301 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 810 ASN Chi-restraints excluded: chain B residue 921 ARG Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 857 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 0.0030 chunk 156 optimal weight: 1.9990 chunk 185 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 0.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 HIS A 922 ASN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 924 GLN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D1022 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.106181 restraints weight = 20879.082| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3115 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17954 Z= 0.153 Angle : 0.528 15.653 24413 Z= 0.264 Chirality : 0.042 0.194 2686 Planarity : 0.004 0.041 3042 Dihedral : 4.083 55.121 2485 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.18 % Allowed : 17.41 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.18), residues: 2151 helix: 2.16 (0.15), residues: 1159 sheet: 1.63 (0.49), residues: 131 loop : -0.84 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 911 HIS 0.005 0.001 HIS D 291 PHE 0.011 0.001 PHE D 925 TYR 0.016 0.001 TYR B 552 ARG 0.007 0.001 ARG D1012 Details of bonding type rmsd link_BETA1-4 : bond 0.00331 ( 3) link_BETA1-4 : angle 1.05969 ( 9) hydrogen bonds : bond 0.04138 ( 898) hydrogen bonds : angle 3.94879 ( 2658) glycosidic custom : bond 0.00181 ( 3) glycosidic custom : angle 0.83632 ( 9) covalent geometry : bond 0.00376 (17948) covalent geometry : angle 0.52707 (24395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 276 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.8019 (t0) cc_final: 0.7125 (m-30) REVERT: A 572 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8433 (mpp) REVERT: A 840 TYR cc_start: 0.6616 (m-80) cc_final: 0.6343 (m-80) REVERT: A 921 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7249 (ttm110) REVERT: A 933 SER cc_start: 0.8635 (m) cc_final: 0.8187 (p) REVERT: A 936 PHE cc_start: 0.7823 (m-80) cc_final: 0.7604 (m-80) REVERT: B 256 LEU cc_start: 0.7152 (mt) cc_final: 0.6845 (mp) REVERT: B 259 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7666 (mppt) REVERT: B 307 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: B 317 ASP cc_start: 0.8082 (t0) cc_final: 0.7005 (m-30) REVERT: B 360 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7892 (mpp) REVERT: B 426 GLU cc_start: 0.8658 (tp30) cc_final: 0.8018 (tp30) REVERT: B 427 TRP cc_start: 0.9013 (m-90) cc_final: 0.8783 (m-90) REVERT: B 637 PHE cc_start: 0.8500 (m-10) cc_final: 0.8277 (m-10) REVERT: B 820 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7415 (ttp80) REVERT: B 880 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7592 (mppt) REVERT: B 907 LEU cc_start: 0.7533 (mt) cc_final: 0.7324 (mp) REVERT: B 935 LEU cc_start: 0.7808 (mt) cc_final: 0.7450 (tt) REVERT: D 307 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6336 (mp0) REVERT: D 349 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: D 426 GLU cc_start: 0.8617 (tp30) cc_final: 0.8340 (tp30) REVERT: D 528 TYR cc_start: 0.7968 (m-80) cc_final: 0.7672 (m-80) REVERT: D 624 ILE cc_start: 0.8747 (mt) cc_final: 0.8474 (mp) REVERT: D 749 LYS cc_start: 0.7602 (tptp) cc_final: 0.7036 (mtpp) REVERT: D 792 ARG cc_start: 0.7549 (mpt180) cc_final: 0.7133 (mpp-170) REVERT: D 808 PRO cc_start: 0.7913 (Cg_exo) cc_final: 0.7704 (Cg_endo) REVERT: D 860 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6488 (mt) REVERT: D 906 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6819 (mp) REVERT: D 938 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6982 (mp) outliers start: 78 outliers final: 40 residues processed: 320 average time/residue: 1.0301 time to fit residues: 379.7162 Evaluate side-chains 310 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 857 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 156 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 83 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN B 606 ASN B 922 ASN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108836 restraints weight = 20980.362| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.27 r_work: 0.3117 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17954 Z= 0.162 Angle : 0.531 9.410 24413 Z= 0.267 Chirality : 0.042 0.201 2686 Planarity : 0.004 0.040 3042 Dihedral : 3.973 43.531 2483 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.07 % Allowed : 17.73 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 2151 helix: 2.15 (0.15), residues: 1155 sheet: 1.57 (0.49), residues: 131 loop : -0.86 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 911 HIS 0.005 0.001 HIS D 291 PHE 0.012 0.001 PHE D 925 TYR 0.016 0.001 TYR D 858 ARG 0.019 0.001 ARG B 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00375 ( 3) link_BETA1-4 : angle 1.07453 ( 9) hydrogen bonds : bond 0.04213 ( 898) hydrogen bonds : angle 3.94712 ( 2658) glycosidic custom : bond 0.00181 ( 3) glycosidic custom : angle 0.86160 ( 9) covalent geometry : bond 0.00398 (17948) covalent geometry : angle 0.53087 (24395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 272 time to evaluate : 2.717 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7921 (t0) cc_final: 0.7012 (m-30) REVERT: A 427 TRP cc_start: 0.9120 (m-90) cc_final: 0.8901 (m-90) REVERT: A 433 VAL cc_start: 0.7665 (t) cc_final: 0.7442 (m) REVERT: A 572 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8401 (mpp) REVERT: A 808 PRO cc_start: 0.7869 (Cg_exo) cc_final: 0.7568 (Cg_endo) REVERT: A 921 ARG cc_start: 0.7383 (ttm110) cc_final: 0.7181 (ttm110) REVERT: A 933 SER cc_start: 0.8617 (m) cc_final: 0.8166 (p) REVERT: A 936 PHE cc_start: 0.7847 (m-80) cc_final: 0.7273 (m-80) REVERT: B 256 LEU cc_start: 0.7168 (mt) cc_final: 0.6851 (mp) REVERT: B 259 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7661 (mppt) REVERT: B 307 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: B 317 ASP cc_start: 0.8085 (t0) cc_final: 0.7020 (m-30) REVERT: B 360 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7950 (mpp) REVERT: B 426 GLU cc_start: 0.8641 (tp30) cc_final: 0.8040 (tp30) REVERT: B 820 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7429 (ttp80) REVERT: D 307 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: D 349 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: D 528 TYR cc_start: 0.7953 (m-80) cc_final: 0.7689 (m-80) REVERT: D 611 ASP cc_start: 0.8034 (m-30) cc_final: 0.7013 (t0) REVERT: D 624 ILE cc_start: 0.8766 (mt) cc_final: 0.8496 (mp) REVERT: D 740 LYS cc_start: 0.8097 (mppt) cc_final: 0.7868 (mmmt) REVERT: D 792 ARG cc_start: 0.7542 (mpt180) cc_final: 0.7132 (mpp-170) REVERT: D 860 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6292 (mt) REVERT: D 906 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6742 (mp) REVERT: D 938 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6918 (mp) outliers start: 76 outliers final: 42 residues processed: 318 average time/residue: 1.1661 time to fit residues: 431.9613 Evaluate side-chains 309 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 857 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 196 optimal weight: 0.0570 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN A 940 GLN B 606 ASN B 924 GLN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107768 restraints weight = 20901.114| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.32 r_work: 0.3094 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17954 Z= 0.166 Angle : 0.539 13.671 24413 Z= 0.270 Chirality : 0.042 0.155 2686 Planarity : 0.004 0.040 3042 Dihedral : 3.996 41.937 2483 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.07 % Allowed : 18.26 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2151 helix: 2.09 (0.15), residues: 1156 sheet: 1.55 (0.49), residues: 131 loop : -0.91 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 919 HIS 0.012 0.001 HIS D 291 PHE 0.012 0.001 PHE D 925 TYR 0.015 0.001 TYR D 858 ARG 0.010 0.001 ARG B 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00303 ( 3) link_BETA1-4 : angle 1.12853 ( 9) hydrogen bonds : bond 0.04271 ( 898) hydrogen bonds : angle 3.97406 ( 2658) glycosidic custom : bond 0.00214 ( 3) glycosidic custom : angle 0.87020 ( 9) covalent geometry : bond 0.00410 (17948) covalent geometry : angle 0.53826 (24395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 266 time to evaluate : 2.337 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7863 (t0) cc_final: 0.6966 (m-30) REVERT: A 427 TRP cc_start: 0.9125 (m-90) cc_final: 0.8885 (m-90) REVERT: A 433 VAL cc_start: 0.7674 (t) cc_final: 0.7433 (m) REVERT: A 572 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8316 (mpp) REVERT: A 596 ILE cc_start: 0.5280 (OUTLIER) cc_final: 0.4938 (pp) REVERT: A 808 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7646 (Cg_endo) REVERT: A 933 SER cc_start: 0.8537 (m) cc_final: 0.8088 (p) REVERT: A 936 PHE cc_start: 0.7658 (m-80) cc_final: 0.7330 (m-80) REVERT: B 256 LEU cc_start: 0.6924 (mt) cc_final: 0.6616 (mp) REVERT: B 259 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7617 (mppt) REVERT: B 307 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5938 (mp0) REVERT: B 317 ASP cc_start: 0.8032 (t0) cc_final: 0.6964 (m-30) REVERT: B 360 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7882 (mpp) REVERT: B 426 GLU cc_start: 0.8598 (tp30) cc_final: 0.7953 (tp30) REVERT: B 596 ILE cc_start: 0.5638 (OUTLIER) cc_final: 0.5243 (pp) REVERT: B 637 PHE cc_start: 0.8514 (m-10) cc_final: 0.8272 (m-10) REVERT: B 820 ARG cc_start: 0.7868 (ttp-110) cc_final: 0.7410 (ttp80) REVERT: D 259 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7588 (mppt) REVERT: D 307 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: D 349 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: D 433 VAL cc_start: 0.7613 (t) cc_final: 0.7341 (m) REVERT: D 437 LYS cc_start: 0.8663 (ttmt) cc_final: 0.7962 (tttp) REVERT: D 528 TYR cc_start: 0.7909 (m-80) cc_final: 0.7670 (m-80) REVERT: D 624 ILE cc_start: 0.8723 (mt) cc_final: 0.8433 (mp) REVERT: D 792 ARG cc_start: 0.7511 (mpt180) cc_final: 0.7099 (mpp-170) REVERT: D 860 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6197 (mt) REVERT: D 906 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6674 (mp) REVERT: D 938 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6865 (mp) outliers start: 76 outliers final: 45 residues processed: 315 average time/residue: 1.1023 time to fit residues: 402.4875 Evaluate side-chains 316 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 857 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 7 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 204 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN B 606 ASN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS ** D 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108293 restraints weight = 20840.830| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.31 r_work: 0.3115 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17954 Z= 0.149 Angle : 0.544 14.051 24413 Z= 0.270 Chirality : 0.042 0.154 2686 Planarity : 0.004 0.040 3042 Dihedral : 3.982 39.788 2483 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.45 % Allowed : 18.32 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.18), residues: 2151 helix: 2.11 (0.15), residues: 1156 sheet: 1.57 (0.50), residues: 131 loop : -0.91 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 911 HIS 0.005 0.001 HIS D 291 PHE 0.013 0.001 PHE D 284 TYR 0.015 0.001 TYR D 858 ARG 0.010 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00370 ( 3) link_BETA1-4 : angle 1.08484 ( 9) hydrogen bonds : bond 0.04154 ( 898) hydrogen bonds : angle 3.96312 ( 2658) glycosidic custom : bond 0.00195 ( 3) glycosidic custom : angle 0.82090 ( 9) covalent geometry : bond 0.00364 (17948) covalent geometry : angle 0.54335 (24395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 271 time to evaluate : 3.104 Fit side-chains revert: symmetry clash REVERT: A 317 ASP cc_start: 0.7976 (t0) cc_final: 0.7101 (m-30) REVERT: A 427 TRP cc_start: 0.9159 (m-90) cc_final: 0.8938 (m-90) REVERT: A 433 VAL cc_start: 0.7680 (t) cc_final: 0.7448 (m) REVERT: A 572 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8446 (mpp) REVERT: A 596 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.5005 (pp) REVERT: A 808 PRO cc_start: 0.8006 (Cg_exo) cc_final: 0.7729 (Cg_endo) REVERT: A 933 SER cc_start: 0.8559 (m) cc_final: 0.8110 (p) REVERT: A 936 PHE cc_start: 0.7644 (m-80) cc_final: 0.7278 (m-80) REVERT: A 940 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6928 (mp10) REVERT: B 256 LEU cc_start: 0.6974 (mt) cc_final: 0.6663 (mp) REVERT: B 259 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7641 (mppt) REVERT: B 307 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6017 (mp0) REVERT: B 317 ASP cc_start: 0.8058 (t0) cc_final: 0.7000 (m-30) REVERT: B 360 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7843 (mpp) REVERT: B 426 GLU cc_start: 0.8596 (tp30) cc_final: 0.7908 (tp30) REVERT: B 596 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.5229 (pp) REVERT: B 637 PHE cc_start: 0.8528 (m-10) cc_final: 0.8287 (m-10) REVERT: B 792 ARG cc_start: 0.7585 (mpt180) cc_final: 0.7209 (mpp-170) REVERT: B 808 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7913 (Cg_endo) REVERT: B 820 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7422 (ttp80) REVERT: B 924 GLN cc_start: 0.6408 (mt0) cc_final: 0.5934 (tt0) REVERT: D 257 TRP cc_start: 0.7056 (p-90) cc_final: 0.6695 (p-90) REVERT: D 259 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7570 (mppt) REVERT: D 307 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6279 (mp0) REVERT: D 349 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: D 433 VAL cc_start: 0.7611 (t) cc_final: 0.7371 (m) REVERT: D 437 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8031 (tttp) REVERT: D 528 TYR cc_start: 0.7930 (m-80) cc_final: 0.7695 (m-80) REVERT: D 611 ASP cc_start: 0.8053 (m-30) cc_final: 0.6993 (t0) REVERT: D 624 ILE cc_start: 0.8755 (mt) cc_final: 0.8486 (mp) REVERT: D 740 LYS cc_start: 0.8051 (mppt) cc_final: 0.7785 (mmmt) REVERT: D 792 ARG cc_start: 0.7663 (mpt180) cc_final: 0.7256 (mpp-170) REVERT: D 860 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6220 (mt) REVERT: D 938 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6889 (mp) outliers start: 83 outliers final: 48 residues processed: 322 average time/residue: 1.2393 time to fit residues: 465.6109 Evaluate side-chains 317 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 809 ILE Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 857 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 113 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 155 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 606 ASN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.164982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109200 restraints weight = 20690.155| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.25 r_work: 0.3115 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17954 Z= 0.137 Angle : 0.544 12.631 24413 Z= 0.270 Chirality : 0.042 0.158 2686 Planarity : 0.004 0.073 3042 Dihedral : 3.953 38.030 2483 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.75 % Allowed : 19.12 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 2151 helix: 2.11 (0.15), residues: 1160 sheet: 1.59 (0.50), residues: 131 loop : -0.93 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 911 HIS 0.006 0.001 HIS D 291 PHE 0.013 0.001 PHE D 284 TYR 0.015 0.001 TYR D 858 ARG 0.016 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00384 ( 3) link_BETA1-4 : angle 1.09017 ( 9) hydrogen bonds : bond 0.04036 ( 898) hydrogen bonds : angle 3.94157 ( 2658) glycosidic custom : bond 0.00172 ( 3) glycosidic custom : angle 0.79481 ( 9) covalent geometry : bond 0.00333 (17948) covalent geometry : angle 0.54318 (24395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 267 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.7959 (mppt) cc_final: 0.7668 (mppt) REVERT: A 317 ASP cc_start: 0.7998 (t0) cc_final: 0.7133 (m-30) REVERT: A 426 GLU cc_start: 0.8702 (tp30) cc_final: 0.8492 (tp30) REVERT: A 427 TRP cc_start: 0.9090 (m-90) cc_final: 0.8885 (m-90) REVERT: A 433 VAL cc_start: 0.7694 (t) cc_final: 0.7477 (m) REVERT: A 572 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8304 (mpp) REVERT: A 596 ILE cc_start: 0.5420 (OUTLIER) cc_final: 0.5033 (pp) REVERT: A 933 SER cc_start: 0.8594 (m) cc_final: 0.8152 (p) REVERT: A 936 PHE cc_start: 0.7723 (m-80) cc_final: 0.7427 (m-80) REVERT: B 256 LEU cc_start: 0.7018 (mt) cc_final: 0.6709 (mp) REVERT: B 259 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7667 (mppt) REVERT: B 307 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: B 317 ASP cc_start: 0.8008 (t0) cc_final: 0.6927 (m-30) REVERT: B 360 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7875 (mpp) REVERT: B 426 GLU cc_start: 0.8623 (tp30) cc_final: 0.8009 (tp30) REVERT: B 427 TRP cc_start: 0.9095 (m-90) cc_final: 0.8820 (m-90) REVERT: B 596 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5250 (pp) REVERT: B 740 LYS cc_start: 0.7775 (mppt) cc_final: 0.7568 (mmmt) REVERT: B 820 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.7444 (ttp80) REVERT: B 924 GLN cc_start: 0.6547 (mt0) cc_final: 0.6100 (tt0) REVERT: D 257 TRP cc_start: 0.7057 (p-90) cc_final: 0.6683 (p-90) REVERT: D 259 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7625 (mppt) REVERT: D 307 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: D 349 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: D 433 VAL cc_start: 0.7636 (t) cc_final: 0.7383 (m) REVERT: D 437 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8188 (tttm) REVERT: D 528 TYR cc_start: 0.7960 (m-80) cc_final: 0.7734 (m-80) REVERT: D 611 ASP cc_start: 0.8063 (m-30) cc_final: 0.7005 (t0) REVERT: D 624 ILE cc_start: 0.8765 (mt) cc_final: 0.8504 (mp) REVERT: D 740 LYS cc_start: 0.8033 (mppt) cc_final: 0.7783 (mmmt) REVERT: D 792 ARG cc_start: 0.7671 (mpt180) cc_final: 0.7277 (mpp-170) REVERT: D 860 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6316 (mt) REVERT: D 938 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6945 (mp) outliers start: 70 outliers final: 51 residues processed: 314 average time/residue: 0.9307 time to fit residues: 338.0412 Evaluate side-chains 319 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 809 ILE Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 938 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 159 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 178 optimal weight: 0.5980 chunk 101 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN B 606 ASN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110095 restraints weight = 20888.153| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.27 r_work: 0.3135 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17954 Z= 0.130 Angle : 0.540 12.045 24413 Z= 0.268 Chirality : 0.042 0.201 2686 Planarity : 0.004 0.076 3042 Dihedral : 3.947 38.161 2483 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.54 % Allowed : 19.50 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 2151 helix: 2.13 (0.15), residues: 1156 sheet: 1.62 (0.49), residues: 131 loop : -0.93 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 911 HIS 0.005 0.001 HIS A 917 PHE 0.015 0.001 PHE D 284 TYR 0.016 0.001 TYR D 858 ARG 0.019 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00418 ( 3) link_BETA1-4 : angle 1.09596 ( 9) hydrogen bonds : bond 0.03957 ( 898) hydrogen bonds : angle 3.91337 ( 2658) glycosidic custom : bond 0.00114 ( 3) glycosidic custom : angle 0.77659 ( 9) covalent geometry : bond 0.00312 (17948) covalent geometry : angle 0.53986 (24395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4302 Ramachandran restraints generated. 2151 Oldfield, 0 Emsley, 2151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 260 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 LYS cc_start: 0.7977 (mppt) cc_final: 0.7693 (mppt) REVERT: A 317 ASP cc_start: 0.7987 (t0) cc_final: 0.7040 (m-30) REVERT: A 427 TRP cc_start: 0.9067 (m-90) cc_final: 0.8863 (m-90) REVERT: A 433 VAL cc_start: 0.7713 (t) cc_final: 0.7507 (m) REVERT: A 572 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8335 (mpp) REVERT: A 596 ILE cc_start: 0.5419 (OUTLIER) cc_final: 0.5037 (pp) REVERT: A 933 SER cc_start: 0.8574 (m) cc_final: 0.8133 (p) REVERT: A 936 PHE cc_start: 0.7654 (m-80) cc_final: 0.7247 (m-80) REVERT: A 940 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: B 256 LEU cc_start: 0.7020 (mt) cc_final: 0.6721 (mp) REVERT: B 307 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: B 317 ASP cc_start: 0.7897 (t0) cc_final: 0.6755 (m-30) REVERT: B 360 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7864 (mpp) REVERT: B 426 GLU cc_start: 0.8617 (tp30) cc_final: 0.7995 (tp30) REVERT: B 427 TRP cc_start: 0.9026 (m-90) cc_final: 0.8752 (m-90) REVERT: B 596 ILE cc_start: 0.5678 (OUTLIER) cc_final: 0.5268 (pp) REVERT: B 637 PHE cc_start: 0.8460 (m-10) cc_final: 0.8175 (m-10) REVERT: B 820 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7448 (ttp80) REVERT: B 924 GLN cc_start: 0.6539 (mt0) cc_final: 0.6132 (tt0) REVERT: D 257 TRP cc_start: 0.7073 (p-90) cc_final: 0.6719 (p-90) REVERT: D 259 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7628 (mppt) REVERT: D 307 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: D 433 VAL cc_start: 0.7635 (t) cc_final: 0.7389 (m) REVERT: D 437 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8149 (tttp) REVERT: D 528 TYR cc_start: 0.7951 (m-80) cc_final: 0.7729 (m-80) REVERT: D 611 ASP cc_start: 0.8053 (m-30) cc_final: 0.6984 (t0) REVERT: D 624 ILE cc_start: 0.8759 (mt) cc_final: 0.8513 (mp) REVERT: D 740 LYS cc_start: 0.8186 (mppt) cc_final: 0.7950 (mmmt) REVERT: D 792 ARG cc_start: 0.7671 (mpt180) cc_final: 0.7276 (mpp-170) REVERT: D 860 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6279 (mt) REVERT: D 906 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6539 (mp) REVERT: D 936 PHE cc_start: 0.7648 (m-80) cc_final: 0.6972 (m-80) REVERT: D 938 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6902 (mp) REVERT: D 940 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6235 (mp10) outliers start: 66 outliers final: 48 residues processed: 304 average time/residue: 1.0081 time to fit residues: 352.7609 Evaluate side-chains 311 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 360 MET Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 319 PHE Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 719 LYS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 809 ILE Chi-restraints excluded: chain D residue 851 SER Chi-restraints excluded: chain D residue 856 VAL Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 940 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 210 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 922 ASN B 268 ASN B 606 ASN ** B1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109015 restraints weight = 20825.482| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.27 r_work: 0.3119 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17954 Z= 0.160 Angle : 0.568 13.852 24413 Z= 0.280 Chirality : 0.043 0.158 2686 Planarity : 0.004 0.073 3042 Dihedral : 3.972 38.210 2483 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.70 % Allowed : 19.44 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.18), residues: 2151 helix: 2.03 (0.15), residues: 1160 sheet: 1.59 (0.50), residues: 131 loop : -0.95 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 919 HIS 0.008 0.001 HIS D 291 PHE 0.014 0.001 PHE D 284 TYR 0.016 0.001 TYR D 858 ARG 0.019 0.001 ARG A 921 Details of bonding type rmsd link_BETA1-4 : bond 0.00332 ( 3) link_BETA1-4 : angle 1.12654 ( 9) hydrogen bonds : bond 0.04167 ( 898) hydrogen bonds : angle 3.95477 ( 2658) glycosidic custom : bond 0.00178 ( 3) glycosidic custom : angle 0.83435 ( 9) covalent geometry : bond 0.00396 (17948) covalent geometry : angle 0.56722 (24395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14104.05 seconds wall clock time: 248 minutes 49.99 seconds (14929.99 seconds total)