Starting phenix.real_space_refine on Mon May 26 04:25:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xr8_22292/05_2025/6xr8_22292.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xr8_22292/05_2025/6xr8_22292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xr8_22292/05_2025/6xr8_22292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xr8_22292/05_2025/6xr8_22292.map" model { file = "/net/cci-nas-00/data/ceres_data/6xr8_22292/05_2025/6xr8_22292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xr8_22292/05_2025/6xr8_22292.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17511 2.51 5 N 4431 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 1.84s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27627 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "B" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "C" Number of atoms: 8666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8666 Classifications: {'peptide': 1107} Link IDs: {'PTRANS': 51, 'TRANS': 1055} Chain breaks: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "GA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "JA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "MA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "PA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "SA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "cA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "fA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "hA" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "kA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "oA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "qA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "sA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "vA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "yA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "1A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 18.75, per 1000 atoms: 0.68 Number of scatterers: 27627 At special positions: 0 Unit cell: (142.725, 143.55, 197.175, 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 120 16.00 O 5565 8.00 N 4431 7.00 C 17511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN n 3 " - " MAN n 4 " " MAN7A 3 " - " MAN7A 4 " " MANSA 3 " - " MANSA 4 " ALPHA1-4 " NAG 5 2 " - " MAN 5 3 " " NAG I 2 " - " MAN I 3 " " NAG Q 2 " - " MAN Q 3 " " NAG Y 2 " - " MAN Y 3 " " NAG b 2 " - " MAN b 3 " " NAG e 2 " - " MAN e 3 " " NAG h 2 " - " MAN h 3 " " NAG k 2 " - " MAN k 3 " " NAG n 2 " - " MAN n 3 " " NAG x 2 " - " MAN x 3 " " NAG1A 2 " - " MAN1A 3 " " NAG4A 2 " - " MAN4A 3 " " NAG7A 2 " - " MAN7A 3 " " NAGDA 2 " - " MANDA 3 " " NAGGA 2 " - " MANGA 3 " " NAGJA 2 " - " MANJA 3 " " NAGMA 2 " - " MANMA 3 " " NAGPA 2 " - " MANPA 3 " " NAGSA 2 " - " MANSA 3 " " NAGcA 2 " - " MANcA 3 " " NAGkA 2 " - " MANkA 3 " " NAGsA 2 " - " MANsA 3 " " NAGvA 2 " - " MANvA 3 " " NAGyA 2 " - " MANyA 3 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 9 1 " - " NAG 9 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG U 1 " - " NAG U 2 " " NAG W 1 " - " NAG W 2 " " NAG Y 1 " - " NAG Y 2 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG h 1 " - " NAG h 2 " " NAG k 1 " - " NAG k 2 " " NAG n 1 " - " NAG n 2 " " NAG x 1 " - " NAG x 2 " " NAG1A 1 " - " NAG1A 2 " " NAG4A 1 " - " NAG4A 2 " " NAG7A 1 " - " NAG7A 2 " " NAGBA 1 " - " NAGBA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGJA 1 " - " NAGJA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGSA 1 " - " NAGSA 2 " " NAGcA 1 " - " NAGcA 2 " " NAGfA 1 " - " NAGfA 2 " " NAGhA 1 " - " NAGhA 2 " " NAGkA 1 " - " NAGkA 2 " " NAGoA 1 " - " NAGoA 2 " " NAGqA 1 " - " NAGqA 2 " " NAGsA 1 " - " NAGsA 2 " " NAGvA 1 " - " NAGvA 2 " " NAGyA 1 " - " NAGyA 2 " BETA1-6 " NAG 2 1 " - " FUC 2 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 3 " " NAGhA 1 " - " FUChA 3 " NAG-ASN " NAG 0 1 " - " ASN B 17 " " NAG 2 1 " - " ASN B1074 " " NAG 5 1 " - " ASN B 122 " " NAG 9 1 " - " ASN B 331 " " NAG A1402 " - " ASN A 343 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 657 " " NAG A1405 " - " ASN A 709 " " NAG A1406 " - " ASN A 149 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 343 " " NAG B1403 " - " ASN B 603 " " NAG B1404 " - " ASN B 657 " " NAG B1405 " - " ASN B 709 " " NAG B1406 " - " ASN B 149 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 343 " " NAG C1403 " - " ASN C 603 " " NAG C1404 " - " ASN C 657 " " NAG C1405 " - " ASN C 709 " " NAG C1406 " - " ASN C 149 " " NAG C1407 " - " ASN C1158 " " NAG I 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 17 " " NAG N 1 " - " ASN A1074 " " NAG Q 1 " - " ASN A 122 " " NAG U 1 " - " ASN A 331 " " NAG W 1 " - " ASN A 165 " " NAG Y 1 " - " ASN A 234 " " NAG b 1 " - " ASN A 282 " " NAG e 1 " - " ASN A 616 " " NAG h 1 " - " ASN A 801 " " NAG k 1 " - " ASN A1098 " " NAG n 1 " - " ASN A1134 " " NAG x 1 " - " ASN B 717 " " NAG1A 1 " - " ASN C 801 " " NAG4A 1 " - " ASN C1098 " " NAG7A 1 " - " ASN C1134 " " NAGBA 1 " - " ASN B 165 " " NAGDA 1 " - " ASN B 234 " " NAGGA 1 " - " ASN B 282 " " NAGJA 1 " - " ASN B 616 " " NAGMA 1 " - " ASN B 801 " " NAGPA 1 " - " ASN B1098 " " NAGSA 1 " - " ASN B1134 " " NAGcA 1 " - " ASN C 717 " " NAGfA 1 " - " ASN C 17 " " NAGhA 1 " - " ASN C1074 " " NAGkA 1 " - " ASN C 122 " " NAGoA 1 " - " ASN C 331 " " NAGqA 1 " - " ASN C 165 " " NAGsA 1 " - " ASN C 234 " " NAGvA 1 " - " ASN C 282 " " NAGyA 1 " - " ASN C 616 " Time building additional restraints: 9.10 Conformation dependent library (CDL) restraints added in 3.6 seconds 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6216 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 56 sheets defined 27.2% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.585A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.259A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.223A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.082A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.564A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 841 removed outlier: 4.038A pdb=" N LEU A 841 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 removed outlier: 3.692A pdb=" N ALA A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.587A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.859A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.702A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.525A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.927A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.871A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.113A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.814A pdb=" N ALA B 846 " --> pdb=" O GLY B 842 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 842 through 848' Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.616A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.682A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.562A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.864A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.277A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.077A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.815A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.361A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.548A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 841 removed outlier: 4.027A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 848 removed outlier: 3.709A pdb=" N ALA C 846 " --> pdb=" O GLY C 842 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.617A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.597A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.792A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 3.850A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.226A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.226A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.591A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.083A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.436A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.250A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.525A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.477A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.883A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.883A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.939A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.690A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.903A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.467A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.841A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.270A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC2, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.991A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.991A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.583A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.012A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.908A pdb=" N PHE B 238 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 12.564A pdb=" N PHE B 135 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 13.089A pdb=" N THR B 240 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N ASN B 137 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N LEU B 242 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.495A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.856A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.907A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.683A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.835A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.614A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.884A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.335A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.338A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.268A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.268A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.663A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.717A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.995A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.295A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.510A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.868A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.875A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.745A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.881A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF8, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.893A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG2, first strand: chain 'C' and resid 1094 through 1097 1150 hydrogen bonds defined for protein. 3126 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: 13.10 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8575 1.34 - 1.46: 6894 1.46 - 1.58: 12606 1.58 - 1.70: 2 1.70 - 1.82: 150 Bond restraints: 28227 Sorted by residual: bond pdb=" C1 FUChA 3 " pdb=" C2 FUChA 3 " ideal model delta sigma weight residual 1.528 1.590 -0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 1.459 1.424 0.035 1.19e-02 7.06e+03 8.65e+00 bond pdb=" C1 FUC N 3 " pdb=" C2 FUC N 3 " ideal model delta sigma weight residual 1.528 1.585 -0.057 2.00e-02 2.50e+03 8.15e+00 bond pdb=" C5 MANPA 3 " pdb=" O5 MANPA 3 " ideal model delta sigma weight residual 1.418 1.472 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C1 NAG C1401 " pdb=" O5 NAG C1401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 28222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 36568 1.46 - 2.92: 1397 2.92 - 4.39: 327 4.39 - 5.85: 57 5.85 - 7.31: 39 Bond angle restraints: 38388 Sorted by residual: angle pdb=" N VAL A 62 " pdb=" CA VAL A 62 " pdb=" C VAL A 62 " ideal model delta sigma weight residual 108.23 101.58 6.65 1.53e+00 4.27e-01 1.89e+01 angle pdb=" N TRP A 258 " pdb=" CA TRP A 258 " pdb=" C TRP A 258 " ideal model delta sigma weight residual 108.19 113.32 -5.13 1.29e+00 6.01e-01 1.58e+01 angle pdb=" N TRP B 258 " pdb=" CA TRP B 258 " pdb=" C TRP B 258 " ideal model delta sigma weight residual 108.19 113.30 -5.11 1.29e+00 6.01e-01 1.57e+01 angle pdb=" N TRP C 258 " pdb=" CA TRP C 258 " pdb=" C TRP C 258 " ideal model delta sigma weight residual 108.19 113.30 -5.11 1.29e+00 6.01e-01 1.57e+01 angle pdb=" N THR A 602 " pdb=" CA THR A 602 " pdb=" C THR A 602 " ideal model delta sigma weight residual 111.28 107.60 3.68 1.09e+00 8.42e-01 1.14e+01 ... (remaining 38383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 17499 24.60 - 49.19: 625 49.19 - 73.79: 130 73.79 - 98.38: 87 98.38 - 122.98: 40 Dihedral angle restraints: 18381 sinusoidal: 8712 harmonic: 9669 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -157.93 71.93 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -157.19 71.19 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -150.93 64.93 1 1.00e+01 1.00e-02 5.53e+01 ... (remaining 18378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 4682 0.338 - 0.676: 10 0.676 - 1.013: 0 1.013 - 1.351: 1 1.351 - 1.689: 1 Chirality restraints: 4694 Sorted by residual: chirality pdb=" C1 NAG A1407 " pdb=" ND2 ASN A1158 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.60 2.00e-01 2.50e+01 8.87e+00 ... (remaining 4691 not shown) Planarity restraints: 4844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.275 2.00e-02 2.50e+03 4.08e-01 2.08e+03 pdb=" CG ASN A 331 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.146 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.733 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.429 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.270 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 657 " -0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.495 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " 0.327 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.245 2.00e-02 2.50e+03 2.32e-01 6.72e+02 pdb=" CG ASN A 717 " -0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " -0.106 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.336 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.279 2.00e-02 2.50e+03 ... (remaining 4841 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 387 2.65 - 3.21: 25952 3.21 - 3.78: 40993 3.78 - 4.34: 61575 4.34 - 4.90: 99461 Nonbonded interactions: 228368 Sorted by model distance: nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.089 3.040 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.101 3.040 nonbonded pdb=" NZ LYS C 97 " pdb=" O GLN C 183 " model vdw 2.112 3.120 nonbonded pdb=" ND2 ASN A 61 " pdb=" C1 NAG A1401 " model vdw 2.149 3.550 nonbonded pdb=" C HIS A 69 " pdb=" N ALA A 260 " model vdw 2.167 3.350 ... (remaining 228363 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: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain '9' selection = chain 'BA' selection = chain 'L' selection = chain 'U' selection = chain 'W' selection = chain 'fA' selection = chain 'oA' selection = chain 'qA' } ncs_group { reference = (chain '1A' and resid 1 through 2) selection = (chain '2' and resid 1 through 2) selection = (chain '4A' and resid 1 through 2) selection = (chain '5' and resid 1 through 2) selection = (chain 'DA' and resid 1 through 2) selection = (chain 'GA' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'JA' and resid 1 through 2) selection = (chain 'MA' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'PA' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'cA' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'h' and resid 1 through 2) selection = (chain 'hA' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'kA' and resid 1 through 2) selection = (chain 'sA' and resid 1 through 2) selection = (chain 'vA' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) selection = (chain 'yA' and resid 1 through 2) } ncs_group { reference = chain '7A' selection = chain 'SA' selection = chain 'n' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 7.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 68.580 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.008 0.455 28394 Z= 0.419 Angle : 0.893 25.744 38844 Z= 0.403 Chirality : 0.060 1.689 4694 Planarity : 0.003 0.057 4788 Dihedral : 15.807 122.977 12030 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 0.73 % Allowed : 4.04 % Favored : 95.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.13), residues: 3291 helix: -0.83 (0.17), residues: 756 sheet: 0.41 (0.19), residues: 738 loop : -1.39 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 258 HIS 0.004 0.001 HIS A 146 PHE 0.012 0.001 PHE A 79 TYR 0.010 0.001 TYR A 145 ARG 0.003 0.000 ARG B 509 Details of bonding type rmsd link_NAG-ASN : bond 0.15154 ( 56) link_NAG-ASN : angle 7.80205 ( 168) link_ALPHA1-4 : bond 0.00900 ( 24) link_ALPHA1-4 : angle 2.54228 ( 72) link_BETA1-4 : bond 0.00852 ( 36) link_BETA1-4 : angle 2.08840 ( 108) link_ALPHA1-3 : bond 0.00673 ( 3) link_ALPHA1-3 : angle 1.96291 ( 9) hydrogen bonds : bond 0.21353 ( 1118) hydrogen bonds : angle 9.19748 ( 3126) link_BETA1-6 : bond 0.01794 ( 3) link_BETA1-6 : angle 2.74600 ( 9) SS BOND : bond 0.00337 ( 45) SS BOND : angle 1.26286 ( 90) covalent geometry : bond 0.00509 (28227) covalent geometry : angle 0.71355 (38388) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 583 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.8529 (t80) cc_final: 0.8301 (t80) REVERT: A 567 ARG cc_start: 0.7236 (mtt90) cc_final: 0.6994 (mpt180) REVERT: A 661 GLU cc_start: 0.7726 (tt0) cc_final: 0.7431 (mp0) REVERT: A 872 GLN cc_start: 0.8458 (mt0) cc_final: 0.7982 (mt0) REVERT: B 528 LYS cc_start: 0.7658 (mtpp) cc_final: 0.7349 (mttp) REVERT: B 844 ILE cc_start: 0.4401 (OUTLIER) cc_final: 0.3840 (mm) REVERT: C 265 TYR cc_start: 0.8257 (p90) cc_final: 0.7981 (p90) REVERT: C 462 LYS cc_start: 0.7580 (mtmt) cc_final: 0.7294 (mmtt) REVERT: C 755 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6735 (mt0) REVERT: C 844 ILE cc_start: 0.4195 (OUTLIER) cc_final: 0.3761 (mm) outliers start: 21 outliers final: 10 residues processed: 600 average time/residue: 1.3344 time to fit residues: 936.5601 Evaluate side-chains 296 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 1146 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 844 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 85 optimal weight: 0.0020 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 0.0980 chunk 192 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 409 GLN A 437 ASN A 474 GLN A 606 ASN A 764 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 317 ASN B 409 GLN B 437 ASN B 474 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 764 ASN B 919 ASN C 115 GLN C 188 ASN C 437 ASN C 474 GLN C 519 HIS C 779 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.163593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119969 restraints weight = 34424.405| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.16 r_work: 0.3237 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28394 Z= 0.204 Angle : 0.782 14.827 38844 Z= 0.371 Chirality : 0.049 0.725 4694 Planarity : 0.004 0.045 4788 Dihedral : 13.620 107.019 6101 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.14 % Allowed : 11.26 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3291 helix: 0.76 (0.18), residues: 780 sheet: 0.55 (0.19), residues: 738 loop : -1.25 (0.13), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 258 HIS 0.006 0.001 HIS A 69 PHE 0.022 0.002 PHE C 157 TYR 0.021 0.002 TYR C1067 ARG 0.008 0.001 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 56) link_NAG-ASN : angle 3.96396 ( 168) link_ALPHA1-4 : bond 0.01467 ( 24) link_ALPHA1-4 : angle 2.87898 ( 72) link_BETA1-4 : bond 0.00367 ( 36) link_BETA1-4 : angle 1.28009 ( 108) link_ALPHA1-3 : bond 0.01181 ( 3) link_ALPHA1-3 : angle 1.32817 ( 9) hydrogen bonds : bond 0.04657 ( 1118) hydrogen bonds : angle 6.31355 ( 3126) link_BETA1-6 : bond 0.01582 ( 3) link_BETA1-6 : angle 2.25716 ( 9) SS BOND : bond 0.00596 ( 45) SS BOND : angle 1.42754 ( 90) covalent geometry : bond 0.00472 (28227) covalent geometry : angle 0.72315 (38388) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 309 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.6172 (t-90) REVERT: A 81 ASN cc_start: 0.7920 (p0) cc_final: 0.7489 (p0) REVERT: A 319 ARG cc_start: 0.7389 (ptp90) cc_final: 0.7040 (ptm160) REVERT: A 462 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7394 (mmtt) REVERT: A 568 ASP cc_start: 0.7737 (m-30) cc_final: 0.7256 (m-30) REVERT: A 586 ASP cc_start: 0.8476 (m-30) cc_final: 0.8264 (m-30) REVERT: A 602 THR cc_start: 0.7359 (m) cc_final: 0.6851 (p) REVERT: A 618 THR cc_start: 0.6279 (OUTLIER) cc_final: 0.5952 (p) REVERT: A 661 GLU cc_start: 0.7931 (tt0) cc_final: 0.7523 (mp0) REVERT: A 755 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6134 (mp10) REVERT: A 872 GLN cc_start: 0.8610 (mt0) cc_final: 0.8191 (mt0) REVERT: A 900 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8801 (mtm) REVERT: A 1045 LYS cc_start: 0.8867 (mtpm) cc_final: 0.8636 (tmmt) REVERT: B 66 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.6432 (t-90) REVERT: B 81 ASN cc_start: 0.8022 (p0) cc_final: 0.7698 (p0) REVERT: B 568 ASP cc_start: 0.7800 (m-30) cc_final: 0.7313 (m-30) REVERT: B 755 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.5801 (mp10) REVERT: B 839 ASP cc_start: 0.6680 (p0) cc_final: 0.6153 (m-30) REVERT: B 900 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8861 (mtp) REVERT: C 115 GLN cc_start: 0.7845 (mt0) cc_final: 0.7573 (mt0) REVERT: C 157 PHE cc_start: 0.8034 (t80) cc_final: 0.7723 (t80) REVERT: C 386 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8012 (mmmt) REVERT: C 462 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7330 (mmtt) REVERT: C 755 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6431 (mt0) outliers start: 91 outliers final: 40 residues processed: 376 average time/residue: 1.1729 time to fit residues: 528.4516 Evaluate side-chains 305 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 183 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 167 optimal weight: 0.3980 chunk 226 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 195 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A1113 GLN B 474 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 52 GLN C 474 GLN C 580 GLN C 919 ASN C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.164310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131336 restraints weight = 34221.002| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.26 r_work: 0.3134 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28394 Z= 0.139 Angle : 0.702 14.609 38844 Z= 0.323 Chirality : 0.045 0.416 4694 Planarity : 0.004 0.038 4788 Dihedral : 12.972 107.254 6091 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.07 % Allowed : 13.68 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3291 helix: 1.21 (0.19), residues: 780 sheet: 0.39 (0.18), residues: 765 loop : -1.14 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 152 HIS 0.002 0.001 HIS C1048 PHE 0.011 0.001 PHE C 32 TYR 0.023 0.001 TYR B 265 ARG 0.010 0.000 ARG C 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 56) link_NAG-ASN : angle 3.69231 ( 168) link_ALPHA1-4 : bond 0.01492 ( 24) link_ALPHA1-4 : angle 2.84149 ( 72) link_BETA1-4 : bond 0.00440 ( 36) link_BETA1-4 : angle 1.18307 ( 108) link_ALPHA1-3 : bond 0.01021 ( 3) link_ALPHA1-3 : angle 1.48771 ( 9) hydrogen bonds : bond 0.04207 ( 1118) hydrogen bonds : angle 5.94249 ( 3126) link_BETA1-6 : bond 0.01697 ( 3) link_BETA1-6 : angle 2.23396 ( 9) SS BOND : bond 0.00312 ( 45) SS BOND : angle 1.94179 ( 90) covalent geometry : bond 0.00303 (28227) covalent geometry : angle 0.63939 (38388) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 279 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.6080 (t-90) REVERT: A 81 ASN cc_start: 0.7905 (p0) cc_final: 0.7465 (p0) REVERT: A 218 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6259 (tm-30) REVERT: A 319 ARG cc_start: 0.7381 (ptp90) cc_final: 0.7078 (ptm160) REVERT: A 422 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.8085 (p0) REVERT: A 462 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7406 (mmtt) REVERT: A 568 ASP cc_start: 0.7692 (m-30) cc_final: 0.7217 (m-30) REVERT: A 602 THR cc_start: 0.7327 (m) cc_final: 0.6851 (p) REVERT: A 661 GLU cc_start: 0.7972 (tt0) cc_final: 0.7572 (mp0) REVERT: A 790 LYS cc_start: 0.8085 (ptmt) cc_final: 0.7806 (mtmt) REVERT: A 872 GLN cc_start: 0.8589 (mt0) cc_final: 0.8180 (mt0) REVERT: A 878 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8802 (tt) REVERT: A 990 GLU cc_start: 0.7758 (tt0) cc_final: 0.7558 (tt0) REVERT: B 66 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.6305 (t-90) REVERT: B 81 ASN cc_start: 0.7997 (p0) cc_final: 0.7649 (p0) REVERT: B 153 MET cc_start: 0.7274 (tpp) cc_final: 0.6409 (ttt) REVERT: B 158 ARG cc_start: 0.6404 (mmt90) cc_final: 0.5392 (mmm-85) REVERT: B 462 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7407 (mmtt) REVERT: B 568 ASP cc_start: 0.7614 (m-30) cc_final: 0.7126 (m-30) REVERT: B 839 ASP cc_start: 0.6573 (p0) cc_final: 0.6046 (m-30) REVERT: C 81 ASN cc_start: 0.7258 (p0) cc_final: 0.6958 (p0) REVERT: C 115 GLN cc_start: 0.7873 (mt0) cc_final: 0.7590 (mt0) REVERT: C 152 TRP cc_start: 0.6395 (m100) cc_final: 0.6085 (m100) REVERT: C 157 PHE cc_start: 0.8070 (t80) cc_final: 0.7748 (t80) REVERT: C 462 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7401 (mmtt) REVERT: C 568 ASP cc_start: 0.7667 (m-30) cc_final: 0.7239 (m-30) REVERT: C 586 ASP cc_start: 0.8493 (m-30) cc_final: 0.8213 (m-30) REVERT: C 755 GLN cc_start: 0.6881 (mm-40) cc_final: 0.6410 (mt0) REVERT: C 900 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8864 (mtm) outliers start: 89 outliers final: 39 residues processed: 345 average time/residue: 1.0724 time to fit residues: 449.1105 Evaluate side-chains 296 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 251 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 132 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 606 ASN B 317 ASN B 414 GLN B 474 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 GLN C 52 GLN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.159507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115272 restraints weight = 34622.273| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.06 r_work: 0.3171 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 28394 Z= 0.267 Angle : 0.788 15.793 38844 Z= 0.366 Chirality : 0.048 0.431 4694 Planarity : 0.004 0.043 4788 Dihedral : 12.781 107.807 6088 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.39 % Allowed : 13.40 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3291 helix: 1.06 (0.19), residues: 780 sheet: 0.43 (0.19), residues: 687 loop : -1.17 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 436 HIS 0.005 0.001 HIS B1083 PHE 0.015 0.002 PHE B 543 TYR 0.024 0.002 TYR B 904 ARG 0.006 0.001 ARG C 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 56) link_NAG-ASN : angle 3.70168 ( 168) link_ALPHA1-4 : bond 0.01554 ( 24) link_ALPHA1-4 : angle 3.02772 ( 72) link_BETA1-4 : bond 0.00388 ( 36) link_BETA1-4 : angle 1.20872 ( 108) link_ALPHA1-3 : bond 0.01115 ( 3) link_ALPHA1-3 : angle 1.25813 ( 9) hydrogen bonds : bond 0.04878 ( 1118) hydrogen bonds : angle 6.03706 ( 3126) link_BETA1-6 : bond 0.01456 ( 3) link_BETA1-6 : angle 2.37789 ( 9) SS BOND : bond 0.00773 ( 45) SS BOND : angle 2.08902 ( 90) covalent geometry : bond 0.00635 (28227) covalent geometry : angle 0.73135 (38388) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 268 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6673 (OUTLIER) cc_final: 0.6033 (t-90) REVERT: A 81 ASN cc_start: 0.8179 (p0) cc_final: 0.7781 (p0) REVERT: A 319 ARG cc_start: 0.7487 (ptp90) cc_final: 0.7138 (ptm160) REVERT: A 462 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7373 (mmtt) REVERT: A 568 ASP cc_start: 0.7853 (m-30) cc_final: 0.7441 (m-30) REVERT: A 618 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.6051 (p) REVERT: A 661 GLU cc_start: 0.8008 (tt0) cc_final: 0.7600 (mp0) REVERT: A 725 GLU cc_start: 0.8757 (tt0) cc_final: 0.8430 (tt0) REVERT: A 790 LYS cc_start: 0.8114 (ptmt) cc_final: 0.7913 (mtpt) REVERT: A 872 GLN cc_start: 0.8675 (mt0) cc_final: 0.8259 (mt0) REVERT: B 81 ASN cc_start: 0.8265 (p0) cc_final: 0.7918 (p0) REVERT: B 132 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: B 153 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6471 (ttt) REVERT: B 158 ARG cc_start: 0.6496 (mtt90) cc_final: 0.5486 (mmm-85) REVERT: B 218 GLN cc_start: 0.7520 (tt0) cc_final: 0.7309 (mt0) REVERT: B 398 ASP cc_start: 0.8653 (m-30) cc_final: 0.8398 (m-30) REVERT: B 462 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7429 (mmtt) REVERT: B 568 ASP cc_start: 0.7793 (m-30) cc_final: 0.7355 (m-30) REVERT: B 755 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.5820 (mp10) REVERT: B 839 ASP cc_start: 0.6922 (p0) cc_final: 0.6429 (m-30) REVERT: C 113 LYS cc_start: 0.7502 (mtpt) cc_final: 0.7196 (ttpp) REVERT: C 115 GLN cc_start: 0.7919 (mt0) cc_final: 0.7623 (mt0) REVERT: C 152 TRP cc_start: 0.6513 (m100) cc_final: 0.6183 (m100) REVERT: C 157 PHE cc_start: 0.8058 (t80) cc_final: 0.7785 (t80) REVERT: C 158 ARG cc_start: 0.6785 (mmt90) cc_final: 0.6270 (mmm-85) REVERT: C 409 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: C 422 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.7623 (p0) REVERT: C 462 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7375 (mmtt) REVERT: C 554 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: C 586 ASP cc_start: 0.8541 (m-30) cc_final: 0.8302 (m-30) REVERT: C 725 GLU cc_start: 0.8892 (tt0) cc_final: 0.8582 (tt0) REVERT: C 755 GLN cc_start: 0.7000 (mm-40) cc_final: 0.6387 (mt0) REVERT: C 847 ARG cc_start: 0.5103 (mtm-85) cc_final: 0.4705 (mtt-85) outliers start: 127 outliers final: 59 residues processed: 370 average time/residue: 1.1433 time to fit residues: 505.6629 Evaluate side-chains 304 residues out of total 2895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.6481 > 50: distance: 30 - 77: 36.262 distance: 33 - 74: 33.017 distance: 51 - 56: 34.240 distance: 56 - 57: 44.074 distance: 57 - 58: 45.561 distance: 58 - 59: 40.203 distance: 58 - 60: 8.015 distance: 60 - 61: 50.690 distance: 61 - 62: 55.963 distance: 61 - 64: 56.767 distance: 62 - 69: 39.575 distance: 64 - 65: 68.713 distance: 65 - 66: 38.689 distance: 66 - 67: 50.628 distance: 67 - 68: 9.013 distance: 69 - 70: 68.138 distance: 70 - 71: 70.661 distance: 70 - 73: 55.892 distance: 71 - 72: 56.084 distance: 71 - 74: 68.732 distance: 74 - 75: 57.692 distance: 75 - 76: 55.244 distance: 75 - 78: 69.181 distance: 76 - 77: 40.147 distance: 78 - 79: 55.997 distance: 79 - 80: 67.552 distance: 79 - 81: 55.528 distance: 80 - 82: 54.074 distance: 81 - 83: 56.881 distance: 82 - 83: 40.114 distance: 84 - 85: 41.210 distance: 84 - 195: 32.387 distance: 85 - 86: 67.965 distance: 85 - 88: 69.300 distance: 86 - 87: 41.137 distance: 86 - 95: 40.287 distance: 87 - 192: 32.402 distance: 88 - 89: 39.208 distance: 89 - 91: 40.905 distance: 90 - 92: 40.822 distance: 92 - 94: 57.191 distance: 93 - 94: 55.722 distance: 95 - 96: 57.306 distance: 95 - 101: 38.943 distance: 96 - 97: 38.768 distance: 96 - 99: 40.890 distance: 97 - 98: 42.073 distance: 97 - 102: 29.069 distance: 99 - 100: 55.163 distance: 100 - 101: 57.374 distance: 102 - 103: 50.037 distance: 103 - 104: 70.527 distance: 103 - 106: 56.284 distance: 104 - 105: 38.950 distance: 104 - 113: 40.062 distance: 106 - 107: 57.257 distance: 107 - 108: 39.196 distance: 108 - 109: 56.278 distance: 113 - 114: 41.169 distance: 114 - 115: 39.336 distance: 114 - 117: 14.120 distance: 115 - 116: 39.724 distance: 115 - 122: 55.329 distance: 117 - 118: 48.674 distance: 119 - 120: 67.069 distance: 119 - 121: 56.637 distance: 122 - 123: 39.487 distance: 123 - 124: 55.535 distance: 124 - 125: 39.748 distance: 124 - 126: 57.727 distance: 126 - 127: 46.621 distance: 126 - 160: 33.758 distance: 127 - 128: 43.445 distance: 127 - 130: 27.186 distance: 128 - 129: 56.365 distance: 128 - 133: 34.379 distance: 129 - 157: 33.052 distance: 130 - 131: 55.420 distance: 130 - 132: 57.106