Starting phenix.real_space_refine on Fri Jun 27 00:33:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nb3_0401/06_2025/6nb3_0401.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nb3_0401/06_2025/6nb3_0401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nb3_0401/06_2025/6nb3_0401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nb3_0401/06_2025/6nb3_0401.map" model { file = "/net/cci-nas-00/data/ceres_data/6nb3_0401/06_2025/6nb3_0401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nb3_0401/06_2025/6nb3_0401.cif" } resolution = 3.5 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= 0.002 sd= 0.061 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 155 5.16 5 C 19492 2.51 5 N 4892 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 199 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30960 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9032 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 59, 'TRANS': 1109} Chain breaks: 4 Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 773 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 958 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 951 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 773 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 7402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7402 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 45, 'TRANS': 912} Chain breaks: 5 Chain: "C" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9032 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 59, 'TRANS': 1109} Chain breaks: 4 Chain: "F" 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, '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: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "S" 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: "T" 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: "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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" 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: {'BMA': 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: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "f" 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 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: "i" 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "r" 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: "s" 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: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "v" 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: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 18.55, per 1000 atoms: 0.60 Number of scatterers: 30960 At special positions: 0 Unit cell: (153.44, 147.96, 194.54, 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 155 16.00 O 6421 8.00 N 4892 7.00 C 19492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.06 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.04 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.02 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.07 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.05 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.06 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.23 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.04 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.08 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.02 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.16 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.04 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.02 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.11 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.13 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.04 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.04 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.08 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.04 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.04 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.02 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.04 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.06 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.08 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " 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 ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " " MAN P 4 " - " MAN P 5 " " MAN Z 4 " - " MAN Z 5 " " MAN b 4 " - " MAN b 5 " " MAN c 4 " - " MAN c 5 " " MAN n 4 " - " MAN n 5 " " MAN q 4 " - " MAN q 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 4 " " BMA y 3 " - " MAN y 4 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA K 3 " - " MAN K 6 " " BMA M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 6 " " BMA W 3 " - " MAN W 5 " " BMA Z 3 " - " MAN Z 6 " " BMA b 3 " - " MAN b 6 " " BMA c 3 " - " MAN c 6 " " BMA d 3 " - " MAN d 5 " " BMA k 3 " - " MAN k 5 " " BMA n 3 " - " MAN n 6 " " BMA y 3 " - " MAN y 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " NAG-ASN " NAG A1445 " - " ASN A 592 " " NAG B1442 " - " ASN B 774 " " NAG C1423 " - " ASN C 236 " " NAG C1428 " - " ASN C 487 " " NAG C1429 " - " ASN C 592 " " NAG F 1 " - " ASN A 66 " " NAG G 1 " - " ASN A 104 " " NAG I 1 " - " ASN A 125 " " NAG J 1 " - " ASN A 155 " " NAG K 1 " - " ASN A 166 " " NAG M 1 " - " ASN A 222 " " NAG N 1 " - " ASN A 236 " " NAG O 1 " - " ASN A 244 " " NAG P 1 " - " ASN A 410 " " NAG Q 1 " - " ASN A 487 " " NAG R 1 " - " ASN A 619 " " NAG S 1 " - " ASN A 719 " " NAG T 1 " - " ASN A 774 " " NAG U 1 " - " ASN A 785 " " NAG V 1 " - " ASN A 870 " " NAG W 1 " - " ASN A1213 " " NAG X 1 " - " ASN B 66 " " NAG Y 1 " - " ASN B 104 " " NAG Z 1 " - " ASN B 125 " " NAG a 1 " - " ASN B 155 " " NAG b 1 " - " ASN B 166 " " NAG c 1 " - " ASN B 222 " " NAG d 1 " - " ASN B 236 " " NAG e 1 " - " ASN B 244 " " NAG f 1 " - " ASN B 592 " " NAG g 1 " - " ASN B 619 " " NAG h 1 " - " ASN B 719 " " NAG i 1 " - " ASN B 785 " " NAG j 1 " - " ASN B 870 " " NAG k 1 " - " ASN B1213 " " NAG l 1 " - " ASN C 66 " " NAG m 1 " - " ASN C 104 " " NAG n 1 " - " ASN C 125 " " NAG o 1 " - " ASN C 155 " " NAG p 1 " - " ASN C 166 " " NAG q 1 " - " ASN C 222 " " NAG r 1 " - " ASN C 244 " " NAG s 1 " - " ASN C 410 " " NAG t 1 " - " ASN C 619 " " NAG u 1 " - " ASN C 719 " " NAG v 1 " - " ASN C 774 " " NAG w 1 " - " ASN C 785 " " NAG x 1 " - " ASN C 870 " " NAG y 1 " - " ASN C1213 " Time building additional restraints: 10.54 Conformation dependent library (CDL) restraints added in 3.9 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6928 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 69 sheets defined 22.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.59 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.925A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.760A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 449 through 456 removed outlier: 4.583A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 826 through 854 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.525A pdb=" N GLY A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 removed outlier: 3.697A pdb=" N ALA A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1011 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 4.295A pdb=" N ALA A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 4.842A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'B' and resid 37 through 40 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.137A pdb=" N LYS B 595 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 940 through 954 Processing helix chain 'B' and resid 954 through 959 removed outlier: 4.614A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1008 through 1011 Processing helix chain 'B' and resid 1016 through 1040 removed outlier: 4.056A pdb=" N ALA B1032 " --> pdb=" O ASN B1028 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B1033 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1056 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 3.515A pdb=" N ASP B1064 " --> pdb=" O PRO B1060 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.564A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 417 removed outlier: 3.554A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 449 through 457 removed outlier: 5.268A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.700A pdb=" N GLN C 819 " --> pdb=" O GLN C 815 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C 820 " --> pdb=" O LYS C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 888 through 896 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.761A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 940 through 954 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1010 removed outlier: 4.003A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 3.508A pdb=" N VAL C1022 " --> pdb=" O ALA C1018 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA C1032 " --> pdb=" O ASN C1028 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU C1033 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 5.205A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.402A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.042A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.274A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.687A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.759A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 214 through 215 removed outlier: 3.736A pdb=" N SER A 215 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.483A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 371 through 376 removed outlier: 4.167A pdb=" N GLU A 605 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 373 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER A 607 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 375 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.898A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.086A pdb=" N CYS A 407 " --> pdb=" O CYS A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.535A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.496A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.651A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1184 through 1188 removed outlier: 4.541A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 796 removed outlier: 4.493A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 968 removed outlier: 5.692A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.149A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.474A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AC7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.954A pdb=" N TRP H 33 " --> pdb=" O LEU H 101 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.710A pdb=" N TRP D 33 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AD5, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.477A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AD7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AD9, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.161A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.031A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.562A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AE4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.584A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.514A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AE7, first strand: chain 'B' and resid 214 through 215 removed outlier: 3.742A pdb=" N SER B 215 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.652A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.245A pdb=" N GLU B 605 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 373 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N SER B 607 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 375 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.330A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.718A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 1184 through 1188 removed outlier: 4.698A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 785 through 796 removed outlier: 3.617A pdb=" N ASN B 785 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.609A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.931A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASN B1163 " --> pdb=" O ASP B1157 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AF8, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.075A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.157A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.159A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AG3, first strand: chain 'C' and resid 109 through 111 removed outlier: 6.700A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.611A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AG6, first strand: chain 'C' and resid 214 through 215 removed outlier: 3.938A pdb=" N SER C 215 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.671A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 371 through 376 removed outlier: 4.233A pdb=" N GLU C 605 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER C 373 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER C 607 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL C 375 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.538A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 477 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS C 425 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 479 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C 423 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU C 481 " --> pdb=" O ASN C 421 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AH2, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.592A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 718 through 724 removed outlier: 6.340A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'C' and resid 786 through 796 removed outlier: 4.379A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 802 through 803 Processing sheet with id=AH6, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.058A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN C1163 " --> pdb=" O ASP C1157 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3063 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: 14.97 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5851 1.32 - 1.45: 9056 1.45 - 1.58: 16515 1.58 - 1.71: 6 1.71 - 1.84: 206 Bond restraints: 31634 Sorted by residual: bond pdb=" CA PRO A1220 " pdb=" C PRO A1220 " ideal model delta sigma weight residual 1.517 1.581 -0.064 9.30e-03 1.16e+04 4.71e+01 bond pdb=" CA PRO C1220 " pdb=" C PRO C1220 " ideal model delta sigma weight residual 1.517 1.578 -0.061 9.30e-03 1.16e+04 4.31e+01 bond pdb=" CA PRO B1220 " pdb=" C PRO B1220 " ideal model delta sigma weight residual 1.517 1.573 -0.056 9.30e-03 1.16e+04 3.65e+01 bond pdb=" CA PRO B1219 " pdb=" C PRO B1219 " ideal model delta sigma weight residual 1.517 1.570 -0.053 9.30e-03 1.16e+04 3.23e+01 bond pdb=" N PRO C1221 " pdb=" CD PRO C1221 " ideal model delta sigma weight residual 1.473 1.402 0.071 1.40e-02 5.10e+03 2.59e+01 ... (remaining 31629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.56: 42601 5.56 - 11.12: 409 11.12 - 16.68: 3 16.68 - 22.24: 5 22.24 - 27.79: 2 Bond angle restraints: 43020 Sorted by residual: angle pdb=" C VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta sigma weight residual 111.29 134.84 -23.55 1.64e+00 3.72e-01 2.06e+02 angle pdb=" C TYR C 905 " pdb=" CA TYR C 905 " pdb=" CB TYR C 905 " ideal model delta sigma weight residual 110.42 138.21 -27.79 1.99e+00 2.53e-01 1.95e+02 angle pdb=" N MET C 906 " pdb=" CA MET C 906 " pdb=" C MET C 906 " ideal model delta sigma weight residual 110.28 125.89 -15.61 1.48e+00 4.57e-01 1.11e+02 angle pdb=" N TYR C 905 " pdb=" CA TYR C 905 " pdb=" C TYR C 905 " ideal model delta sigma weight residual 110.80 88.98 21.82 2.13e+00 2.20e-01 1.05e+02 angle pdb=" CD1 LEU C 506 " pdb=" CG LEU C 506 " pdb=" CD2 LEU C 506 " ideal model delta sigma weight residual 110.80 131.55 -20.75 2.20e+00 2.07e-01 8.90e+01 ... (remaining 43015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.11: 19758 22.11 - 44.22: 609 44.22 - 66.34: 149 66.34 - 88.45: 197 88.45 - 110.56: 120 Dihedral angle restraints: 20833 sinusoidal: 9953 harmonic: 10880 Sorted by residual: dihedral pdb=" C VAL B 711 " pdb=" N VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta harmonic sigma weight residual -122.00 -158.42 36.42 0 2.50e+00 1.60e-01 2.12e+02 dihedral pdb=" N VAL B 711 " pdb=" C VAL B 711 " pdb=" CA VAL B 711 " pdb=" CB VAL B 711 " ideal model delta harmonic sigma weight residual 123.40 150.91 -27.51 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" CB CYS C 806 " pdb=" SG CYS C 806 " pdb=" SG CYS C 828 " pdb=" CB CYS C 828 " ideal model delta sinusoidal sigma weight residual 93.00 178.95 -85.95 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 20830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 5215 0.267 - 0.534: 58 0.534 - 0.802: 4 0.802 - 1.069: 0 1.069 - 1.336: 1 Chirality restraints: 5278 Sorted by residual: chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.31e+01 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.22e+01 chirality pdb=" C1 BMA o 3 " pdb=" O4 NAG o 2 " pdb=" C2 BMA o 3 " pdb=" O5 BMA o 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.77e+01 ... (remaining 5275 not shown) Planarity restraints: 5366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 166 " -0.042 2.00e-02 2.50e+03 4.22e-02 2.23e+01 pdb=" CG ASN B 166 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 166 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 166 " 0.064 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 166 " 0.036 2.00e-02 2.50e+03 3.68e-02 1.70e+01 pdb=" CG ASN A 166 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 166 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 166 " -0.056 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 77 " 0.049 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR A 77 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 77 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 77 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 77 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 77 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 77 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 77 " 0.027 2.00e-02 2.50e+03 ... (remaining 5363 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 871 2.69 - 3.24: 29800 3.24 - 3.80: 48629 3.80 - 4.35: 63141 4.35 - 4.90: 102110 Nonbonded interactions: 244551 Sorted by model distance: nonbonded pdb=" OG SER C 419 " pdb=" OG1 THR C 483 " model vdw 2.139 3.040 nonbonded pdb=" OG SER A 419 " pdb=" OG1 THR A 483 " model vdw 2.238 3.040 nonbonded pdb=" N ASN C 592 " pdb=" OD1 ASN C 592 " model vdw 2.253 3.120 nonbonded pdb=" CB SER B 676 " pdb=" O TYR C 905 " model vdw 2.256 3.440 nonbonded pdb=" OG1 THR A 709 " pdb=" O GLY A 712 " model vdw 2.298 3.040 ... (remaining 244546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 18 through 1222 or resid 1423)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 2 through 124) } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'l' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'Y' selection = chain 'a' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 't' selection = chain 'x' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'n' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'd' selection = chain 'k' selection = chain 'q' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 78.180 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.015 0.201 31845 Z= 0.789 Angle : 1.419 27.795 43602 Z= 0.860 Chirality : 0.090 1.336 5278 Planarity : 0.006 0.059 5317 Dihedral : 17.224 110.562 13752 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Rotamer: Outliers : 0.41 % Allowed : 1.44 % Favored : 98.15 % Cbeta Deviations : 0.09 % 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: 0.07 (0.13), residues: 3717 helix: 0.47 (0.19), residues: 682 sheet: 0.59 (0.16), residues: 897 loop : -0.27 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.006 TRP C1184 HIS 0.006 0.001 HIS A1138 PHE 0.030 0.004 PHE C 313 TYR 0.049 0.006 TYR A 77 ARG 0.006 0.001 ARG A 401 Details of bonding type rmsd link_NAG-ASN : bond 0.02549 ( 49) link_NAG-ASN : angle 1.95172 ( 147) link_ALPHA1-6 : bond 0.03038 ( 13) link_ALPHA1-6 : angle 2.24264 ( 39) link_BETA1-4 : bond 0.03616 ( 74) link_BETA1-4 : angle 2.43756 ( 222) link_ALPHA1-2 : bond 0.04072 ( 9) link_ALPHA1-2 : angle 1.84735 ( 27) link_ALPHA1-3 : bond 0.03453 ( 15) link_ALPHA1-3 : angle 1.52567 ( 45) hydrogen bonds : bond 0.18874 ( 1154) hydrogen bonds : angle 7.83260 ( 3063) SS BOND : bond 0.04067 ( 51) SS BOND : angle 3.78031 ( 102) covalent geometry : bond 0.01462 (31634) covalent geometry : angle 1.39741 (43020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 839 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7676 (ttp) cc_final: 0.7233 (ttm) REVERT: A 444 ASP cc_start: 0.7617 (m-30) cc_final: 0.7276 (m-30) REVERT: A 817 CYS cc_start: 0.6670 (t) cc_final: 0.6431 (t) REVERT: H 83 LEU cc_start: 0.5935 (tp) cc_final: 0.5658 (tt) REVERT: H 88 LEU cc_start: 0.7166 (mt) cc_final: 0.6912 (mt) REVERT: H 92 ASP cc_start: 0.6545 (m-30) cc_final: 0.5164 (t70) REVERT: H 100 THR cc_start: 0.6187 (p) cc_final: 0.5960 (p) REVERT: H 108 TRP cc_start: 0.6890 (t-100) cc_final: 0.6405 (t60) REVERT: D 60 THR cc_start: 0.7052 (p) cc_final: 0.6763 (t) REVERT: D 62 TYR cc_start: 0.8067 (m-80) cc_final: 0.7688 (m-10) REVERT: D 72 LEU cc_start: 0.7149 (mp) cc_final: 0.6663 (tt) REVERT: D 95 VAL cc_start: 0.7588 (t) cc_final: 0.7384 (m) REVERT: E 64 PHE cc_start: 0.5375 (m-80) cc_final: 0.4594 (m-10) REVERT: E 97 SER cc_start: 0.8310 (m) cc_final: 0.7875 (p) REVERT: E 108 VAL cc_start: 0.6319 (t) cc_final: 0.6038 (t) REVERT: B 68 THR cc_start: 0.8641 (m) cc_final: 0.8338 (p) REVERT: B 220 ASN cc_start: 0.5262 (t0) cc_final: 0.4687 (t0) REVERT: B 677 VAL cc_start: 0.8872 (t) cc_final: 0.8591 (m) REVERT: B 816 LYS cc_start: 0.8229 (tptt) cc_final: 0.7762 (mmtt) REVERT: B 1054 ILE cc_start: 0.9101 (pt) cc_final: 0.8828 (mt) REVERT: C 84 MET cc_start: 0.7002 (ptm) cc_final: 0.6651 (ptm) REVERT: C 144 TYR cc_start: 0.7922 (m-80) cc_final: 0.7698 (m-10) REVERT: C 245 ILE cc_start: 0.8034 (mt) cc_final: 0.7814 (mt) REVERT: C 292 TYR cc_start: 0.8153 (m-80) cc_final: 0.7918 (m-10) REVERT: C 859 SER cc_start: 0.8795 (m) cc_final: 0.8515 (p) REVERT: C 1040 LEU cc_start: 0.8398 (tp) cc_final: 0.7853 (tp) outliers start: 13 outliers final: 1 residues processed: 848 average time/residue: 0.4139 time to fit residues: 556.5990 Evaluate side-chains 397 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 592 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 0.0970 chunk 281 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 216 optimal weight: 0.7980 chunk 336 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN A 466 GLN A 522 GLN A 833 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 119 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 277 ASN B 298 HIS B 346 GLN B 914 GLN B 993 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 60 GLN ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN C 708 GLN C1056 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.150183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.121240 restraints weight = 59875.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124263 restraints weight = 33020.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.124687 restraints weight = 22112.529| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31845 Z= 0.175 Angle : 0.771 11.778 43602 Z= 0.377 Chirality : 0.047 0.358 5278 Planarity : 0.005 0.058 5317 Dihedral : 13.398 85.021 7299 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.44 % Rotamer: Outliers : 2.38 % Allowed : 8.64 % Favored : 88.98 % 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: 0.36 (0.13), residues: 3717 helix: 1.53 (0.20), residues: 698 sheet: 0.45 (0.16), residues: 913 loop : -0.25 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 253 HIS 0.008 0.001 HIS C 681 PHE 0.027 0.002 PHE A 977 TYR 0.023 0.002 TYR B 794 ARG 0.009 0.001 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 49) link_NAG-ASN : angle 2.24251 ( 147) link_ALPHA1-6 : bond 0.00739 ( 13) link_ALPHA1-6 : angle 2.04803 ( 39) link_BETA1-4 : bond 0.01371 ( 74) link_BETA1-4 : angle 2.71230 ( 222) link_ALPHA1-2 : bond 0.00297 ( 9) link_ALPHA1-2 : angle 1.66153 ( 27) link_ALPHA1-3 : bond 0.00790 ( 15) link_ALPHA1-3 : angle 2.90549 ( 45) hydrogen bonds : bond 0.06442 ( 1154) hydrogen bonds : angle 6.07941 ( 3063) SS BOND : bond 0.00425 ( 51) SS BOND : angle 1.58061 ( 102) covalent geometry : bond 0.00384 (31634) covalent geometry : angle 0.72576 (43020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 470 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7724 (ttp) cc_final: 0.7450 (ttm) REVERT: A 161 MET cc_start: 0.7666 (mmt) cc_final: 0.7181 (tpp) REVERT: A 686 MET cc_start: 0.8012 (ttt) cc_final: 0.7596 (ttt) REVERT: A 1137 MET cc_start: 0.7913 (mpp) cc_final: 0.7490 (mtm) REVERT: A 1190 SER cc_start: 0.8577 (m) cc_final: 0.8309 (p) REVERT: L 87 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: H 108 TRP cc_start: 0.6928 (t-100) cc_final: 0.6681 (t60) REVERT: D 28 THR cc_start: 0.8329 (t) cc_final: 0.7739 (t) REVERT: D 62 TYR cc_start: 0.7994 (m-80) cc_final: 0.7653 (m-10) REVERT: E 87 ASP cc_start: 0.7358 (m-30) cc_final: 0.7125 (m-30) REVERT: B 57 ILE cc_start: 0.8339 (mt) cc_final: 0.8123 (pt) REVERT: B 644 ASP cc_start: 0.7296 (m-30) cc_final: 0.6848 (m-30) REVERT: B 808 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7339 (tp40) REVERT: B 943 MET cc_start: 0.7473 (mtm) cc_final: 0.7178 (ttm) REVERT: B 977 PHE cc_start: 0.7613 (m-80) cc_final: 0.7386 (m-80) REVERT: B 1054 ILE cc_start: 0.9015 (pt) cc_final: 0.8810 (mt) REVERT: B 1084 GLN cc_start: 0.8110 (tp40) cc_final: 0.7705 (tp40) REVERT: B 1186 TYR cc_start: 0.8550 (t80) cc_final: 0.8246 (t80) REVERT: C 84 MET cc_start: 0.6406 (ptm) cc_final: 0.6084 (ptm) REVERT: C 254 PHE cc_start: 0.7978 (t80) cc_final: 0.7770 (t80) REVERT: C 292 TYR cc_start: 0.8235 (m-80) cc_final: 0.8013 (m-10) REVERT: C 563 MET cc_start: 0.8024 (tpt) cc_final: 0.7742 (tpt) REVERT: C 664 ASP cc_start: 0.7419 (t0) cc_final: 0.7082 (t70) REVERT: C 859 SER cc_start: 0.8994 (m) cc_final: 0.8745 (p) REVERT: C 970 ILE cc_start: 0.8577 (mm) cc_final: 0.8352 (mm) REVERT: C 1024 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8244 (t0) REVERT: C 1040 LEU cc_start: 0.8535 (tp) cc_final: 0.7965 (tp) REVERT: C 1161 PRO cc_start: 0.7728 (Cg_endo) cc_final: 0.7479 (Cg_exo) outliers start: 76 outliers final: 40 residues processed: 515 average time/residue: 0.4187 time to fit residues: 357.0454 Evaluate side-chains 374 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 332 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 978 TYR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 993 ASN Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 1024 ASP Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 316 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 360 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 284 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN A 708 GLN A 842 GLN A 857 GLN L 39 GLN H 119 GLN D 39 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 GLN B1122 HIS ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN C 927 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.140577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110645 restraints weight = 60407.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.113744 restraints weight = 34814.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114029 restraints weight = 22646.410| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 31845 Z= 0.282 Angle : 0.836 13.057 43602 Z= 0.410 Chirality : 0.049 0.405 5278 Planarity : 0.005 0.057 5317 Dihedral : 10.901 76.270 7299 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.54 % Allowed : 11.05 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.27 (0.13), residues: 3717 helix: 1.04 (0.21), residues: 684 sheet: 0.17 (0.16), residues: 934 loop : -0.74 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 108 HIS 0.011 0.003 HIS C1138 PHE 0.027 0.003 PHE C 116 TYR 0.029 0.002 TYR L 88 ARG 0.012 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 49) link_NAG-ASN : angle 2.28324 ( 147) link_ALPHA1-6 : bond 0.00898 ( 13) link_ALPHA1-6 : angle 1.78344 ( 39) link_BETA1-4 : bond 0.01298 ( 74) link_BETA1-4 : angle 2.55381 ( 222) link_ALPHA1-2 : bond 0.00477 ( 9) link_ALPHA1-2 : angle 1.59666 ( 27) link_ALPHA1-3 : bond 0.01005 ( 15) link_ALPHA1-3 : angle 2.56319 ( 45) hydrogen bonds : bond 0.06886 ( 1154) hydrogen bonds : angle 5.95925 ( 3063) SS BOND : bond 0.00724 ( 51) SS BOND : angle 2.00360 ( 102) covalent geometry : bond 0.00663 (31634) covalent geometry : angle 0.79798 (43020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 347 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8004 (ttp) cc_final: 0.7792 (ttm) REVERT: A 444 ASP cc_start: 0.8201 (m-30) cc_final: 0.7803 (m-30) REVERT: A 576 GLN cc_start: 0.8235 (tt0) cc_final: 0.8008 (tt0) REVERT: A 871 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7514 (pp) REVERT: A 943 MET cc_start: 0.7692 (mmt) cc_final: 0.7385 (tpp) REVERT: A 1020 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 1068 ASP cc_start: 0.7981 (t0) cc_final: 0.7637 (m-30) REVERT: L 87 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6728 (m-30) REVERT: H 51 ILE cc_start: 0.6864 (tp) cc_final: 0.6623 (tt) REVERT: D 62 TYR cc_start: 0.8162 (m-80) cc_final: 0.7784 (m-10) REVERT: D 115 ASP cc_start: 0.8351 (p0) cc_final: 0.7874 (p0) REVERT: B 179 LEU cc_start: 0.8913 (pp) cc_final: 0.8601 (pp) REVERT: B 240 MET cc_start: 0.7710 (ttt) cc_final: 0.6745 (ttt) REVERT: B 911 ASP cc_start: 0.7505 (t0) cc_final: 0.6595 (t0) REVERT: B 943 MET cc_start: 0.7923 (mtm) cc_final: 0.7512 (ttm) REVERT: B 1031 GLN cc_start: 0.8464 (mt0) cc_final: 0.7992 (tm-30) REVERT: B 1084 GLN cc_start: 0.8204 (tp40) cc_final: 0.7945 (tp40) REVERT: C 84 MET cc_start: 0.6520 (ptm) cc_final: 0.6208 (ptm) REVERT: C 254 PHE cc_start: 0.8364 (t80) cc_final: 0.8123 (t80) REVERT: C 580 ASP cc_start: 0.7899 (t70) cc_final: 0.7674 (t0) REVERT: C 1008 MET cc_start: 0.8577 (tmm) cc_final: 0.8286 (tmm) outliers start: 113 outliers final: 78 residues processed: 431 average time/residue: 0.3982 time to fit residues: 284.0278 Evaluate side-chains 372 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 292 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 87 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 993 ASN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1125 SER Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1214 ILE Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 295 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 354 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 348 HIS ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 836 HIS B 993 ASN B1042 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS C1129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.141000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111772 restraints weight = 60412.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114963 restraints weight = 35761.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.114984 restraints weight = 24301.337| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31845 Z= 0.186 Angle : 0.718 13.529 43602 Z= 0.347 Chirality : 0.046 0.332 5278 Planarity : 0.004 0.064 5317 Dihedral : 9.689 71.395 7299 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 3.41 % Allowed : 12.34 % Favored : 84.25 % 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: -0.26 (0.13), residues: 3717 helix: 1.32 (0.21), residues: 673 sheet: 0.08 (0.16), residues: 977 loop : -0.79 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 108 HIS 0.008 0.001 HIS C1138 PHE 0.028 0.002 PHE C 313 TYR 0.038 0.002 TYR L 88 ARG 0.004 0.000 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 49) link_NAG-ASN : angle 2.06862 ( 147) link_ALPHA1-6 : bond 0.00936 ( 13) link_ALPHA1-6 : angle 1.73925 ( 39) link_BETA1-4 : bond 0.01255 ( 74) link_BETA1-4 : angle 2.41667 ( 222) link_ALPHA1-2 : bond 0.00472 ( 9) link_ALPHA1-2 : angle 1.48238 ( 27) link_ALPHA1-3 : bond 0.01069 ( 15) link_ALPHA1-3 : angle 2.70908 ( 45) hydrogen bonds : bond 0.05855 ( 1154) hydrogen bonds : angle 5.57620 ( 3063) SS BOND : bond 0.00350 ( 51) SS BOND : angle 1.44326 ( 102) covalent geometry : bond 0.00422 (31634) covalent geometry : angle 0.67949 (43020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 322 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7831 (ttp) cc_final: 0.7554 (ttm) REVERT: A 161 MET cc_start: 0.7283 (mmt) cc_final: 0.6833 (tpp) REVERT: A 369 LYS cc_start: 0.7660 (mmtm) cc_final: 0.7418 (mmtp) REVERT: A 686 MET cc_start: 0.8278 (ttt) cc_final: 0.7986 (ttt) REVERT: A 871 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7751 (pp) REVERT: A 943 MET cc_start: 0.7564 (mmt) cc_final: 0.7205 (mmt) REVERT: A 1020 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 1068 ASP cc_start: 0.7905 (t0) cc_final: 0.7636 (m-30) REVERT: L 87 ASP cc_start: 0.7293 (m-30) cc_final: 0.6751 (m-30) REVERT: H 27 LEU cc_start: 0.1097 (OUTLIER) cc_final: 0.0774 (pp) REVERT: D 52 LYS cc_start: 0.8296 (mttp) cc_final: 0.7920 (mtmt) REVERT: D 62 TYR cc_start: 0.8255 (m-80) cc_final: 0.7993 (m-80) REVERT: D 115 ASP cc_start: 0.8387 (p0) cc_final: 0.7885 (p0) REVERT: E 88 TYR cc_start: 0.6540 (m-80) cc_final: 0.5367 (m-80) REVERT: E 107 LYS cc_start: 0.6838 (tptt) cc_final: 0.6607 (tptt) REVERT: B 78 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7670 (tp-100) REVERT: B 174 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8327 (m-30) REVERT: B 213 ASP cc_start: 0.6619 (m-30) cc_final: 0.6242 (m-30) REVERT: B 240 MET cc_start: 0.7271 (ttt) cc_final: 0.6230 (ttt) REVERT: B 686 MET cc_start: 0.8066 (mmm) cc_final: 0.7499 (tpp) REVERT: B 822 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7902 (mtm-85) REVERT: B 873 LEU cc_start: 0.8231 (pp) cc_final: 0.7992 (pp) REVERT: B 943 MET cc_start: 0.7633 (mtm) cc_final: 0.7180 (ttm) REVERT: B 1031 GLN cc_start: 0.8414 (mt0) cc_final: 0.8021 (tm-30) REVERT: B 1084 GLN cc_start: 0.8267 (tp40) cc_final: 0.7812 (tp40) REVERT: C 84 MET cc_start: 0.6457 (ptm) cc_final: 0.6188 (ptm) REVERT: C 628 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: C 827 PHE cc_start: 0.8031 (t80) cc_final: 0.7783 (t80) REVERT: C 994 GLN cc_start: 0.7283 (pm20) cc_final: 0.6919 (pm20) outliers start: 109 outliers final: 70 residues processed: 404 average time/residue: 0.3881 time to fit residues: 263.0994 Evaluate side-chains 369 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 293 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 822 ARG Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 249 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 354 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 359 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 268 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 421 ASN A 516 GLN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B1042 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.141015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111820 restraints weight = 59792.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.114238 restraints weight = 34075.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.114906 restraints weight = 23583.683| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31845 Z= 0.178 Angle : 0.711 12.853 43602 Z= 0.340 Chirality : 0.046 0.313 5278 Planarity : 0.004 0.062 5317 Dihedral : 8.917 68.003 7299 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 3.48 % Allowed : 13.21 % Favored : 83.31 % 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: -0.32 (0.13), residues: 3717 helix: 1.36 (0.21), residues: 673 sheet: -0.00 (0.16), residues: 955 loop : -0.83 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 33 HIS 0.007 0.001 HIS C1138 PHE 0.024 0.002 PHE C 40 TYR 0.035 0.002 TYR L 88 ARG 0.003 0.000 ARG B 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 49) link_NAG-ASN : angle 2.04361 ( 147) link_ALPHA1-6 : bond 0.01021 ( 13) link_ALPHA1-6 : angle 1.71092 ( 39) link_BETA1-4 : bond 0.01228 ( 74) link_BETA1-4 : angle 2.41043 ( 222) link_ALPHA1-2 : bond 0.00510 ( 9) link_ALPHA1-2 : angle 1.48219 ( 27) link_ALPHA1-3 : bond 0.01119 ( 15) link_ALPHA1-3 : angle 2.70897 ( 45) hydrogen bonds : bond 0.05624 ( 1154) hydrogen bonds : angle 5.46968 ( 3063) SS BOND : bond 0.00412 ( 51) SS BOND : angle 1.58951 ( 102) covalent geometry : bond 0.00404 (31634) covalent geometry : angle 0.67096 (43020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 317 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7848 (ttp) cc_final: 0.7547 (ttm) REVERT: A 161 MET cc_start: 0.6998 (mmt) cc_final: 0.6569 (tpp) REVERT: A 686 MET cc_start: 0.7974 (ttt) cc_final: 0.7767 (ttt) REVERT: A 871 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7661 (pp) REVERT: A 943 MET cc_start: 0.7585 (mmt) cc_final: 0.7264 (tpp) REVERT: A 1020 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7505 (tm-30) REVERT: H 13 LYS cc_start: 0.8258 (tppt) cc_final: 0.7787 (tppt) REVERT: H 92 ASP cc_start: 0.7724 (m-30) cc_final: 0.5596 (t70) REVERT: H 108 TRP cc_start: 0.7043 (t-100) cc_final: 0.6757 (t-100) REVERT: D 52 LYS cc_start: 0.8276 (mttp) cc_final: 0.7881 (mtmt) REVERT: D 62 TYR cc_start: 0.8195 (m-80) cc_final: 0.7945 (m-80) REVERT: D 115 ASP cc_start: 0.8395 (p0) cc_final: 0.7922 (p0) REVERT: E 81 GLN cc_start: 0.7849 (pp30) cc_final: 0.7457 (pp30) REVERT: E 87 ASP cc_start: 0.7042 (m-30) cc_final: 0.6836 (m-30) REVERT: B 179 LEU cc_start: 0.8888 (pp) cc_final: 0.8510 (pp) REVERT: B 240 MET cc_start: 0.6992 (ttt) cc_final: 0.5930 (ttt) REVERT: B 245 ILE cc_start: 0.8409 (mm) cc_final: 0.8201 (mt) REVERT: B 939 MET cc_start: 0.8258 (tpp) cc_final: 0.8054 (tpp) REVERT: B 943 MET cc_start: 0.7729 (mtm) cc_final: 0.7276 (ttm) REVERT: B 1031 GLN cc_start: 0.8463 (mt0) cc_final: 0.8096 (tm-30) REVERT: B 1084 GLN cc_start: 0.8271 (tp40) cc_final: 0.7815 (tp40) REVERT: B 1137 MET cc_start: 0.8571 (mtm) cc_final: 0.8362 (ptp) REVERT: C 84 MET cc_start: 0.6466 (ptm) cc_final: 0.6219 (ptm) REVERT: C 156 PHE cc_start: 0.5180 (OUTLIER) cc_final: 0.4737 (m-10) REVERT: C 628 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: C 827 PHE cc_start: 0.8223 (t80) cc_final: 0.7959 (t80) REVERT: C 1008 MET cc_start: 0.8442 (tmm) cc_final: 0.8206 (tmm) outliers start: 111 outliers final: 83 residues processed: 401 average time/residue: 0.3759 time to fit residues: 253.8782 Evaluate side-chains 373 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 287 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1059 ASP Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 368 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 288 optimal weight: 0.1980 chunk 161 optimal weight: 0.4980 chunk 336 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN D 119 GLN B1042 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.141069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111675 restraints weight = 60010.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115037 restraints weight = 35512.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115111 restraints weight = 23475.114| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31845 Z= 0.172 Angle : 0.714 14.126 43602 Z= 0.340 Chirality : 0.046 0.303 5278 Planarity : 0.004 0.064 5317 Dihedral : 8.504 65.757 7299 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 3.57 % Allowed : 13.65 % Favored : 82.78 % 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: -0.30 (0.13), residues: 3717 helix: 1.41 (0.21), residues: 673 sheet: 0.01 (0.16), residues: 952 loop : -0.83 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.006 0.001 HIS C 681 PHE 0.024 0.002 PHE C 40 TYR 0.039 0.001 TYR L 88 ARG 0.008 0.000 ARG D 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 49) link_NAG-ASN : angle 2.01126 ( 147) link_ALPHA1-6 : bond 0.01052 ( 13) link_ALPHA1-6 : angle 1.70138 ( 39) link_BETA1-4 : bond 0.01203 ( 74) link_BETA1-4 : angle 2.44128 ( 222) link_ALPHA1-2 : bond 0.00516 ( 9) link_ALPHA1-2 : angle 1.45186 ( 27) link_ALPHA1-3 : bond 0.01124 ( 15) link_ALPHA1-3 : angle 2.69535 ( 45) hydrogen bonds : bond 0.05491 ( 1154) hydrogen bonds : angle 5.47567 ( 3063) SS BOND : bond 0.00314 ( 51) SS BOND : angle 2.08417 ( 102) covalent geometry : bond 0.00389 (31634) covalent geometry : angle 0.67073 (43020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 311 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7734 (ttp) cc_final: 0.7388 (ttm) REVERT: A 161 MET cc_start: 0.7153 (mmt) cc_final: 0.6766 (tpp) REVERT: A 850 PHE cc_start: 0.8553 (m-80) cc_final: 0.8202 (m-10) REVERT: A 871 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7682 (pp) REVERT: A 943 MET cc_start: 0.7605 (mmt) cc_final: 0.7278 (tpp) REVERT: A 1020 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7395 (tm-30) REVERT: L 88 TYR cc_start: 0.7473 (m-80) cc_final: 0.7112 (m-80) REVERT: H 27 LEU cc_start: 0.1708 (OUTLIER) cc_final: 0.1246 (pp) REVERT: H 92 ASP cc_start: 0.7653 (m-30) cc_final: 0.5599 (t70) REVERT: H 108 TRP cc_start: 0.6933 (t-100) cc_final: 0.6679 (t-100) REVERT: D 28 THR cc_start: 0.9460 (t) cc_final: 0.9111 (p) REVERT: D 52 LYS cc_start: 0.8200 (mttp) cc_final: 0.7908 (mtmt) REVERT: D 62 TYR cc_start: 0.8170 (m-80) cc_final: 0.7885 (m-80) REVERT: E 81 GLN cc_start: 0.7876 (pp30) cc_final: 0.7586 (pp30) REVERT: B 78 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8067 (tp-100) REVERT: B 174 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: B 179 LEU cc_start: 0.8859 (pp) cc_final: 0.8507 (pp) REVERT: B 240 MET cc_start: 0.6875 (ttt) cc_final: 0.5837 (ttt) REVERT: B 943 MET cc_start: 0.7613 (mtm) cc_final: 0.7190 (ttm) REVERT: B 1031 GLN cc_start: 0.8467 (mt0) cc_final: 0.8107 (tm-30) REVERT: B 1084 GLN cc_start: 0.8241 (tp40) cc_final: 0.7785 (tp40) REVERT: B 1137 MET cc_start: 0.8535 (mtm) cc_final: 0.8321 (ptp) REVERT: C 84 MET cc_start: 0.6568 (ptm) cc_final: 0.6328 (ptm) REVERT: C 156 PHE cc_start: 0.5189 (OUTLIER) cc_final: 0.4724 (m-10) REVERT: C 628 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: C 1200 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8447 (mm) outliers start: 114 outliers final: 83 residues processed: 394 average time/residue: 0.3808 time to fit residues: 250.1849 Evaluate side-chains 382 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 292 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 288 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 236 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 342 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 319 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.139256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109998 restraints weight = 59986.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.113072 restraints weight = 35908.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.113027 restraints weight = 24354.336| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31845 Z= 0.210 Angle : 0.749 12.767 43602 Z= 0.358 Chirality : 0.047 0.315 5278 Planarity : 0.005 0.063 5317 Dihedral : 8.313 64.156 7299 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 4.04 % Allowed : 13.84 % Favored : 82.12 % 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: -0.46 (0.13), residues: 3717 helix: 1.30 (0.21), residues: 673 sheet: 0.01 (0.16), residues: 931 loop : -0.99 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 33 HIS 0.007 0.001 HIS C 681 PHE 0.023 0.002 PHE B 786 TYR 0.027 0.002 TYR L 88 ARG 0.009 0.001 ARG B 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 49) link_NAG-ASN : angle 2.09232 ( 147) link_ALPHA1-6 : bond 0.01033 ( 13) link_ALPHA1-6 : angle 1.71394 ( 39) link_BETA1-4 : bond 0.01189 ( 74) link_BETA1-4 : angle 2.48344 ( 222) link_ALPHA1-2 : bond 0.00548 ( 9) link_ALPHA1-2 : angle 1.49733 ( 27) link_ALPHA1-3 : bond 0.01139 ( 15) link_ALPHA1-3 : angle 2.77033 ( 45) hydrogen bonds : bond 0.05820 ( 1154) hydrogen bonds : angle 5.59358 ( 3063) SS BOND : bond 0.00371 ( 51) SS BOND : angle 1.95900 ( 102) covalent geometry : bond 0.00487 (31634) covalent geometry : angle 0.70782 (43020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 315 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7741 (ttp) cc_final: 0.7380 (ttm) REVERT: A 871 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7821 (pp) REVERT: A 943 MET cc_start: 0.7680 (mmt) cc_final: 0.7408 (tpp) REVERT: A 1020 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 1102 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8600 (tttm) REVERT: H 27 LEU cc_start: 0.1775 (OUTLIER) cc_final: 0.1292 (pp) REVERT: H 29 PHE cc_start: 0.5592 (t80) cc_final: 0.5224 (t80) REVERT: H 92 ASP cc_start: 0.7679 (m-30) cc_final: 0.5603 (t70) REVERT: H 108 TRP cc_start: 0.7039 (t-100) cc_final: 0.6719 (t-100) REVERT: D 28 THR cc_start: 0.9444 (t) cc_final: 0.9224 (p) REVERT: D 52 LYS cc_start: 0.8325 (mttp) cc_final: 0.7905 (mtmt) REVERT: D 62 TYR cc_start: 0.8207 (m-80) cc_final: 0.7977 (m-80) REVERT: D 98 CYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6594 (t) REVERT: B 78 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8098 (tp-100) REVERT: B 240 MET cc_start: 0.6902 (ttt) cc_final: 0.5942 (ttt) REVERT: B 303 ILE cc_start: 0.7302 (pp) cc_final: 0.6950 (mm) REVERT: B 943 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7172 (ttm) REVERT: B 1031 GLN cc_start: 0.8502 (mt0) cc_final: 0.8141 (tm-30) REVERT: B 1084 GLN cc_start: 0.8260 (tp40) cc_final: 0.7784 (tp40) REVERT: B 1105 GLU cc_start: 0.7110 (tt0) cc_final: 0.6883 (tt0) REVERT: C 84 MET cc_start: 0.6623 (ptm) cc_final: 0.6376 (ptm) REVERT: C 156 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4802 (m-10) REVERT: C 628 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: C 830 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8062 (ptmt) REVERT: C 1200 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8315 (mm) outliers start: 129 outliers final: 101 residues processed: 410 average time/residue: 0.3962 time to fit residues: 271.5231 Evaluate side-chains 405 residues out of total 3194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 295 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1121 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 78 GLN Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 592 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1197 ILE Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain B residue 1222 LEU Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 87 TYR Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 513 GLU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 689 TYR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 830 LYS Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 939 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 989 VAL Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1070 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1086 LEU Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1200 LEU Chi-restraints excluded: chain C residue 1205 VAL Chi-restraints excluded: chain C residue 1218 LEU Chi-restraints excluded: chain C residue 1222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 53.3614 > 50: distance: 51 - 52: 3.504 distance: 52 - 53: 9.006 distance: 52 - 59: 7.795 distance: 54 - 55: 5.010 distance: 55 - 56: 7.584 distance: 56 - 57: 7.392 distance: 57 - 58: 5.330 distance: 59 - 60: 5.074 distance: 60 - 63: 3.056 distance: 61 - 62: 6.373 distance: 61 - 67: 7.335 distance: 64 - 65: 8.120 distance: 64 - 66: 5.536 distance: 67 - 68: 3.522 distance: 68 - 69: 9.847 distance: 68 - 71: 5.919 distance: 69 - 70: 27.959 distance: 69 - 76: 25.417 distance: 71 - 72: 5.518 distance: 72 - 73: 5.814 distance: 73 - 75: 5.343 distance: 76 - 77: 6.741 distance: 77 - 78: 13.863 distance: 77 - 80: 11.684 distance: 78 - 79: 7.221 distance: 78 - 87: 10.162 distance: 80 - 81: 3.297 distance: 81 - 82: 19.691 distance: 81 - 83: 3.467 distance: 82 - 84: 10.444 distance: 83 - 85: 5.479 distance: 84 - 86: 8.433 distance: 85 - 86: 10.704 distance: 88 - 89: 6.613 distance: 88 - 91: 3.184 distance: 89 - 90: 3.910 distance: 89 - 92: 3.266 distance: 92 - 93: 3.959 distance: 93 - 94: 4.010 distance: 94 - 95: 4.557 distance: 97 - 98: 3.464 distance: 97 - 99: 5.210 distance: 99 - 172: 3.742 distance: 101 - 104: 3.581 distance: 102 - 103: 4.078 distance: 108 - 109: 5.231 distance: 109 - 110: 3.502 distance: 110 - 111: 7.169 distance: 112 - 113: 6.495 distance: 115 - 116: 4.001 distance: 116 - 117: 3.420 distance: 116 - 119: 5.868 distance: 117 - 118: 13.688 distance: 117 - 124: 5.517 distance: 119 - 120: 9.035 distance: 120 - 121: 8.465 distance: 121 - 122: 3.525 distance: 122 - 123: 4.057 distance: 124 - 125: 5.070 distance: 125 - 126: 5.528 distance: 125 - 128: 5.230 distance: 126 - 127: 10.042 distance: 126 - 132: 7.494 distance: 128 - 130: 7.519 distance: 129 - 131: 5.603