Starting phenix.real_space_refine on Wed Aug 27 02:46:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ozj_17311/08_2025/8ozj_17311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ozj_17311/08_2025/8ozj_17311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ozj_17311/08_2025/8ozj_17311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ozj_17311/08_2025/8ozj_17311.map" model { file = "/net/cci-nas-00/data/ceres_data/8ozj_17311/08_2025/8ozj_17311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ozj_17311/08_2025/8ozj_17311.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 222 5.16 5 C 29220 2.51 5 N 7188 2.21 5 O 8952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45588 Number of models: 1 Model: "" Number of chains: 82 Chain: "A" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "D" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "J" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "H" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} Chain: "L" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} Chain: "E" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "I" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3380 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 382} Chain breaks: 2 Chain: "G" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3328 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 377} Chain breaks: 2 Chain: "K" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3328 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 377} Chain breaks: 2 Chain: "M" 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: "e" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" 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: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "c" 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: 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: "g" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" 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: 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: 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: "O" 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: 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: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} 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: "P" 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: "Y" 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: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} 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: "Z" 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: 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: "X" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} 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: "R" 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: "a" 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: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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 Chain: "G" 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 Chain: "K" 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 Chain: "B" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "0" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} Chain: "1" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "2" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 94 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 2, 'TRANS': 8} Chain: "3" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} Chain: "4" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3190 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 386} Chain: "5" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "6" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "7" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3380 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 382} Chain breaks: 2 Chain: "8" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3328 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 377} Chain breaks: 2 Chain: "9" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3328 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 377} Chain breaks: 2 Chain: "k" 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: "l" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "p" 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: "q" 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: "r" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 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: "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: 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: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} 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: "y" 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: "z" 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: "AA" 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: "AB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} 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: "AC" 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: "AD" 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: "AE" 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: "AF" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} 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: "AG" 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: "AH" 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: "0" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CLR': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" 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 Chain: "8" 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 Chain: "9" 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: 11.46, per 1000 atoms: 0.25 Number of scatterers: 45588 At special positions: 0 Unit cell: (195.48, 191.16, 213.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 222 16.00 P 6 15.00 O 8952 8.00 N 7188 7.00 C 29220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS D 763 " - pdb=" SG CYS D 771 " distance=2.08 Simple disulfide: pdb=" SG CYS D 780 " - pdb=" SG CYS D 789 " distance=2.05 Simple disulfide: pdb=" SG CYS D 820 " - pdb=" SG CYS D 838 " distance=2.05 Simple disulfide: pdb=" SG CYS H 763 " - pdb=" SG CYS H 771 " distance=2.08 Simple disulfide: pdb=" SG CYS H 780 " - pdb=" SG CYS H 789 " distance=2.05 Simple disulfide: pdb=" SG CYS H 820 " - pdb=" SG CYS H 838 " distance=2.05 Simple disulfide: pdb=" SG CYS L 763 " - pdb=" SG CYS L 771 " distance=2.08 Simple disulfide: pdb=" SG CYS L 780 " - pdb=" SG CYS L 789 " distance=2.05 Simple disulfide: pdb=" SG CYS L 820 " - pdb=" SG CYS L 838 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 506 " distance=2.06 Simple disulfide: pdb=" SG CYS C 235 " - pdb=" SG CYS C 318 " distance=2.07 Simple disulfide: pdb=" SG CYS C 256 " - pdb=" SG CYS C 381 " distance=2.05 Simple disulfide: pdb=" SG CYS C 449 " - pdb=" SG CYS C 457 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 506 " distance=2.06 Simple disulfide: pdb=" SG CYS G 235 " - pdb=" SG CYS G 318 " distance=2.07 Simple disulfide: pdb=" SG CYS G 256 " - pdb=" SG CYS G 381 " distance=2.05 Simple disulfide: pdb=" SG CYS G 449 " - pdb=" SG CYS G 457 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 506 " distance=2.06 Simple disulfide: pdb=" SG CYS K 235 " - pdb=" SG CYS K 318 " distance=2.07 Simple disulfide: pdb=" SG CYS K 256 " - pdb=" SG CYS K 381 " distance=2.05 Simple disulfide: pdb=" SG CYS K 449 " - pdb=" SG CYS K 457 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 763 " - pdb=" SG CYS 0 771 " distance=2.08 Simple disulfide: pdb=" SG CYS 0 780 " - pdb=" SG CYS 0 789 " distance=2.05 Simple disulfide: pdb=" SG CYS 0 820 " - pdb=" SG CYS 0 838 " distance=2.05 Simple disulfide: pdb=" SG CYS 3 763 " - pdb=" SG CYS 3 771 " distance=2.08 Simple disulfide: pdb=" SG CYS 3 780 " - pdb=" SG CYS 3 789 " distance=2.05 Simple disulfide: pdb=" SG CYS 3 820 " - pdb=" SG CYS 3 838 " distance=2.05 Simple disulfide: pdb=" SG CYS 4 763 " - pdb=" SG CYS 4 771 " distance=2.08 Simple disulfide: pdb=" SG CYS 4 780 " - pdb=" SG CYS 4 789 " distance=2.05 Simple disulfide: pdb=" SG CYS 4 820 " - pdb=" SG CYS 4 838 " distance=2.05 Simple disulfide: pdb=" SG CYS 7 228 " - pdb=" SG CYS 7 506 " distance=2.06 Simple disulfide: pdb=" SG CYS 7 235 " - pdb=" SG CYS 7 318 " distance=2.07 Simple disulfide: pdb=" SG CYS 7 256 " - pdb=" SG CYS 7 381 " distance=2.05 Simple disulfide: pdb=" SG CYS 7 449 " - pdb=" SG CYS 7 457 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 228 " - pdb=" SG CYS 8 506 " distance=2.06 Simple disulfide: pdb=" SG CYS 8 235 " - pdb=" SG CYS 8 318 " distance=2.07 Simple disulfide: pdb=" SG CYS 8 256 " - pdb=" SG CYS 8 381 " distance=2.05 Simple disulfide: pdb=" SG CYS 8 449 " - pdb=" SG CYS 8 457 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 228 " - pdb=" SG CYS 9 506 " distance=2.06 Simple disulfide: pdb=" SG CYS 9 235 " - pdb=" SG CYS 9 318 " distance=2.07 Simple disulfide: pdb=" SG CYS 9 256 " - pdb=" SG CYS 9 381 " distance=2.05 Simple disulfide: pdb=" SG CYS 9 449 " - pdb=" SG CYS 9 457 " 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 e 5 " - " MAN e 6 " " MAN f 5 " - " MAN f 6 " " MAN g 5 " - " MAN g 6 " " MAN l 5 " - " MAN l 6 " " MAN o 5 " - " MAN o 6 " " MAN r 5 " - " MAN r 6 " ALPHA1-3 " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA e 3 " - " MAN e 8 " " MAN e 4 " - " MAN e 5 " " BMA f 3 " - " MAN f 8 " " MAN f 4 " - " MAN f 5 " " BMA g 3 " - " MAN g 8 " " MAN g 4 " - " MAN g 5 " " BMA h 3 " - " MAN h 6 " " MAN h 4 " - " MAN h 5 " " BMA i 3 " - " MAN i 6 " " MAN i 4 " - " MAN i 5 " " BMA j 3 " - " MAN j 6 " " MAN j 4 " - " MAN j 5 " " BMA l 3 " - " MAN l 8 " " MAN l 4 " - " MAN l 5 " " BMA n 3 " - " MAN n 6 " " MAN n 4 " - " MAN n 5 " " BMA o 3 " - " MAN o 8 " " MAN o 4 " - " MAN o 5 " " BMA q 3 " - " MAN q 6 " " MAN q 4 " - " MAN q 5 " " BMA r 3 " - " MAN r 8 " " MAN r 4 " - " MAN r 5 " " BMA t 3 " - " MAN t 6 " " MAN t 4 " - " MAN t 5 " " BMA x 3 " - " MAN x 4 " " BMAAB 3 " - " MANAB 4 " " BMAAF 3 " - " MANAF 4 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 6 " " BMA W 3 " - " MAN W 6 " " BMA X 3 " - " MAN X 6 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 7 " " BMA f 3 " - " MAN f 4 " " MAN f 4 " - " MAN f 7 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 7 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " MAN l 4 " - " MAN l 7 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 4 " " MAN o 4 " - " MAN o 7 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " MAN r 4 " - " MAN r 7 " " BMA t 3 " - " MAN t 4 " " BMA x 3 " - " MAN x 6 " " BMA y 3 " - " MAN y 4 " " BMAAB 3 " - " MANAB 6 " " BMAAC 3 " - " MANAC 4 " " BMAAF 3 " - " MANAF 6 " " BMAAG 3 " - " MANAG 4 " BETA1-2 " MAN V 4 " - " NAG V 5 " " MAN W 4 " - " NAG W 5 " " MAN X 4 " - " NAG X 5 " " MAN x 4 " - " NAG x 5 " " MANAB 4 " - " NAGAB 5 " " MANAF 4 " - " NAGAF 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 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 l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " 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 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 t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " 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 z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGAB 1 " - " NAGAB 2 " " NAGAB 2 " - " BMAAB 3 " " NAGAC 1 " - " NAGAC 2 " " NAGAC 2 " - " BMAAC 3 " " NAGAD 1 " - " NAGAD 2 " " NAGAE 1 " - " NAGAE 2 " " NAGAE 2 " - " BMAAE 3 " " NAGAF 1 " - " NAGAF 2 " " NAGAF 2 " - " BMAAF 3 " " NAGAG 1 " - " NAGAG 2 " " NAGAG 2 " - " BMAAG 3 " " NAGAH 1 " - " NAGAH 2 " NAG-ASN " NAG 71001 " - " ASN 7 405 " " NAG 71002 " - " ASN 7 311 " " NAG 71003 " - " ASN 7 556 " " NAG 81001 " - " ASN 8 405 " " NAG 81002 " - " ASN 8 311 " " NAG 81003 " - " ASN 8 556 " " NAG 91001 " - " ASN 9 405 " " NAG 91002 " - " ASN 9 311 " " NAG 91003 " - " ASN 9 556 " " NAG C1001 " - " ASN C 405 " " NAG C1002 " - " ASN C 311 " " NAG C1003 " - " ASN C 556 " " NAG G1001 " - " ASN G 405 " " NAG G1002 " - " ASN G 311 " " NAG G1003 " - " ASN G 556 " " NAG K1001 " - " ASN K 405 " " NAG K1002 " - " ASN K 311 " " NAG K1003 " - " ASN K 556 " " NAG M 1 " - " ASN A 109 " " NAG N 1 " - " ASN E 109 " " NAG O 1 " - " ASN I 109 " " NAG P 1 " - " ASN C 141 " " NAG Q 1 " - " ASN G 141 " " NAG R 1 " - " ASN K 141 " " NAG S 1 " - " ASN C 183 " " NAG T 1 " - " ASN G 183 " " NAG U 1 " - " ASN K 183 " " NAG V 1 " - " ASN C 391 " " NAG W 1 " - " ASN G 391 " " NAG X 1 " - " ASN K 391 " " NAG Y 1 " - " ASN C 527 " " NAG Z 1 " - " ASN G 527 " " NAG a 1 " - " ASN K 527 " " NAG b 1 " - " ASN D 833 " " NAG c 1 " - " ASN H 833 " " NAG d 1 " - " ASN L 833 " " NAG e 1 " - " ASN D 808 " " NAG f 1 " - " ASN H 808 " " NAG g 1 " - " ASN L 808 " " NAG h 1 " - " ASN D 782 " " NAG i 1 " - " ASN H 782 " " NAG j 1 " - " ASN L 782 " " NAG k 1 " - " ASN B 109 " " NAG l 1 " - " ASN 0 808 " " NAG m 1 " - " ASN 0 833 " " NAG n 1 " - " ASN 0 782 " " NAG o 1 " - " ASN 3 808 " " NAG p 1 " - " ASN 3 833 " " NAG q 1 " - " ASN 3 782 " " NAG r 1 " - " ASN 4 808 " " NAG s 1 " - " ASN 4 833 " " NAG t 1 " - " ASN 4 782 " " NAG u 1 " - " ASN 5 109 " " NAG v 1 " - " ASN 6 109 " " NAG w 1 " - " ASN 7 183 " " NAG x 1 " - " ASN 7 391 " " NAG y 1 " - " ASN 7 141 " " NAG z 1 " - " ASN 7 527 " " NAGAA 1 " - " ASN 8 183 " " NAGAB 1 " - " ASN 8 391 " " NAGAC 1 " - " ASN 8 141 " " NAGAD 1 " - " ASN 8 527 " " NAGAE 1 " - " ASN 9 183 " " NAGAF 1 " - " ASN 9 391 " " NAGAG 1 " - " ASN 9 141 " " NAGAH 1 " - " ASN 9 527 " Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.2 microseconds 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10072 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 66 sheets defined 40.3% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 59 through 101 removed outlier: 3.507A pdb=" N ILE A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.563A pdb=" N ALA A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 602 Processing helix chain 'D' and resid 620 through 624 Processing helix chain 'D' and resid 624 through 629 removed outlier: 4.209A pdb=" N SER D 628 " --> pdb=" O LEU D 624 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 629 " --> pdb=" O HIS D 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 624 through 629' Processing helix chain 'D' and resid 631 through 652 removed outlier: 3.518A pdb=" N ALA D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 652 " --> pdb=" O THR D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.901A pdb=" N TYR D 659 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET D 660 " --> pdb=" O TRP D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 660' Processing helix chain 'D' and resid 661 through 670 Processing helix chain 'D' and resid 672 through 683 removed outlier: 3.504A pdb=" N LYS D 677 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 876 Processing helix chain 'D' and resid 889 through 895 Processing helix chain 'D' and resid 897 through 903 Processing helix chain 'D' and resid 910 through 923 removed outlier: 3.564A pdb=" N GLN D 917 " --> pdb=" O ALA D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 942 removed outlier: 3.618A pdb=" N LEU D 940 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 979 removed outlier: 3.582A pdb=" N LYS D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) Proline residue: D 960 - end of helix removed outlier: 3.643A pdb=" N PHE D 975 " --> pdb=" O VAL D 971 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 602 Processing helix chain 'H' and resid 620 through 624 Processing helix chain 'H' and resid 624 through 629 removed outlier: 4.209A pdb=" N SER H 628 " --> pdb=" O LEU H 624 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL H 629 " --> pdb=" O HIS H 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 624 through 629' Processing helix chain 'H' and resid 631 through 652 removed outlier: 3.519A pdb=" N ALA H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU H 652 " --> pdb=" O THR H 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 656 through 660 removed outlier: 3.901A pdb=" N TYR H 659 " --> pdb=" O ASP H 656 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET H 660 " --> pdb=" O TRP H 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 656 through 660' Processing helix chain 'H' and resid 661 through 670 Processing helix chain 'H' and resid 672 through 683 removed outlier: 3.504A pdb=" N LYS H 677 " --> pdb=" O ASP H 673 " (cutoff:3.500A) Processing helix chain 'H' and resid 869 through 876 Processing helix chain 'H' and resid 889 through 895 Processing helix chain 'H' and resid 897 through 903 Processing helix chain 'H' and resid 910 through 923 removed outlier: 3.563A pdb=" N GLN H 917 " --> pdb=" O ALA H 913 " (cutoff:3.500A) Processing helix chain 'H' and resid 926 through 942 removed outlier: 3.618A pdb=" N LEU H 940 " --> pdb=" O ILE H 936 " (cutoff:3.500A) Processing helix chain 'H' and resid 946 through 979 removed outlier: 3.582A pdb=" N LYS H 959 " --> pdb=" O LEU H 955 " (cutoff:3.500A) Proline residue: H 960 - end of helix removed outlier: 3.643A pdb=" N PHE H 975 " --> pdb=" O VAL H 971 " (cutoff:3.500A) Processing helix chain 'L' and resid 596 through 602 Processing helix chain 'L' and resid 620 through 624 Processing helix chain 'L' and resid 624 through 629 removed outlier: 4.210A pdb=" N SER L 628 " --> pdb=" O LEU L 624 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL L 629 " --> pdb=" O HIS L 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 624 through 629' Processing helix chain 'L' and resid 631 through 652 removed outlier: 3.519A pdb=" N ALA L 635 " --> pdb=" O GLU L 631 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU L 652 " --> pdb=" O THR L 648 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 660 removed outlier: 3.902A pdb=" N TYR L 659 " --> pdb=" O ASP L 656 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET L 660 " --> pdb=" O TRP L 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 656 through 660' Processing helix chain 'L' and resid 661 through 670 Processing helix chain 'L' and resid 672 through 683 removed outlier: 3.506A pdb=" N LYS L 677 " --> pdb=" O ASP L 673 " (cutoff:3.500A) Processing helix chain 'L' and resid 869 through 876 Processing helix chain 'L' and resid 889 through 895 Processing helix chain 'L' and resid 897 through 903 Processing helix chain 'L' and resid 910 through 923 removed outlier: 3.562A pdb=" N GLN L 917 " --> pdb=" O ALA L 913 " (cutoff:3.500A) Processing helix chain 'L' and resid 926 through 942 removed outlier: 3.618A pdb=" N LEU L 940 " --> pdb=" O ILE L 936 " (cutoff:3.500A) Processing helix chain 'L' and resid 946 through 979 removed outlier: 3.582A pdb=" N LYS L 959 " --> pdb=" O LEU L 955 " (cutoff:3.500A) Proline residue: L 960 - end of helix removed outlier: 3.643A pdb=" N PHE L 975 " --> pdb=" O VAL L 971 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 101 removed outlier: 3.506A pdb=" N ILE E 77 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.564A pdb=" N ALA E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 101 removed outlier: 3.507A pdb=" N ILE I 77 " --> pdb=" O PHE I 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN I 100 " --> pdb=" O ASN I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 114 removed outlier: 3.563A pdb=" N ALA I 114 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 175 through 182 removed outlier: 3.669A pdb=" N ASN C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 205 removed outlier: 3.633A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 219 Processing helix chain 'C' and resid 220 through 233 Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.558A pdb=" N TRP C 273 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.925A pdb=" N LYS C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 332 through 347 removed outlier: 3.522A pdb=" N ARG C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.936A pdb=" N SER C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 removed outlier: 3.650A pdb=" N VAL C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 471 through 478 Processing helix chain 'C' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS C 511 " --> pdb=" O LYS C 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA C 512 " --> pdb=" O ILE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 526 removed outlier: 3.552A pdb=" N PHE C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 537 through 540 Processing helix chain 'G' and resid 145 through 147 No H-bonds generated for 'chain 'G' and resid 145 through 147' Processing helix chain 'G' and resid 175 through 182 removed outlier: 3.669A pdb=" N ASN G 181 " --> pdb=" O ASN G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 205 removed outlier: 3.632A pdb=" N LYS G 190 " --> pdb=" O GLN G 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G 203 " --> pdb=" O GLU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 219 Processing helix chain 'G' and resid 220 through 233 Processing helix chain 'G' and resid 270 through 276 removed outlier: 3.558A pdb=" N TRP G 273 " --> pdb=" O GLN G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 removed outlier: 3.924A pdb=" N LYS G 292 " --> pdb=" O THR G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 332 through 347 removed outlier: 3.521A pdb=" N ARG G 338 " --> pdb=" O GLU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 359 Processing helix chain 'G' and resid 378 through 383 removed outlier: 3.937A pdb=" N SER G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 391 removed outlier: 3.651A pdb=" N VAL G 387 " --> pdb=" O LYS G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 406 Processing helix chain 'G' and resid 471 through 478 Processing helix chain 'G' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS G 511 " --> pdb=" O LYS G 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA G 512 " --> pdb=" O ILE G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 526 removed outlier: 3.552A pdb=" N PHE G 520 " --> pdb=" O ASP G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 536 Processing helix chain 'G' and resid 537 through 540 Processing helix chain 'K' and resid 145 through 147 No H-bonds generated for 'chain 'K' and resid 145 through 147' Processing helix chain 'K' and resid 175 through 182 removed outlier: 3.670A pdb=" N ASN K 181 " --> pdb=" O ASN K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 205 removed outlier: 3.633A pdb=" N LYS K 190 " --> pdb=" O GLN K 186 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 203 " --> pdb=" O GLU K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 219 Processing helix chain 'K' and resid 220 through 233 Processing helix chain 'K' and resid 270 through 276 removed outlier: 3.557A pdb=" N TRP K 273 " --> pdb=" O GLN K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 293 removed outlier: 3.925A pdb=" N LYS K 292 " --> pdb=" O THR K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 Processing helix chain 'K' and resid 332 through 347 removed outlier: 3.520A pdb=" N ARG K 338 " --> pdb=" O GLU K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 359 Processing helix chain 'K' and resid 378 through 383 removed outlier: 3.936A pdb=" N SER K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 391 removed outlier: 3.650A pdb=" N VAL K 387 " --> pdb=" O LYS K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 402 through 406 Processing helix chain 'K' and resid 471 through 478 Processing helix chain 'K' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS K 511 " --> pdb=" O LYS K 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA K 512 " --> pdb=" O ILE K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 514 through 526 removed outlier: 3.552A pdb=" N PHE K 520 " --> pdb=" O ASP K 516 " (cutoff:3.500A) Processing helix chain 'K' and resid 532 through 536 Processing helix chain 'K' and resid 537 through 540 Processing helix chain 'B' and resid 59 through 101 removed outlier: 3.507A pdb=" N ILE B 77 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 100 " --> pdb=" O ASN B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.563A pdb=" N ALA B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain '0' and resid 596 through 602 Processing helix chain '0' and resid 620 through 624 Processing helix chain '0' and resid 624 through 629 removed outlier: 4.209A pdb=" N SER 0 628 " --> pdb=" O LEU 0 624 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL 0 629 " --> pdb=" O HIS 0 625 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 624 through 629' Processing helix chain '0' and resid 631 through 652 removed outlier: 3.518A pdb=" N ALA 0 635 " --> pdb=" O GLU 0 631 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU 0 652 " --> pdb=" O THR 0 648 " (cutoff:3.500A) Processing helix chain '0' and resid 656 through 660 removed outlier: 3.901A pdb=" N TYR 0 659 " --> pdb=" O ASP 0 656 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET 0 660 " --> pdb=" O TRP 0 657 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 656 through 660' Processing helix chain '0' and resid 661 through 670 Processing helix chain '0' and resid 672 through 683 removed outlier: 3.504A pdb=" N LYS 0 677 " --> pdb=" O ASP 0 673 " (cutoff:3.500A) Processing helix chain '0' and resid 869 through 876 Processing helix chain '0' and resid 889 through 895 Processing helix chain '0' and resid 897 through 903 Processing helix chain '0' and resid 910 through 923 removed outlier: 3.564A pdb=" N GLN 0 917 " --> pdb=" O ALA 0 913 " (cutoff:3.500A) Processing helix chain '0' and resid 926 through 942 removed outlier: 3.618A pdb=" N LEU 0 940 " --> pdb=" O ILE 0 936 " (cutoff:3.500A) Processing helix chain '0' and resid 946 through 979 removed outlier: 3.582A pdb=" N LYS 0 959 " --> pdb=" O LEU 0 955 " (cutoff:3.500A) Proline residue: 0 960 - end of helix removed outlier: 3.643A pdb=" N PHE 0 975 " --> pdb=" O VAL 0 971 " (cutoff:3.500A) Processing helix chain '3' and resid 596 through 602 Processing helix chain '3' and resid 620 through 624 Processing helix chain '3' and resid 624 through 629 removed outlier: 4.209A pdb=" N SER 3 628 " --> pdb=" O LEU 3 624 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL 3 629 " --> pdb=" O HIS 3 625 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 624 through 629' Processing helix chain '3' and resid 631 through 652 removed outlier: 3.519A pdb=" N ALA 3 635 " --> pdb=" O GLU 3 631 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU 3 652 " --> pdb=" O THR 3 648 " (cutoff:3.500A) Processing helix chain '3' and resid 656 through 660 removed outlier: 3.901A pdb=" N TYR 3 659 " --> pdb=" O ASP 3 656 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET 3 660 " --> pdb=" O TRP 3 657 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 656 through 660' Processing helix chain '3' and resid 661 through 670 Processing helix chain '3' and resid 672 through 683 removed outlier: 3.504A pdb=" N LYS 3 677 " --> pdb=" O ASP 3 673 " (cutoff:3.500A) Processing helix chain '3' and resid 869 through 876 Processing helix chain '3' and resid 889 through 895 Processing helix chain '3' and resid 897 through 903 Processing helix chain '3' and resid 910 through 923 removed outlier: 3.563A pdb=" N GLN 3 917 " --> pdb=" O ALA 3 913 " (cutoff:3.500A) Processing helix chain '3' and resid 926 through 942 removed outlier: 3.618A pdb=" N LEU 3 940 " --> pdb=" O ILE 3 936 " (cutoff:3.500A) Processing helix chain '3' and resid 946 through 979 removed outlier: 3.582A pdb=" N LYS 3 959 " --> pdb=" O LEU 3 955 " (cutoff:3.500A) Proline residue: 3 960 - end of helix removed outlier: 3.643A pdb=" N PHE 3 975 " --> pdb=" O VAL 3 971 " (cutoff:3.500A) Processing helix chain '4' and resid 596 through 602 Processing helix chain '4' and resid 620 through 624 Processing helix chain '4' and resid 624 through 629 removed outlier: 4.210A pdb=" N SER 4 628 " --> pdb=" O LEU 4 624 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL 4 629 " --> pdb=" O HIS 4 625 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 624 through 629' Processing helix chain '4' and resid 631 through 652 removed outlier: 3.519A pdb=" N ALA 4 635 " --> pdb=" O GLU 4 631 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU 4 652 " --> pdb=" O THR 4 648 " (cutoff:3.500A) Processing helix chain '4' and resid 656 through 660 removed outlier: 3.902A pdb=" N TYR 4 659 " --> pdb=" O ASP 4 656 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET 4 660 " --> pdb=" O TRP 4 657 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 656 through 660' Processing helix chain '4' and resid 661 through 670 Processing helix chain '4' and resid 672 through 683 removed outlier: 3.506A pdb=" N LYS 4 677 " --> pdb=" O ASP 4 673 " (cutoff:3.500A) Processing helix chain '4' and resid 869 through 876 Processing helix chain '4' and resid 889 through 895 Processing helix chain '4' and resid 897 through 903 Processing helix chain '4' and resid 910 through 923 removed outlier: 3.562A pdb=" N GLN 4 917 " --> pdb=" O ALA 4 913 " (cutoff:3.500A) Processing helix chain '4' and resid 926 through 942 removed outlier: 3.618A pdb=" N LEU 4 940 " --> pdb=" O ILE 4 936 " (cutoff:3.500A) Processing helix chain '4' and resid 946 through 979 removed outlier: 3.582A pdb=" N LYS 4 959 " --> pdb=" O LEU 4 955 " (cutoff:3.500A) Proline residue: 4 960 - end of helix removed outlier: 3.643A pdb=" N PHE 4 975 " --> pdb=" O VAL 4 971 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 101 removed outlier: 3.506A pdb=" N ILE 5 77 " --> pdb=" O PHE 5 73 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN 5 100 " --> pdb=" O ASN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 110 through 114 removed outlier: 3.564A pdb=" N ALA 5 114 " --> pdb=" O THR 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 101 removed outlier: 3.507A pdb=" N ILE 6 77 " --> pdb=" O PHE 6 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN 6 100 " --> pdb=" O ASN 6 96 " (cutoff:3.500A) Processing helix chain '6' and resid 110 through 114 removed outlier: 3.563A pdb=" N ALA 6 114 " --> pdb=" O THR 6 111 " (cutoff:3.500A) Processing helix chain '7' and resid 145 through 147 No H-bonds generated for 'chain '7' and resid 145 through 147' Processing helix chain '7' and resid 175 through 182 removed outlier: 3.669A pdb=" N ASN 7 181 " --> pdb=" O ASN 7 177 " (cutoff:3.500A) Processing helix chain '7' and resid 185 through 205 removed outlier: 3.633A pdb=" N LYS 7 190 " --> pdb=" O GLN 7 186 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU 7 191 " --> pdb=" O GLU 7 187 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU 7 203 " --> pdb=" O GLU 7 199 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 219 Processing helix chain '7' and resid 220 through 233 Processing helix chain '7' and resid 270 through 276 removed outlier: 3.558A pdb=" N TRP 7 273 " --> pdb=" O GLN 7 270 " (cutoff:3.500A) Processing helix chain '7' and resid 288 through 293 removed outlier: 3.925A pdb=" N LYS 7 292 " --> pdb=" O THR 7 288 " (cutoff:3.500A) Processing helix chain '7' and resid 304 through 308 Processing helix chain '7' and resid 332 through 347 removed outlier: 3.522A pdb=" N ARG 7 338 " --> pdb=" O GLU 7 334 " (cutoff:3.500A) Processing helix chain '7' and resid 355 through 359 Processing helix chain '7' and resid 378 through 383 removed outlier: 3.936A pdb=" N SER 7 382 " --> pdb=" O LEU 7 378 " (cutoff:3.500A) Processing helix chain '7' and resid 383 through 391 removed outlier: 3.650A pdb=" N VAL 7 387 " --> pdb=" O LYS 7 383 " (cutoff:3.500A) Processing helix chain '7' and resid 402 through 406 Processing helix chain '7' and resid 471 through 478 Processing helix chain '7' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS 7 511 " --> pdb=" O LYS 7 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA 7 512 " --> pdb=" O ILE 7 508 " (cutoff:3.500A) Processing helix chain '7' and resid 514 through 526 removed outlier: 3.552A pdb=" N PHE 7 520 " --> pdb=" O ASP 7 516 " (cutoff:3.500A) Processing helix chain '7' and resid 532 through 536 Processing helix chain '7' and resid 537 through 540 Processing helix chain '8' and resid 145 through 147 No H-bonds generated for 'chain '8' and resid 145 through 147' Processing helix chain '8' and resid 175 through 182 removed outlier: 3.669A pdb=" N ASN 8 181 " --> pdb=" O ASN 8 177 " (cutoff:3.500A) Processing helix chain '8' and resid 185 through 205 removed outlier: 3.632A pdb=" N LYS 8 190 " --> pdb=" O GLN 8 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU 8 191 " --> pdb=" O GLU 8 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU 8 203 " --> pdb=" O GLU 8 199 " (cutoff:3.500A) Processing helix chain '8' and resid 216 through 219 Processing helix chain '8' and resid 220 through 233 Processing helix chain '8' and resid 270 through 276 removed outlier: 3.558A pdb=" N TRP 8 273 " --> pdb=" O GLN 8 270 " (cutoff:3.500A) Processing helix chain '8' and resid 288 through 293 removed outlier: 3.924A pdb=" N LYS 8 292 " --> pdb=" O THR 8 288 " (cutoff:3.500A) Processing helix chain '8' and resid 304 through 308 Processing helix chain '8' and resid 332 through 347 removed outlier: 3.521A pdb=" N ARG 8 338 " --> pdb=" O GLU 8 334 " (cutoff:3.500A) Processing helix chain '8' and resid 355 through 359 Processing helix chain '8' and resid 378 through 383 removed outlier: 3.937A pdb=" N SER 8 382 " --> pdb=" O LEU 8 378 " (cutoff:3.500A) Processing helix chain '8' and resid 383 through 391 removed outlier: 3.651A pdb=" N VAL 8 387 " --> pdb=" O LYS 8 383 " (cutoff:3.500A) Processing helix chain '8' and resid 402 through 406 Processing helix chain '8' and resid 471 through 478 Processing helix chain '8' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS 8 511 " --> pdb=" O LYS 8 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA 8 512 " --> pdb=" O ILE 8 508 " (cutoff:3.500A) Processing helix chain '8' and resid 514 through 526 removed outlier: 3.552A pdb=" N PHE 8 520 " --> pdb=" O ASP 8 516 " (cutoff:3.500A) Processing helix chain '8' and resid 532 through 536 Processing helix chain '8' and resid 537 through 540 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 175 through 182 removed outlier: 3.670A pdb=" N ASN 9 181 " --> pdb=" O ASN 9 177 " (cutoff:3.500A) Processing helix chain '9' and resid 185 through 205 removed outlier: 3.633A pdb=" N LYS 9 190 " --> pdb=" O GLN 9 186 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU 9 191 " --> pdb=" O GLU 9 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU 9 203 " --> pdb=" O GLU 9 199 " (cutoff:3.500A) Processing helix chain '9' and resid 216 through 219 Processing helix chain '9' and resid 220 through 233 Processing helix chain '9' and resid 270 through 276 removed outlier: 3.557A pdb=" N TRP 9 273 " --> pdb=" O GLN 9 270 " (cutoff:3.500A) Processing helix chain '9' and resid 288 through 293 removed outlier: 3.925A pdb=" N LYS 9 292 " --> pdb=" O THR 9 288 " (cutoff:3.500A) Processing helix chain '9' and resid 304 through 308 Processing helix chain '9' and resid 332 through 347 removed outlier: 3.520A pdb=" N ARG 9 338 " --> pdb=" O GLU 9 334 " (cutoff:3.500A) Processing helix chain '9' and resid 355 through 359 Processing helix chain '9' and resid 378 through 383 removed outlier: 3.936A pdb=" N SER 9 382 " --> pdb=" O LEU 9 378 " (cutoff:3.500A) Processing helix chain '9' and resid 383 through 391 removed outlier: 3.650A pdb=" N VAL 9 387 " --> pdb=" O LYS 9 383 " (cutoff:3.500A) Processing helix chain '9' and resid 402 through 406 Processing helix chain '9' and resid 471 through 478 Processing helix chain '9' and resid 502 through 514 removed outlier: 3.692A pdb=" N LYS 9 511 " --> pdb=" O LYS 9 507 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA 9 512 " --> pdb=" O ILE 9 508 " (cutoff:3.500A) Processing helix chain '9' and resid 514 through 526 removed outlier: 3.552A pdb=" N PHE 9 520 " --> pdb=" O ASP 9 516 " (cutoff:3.500A) Processing helix chain '9' and resid 532 through 536 Processing helix chain '9' and resid 537 through 540 Processing sheet with id=1, first strand: chain 'A' and resid 105 through 106 Processing sheet with id=2, first strand: chain 'D' and resid 590 through 591 Processing sheet with id=3, first strand: chain 'D' and resid 593 through 594 removed outlier: 5.554A pdb=" N SER C 168 " --> pdb=" O LEU D 612 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 158 " --> pdb=" O ILE D 716 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE D 716 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 160 " --> pdb=" O LYS D 714 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE D 712 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL C 164 " --> pdb=" O LEU D 710 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU D 710 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY C 166 " --> pdb=" O TYR D 708 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR D 708 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER C 168 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 706 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE C 170 " --> pdb=" O ILE D 704 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 704 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET C 172 " --> pdb=" O TRP D 702 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP D 702 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN C 174 " --> pdb=" O THR D 700 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR D 700 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA D 701 " --> pdb=" O GLN D 692 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN D 692 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU D 703 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL D 690 " --> pdb=" O GLU D 703 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY D 705 " --> pdb=" O TYR D 688 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 616 through 619 removed outlier: 6.347A pdb=" N VAL D 616 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N MET C 172 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR D 618 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ASN C 174 " --> pdb=" O THR D 618 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL D 769 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LYS C 161 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS D 771 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ARG C 163 " --> pdb=" O CYS D 771 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N VAL D 773 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 17.923A pdb=" N LEU C 165 " --> pdb=" O VAL D 773 " (cutoff:3.500A) removed outlier: 22.908A pdb=" N LYS D 775 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 29.827A pdb=" N LEU C 167 " --> pdb=" O LYS D 775 " (cutoff:3.500A) removed outlier: 35.422A pdb=" N VAL D 777 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 41.769A pdb=" N GLN C 169 " --> pdb=" O VAL D 777 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG D 765 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS D 771 " --> pdb=" O CYS D 763 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS D 763 " --> pdb=" O CYS D 771 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR D 757 " --> pdb=" O VAL D 777 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN D 720 " --> pdb=" O HIS C 154 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'D' and resid 728 through 732 removed outlier: 6.902A pdb=" N VAL D 791 " --> pdb=" O VAL D 883 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'D' and resid 801 through 805 Processing sheet with id=7, first strand: chain 'D' and resid 836 through 838 Processing sheet with id=8, first strand: chain 'D' and resid 850 through 851 Processing sheet with id=9, first strand: chain 'D' and resid 864 through 867 Processing sheet with id=10, first strand: chain 'F' and resid 128 through 132 Processing sheet with id=11, first strand: chain 'J' and resid 128 through 132 Processing sheet with id=12, first strand: chain 'H' and resid 593 through 594 removed outlier: 5.627A pdb=" N SER G 168 " --> pdb=" O LEU H 612 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE G 158 " --> pdb=" O ILE H 716 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE H 716 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL G 160 " --> pdb=" O LYS H 714 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE H 712 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL G 164 " --> pdb=" O LEU H 710 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU H 710 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY G 166 " --> pdb=" O TYR H 708 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR H 708 " --> pdb=" O GLY G 166 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER G 168 " --> pdb=" O LEU H 706 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU H 706 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE G 170 " --> pdb=" O ILE H 704 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE H 704 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET G 172 " --> pdb=" O TRP H 702 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP H 702 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN G 174 " --> pdb=" O THR H 700 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR H 700 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA H 701 " --> pdb=" O GLN H 692 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN H 692 " --> pdb=" O ALA H 701 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU H 703 " --> pdb=" O VAL H 690 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL H 690 " --> pdb=" O GLU H 703 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY H 705 " --> pdb=" O TYR H 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG H 684 " --> pdb=" O GLU H 709 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'H' and resid 616 through 619 removed outlier: 6.660A pdb=" N VAL H 769 " --> pdb=" O VAL G 159 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS G 161 " --> pdb=" O VAL H 769 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N CYS H 771 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ARG G 163 " --> pdb=" O CYS H 771 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N VAL H 773 " --> pdb=" O ARG G 163 " (cutoff:3.500A) removed outlier: 18.000A pdb=" N LEU G 165 " --> pdb=" O VAL H 773 " (cutoff:3.500A) removed outlier: 22.989A pdb=" N LYS H 775 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 29.910A pdb=" N LEU G 167 " --> pdb=" O LYS H 775 " (cutoff:3.500A) removed outlier: 35.505A pdb=" N VAL H 777 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 41.850A pdb=" N GLN G 169 " --> pdb=" O VAL H 777 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL H 769 " --> pdb=" O ARG H 765 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG H 765 " --> pdb=" O VAL H 769 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS H 771 " --> pdb=" O CYS H 763 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS H 763 " --> pdb=" O CYS H 771 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR H 757 " --> pdb=" O VAL H 777 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN H 720 " --> pdb=" O HIS G 154 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'H' and resid 728 through 732 removed outlier: 6.901A pdb=" N VAL H 791 " --> pdb=" O VAL H 883 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 836 through 838 Processing sheet with id=16, first strand: chain 'H' and resid 850 through 851 Processing sheet with id=17, first strand: chain 'L' and resid 593 through 594 removed outlier: 5.580A pdb=" N SER K 168 " --> pdb=" O LEU L 612 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS L 715 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU K 162 " --> pdb=" O PRO L 713 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL K 164 " --> pdb=" O VAL L 711 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL L 711 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY K 166 " --> pdb=" O GLU L 709 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU L 709 " --> pdb=" O GLY K 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER K 168 " --> pdb=" O TYR L 707 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR L 707 " --> pdb=" O SER K 168 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE K 170 " --> pdb=" O GLY L 705 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLY L 705 " --> pdb=" O ILE K 170 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET K 172 " --> pdb=" O GLU L 703 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU L 703 " --> pdb=" O MET K 172 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN K 174 " --> pdb=" O ALA L 701 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA L 701 " --> pdb=" O ASN K 174 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA L 701 " --> pdb=" O GLN L 692 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN L 692 " --> pdb=" O ALA L 701 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU L 703 " --> pdb=" O VAL L 690 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL L 690 " --> pdb=" O GLU L 703 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY L 705 " --> pdb=" O TYR L 688 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG L 684 " --> pdb=" O GLU L 709 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'L' and resid 616 through 619 removed outlier: 6.371A pdb=" N VAL L 616 " --> pdb=" O ILE K 170 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET K 172 " --> pdb=" O VAL L 616 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR L 618 " --> pdb=" O MET K 172 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN K 174 " --> pdb=" O THR L 618 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL L 769 " --> pdb=" O VAL K 159 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LYS K 161 " --> pdb=" O VAL L 769 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS L 771 " --> pdb=" O LYS K 161 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ARG K 163 " --> pdb=" O CYS L 771 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N VAL L 773 " --> pdb=" O ARG K 163 " (cutoff:3.500A) removed outlier: 17.944A pdb=" N LEU K 165 " --> pdb=" O VAL L 773 " (cutoff:3.500A) removed outlier: 22.933A pdb=" N LYS L 775 " --> pdb=" O LEU K 165 " (cutoff:3.500A) removed outlier: 29.851A pdb=" N LEU K 167 " --> pdb=" O LYS L 775 " (cutoff:3.500A) removed outlier: 35.446A pdb=" N VAL L 777 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 41.794A pdb=" N GLN K 169 " --> pdb=" O VAL L 777 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL L 769 " --> pdb=" O ARG L 765 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG L 765 " --> pdb=" O VAL L 769 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS L 771 " --> pdb=" O CYS L 763 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS L 763 " --> pdb=" O CYS L 771 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR L 757 " --> pdb=" O VAL L 777 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN L 720 " --> pdb=" O HIS K 154 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'L' and resid 728 through 732 removed outlier: 6.902A pdb=" N VAL L 791 " --> pdb=" O VAL L 883 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'L' and resid 836 through 838 Processing sheet with id=21, first strand: chain 'L' and resid 864 through 865 Processing sheet with id=22, first strand: chain 'C' and resid 498 through 501 Processing sheet with id=23, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.675A pdb=" N PHE C 301 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=25, first strand: chain 'C' and resid 393 through 395 Processing sheet with id=26, first strand: chain 'G' and resid 498 through 501 Processing sheet with id=27, first strand: chain 'G' and resid 250 through 251 removed outlier: 3.675A pdb=" N PHE G 301 " --> pdb=" O LEU G 251 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=29, first strand: chain 'G' and resid 393 through 395 Processing sheet with id=30, first strand: chain 'K' and resid 498 through 501 Processing sheet with id=31, first strand: chain 'K' and resid 250 through 251 removed outlier: 3.674A pdb=" N PHE K 301 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'K' and resid 282 through 283 Processing sheet with id=33, first strand: chain 'K' and resid 393 through 395 Processing sheet with id=34, first strand: chain 'B' and resid 105 through 106 Processing sheet with id=35, first strand: chain '0' and resid 590 through 591 Processing sheet with id=36, first strand: chain '0' and resid 593 through 594 removed outlier: 5.554A pdb=" N SER 7 168 " --> pdb=" O LEU 0 612 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE 7 158 " --> pdb=" O ILE 0 716 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE 0 716 " --> pdb=" O ILE 7 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL 7 160 " --> pdb=" O LYS 0 714 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE 0 712 " --> pdb=" O GLU 7 162 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL 7 164 " --> pdb=" O LEU 0 710 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU 0 710 " --> pdb=" O VAL 7 164 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY 7 166 " --> pdb=" O TYR 0 708 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR 0 708 " --> pdb=" O GLY 7 166 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER 7 168 " --> pdb=" O LEU 0 706 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU 0 706 " --> pdb=" O SER 7 168 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE 7 170 " --> pdb=" O ILE 0 704 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE 0 704 " --> pdb=" O ILE 7 170 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N MET 7 172 " --> pdb=" O TRP 0 702 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP 0 702 " --> pdb=" O MET 7 172 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN 7 174 " --> pdb=" O THR 0 700 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR 0 700 " --> pdb=" O ASN 7 174 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA 0 701 " --> pdb=" O GLN 0 692 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN 0 692 " --> pdb=" O ALA 0 701 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU 0 703 " --> pdb=" O VAL 0 690 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL 0 690 " --> pdb=" O GLU 0 703 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY 0 705 " --> pdb=" O TYR 0 688 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain '0' and resid 616 through 619 removed outlier: 6.347A pdb=" N VAL 0 616 " --> pdb=" O ILE 7 170 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N MET 7 172 " --> pdb=" O VAL 0 616 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR 0 618 " --> pdb=" O MET 7 172 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ASN 7 174 " --> pdb=" O THR 0 618 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL 0 769 " --> pdb=" O VAL 7 159 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LYS 7 161 " --> pdb=" O VAL 0 769 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS 0 771 " --> pdb=" O LYS 7 161 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ARG 7 163 " --> pdb=" O CYS 0 771 " (cutoff:3.500A) removed outlier: 10.979A pdb=" N VAL 0 773 " --> pdb=" O ARG 7 163 " (cutoff:3.500A) removed outlier: 17.923A pdb=" N LEU 7 165 " --> pdb=" O VAL 0 773 " (cutoff:3.500A) removed outlier: 22.908A pdb=" N LYS 0 775 " --> pdb=" O LEU 7 165 " (cutoff:3.500A) removed outlier: 29.827A pdb=" N LEU 7 167 " --> pdb=" O LYS 0 775 " (cutoff:3.500A) removed outlier: 35.422A pdb=" N VAL 0 777 " --> pdb=" O LEU 7 167 " (cutoff:3.500A) removed outlier: 41.769A pdb=" N GLN 7 169 " --> pdb=" O VAL 0 777 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL 0 769 " --> pdb=" O ARG 0 765 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG 0 765 " --> pdb=" O VAL 0 769 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N CYS 0 771 " --> pdb=" O CYS 0 763 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS 0 763 " --> pdb=" O CYS 0 771 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR 0 757 " --> pdb=" O VAL 0 777 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN 0 720 " --> pdb=" O HIS 7 154 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain '0' and resid 728 through 732 removed outlier: 6.902A pdb=" N VAL 0 791 " --> pdb=" O VAL 0 883 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain '0' and resid 801 through 805 Processing sheet with id=40, first strand: chain '0' and resid 836 through 838 Processing sheet with id=41, first strand: chain '0' and resid 850 through 851 Processing sheet with id=42, first strand: chain '0' and resid 864 through 867 Processing sheet with id=43, first strand: chain '1' and resid 128 through 132 Processing sheet with id=44, first strand: chain '2' and resid 128 through 132 Processing sheet with id=45, first strand: chain '3' and resid 593 through 594 removed outlier: 5.627A pdb=" N SER 8 168 " --> pdb=" O LEU 3 612 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE 8 158 " --> pdb=" O ILE 3 716 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE 3 716 " --> pdb=" O ILE 8 158 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL 8 160 " --> pdb=" O LYS 3 714 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE 3 712 " --> pdb=" O GLU 8 162 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL 8 164 " --> pdb=" O LEU 3 710 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU 3 710 " --> pdb=" O VAL 8 164 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY 8 166 " --> pdb=" O TYR 3 708 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR 3 708 " --> pdb=" O GLY 8 166 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER 8 168 " --> pdb=" O LEU 3 706 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU 3 706 " --> pdb=" O SER 8 168 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE 8 170 " --> pdb=" O ILE 3 704 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE 3 704 " --> pdb=" O ILE 8 170 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET 8 172 " --> pdb=" O TRP 3 702 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP 3 702 " --> pdb=" O MET 8 172 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN 8 174 " --> pdb=" O THR 3 700 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR 3 700 " --> pdb=" O ASN 8 174 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA 3 701 " --> pdb=" O GLN 3 692 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN 3 692 " --> pdb=" O ALA 3 701 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU 3 703 " --> pdb=" O VAL 3 690 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL 3 690 " --> pdb=" O GLU 3 703 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY 3 705 " --> pdb=" O TYR 3 688 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG 3 684 " --> pdb=" O GLU 3 709 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain '3' and resid 616 through 619 removed outlier: 6.660A pdb=" N VAL 3 769 " --> pdb=" O VAL 8 159 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS 8 161 " --> pdb=" O VAL 3 769 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N CYS 3 771 " --> pdb=" O LYS 8 161 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ARG 8 163 " --> pdb=" O CYS 3 771 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N VAL 3 773 " --> pdb=" O ARG 8 163 " (cutoff:3.500A) removed outlier: 18.000A pdb=" N LEU 8 165 " --> pdb=" O VAL 3 773 " (cutoff:3.500A) removed outlier: 22.989A pdb=" N LYS 3 775 " --> pdb=" O LEU 8 165 " (cutoff:3.500A) removed outlier: 29.910A pdb=" N LEU 8 167 " --> pdb=" O LYS 3 775 " (cutoff:3.500A) removed outlier: 35.505A pdb=" N VAL 3 777 " --> pdb=" O LEU 8 167 " (cutoff:3.500A) removed outlier: 41.850A pdb=" N GLN 8 169 " --> pdb=" O VAL 3 777 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL 3 769 " --> pdb=" O ARG 3 765 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG 3 765 " --> pdb=" O VAL 3 769 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS 3 771 " --> pdb=" O CYS 3 763 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS 3 763 " --> pdb=" O CYS 3 771 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR 3 757 " --> pdb=" O VAL 3 777 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN 3 720 " --> pdb=" O HIS 8 154 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain '3' and resid 728 through 732 removed outlier: 6.901A pdb=" N VAL 3 791 " --> pdb=" O VAL 3 883 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain '3' and resid 836 through 838 Processing sheet with id=49, first strand: chain '3' and resid 850 through 851 Processing sheet with id=50, first strand: chain '4' and resid 593 through 594 removed outlier: 5.580A pdb=" N SER 9 168 " --> pdb=" O LEU 4 612 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS 4 715 " --> pdb=" O VAL 9 160 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU 9 162 " --> pdb=" O PRO 4 713 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL 9 164 " --> pdb=" O VAL 4 711 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL 4 711 " --> pdb=" O VAL 9 164 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY 9 166 " --> pdb=" O GLU 4 709 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU 4 709 " --> pdb=" O GLY 9 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER 9 168 " --> pdb=" O TYR 4 707 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR 4 707 " --> pdb=" O SER 9 168 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE 9 170 " --> pdb=" O GLY 4 705 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLY 4 705 " --> pdb=" O ILE 9 170 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET 9 172 " --> pdb=" O GLU 4 703 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU 4 703 " --> pdb=" O MET 9 172 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN 9 174 " --> pdb=" O ALA 4 701 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA 4 701 " --> pdb=" O ASN 9 174 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA 4 701 " --> pdb=" O GLN 4 692 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN 4 692 " --> pdb=" O ALA 4 701 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU 4 703 " --> pdb=" O VAL 4 690 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL 4 690 " --> pdb=" O GLU 4 703 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY 4 705 " --> pdb=" O TYR 4 688 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG 4 684 " --> pdb=" O GLU 4 709 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain '4' and resid 616 through 619 removed outlier: 6.371A pdb=" N VAL 4 616 " --> pdb=" O ILE 9 170 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N MET 9 172 " --> pdb=" O VAL 4 616 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR 4 618 " --> pdb=" O MET 9 172 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN 9 174 " --> pdb=" O THR 4 618 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL 4 769 " --> pdb=" O VAL 9 159 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LYS 9 161 " --> pdb=" O VAL 4 769 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS 4 771 " --> pdb=" O LYS 9 161 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ARG 9 163 " --> pdb=" O CYS 4 771 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N VAL 4 773 " --> pdb=" O ARG 9 163 " (cutoff:3.500A) removed outlier: 17.944A pdb=" N LEU 9 165 " --> pdb=" O VAL 4 773 " (cutoff:3.500A) removed outlier: 22.933A pdb=" N LYS 4 775 " --> pdb=" O LEU 9 165 " (cutoff:3.500A) removed outlier: 29.851A pdb=" N LEU 9 167 " --> pdb=" O LYS 4 775 " (cutoff:3.500A) removed outlier: 35.446A pdb=" N VAL 4 777 " --> pdb=" O LEU 9 167 " (cutoff:3.500A) removed outlier: 41.794A pdb=" N GLN 9 169 " --> pdb=" O VAL 4 777 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL 4 769 " --> pdb=" O ARG 4 765 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG 4 765 " --> pdb=" O VAL 4 769 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS 4 771 " --> pdb=" O CYS 4 763 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS 4 763 " --> pdb=" O CYS 4 771 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR 4 757 " --> pdb=" O VAL 4 777 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN 4 720 " --> pdb=" O HIS 9 154 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain '4' and resid 728 through 732 removed outlier: 6.902A pdb=" N VAL 4 791 " --> pdb=" O VAL 4 883 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain '4' and resid 836 through 838 Processing sheet with id=54, first strand: chain '4' and resid 864 through 865 Processing sheet with id=55, first strand: chain '7' and resid 498 through 501 Processing sheet with id=56, first strand: chain '7' and resid 250 through 251 removed outlier: 3.675A pdb=" N PHE 7 301 " --> pdb=" O LEU 7 251 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain '7' and resid 282 through 283 Processing sheet with id=58, first strand: chain '7' and resid 393 through 395 Processing sheet with id=59, first strand: chain '8' and resid 498 through 501 Processing sheet with id=60, first strand: chain '8' and resid 250 through 251 removed outlier: 3.675A pdb=" N PHE 8 301 " --> pdb=" O LEU 8 251 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain '8' and resid 282 through 283 Processing sheet with id=62, first strand: chain '8' and resid 393 through 395 Processing sheet with id=63, first strand: chain '9' and resid 498 through 501 Processing sheet with id=64, first strand: chain '9' and resid 250 through 251 removed outlier: 3.674A pdb=" N PHE 9 301 " --> pdb=" O LEU 9 251 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain '9' and resid 282 through 283 Processing sheet with id=66, first strand: chain '9' and resid 393 through 395 1738 hydrogen bonds defined for protein. 4596 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: 10.99 Time building geometry restraints manager: 5.94 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: 7062 1.32 - 1.45: 12834 1.45 - 1.57: 26402 1.57 - 1.70: 12 1.70 - 1.83: 312 Bond restraints: 46622 Sorted by residual: bond pdb=" N ILE K 303 " pdb=" CA ILE K 303 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.38e+01 bond pdb=" N ILE 9 303 " pdb=" CA ILE 9 303 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.38e+01 bond pdb=" N ILE 7 303 " pdb=" CA ILE 7 303 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.37e+01 bond pdb=" N ILE C 303 " pdb=" CA ILE C 303 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.37e+01 bond pdb=" N ILE G 303 " pdb=" CA ILE G 303 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.32e+01 ... (remaining 46617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 49916 2.19 - 4.37: 12548 4.37 - 6.56: 872 6.56 - 8.75: 8 8.75 - 10.93: 18 Bond angle restraints: 63362 Sorted by residual: angle pdb=" N PRO 8 135 " pdb=" CA PRO 8 135 " pdb=" C PRO 8 135 " ideal model delta sigma weight residual 111.34 120.29 -8.95 1.55e+00 4.16e-01 3.33e+01 angle pdb=" N PRO G 135 " pdb=" CA PRO G 135 " pdb=" C PRO G 135 " ideal model delta sigma weight residual 111.34 120.29 -8.95 1.55e+00 4.16e-01 3.33e+01 angle pdb=" N PRO K 135 " pdb=" CA PRO K 135 " pdb=" C PRO K 135 " ideal model delta sigma weight residual 111.34 120.17 -8.83 1.55e+00 4.16e-01 3.25e+01 angle pdb=" N PRO 9 135 " pdb=" CA PRO 9 135 " pdb=" C PRO 9 135 " ideal model delta sigma weight residual 111.34 120.17 -8.83 1.55e+00 4.16e-01 3.25e+01 angle pdb=" N PRO 7 135 " pdb=" CA PRO 7 135 " pdb=" C PRO 7 135 " ideal model delta sigma weight residual 111.34 120.15 -8.81 1.55e+00 4.16e-01 3.23e+01 ... (remaining 63357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 29118 23.79 - 47.58: 1474 47.58 - 71.38: 366 71.38 - 95.17: 186 95.17 - 118.96: 108 Dihedral angle restraints: 31252 sinusoidal: 15682 harmonic: 15570 Sorted by residual: dihedral pdb=" CA TRP K 246 " pdb=" C TRP K 246 " pdb=" N PRO K 247 " pdb=" CA PRO K 247 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TRP 9 246 " pdb=" C TRP 9 246 " pdb=" N PRO 9 247 " pdb=" CA PRO 9 247 " ideal model delta harmonic sigma weight residual 180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TRP G 246 " pdb=" C TRP G 246 " pdb=" N PRO G 247 " pdb=" CA PRO G 247 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 31249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5394 0.098 - 0.196: 2190 0.196 - 0.294: 198 0.294 - 0.391: 6 0.391 - 0.489: 12 Chirality restraints: 7800 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.79e+01 chirality pdb=" C1 NAG w 2 " pdb=" O4 NAG w 1 " pdb=" C2 NAG w 2 " pdb=" O5 NAG w 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.79e+01 chirality pdb=" C1 NAGAE 2 " pdb=" O4 NAGAE 1 " pdb=" C2 NAGAE 2 " pdb=" O5 NAGAE 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.64e+01 ... (remaining 7797 not shown) Planarity restraints: 7638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG y 1 " -0.067 2.00e-02 2.50e+03 5.62e-02 3.95e+01 pdb=" C7 NAG y 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG y 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG y 1 " 0.085 2.00e-02 2.50e+03 pdb=" O7 NAG y 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG P 1 " -0.067 2.00e-02 2.50e+03 5.62e-02 3.95e+01 pdb=" C7 NAG P 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG P 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG P 1 " 0.085 2.00e-02 2.50e+03 pdb=" O7 NAG P 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.067 2.00e-02 2.50e+03 5.61e-02 3.94e+01 pdb=" C7 NAG R 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.006 2.00e-02 2.50e+03 ... (remaining 7635 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1518 2.74 - 3.28: 42794 3.28 - 3.82: 64200 3.82 - 4.36: 87628 4.36 - 4.90: 144093 Nonbonded interactions: 340233 Sorted by model distance: nonbonded pdb=" OE2 GLU 4 856 " pdb=" OH TYR 9 151 " model vdw 2.204 3.040 nonbonded pdb=" OE2 GLU L 856 " pdb=" OH TYR K 151 " model vdw 2.204 3.040 nonbonded pdb=" OE2 GLU D 856 " pdb=" OH TYR C 151 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU 0 856 " pdb=" OH TYR 7 151 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU 3 856 " pdb=" OH TYR 8 151 " model vdw 2.259 3.040 ... (remaining 340228 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: 0.06 Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '4' selection = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain '1' selection = chain '2' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain '5' selection = chain '6' selection = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain '7' and resid 133 through 1003) selection = chain '8' selection = chain '9' selection = (chain 'C' and resid 133 through 1003) selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'AA' selection = chain 'AE' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'w' } ncs_group { reference = (chain 'AB' and (resid 1 through 4 or resid 6)) selection = (chain 'AF' and (resid 1 through 4 or resid 6)) selection = (chain 'V' and (resid 1 through 4 or resid 6)) selection = (chain 'W' and (resid 1 through 4 or resid 6)) selection = (chain 'X' and (resid 1 through 4 or resid 6)) selection = (chain 'h' and (resid 1 through 4 or resid 6)) selection = (chain 'i' and (resid 1 through 4 or resid 6)) selection = (chain 'j' and (resid 1 through 4 or resid 6)) selection = (chain 'n' and (resid 1 through 4 or resid 6)) selection = (chain 'q' and (resid 1 through 4 or resid 6)) selection = (chain 't' and (resid 1 through 4 or resid 6)) selection = (chain 'x' and (resid 1 through 4 or resid 6)) } ncs_group { reference = chain 'AC' selection = chain 'AG' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'y' } ncs_group { reference = chain 'AD' selection = chain 'AH' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'k' selection = chain 'm' selection = chain 'p' selection = chain 's' selection = chain 'u' selection = chain 'v' selection = chain 'z' } ncs_group { reference = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'o' selection = chain 'r' } 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: 7.720 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: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 43.830 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 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 : 0.014 0.053 46880 Z= 1.054 Angle : 1.758 10.932 64094 Z= 1.248 Chirality : 0.094 0.489 7800 Planarity : 0.005 0.056 7572 Dihedral : 17.502 118.958 21054 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.75 % Allowed : 5.41 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.10), residues: 5196 helix: -2.52 (0.09), residues: 1704 sheet: -1.02 (0.20), residues: 546 loop : -1.69 (0.10), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 92 TYR 0.032 0.004 TYR 0 688 PHE 0.024 0.003 PHE 5 87 TRP 0.014 0.003 TRP L 721 HIS 0.011 0.003 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.01414 (46622) covalent geometry : angle 1.73462 (63362) SS BOND : bond 0.02813 ( 42) SS BOND : angle 2.97426 ( 84) hydrogen bonds : bond 0.25874 ( 1738) hydrogen bonds : angle 7.73131 ( 4596) link_ALPHA1-2 : bond 0.00973 ( 6) link_ALPHA1-2 : angle 5.21404 ( 18) link_ALPHA1-3 : bond 0.00695 ( 30) link_ALPHA1-3 : angle 2.94434 ( 90) link_ALPHA1-6 : bond 0.00648 ( 30) link_ALPHA1-6 : angle 2.24842 ( 90) link_BETA1-2 : bond 0.00949 ( 6) link_BETA1-2 : angle 6.18944 ( 18) link_BETA1-4 : bond 0.00755 ( 78) link_BETA1-4 : angle 3.20706 ( 234) link_NAG-ASN : bond 0.00850 ( 66) link_NAG-ASN : angle 3.07900 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1340 time to evaluate : 1.483 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 625 HIS cc_start: 0.7099 (t-90) cc_final: 0.6708 (m-70) REVERT: D 884 THR cc_start: 0.8387 (p) cc_final: 0.7866 (t) REVERT: D 924 ASP cc_start: 0.7176 (m-30) cc_final: 0.6969 (t0) REVERT: J 128 LEU cc_start: 0.7347 (tp) cc_final: 0.7050 (tt) REVERT: H 607 GLN cc_start: 0.8488 (tt0) cc_final: 0.7779 (tt0) REVERT: H 626 ASP cc_start: 0.5522 (p0) cc_final: 0.4967 (p0) REVERT: H 670 GLN cc_start: 0.7068 (mm-40) cc_final: 0.6568 (mp10) REVERT: H 690 VAL cc_start: 0.8301 (t) cc_final: 0.8054 (p) REVERT: H 761 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7587 (mt-10) REVERT: H 772 ASP cc_start: 0.7914 (m-30) cc_final: 0.7682 (m-30) REVERT: H 936 ILE cc_start: 0.7157 (mt) cc_final: 0.6700 (mt) REVERT: L 623 THR cc_start: 0.8097 (m) cc_final: 0.7743 (p) REVERT: L 730 VAL cc_start: 0.8014 (t) cc_final: 0.7614 (m) REVERT: L 792 TRP cc_start: 0.6181 (m100) cc_final: 0.5962 (m-10) REVERT: L 814 LEU cc_start: 0.7434 (tp) cc_final: 0.7128 (tt) REVERT: L 892 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7127 (mm-30) REVERT: L 926 TRP cc_start: 0.6914 (t60) cc_final: 0.6687 (t-100) REVERT: E 107 ASP cc_start: 0.7397 (p0) cc_final: 0.7167 (p0) REVERT: C 170 ILE cc_start: 0.8362 (mt) cc_final: 0.7914 (tt) REVERT: C 172 MET cc_start: 0.8207 (mtp) cc_final: 0.7976 (mtp) REVERT: C 211 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6259 (tp30) REVERT: C 268 ASN cc_start: 0.7436 (m-40) cc_final: 0.7130 (p0) REVERT: C 271 SER cc_start: 0.8081 (m) cc_final: 0.7685 (p) REVERT: C 303 ILE cc_start: 0.8199 (mm) cc_final: 0.7940 (pt) REVERT: C 332 THR cc_start: 0.7150 (m) cc_final: 0.6897 (p) REVERT: C 349 SER cc_start: 0.6901 (p) cc_final: 0.6508 (m) REVERT: C 500 TYR cc_start: 0.6493 (m-80) cc_final: 0.6017 (m-10) REVERT: C 510 SER cc_start: 0.7235 (m) cc_final: 0.6575 (p) REVERT: C 543 VAL cc_start: 0.5699 (t) cc_final: 0.5483 (p) REVERT: C 547 ASP cc_start: 0.7670 (m-30) cc_final: 0.7126 (t70) REVERT: C 550 PHE cc_start: 0.6389 (t80) cc_final: 0.6022 (t80) REVERT: G 142 MET cc_start: 0.8330 (mtm) cc_final: 0.7816 (mpp) REVERT: G 152 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7832 (mm-30) REVERT: G 162 GLU cc_start: 0.6692 (tt0) cc_final: 0.6456 (tt0) REVERT: G 278 LYS cc_start: 0.7303 (tttt) cc_final: 0.6991 (mmtt) REVERT: G 283 ARG cc_start: 0.5213 (mmt180) cc_final: 0.4620 (mmt180) REVERT: G 320 ASP cc_start: 0.6974 (p0) cc_final: 0.6692 (t0) REVERT: G 331 ASN cc_start: 0.5898 (m-40) cc_final: 0.5064 (m110) REVERT: G 405 ASN cc_start: 0.3027 (OUTLIER) cc_final: 0.2589 (m-40) REVERT: G 439 ARG cc_start: 0.6728 (mtm180) cc_final: 0.5765 (ttm-80) REVERT: G 531 THR cc_start: 0.6450 (m) cc_final: 0.6152 (p) REVERT: G 538 ASN cc_start: 0.7924 (t0) cc_final: 0.7655 (t0) REVERT: G 547 ASP cc_start: 0.8271 (m-30) cc_final: 0.7794 (t0) REVERT: G 549 LYS cc_start: 0.6746 (tttt) cc_final: 0.6430 (mtmm) REVERT: G 562 TYR cc_start: 0.5569 (t80) cc_final: 0.4991 (t80) REVERT: K 172 MET cc_start: 0.8373 (mtp) cc_final: 0.8034 (mtm) REVERT: K 174 ASN cc_start: 0.6872 (t0) cc_final: 0.6509 (t0) REVERT: K 258 LEU cc_start: 0.6956 (mt) cc_final: 0.6635 (tp) REVERT: K 277 ILE cc_start: 0.5870 (mt) cc_final: 0.5387 (pt) REVERT: K 326 TRP cc_start: 0.7875 (p-90) cc_final: 0.7617 (p-90) REVERT: K 335 GLN cc_start: 0.6118 (mt0) cc_final: 0.5820 (mt0) REVERT: K 397 PHE cc_start: 0.5368 (t80) cc_final: 0.3987 (t80) REVERT: K 401 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6358 (pt0) REVERT: K 439 ARG cc_start: 0.7195 (mtm180) cc_final: 0.6535 (mmm-85) REVERT: K 479 LYS cc_start: 0.7705 (mttm) cc_final: 0.7472 (mmmt) REVERT: K 499 VAL cc_start: 0.7766 (t) cc_final: 0.7541 (m) REVERT: K 538 ASN cc_start: 0.7893 (t0) cc_final: 0.7599 (t0) REVERT: 0 625 HIS cc_start: 0.7099 (t-90) cc_final: 0.6709 (m-70) REVERT: 0 884 THR cc_start: 0.8386 (p) cc_final: 0.7864 (t) REVERT: 0 924 ASP cc_start: 0.7176 (m-30) cc_final: 0.6968 (t0) REVERT: 2 128 LEU cc_start: 0.7348 (tp) cc_final: 0.7052 (tt) REVERT: 3 607 GLN cc_start: 0.8488 (tt0) cc_final: 0.7781 (tt0) REVERT: 3 626 ASP cc_start: 0.5521 (p0) cc_final: 0.4966 (p0) REVERT: 3 670 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6567 (mp10) REVERT: 3 690 VAL cc_start: 0.8302 (t) cc_final: 0.8056 (p) REVERT: 3 761 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7587 (mt-10) REVERT: 3 772 ASP cc_start: 0.7914 (m-30) cc_final: 0.7681 (m-30) REVERT: 3 936 ILE cc_start: 0.7155 (mt) cc_final: 0.6698 (mt) REVERT: 4 623 THR cc_start: 0.8097 (m) cc_final: 0.7743 (p) REVERT: 4 730 VAL cc_start: 0.8014 (t) cc_final: 0.7615 (m) REVERT: 4 792 TRP cc_start: 0.6183 (m100) cc_final: 0.5962 (m-10) REVERT: 4 814 LEU cc_start: 0.7430 (tp) cc_final: 0.7124 (tt) REVERT: 4 892 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7125 (mm-30) REVERT: 4 926 TRP cc_start: 0.6916 (t60) cc_final: 0.6687 (t-100) REVERT: 5 107 ASP cc_start: 0.7400 (p0) cc_final: 0.7169 (p0) REVERT: 7 170 ILE cc_start: 0.8365 (mt) cc_final: 0.7916 (tt) REVERT: 7 172 MET cc_start: 0.8209 (mtp) cc_final: 0.7975 (mtp) REVERT: 7 211 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: 7 268 ASN cc_start: 0.7434 (m-40) cc_final: 0.7129 (p0) REVERT: 7 271 SER cc_start: 0.8085 (m) cc_final: 0.7689 (p) REVERT: 7 303 ILE cc_start: 0.8199 (mm) cc_final: 0.7940 (pt) REVERT: 7 332 THR cc_start: 0.7155 (m) cc_final: 0.6901 (p) REVERT: 7 349 SER cc_start: 0.6897 (p) cc_final: 0.6506 (m) REVERT: 7 500 TYR cc_start: 0.6489 (m-80) cc_final: 0.6015 (m-10) REVERT: 7 510 SER cc_start: 0.7233 (m) cc_final: 0.6573 (p) REVERT: 7 543 VAL cc_start: 0.5701 (t) cc_final: 0.5487 (p) REVERT: 7 547 ASP cc_start: 0.7669 (m-30) cc_final: 0.7125 (t70) REVERT: 7 550 PHE cc_start: 0.6390 (t80) cc_final: 0.6020 (t80) REVERT: 8 142 MET cc_start: 0.8329 (mtm) cc_final: 0.7817 (mpp) REVERT: 8 152 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7831 (mm-30) REVERT: 8 162 GLU cc_start: 0.6692 (tt0) cc_final: 0.6457 (tt0) REVERT: 8 278 LYS cc_start: 0.7301 (tttt) cc_final: 0.6990 (mmtt) REVERT: 8 283 ARG cc_start: 0.5219 (mmt180) cc_final: 0.4621 (mmt180) REVERT: 8 320 ASP cc_start: 0.6978 (p0) cc_final: 0.6694 (t0) REVERT: 8 331 ASN cc_start: 0.5899 (m-40) cc_final: 0.5066 (m110) REVERT: 8 405 ASN cc_start: 0.3021 (OUTLIER) cc_final: 0.2585 (m-40) REVERT: 8 439 ARG cc_start: 0.6721 (mtm180) cc_final: 0.5766 (ttm-80) REVERT: 8 531 THR cc_start: 0.6454 (m) cc_final: 0.6155 (p) REVERT: 8 538 ASN cc_start: 0.7924 (t0) cc_final: 0.7655 (t0) REVERT: 8 547 ASP cc_start: 0.8270 (m-30) cc_final: 0.7794 (t0) REVERT: 8 549 LYS cc_start: 0.6744 (tttt) cc_final: 0.6429 (mtmm) REVERT: 8 562 TYR cc_start: 0.5573 (t80) cc_final: 0.4994 (t80) REVERT: 9 172 MET cc_start: 0.8376 (mtp) cc_final: 0.8036 (mtm) REVERT: 9 174 ASN cc_start: 0.6871 (t0) cc_final: 0.6509 (t0) REVERT: 9 258 LEU cc_start: 0.6954 (mt) cc_final: 0.6633 (tp) REVERT: 9 277 ILE cc_start: 0.5869 (mt) cc_final: 0.5387 (pt) REVERT: 9 326 TRP cc_start: 0.7874 (p-90) cc_final: 0.7616 (p-90) REVERT: 9 335 GLN cc_start: 0.6118 (mt0) cc_final: 0.5821 (mt0) REVERT: 9 397 PHE cc_start: 0.5369 (t80) cc_final: 0.3981 (t80) REVERT: 9 401 GLU cc_start: 0.6577 (tm-30) cc_final: 0.6360 (pt0) REVERT: 9 439 ARG cc_start: 0.7193 (mtm180) cc_final: 0.6533 (mmm-85) REVERT: 9 479 LYS cc_start: 0.7703 (mttm) cc_final: 0.7470 (mmmt) REVERT: 9 499 VAL cc_start: 0.7765 (t) cc_final: 0.7541 (m) REVERT: 9 538 ASN cc_start: 0.7894 (t0) cc_final: 0.7599 (t0) outliers start: 36 outliers final: 8 residues processed: 1360 average time/residue: 0.2448 time to fit residues: 555.8097 Evaluate side-chains 712 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 700 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 211 GLU Chi-restraints excluded: chain 7 residue 211 GLU Chi-restraints excluded: chain 7 residue 405 ASN Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 405 ASN Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 211 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 592 GLN D 638 HIS ** D 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 893 GLN D 907 HIS J 131 GLN ** H 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 743 HIS H 893 GLN H 907 HIS L 625 HIS L 692 GLN L 907 HIS L 917 GLN C 230 GLN C 366 GLN C 480 ASN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 GLN G 489 GLN K 225 HIS K 230 GLN 0 592 GLN 0 638 HIS ** 0 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 893 GLN 0 907 HIS 2 131 GLN ** 3 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 743 HIS 3 893 GLN 3 907 HIS 4 625 HIS 4 907 HIS 4 917 GLN 7 366 GLN 7 480 ASN ** 8 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 478 GLN 8 489 GLN 9 225 HIS 9 230 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.164365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130748 restraints weight = 71533.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.128900 restraints weight = 77678.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130016 restraints weight = 77013.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130662 restraints weight = 49485.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131718 restraints weight = 42452.222| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 46880 Z= 0.239 Angle : 0.901 13.420 64094 Z= 0.423 Chirality : 0.054 0.373 7800 Planarity : 0.005 0.053 7572 Dihedral : 12.147 83.625 10716 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.25 % Allowed : 11.84 % Favored : 84.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.11), residues: 5196 helix: 0.58 (0.12), residues: 1752 sheet: -0.39 (0.19), residues: 692 loop : -1.22 (0.11), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 226 TYR 0.028 0.003 TYR G 323 PHE 0.022 0.002 PHE B 87 TRP 0.023 0.002 TRP G 326 HIS 0.011 0.002 HIS L 625 Details of bonding type rmsd covalent geometry : bond 0.00547 (46622) covalent geometry : angle 0.85318 (63362) SS BOND : bond 0.00345 ( 42) SS BOND : angle 1.20337 ( 84) hydrogen bonds : bond 0.05872 ( 1738) hydrogen bonds : angle 5.13885 ( 4596) link_ALPHA1-2 : bond 0.00947 ( 6) link_ALPHA1-2 : angle 1.93733 ( 18) link_ALPHA1-3 : bond 0.01128 ( 30) link_ALPHA1-3 : angle 1.99446 ( 90) link_ALPHA1-6 : bond 0.00724 ( 30) link_ALPHA1-6 : angle 1.94733 ( 90) link_BETA1-2 : bond 0.01061 ( 6) link_BETA1-2 : angle 4.71750 ( 18) link_BETA1-4 : bond 0.00560 ( 78) link_BETA1-4 : angle 2.71887 ( 234) link_NAG-ASN : bond 0.01205 ( 66) link_NAG-ASN : angle 3.81735 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 720 time to evaluate : 1.789 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: H 595 SER cc_start: 0.7075 (p) cc_final: 0.6871 (p) REVERT: C 271 SER cc_start: 0.8215 (m) cc_final: 0.8006 (p) REVERT: G 273 TRP cc_start: 0.8442 (m-10) cc_final: 0.8213 (m-10) REVERT: G 278 LYS cc_start: 0.7800 (tttt) cc_final: 0.7447 (tttp) REVERT: G 531 THR cc_start: 0.7407 (m) cc_final: 0.7136 (p) REVERT: G 549 LYS cc_start: 0.7731 (tttt) cc_final: 0.7290 (mtmm) REVERT: K 195 MET cc_start: 0.6907 (mmm) cc_final: 0.6689 (mmm) REVERT: 3 595 SER cc_start: 0.7087 (p) cc_final: 0.6880 (p) REVERT: 5 73 PHE cc_start: 0.6318 (t80) cc_final: 0.6087 (t80) REVERT: 7 271 SER cc_start: 0.8221 (m) cc_final: 0.8008 (p) REVERT: 8 273 TRP cc_start: 0.8441 (m-10) cc_final: 0.8216 (m-10) REVERT: 8 278 LYS cc_start: 0.7803 (tttt) cc_final: 0.7451 (tttp) REVERT: 8 531 THR cc_start: 0.7404 (m) cc_final: 0.7134 (p) REVERT: 8 549 LYS cc_start: 0.7738 (tttt) cc_final: 0.7287 (mtmm) REVERT: 9 195 MET cc_start: 0.6917 (mmm) cc_final: 0.6705 (mmm) outliers start: 155 outliers final: 75 residues processed: 829 average time/residue: 0.2359 time to fit residues: 331.5964 Evaluate side-chains 579 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 504 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 881 ILE Chi-restraints excluded: chain D residue 889 SER Chi-restraints excluded: chain D residue 931 SER Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 803 VAL Chi-restraints excluded: chain H residue 863 GLN Chi-restraints excluded: chain H residue 884 THR Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 812 LEU Chi-restraints excluded: chain L residue 818 THR Chi-restraints excluded: chain L residue 830 VAL Chi-restraints excluded: chain L residue 862 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain C residue 435 CYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 483 SER Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 230 GLN Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 318 CYS Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 365 SER Chi-restraints excluded: chain K residue 435 CYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain 0 residue 588 THR Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 806 LEU Chi-restraints excluded: chain 0 residue 841 LEU Chi-restraints excluded: chain 0 residue 881 ILE Chi-restraints excluded: chain 0 residue 889 SER Chi-restraints excluded: chain 0 residue 931 SER Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 803 VAL Chi-restraints excluded: chain 3 residue 863 GLN Chi-restraints excluded: chain 3 residue 884 THR Chi-restraints excluded: chain 4 residue 739 VAL Chi-restraints excluded: chain 4 residue 812 LEU Chi-restraints excluded: chain 4 residue 818 THR Chi-restraints excluded: chain 4 residue 830 VAL Chi-restraints excluded: chain 4 residue 862 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 333 ILE Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 7 residue 435 CYS Chi-restraints excluded: chain 7 residue 475 LEU Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 378 LEU Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 483 SER Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 230 GLN Chi-restraints excluded: chain 9 residue 306 SER Chi-restraints excluded: chain 9 residue 318 CYS Chi-restraints excluded: chain 9 residue 344 LEU Chi-restraints excluded: chain 9 residue 365 SER Chi-restraints excluded: chain 9 residue 435 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 160 optimal weight: 10.0000 chunk 346 optimal weight: 0.9990 chunk 41 optimal weight: 0.0170 chunk 214 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 488 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 434 optimal weight: 10.0000 chunk 111 optimal weight: 0.2980 chunk 385 optimal weight: 20.0000 overall best weight: 1.8624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 668 GLN ** D 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 615 HIS H 694 HIS L 694 HIS L 722 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 ASN G 230 GLN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN K 174 ASN K 181 ASN K 230 GLN K 480 ASN 0 668 GLN ** 0 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 694 HIS 4 694 HIS 4 722 ASN 7 230 GLN 8 174 ASN 8 230 GLN ** 8 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 480 ASN 9 174 ASN 9 181 ASN 9 230 GLN 9 480 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.162269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128078 restraints weight = 71300.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126268 restraints weight = 78406.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127442 restraints weight = 78369.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128087 restraints weight = 50378.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128918 restraints weight = 43040.366| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 46880 Z= 0.182 Angle : 0.725 13.300 64094 Z= 0.347 Chirality : 0.048 0.292 7800 Planarity : 0.004 0.065 7572 Dihedral : 10.810 81.630 10696 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.83 % Allowed : 13.83 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.11), residues: 5196 helix: 1.44 (0.13), residues: 1742 sheet: -0.47 (0.19), residues: 688 loop : -1.02 (0.11), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 613 TYR 0.024 0.002 TYR 4 688 PHE 0.018 0.002 PHE 7 372 TRP 0.034 0.002 TRP K 326 HIS 0.008 0.001 HIS D 743 Details of bonding type rmsd covalent geometry : bond 0.00386 (46622) covalent geometry : angle 0.68090 (63362) SS BOND : bond 0.01174 ( 42) SS BOND : angle 1.24444 ( 84) hydrogen bonds : bond 0.05587 ( 1738) hydrogen bonds : angle 4.75184 ( 4596) link_ALPHA1-2 : bond 0.00994 ( 6) link_ALPHA1-2 : angle 2.49717 ( 18) link_ALPHA1-3 : bond 0.01067 ( 30) link_ALPHA1-3 : angle 1.64611 ( 90) link_ALPHA1-6 : bond 0.00663 ( 30) link_ALPHA1-6 : angle 1.84647 ( 90) link_BETA1-2 : bond 0.00812 ( 6) link_BETA1-2 : angle 4.56747 ( 18) link_BETA1-4 : bond 0.00738 ( 78) link_BETA1-4 : angle 2.14413 ( 234) link_NAG-ASN : bond 0.01045 ( 66) link_NAG-ASN : angle 3.23787 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 572 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 583 MET cc_start: 0.8105 (mmt) cc_final: 0.7779 (mmt) REVERT: H 595 SER cc_start: 0.7535 (p) cc_final: 0.7316 (p) REVERT: H 792 TRP cc_start: 0.8723 (m-10) cc_final: 0.8177 (m100) REVERT: H 892 GLU cc_start: 0.6687 (tp30) cc_final: 0.6305 (tp30) REVERT: E 73 PHE cc_start: 0.6100 (t80) cc_final: 0.5501 (t80) REVERT: E 97 LYS cc_start: 0.8038 (tppt) cc_final: 0.7304 (tppt) REVERT: C 363 TRP cc_start: 0.6713 (m-10) cc_final: 0.6466 (m-10) REVERT: G 181 ASN cc_start: 0.8089 (m-40) cc_final: 0.7428 (t0) REVERT: G 273 TRP cc_start: 0.8615 (m-10) cc_final: 0.8380 (m-10) REVERT: G 278 LYS cc_start: 0.7962 (tttt) cc_final: 0.7567 (mttm) REVERT: G 283 ARG cc_start: 0.5085 (mmt180) cc_final: 0.4884 (mmt180) REVERT: G 531 THR cc_start: 0.7508 (m) cc_final: 0.7256 (p) REVERT: G 549 LYS cc_start: 0.7685 (tttt) cc_final: 0.7330 (mtmm) REVERT: G 556 ASN cc_start: 0.5793 (OUTLIER) cc_final: 0.5334 (t0) REVERT: K 195 MET cc_start: 0.7148 (mmm) cc_final: 0.6928 (mmm) REVERT: K 211 GLU cc_start: 0.7601 (tp30) cc_final: 0.7324 (tp30) REVERT: K 561 HIS cc_start: 0.7524 (p-80) cc_final: 0.7256 (p-80) REVERT: 3 583 MET cc_start: 0.8163 (mmt) cc_final: 0.7831 (mmt) REVERT: 3 595 SER cc_start: 0.7551 (p) cc_final: 0.7330 (p) REVERT: 3 792 TRP cc_start: 0.8714 (m-10) cc_final: 0.8168 (m100) REVERT: 3 892 GLU cc_start: 0.6685 (tp30) cc_final: 0.6300 (tp30) REVERT: 5 97 LYS cc_start: 0.8036 (tppt) cc_final: 0.7302 (tppt) REVERT: 7 363 TRP cc_start: 0.6714 (m-10) cc_final: 0.6469 (m-10) REVERT: 8 181 ASN cc_start: 0.8082 (m-40) cc_final: 0.7430 (t0) REVERT: 8 273 TRP cc_start: 0.8612 (m-10) cc_final: 0.8381 (m-10) REVERT: 8 278 LYS cc_start: 0.7956 (tttt) cc_final: 0.7565 (mttm) REVERT: 8 283 ARG cc_start: 0.5095 (mmt180) cc_final: 0.4895 (mmt180) REVERT: 8 531 THR cc_start: 0.7507 (m) cc_final: 0.7255 (p) REVERT: 8 549 LYS cc_start: 0.7672 (tttt) cc_final: 0.7324 (mtmm) REVERT: 8 556 ASN cc_start: 0.5777 (OUTLIER) cc_final: 0.5323 (t0) REVERT: 9 195 MET cc_start: 0.7137 (mmm) cc_final: 0.6925 (mmm) REVERT: 9 211 GLU cc_start: 0.7590 (tp30) cc_final: 0.7304 (tp30) REVERT: 9 561 HIS cc_start: 0.7517 (p-80) cc_final: 0.7251 (p-80) outliers start: 135 outliers final: 76 residues processed: 677 average time/residue: 0.2368 time to fit residues: 278.0099 Evaluate side-chains 563 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 485 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 931 SER Chi-restraints excluded: chain D residue 936 ILE Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 801 VAL Chi-restraints excluded: chain H residue 803 VAL Chi-restraints excluded: chain H residue 863 GLN Chi-restraints excluded: chain L residue 628 SER Chi-restraints excluded: chain L residue 803 VAL Chi-restraints excluded: chain L residue 818 THR Chi-restraints excluded: chain L residue 830 VAL Chi-restraints excluded: chain L residue 836 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 331 ASN Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 230 GLN Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain 0 residue 588 THR Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 806 LEU Chi-restraints excluded: chain 0 residue 810 SER Chi-restraints excluded: chain 0 residue 830 VAL Chi-restraints excluded: chain 0 residue 931 SER Chi-restraints excluded: chain 0 residue 936 ILE Chi-restraints excluded: chain 3 residue 626 ASP Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 801 VAL Chi-restraints excluded: chain 3 residue 803 VAL Chi-restraints excluded: chain 3 residue 863 GLN Chi-restraints excluded: chain 4 residue 628 SER Chi-restraints excluded: chain 4 residue 803 VAL Chi-restraints excluded: chain 4 residue 818 THR Chi-restraints excluded: chain 4 residue 830 VAL Chi-restraints excluded: chain 4 residue 836 THR Chi-restraints excluded: chain 5 residue 82 VAL Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 6 residue 89 THR Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 151 TYR Chi-restraints excluded: chain 7 residue 348 THR Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 300 SER Chi-restraints excluded: chain 8 residue 331 ASN Chi-restraints excluded: chain 8 residue 378 LEU Chi-restraints excluded: chain 8 residue 386 SER Chi-restraints excluded: chain 8 residue 389 LEU Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 487 ILE Chi-restraints excluded: chain 8 residue 521 SER Chi-restraints excluded: chain 8 residue 556 ASN Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 230 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 210 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 284 optimal weight: 8.9990 chunk 213 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 458 optimal weight: 0.9980 chunk 249 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 366 optimal weight: 5.9990 chunk 493 optimal weight: 0.2980 chunk 282 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 725 ASN D 743 HIS H 607 GLN ** H 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 722 ASN L 625 HIS L 893 GLN ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN K 181 ASN K 369 ASN 0 725 ASN 0 743 HIS 3 607 GLN 3 722 ASN 4 625 HIS 4 893 GLN ** 7 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 234 ASN 9 181 ASN 9 369 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.163446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128954 restraints weight = 71372.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127619 restraints weight = 76952.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128797 restraints weight = 74160.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129282 restraints weight = 50516.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130211 restraints weight = 43260.987| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 46880 Z= 0.122 Angle : 0.642 12.205 64094 Z= 0.303 Chirality : 0.045 0.283 7800 Planarity : 0.004 0.054 7572 Dihedral : 9.627 79.939 10696 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.77 % Allowed : 14.59 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.12), residues: 5196 helix: 1.76 (0.13), residues: 1748 sheet: -0.19 (0.20), residues: 658 loop : -0.90 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 308 TYR 0.024 0.001 TYR 9 474 PHE 0.013 0.001 PHE 7 372 TRP 0.010 0.001 TRP K 326 HIS 0.012 0.001 HIS 4 625 Details of bonding type rmsd covalent geometry : bond 0.00261 (46622) covalent geometry : angle 0.59735 (63362) SS BOND : bond 0.00895 ( 42) SS BOND : angle 2.00228 ( 84) hydrogen bonds : bond 0.04433 ( 1738) hydrogen bonds : angle 4.50169 ( 4596) link_ALPHA1-2 : bond 0.01023 ( 6) link_ALPHA1-2 : angle 2.14881 ( 18) link_ALPHA1-3 : bond 0.01109 ( 30) link_ALPHA1-3 : angle 1.69006 ( 90) link_ALPHA1-6 : bond 0.00685 ( 30) link_ALPHA1-6 : angle 1.84559 ( 90) link_BETA1-2 : bond 0.00847 ( 6) link_BETA1-2 : angle 4.30334 ( 18) link_BETA1-4 : bond 0.00573 ( 78) link_BETA1-4 : angle 1.87144 ( 234) link_NAG-ASN : bond 0.00453 ( 66) link_NAG-ASN : angle 2.92767 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 536 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6685 (m-30) REVERT: H 583 MET cc_start: 0.8201 (mmt) cc_final: 0.7881 (mmt) REVERT: H 792 TRP cc_start: 0.8756 (m-10) cc_final: 0.8279 (m100) REVERT: H 892 GLU cc_start: 0.6636 (tp30) cc_final: 0.6225 (tp30) REVERT: E 97 LYS cc_start: 0.7989 (tppt) cc_final: 0.7269 (tppt) REVERT: C 198 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: C 363 TRP cc_start: 0.6735 (m-10) cc_final: 0.6389 (m-10) REVERT: G 273 TRP cc_start: 0.8661 (m-10) cc_final: 0.8386 (m-10) REVERT: G 278 LYS cc_start: 0.8025 (tttt) cc_final: 0.7632 (tttp) REVERT: G 283 ARG cc_start: 0.5218 (mmt180) cc_final: 0.4975 (mmt180) REVERT: G 327 TYR cc_start: 0.7236 (t80) cc_final: 0.6924 (t80) REVERT: G 549 LYS cc_start: 0.7673 (tttt) cc_final: 0.7320 (mtmm) REVERT: G 556 ASN cc_start: 0.6059 (OUTLIER) cc_final: 0.5700 (t0) REVERT: K 389 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7678 (mm) REVERT: B 107 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: 3 583 MET cc_start: 0.8208 (mmt) cc_final: 0.7882 (mmt) REVERT: 3 792 TRP cc_start: 0.8741 (m-10) cc_final: 0.8273 (m100) REVERT: 3 892 GLU cc_start: 0.6638 (tp30) cc_final: 0.6226 (tp30) REVERT: 5 97 LYS cc_start: 0.7987 (tppt) cc_final: 0.7264 (tppt) REVERT: 7 198 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: 7 363 TRP cc_start: 0.6749 (m-10) cc_final: 0.6402 (m-10) REVERT: 8 273 TRP cc_start: 0.8660 (m-10) cc_final: 0.8390 (m-10) REVERT: 8 278 LYS cc_start: 0.8024 (tttt) cc_final: 0.7618 (mttm) REVERT: 8 283 ARG cc_start: 0.5230 (mmt180) cc_final: 0.4972 (mmt180) REVERT: 8 327 TYR cc_start: 0.7234 (t80) cc_final: 0.6928 (t80) REVERT: 8 549 LYS cc_start: 0.7669 (tttt) cc_final: 0.7321 (mtmm) REVERT: 8 556 ASN cc_start: 0.6049 (OUTLIER) cc_final: 0.5690 (t0) REVERT: 9 389 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7684 (mm) outliers start: 132 outliers final: 80 residues processed: 642 average time/residue: 0.2090 time to fit residues: 232.1821 Evaluate side-chains 554 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 466 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain H residue 628 SER Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 801 VAL Chi-restraints excluded: chain H residue 803 VAL Chi-restraints excluded: chain H residue 831 THR Chi-restraints excluded: chain L residue 625 HIS Chi-restraints excluded: chain L residue 723 VAL Chi-restraints excluded: chain L residue 803 VAL Chi-restraints excluded: chain L residue 812 LEU Chi-restraints excluded: chain L residue 818 THR Chi-restraints excluded: chain L residue 831 THR Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 528 TYR Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 318 CYS Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 405 ASN Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 810 SER Chi-restraints excluded: chain 0 residue 831 THR Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 3 residue 628 SER Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 801 VAL Chi-restraints excluded: chain 3 residue 803 VAL Chi-restraints excluded: chain 3 residue 831 THR Chi-restraints excluded: chain 4 residue 625 HIS Chi-restraints excluded: chain 4 residue 723 VAL Chi-restraints excluded: chain 4 residue 803 VAL Chi-restraints excluded: chain 4 residue 812 LEU Chi-restraints excluded: chain 4 residue 818 THR Chi-restraints excluded: chain 4 residue 831 THR Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 151 TYR Chi-restraints excluded: chain 7 residue 167 LEU Chi-restraints excluded: chain 7 residue 198 GLU Chi-restraints excluded: chain 7 residue 235 CYS Chi-restraints excluded: chain 7 residue 348 THR Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 300 SER Chi-restraints excluded: chain 8 residue 345 ASN Chi-restraints excluded: chain 8 residue 378 LEU Chi-restraints excluded: chain 8 residue 386 SER Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 521 SER Chi-restraints excluded: chain 8 residue 528 TYR Chi-restraints excluded: chain 8 residue 556 ASN Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 185 THR Chi-restraints excluded: chain 9 residue 242 GLU Chi-restraints excluded: chain 9 residue 318 CYS Chi-restraints excluded: chain 9 residue 344 LEU Chi-restraints excluded: chain 9 residue 389 LEU Chi-restraints excluded: chain 9 residue 405 ASN Chi-restraints excluded: chain 9 residue 483 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 285 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 510 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 389 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 462 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 692 GLN H 863 GLN L 640 HIS L 893 GLN C 220 GLN ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 ASN C 489 GLN ** G 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 ASN K 478 GLN 0 692 GLN ** 3 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 863 GLN 4 640 HIS 4 893 GLN 4 934 GLN 7 220 GLN ** 7 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 480 ASN ** 8 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 181 ASN 9 478 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.155891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120841 restraints weight = 71858.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117559 restraints weight = 75070.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119923 restraints weight = 73482.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119743 restraints weight = 48572.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120801 restraints weight = 43549.892| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 46880 Z= 0.258 Angle : 0.819 12.159 64094 Z= 0.391 Chirality : 0.050 0.278 7800 Planarity : 0.005 0.063 7572 Dihedral : 9.965 84.788 10696 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.94 % Allowed : 14.92 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.11), residues: 5196 helix: 1.36 (0.13), residues: 1692 sheet: -0.75 (0.19), residues: 710 loop : -1.13 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 436 TYR 0.024 0.002 TYR 0 688 PHE 0.022 0.002 PHE 7 481 TRP 0.021 0.002 TRP A 95 HIS 0.026 0.002 HIS L 625 Details of bonding type rmsd covalent geometry : bond 0.00625 (46622) covalent geometry : angle 0.77401 (63362) SS BOND : bond 0.01076 ( 42) SS BOND : angle 2.30457 ( 84) hydrogen bonds : bond 0.06459 ( 1738) hydrogen bonds : angle 4.95856 ( 4596) link_ALPHA1-2 : bond 0.00854 ( 6) link_ALPHA1-2 : angle 2.50208 ( 18) link_ALPHA1-3 : bond 0.01074 ( 30) link_ALPHA1-3 : angle 2.04961 ( 90) link_ALPHA1-6 : bond 0.00721 ( 30) link_ALPHA1-6 : angle 2.01074 ( 90) link_BETA1-2 : bond 0.00833 ( 6) link_BETA1-2 : angle 4.72808 ( 18) link_BETA1-4 : bond 0.00875 ( 78) link_BETA1-4 : angle 2.07111 ( 234) link_NAG-ASN : bond 0.00596 ( 66) link_NAG-ASN : angle 3.46186 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 478 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 633 MET cc_start: 0.6980 (mmm) cc_final: 0.6776 (mmm) REVERT: D 845 ARG cc_start: 0.7747 (ttt90) cc_final: 0.7100 (ptm160) REVERT: D 912 PRO cc_start: 0.8351 (Cg_endo) cc_final: 0.8044 (Cg_exo) REVERT: H 792 TRP cc_start: 0.8744 (m-10) cc_final: 0.8436 (m100) REVERT: H 890 ILE cc_start: 0.8412 (mm) cc_final: 0.8185 (mt) REVERT: H 892 GLU cc_start: 0.7141 (tp30) cc_final: 0.6723 (tp30) REVERT: E 97 LYS cc_start: 0.8124 (tppt) cc_final: 0.7293 (tppt) REVERT: C 314 HIS cc_start: 0.5812 (m90) cc_final: 0.5008 (m90) REVERT: C 363 TRP cc_start: 0.7254 (m-10) cc_final: 0.6886 (m-10) REVERT: G 278 LYS cc_start: 0.8185 (tttt) cc_final: 0.7756 (tttp) REVERT: G 549 LYS cc_start: 0.7909 (tttt) cc_final: 0.7689 (mtmm) REVERT: G 556 ASN cc_start: 0.5783 (OUTLIER) cc_final: 0.5449 (t0) REVERT: K 334 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7906 (mm-30) REVERT: K 389 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8119 (mt) REVERT: 0 845 ARG cc_start: 0.7752 (ttt90) cc_final: 0.7099 (ptm160) REVERT: 0 912 PRO cc_start: 0.8348 (Cg_endo) cc_final: 0.8042 (Cg_exo) REVERT: 3 792 TRP cc_start: 0.8825 (m-10) cc_final: 0.8553 (m100) REVERT: 3 890 ILE cc_start: 0.8421 (mm) cc_final: 0.8198 (mt) REVERT: 3 892 GLU cc_start: 0.7144 (tp30) cc_final: 0.6727 (tp30) REVERT: 5 97 LYS cc_start: 0.8120 (tppt) cc_final: 0.7287 (tppt) REVERT: 7 172 MET cc_start: 0.8439 (mtt) cc_final: 0.8176 (mtt) REVERT: 7 314 HIS cc_start: 0.5824 (m90) cc_final: 0.5024 (m90) REVERT: 7 363 TRP cc_start: 0.7258 (m-10) cc_final: 0.6893 (m-10) REVERT: 8 278 LYS cc_start: 0.8198 (tttt) cc_final: 0.7765 (tttp) REVERT: 8 302 TYR cc_start: 0.6737 (t80) cc_final: 0.6536 (t80) REVERT: 8 549 LYS cc_start: 0.7899 (tttt) cc_final: 0.7686 (mtmm) REVERT: 8 556 ASN cc_start: 0.5757 (OUTLIER) cc_final: 0.5421 (t0) REVERT: 9 334 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: 9 389 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8120 (mt) outliers start: 188 outliers final: 120 residues processed: 640 average time/residue: 0.2169 time to fit residues: 240.4101 Evaluate side-chains 571 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 445 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 830 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 889 SER Chi-restraints excluded: chain D residue 931 SER Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 595 SER Chi-restraints excluded: chain H residue 623 THR Chi-restraints excluded: chain H residue 626 ASP Chi-restraints excluded: chain H residue 628 SER Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 771 CYS Chi-restraints excluded: chain H residue 801 VAL Chi-restraints excluded: chain H residue 831 THR Chi-restraints excluded: chain H residue 972 ILE Chi-restraints excluded: chain L residue 627 ILE Chi-restraints excluded: chain L residue 628 SER Chi-restraints excluded: chain L residue 703 GLU Chi-restraints excluded: chain L residue 723 VAL Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 803 VAL Chi-restraints excluded: chain L residue 818 THR Chi-restraints excluded: chain L residue 830 VAL Chi-restraints excluded: chain L residue 831 THR Chi-restraints excluded: chain L residue 836 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 331 ASN Chi-restraints excluded: chain G residue 378 LEU Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 306 SER Chi-restraints excluded: chain K residue 315 VAL Chi-restraints excluded: chain K residue 318 CYS Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 405 ASN Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain 0 residue 753 VAL Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 806 LEU Chi-restraints excluded: chain 0 residue 830 VAL Chi-restraints excluded: chain 0 residue 831 THR Chi-restraints excluded: chain 0 residue 836 THR Chi-restraints excluded: chain 0 residue 841 LEU Chi-restraints excluded: chain 0 residue 889 SER Chi-restraints excluded: chain 0 residue 931 SER Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 3 residue 591 VAL Chi-restraints excluded: chain 3 residue 595 SER Chi-restraints excluded: chain 3 residue 623 THR Chi-restraints excluded: chain 3 residue 626 ASP Chi-restraints excluded: chain 3 residue 628 SER Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 771 CYS Chi-restraints excluded: chain 3 residue 801 VAL Chi-restraints excluded: chain 3 residue 831 THR Chi-restraints excluded: chain 3 residue 972 ILE Chi-restraints excluded: chain 4 residue 627 ILE Chi-restraints excluded: chain 4 residue 628 SER Chi-restraints excluded: chain 4 residue 703 GLU Chi-restraints excluded: chain 4 residue 723 VAL Chi-restraints excluded: chain 4 residue 740 THR Chi-restraints excluded: chain 4 residue 803 VAL Chi-restraints excluded: chain 4 residue 818 THR Chi-restraints excluded: chain 4 residue 830 VAL Chi-restraints excluded: chain 4 residue 831 THR Chi-restraints excluded: chain 4 residue 836 THR Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 5 residue 86 CYS Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 6 residue 89 THR Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 151 TYR Chi-restraints excluded: chain 7 residue 271 SER Chi-restraints excluded: chain 7 residue 348 THR Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 143 THR Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 331 ASN Chi-restraints excluded: chain 8 residue 378 LEU Chi-restraints excluded: chain 8 residue 386 SER Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 487 ILE Chi-restraints excluded: chain 8 residue 521 SER Chi-restraints excluded: chain 8 residue 556 ASN Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 185 THR Chi-restraints excluded: chain 9 residue 306 SER Chi-restraints excluded: chain 9 residue 315 VAL Chi-restraints excluded: chain 9 residue 318 CYS Chi-restraints excluded: chain 9 residue 329 ILE Chi-restraints excluded: chain 9 residue 334 GLU Chi-restraints excluded: chain 9 residue 389 LEU Chi-restraints excluded: chain 9 residue 405 ASN Chi-restraints excluded: chain 9 residue 483 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 191 optimal weight: 5.9990 chunk 337 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 410 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 118 optimal weight: 0.3980 chunk 467 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 749 ASN L 625 HIS ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 321 GLN K 181 ASN K 230 GLN 3 615 HIS 4 625 HIS ** 7 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 321 GLN 9 181 ASN 9 230 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122844 restraints weight = 71658.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119936 restraints weight = 74988.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122331 restraints weight = 69012.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122213 restraints weight = 45598.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123110 restraints weight = 42065.597| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 46880 Z= 0.153 Angle : 0.675 11.218 64094 Z= 0.321 Chirality : 0.045 0.290 7800 Planarity : 0.004 0.059 7572 Dihedral : 9.427 83.648 10696 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.81 % Allowed : 16.62 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.12), residues: 5196 helix: 1.59 (0.13), residues: 1698 sheet: -0.67 (0.19), residues: 704 loop : -0.99 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 865 TYR 0.022 0.002 TYR K 470 PHE 0.025 0.001 PHE 7 481 TRP 0.010 0.001 TRP B 95 HIS 0.007 0.001 HIS L 625 Details of bonding type rmsd covalent geometry : bond 0.00348 (46622) covalent geometry : angle 0.63173 (63362) SS BOND : bond 0.01001 ( 42) SS BOND : angle 2.41251 ( 84) hydrogen bonds : bond 0.05092 ( 1738) hydrogen bonds : angle 4.67274 ( 4596) link_ALPHA1-2 : bond 0.00959 ( 6) link_ALPHA1-2 : angle 1.99606 ( 18) link_ALPHA1-3 : bond 0.01112 ( 30) link_ALPHA1-3 : angle 1.77878 ( 90) link_ALPHA1-6 : bond 0.00705 ( 30) link_ALPHA1-6 : angle 1.88769 ( 90) link_BETA1-2 : bond 0.00860 ( 6) link_BETA1-2 : angle 4.43379 ( 18) link_BETA1-4 : bond 0.00655 ( 78) link_BETA1-4 : angle 1.73493 ( 234) link_NAG-ASN : bond 0.00463 ( 66) link_NAG-ASN : angle 2.95649 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 473 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8721 (t70) cc_final: 0.8283 (t0) REVERT: A 107 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6903 (m-30) REVERT: D 845 ARG cc_start: 0.7759 (ttt90) cc_final: 0.7114 (ptm160) REVERT: D 912 PRO cc_start: 0.8328 (Cg_endo) cc_final: 0.8046 (Cg_exo) REVERT: H 670 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7284 (mt0) REVERT: H 792 TRP cc_start: 0.8774 (m-10) cc_final: 0.8522 (m100) REVERT: H 890 ILE cc_start: 0.8426 (mm) cc_final: 0.8163 (mt) REVERT: H 892 GLU cc_start: 0.7045 (tp30) cc_final: 0.6796 (tp30) REVERT: H 954 LEU cc_start: 0.8540 (mm) cc_final: 0.8304 (mm) REVERT: E 97 LYS cc_start: 0.8109 (tppt) cc_final: 0.7329 (tppt) REVERT: C 251 LEU cc_start: 0.8344 (tp) cc_final: 0.8092 (tt) REVERT: C 252 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7178 (mt) REVERT: C 314 HIS cc_start: 0.5996 (m90) cc_final: 0.5253 (m90) REVERT: C 363 TRP cc_start: 0.7219 (m-10) cc_final: 0.6870 (m-10) REVERT: G 195 MET cc_start: 0.7781 (tmm) cc_final: 0.7570 (tmm) REVERT: G 278 LYS cc_start: 0.8168 (tttt) cc_final: 0.7815 (mttm) REVERT: G 556 ASN cc_start: 0.5731 (OUTLIER) cc_final: 0.5319 (t0) REVERT: K 274 ASP cc_start: 0.6827 (m-30) cc_final: 0.6492 (m-30) REVERT: K 389 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8168 (mt) REVERT: K 528 TYR cc_start: 0.7389 (t80) cc_final: 0.7182 (t80) REVERT: K 540 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7213 (mmm160) REVERT: B 98 ASP cc_start: 0.8720 (t70) cc_final: 0.8284 (t0) REVERT: B 107 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6909 (m-30) REVERT: 0 845 ARG cc_start: 0.7757 (ttt90) cc_final: 0.7108 (ptm160) REVERT: 0 912 PRO cc_start: 0.8328 (Cg_endo) cc_final: 0.8046 (Cg_exo) REVERT: 3 670 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7274 (mt0) REVERT: 3 792 TRP cc_start: 0.8768 (m-10) cc_final: 0.8525 (m100) REVERT: 3 890 ILE cc_start: 0.8425 (mm) cc_final: 0.8161 (mt) REVERT: 3 892 GLU cc_start: 0.7045 (tp30) cc_final: 0.6796 (tp30) REVERT: 3 954 LEU cc_start: 0.8537 (mm) cc_final: 0.8300 (mm) REVERT: 5 97 LYS cc_start: 0.8101 (tppt) cc_final: 0.7321 (tppt) REVERT: 7 172 MET cc_start: 0.8530 (mtt) cc_final: 0.8258 (mtt) REVERT: 7 251 LEU cc_start: 0.8342 (tp) cc_final: 0.8089 (tt) REVERT: 7 252 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7171 (mt) REVERT: 7 314 HIS cc_start: 0.6002 (m90) cc_final: 0.5265 (m90) REVERT: 7 363 TRP cc_start: 0.7222 (m-10) cc_final: 0.6875 (m-10) REVERT: 8 195 MET cc_start: 0.7791 (tmm) cc_final: 0.7574 (tmm) REVERT: 8 278 LYS cc_start: 0.8153 (tttt) cc_final: 0.7798 (mttm) REVERT: 8 556 ASN cc_start: 0.5717 (OUTLIER) cc_final: 0.5302 (t0) REVERT: 9 274 ASP cc_start: 0.6839 (m-30) cc_final: 0.6497 (m-30) REVERT: 9 389 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8173 (mt) REVERT: 9 528 TYR cc_start: 0.7396 (t80) cc_final: 0.7185 (t80) REVERT: 9 540 ARG cc_start: 0.7542 (mmm-85) cc_final: 0.7209 (mmm160) outliers start: 134 outliers final: 90 residues processed: 577 average time/residue: 0.2013 time to fit residues: 199.4251 Evaluate side-chains 539 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 439 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 931 SER Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 627 ILE Chi-restraints excluded: chain H residue 628 SER Chi-restraints excluded: chain H residue 670 GLN Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 771 CYS Chi-restraints excluded: chain H residue 801 VAL Chi-restraints excluded: chain H residue 831 THR Chi-restraints excluded: chain H residue 922 THR Chi-restraints excluded: chain L residue 625 HIS Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 803 VAL Chi-restraints excluded: chain L residue 818 THR Chi-restraints excluded: chain L residue 831 THR Chi-restraints excluded: chain L residue 836 THR Chi-restraints excluded: chain L residue 918 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 318 CYS Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 389 LEU Chi-restraints excluded: chain K residue 405 ASN Chi-restraints excluded: chain K residue 435 CYS Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain 0 residue 753 VAL Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 831 THR Chi-restraints excluded: chain 0 residue 931 SER Chi-restraints excluded: chain 3 residue 591 VAL Chi-restraints excluded: chain 3 residue 627 ILE Chi-restraints excluded: chain 3 residue 628 SER Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 771 CYS Chi-restraints excluded: chain 3 residue 801 VAL Chi-restraints excluded: chain 3 residue 831 THR Chi-restraints excluded: chain 3 residue 922 THR Chi-restraints excluded: chain 4 residue 625 HIS Chi-restraints excluded: chain 4 residue 739 VAL Chi-restraints excluded: chain 4 residue 740 THR Chi-restraints excluded: chain 4 residue 753 VAL Chi-restraints excluded: chain 4 residue 803 VAL Chi-restraints excluded: chain 4 residue 818 THR Chi-restraints excluded: chain 4 residue 831 THR Chi-restraints excluded: chain 4 residue 836 THR Chi-restraints excluded: chain 4 residue 918 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 151 TYR Chi-restraints excluded: chain 7 residue 167 LEU Chi-restraints excluded: chain 7 residue 185 THR Chi-restraints excluded: chain 7 residue 252 ILE Chi-restraints excluded: chain 7 residue 271 SER Chi-restraints excluded: chain 7 residue 348 THR Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 143 THR Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 386 SER Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 487 ILE Chi-restraints excluded: chain 8 residue 521 SER Chi-restraints excluded: chain 8 residue 556 ASN Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 318 CYS Chi-restraints excluded: chain 9 residue 329 ILE Chi-restraints excluded: chain 9 residue 344 LEU Chi-restraints excluded: chain 9 residue 389 LEU Chi-restraints excluded: chain 9 residue 405 ASN Chi-restraints excluded: chain 9 residue 435 CYS Chi-restraints excluded: chain 9 residue 483 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 322 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 427 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 103 optimal weight: 0.0870 chunk 314 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 893 GLN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 ASN ** 3 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 625 HIS 4 893 GLN ** 7 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124165 restraints weight = 71627.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120932 restraints weight = 71694.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122696 restraints weight = 67823.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123827 restraints weight = 44576.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124078 restraints weight = 41721.549| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 46880 Z= 0.123 Angle : 0.634 13.673 64094 Z= 0.300 Chirality : 0.044 0.274 7800 Planarity : 0.004 0.054 7572 Dihedral : 8.988 82.381 10696 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 16.97 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.12), residues: 5196 helix: 1.79 (0.13), residues: 1698 sheet: -0.53 (0.19), residues: 704 loop : -0.91 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 865 TYR 0.021 0.001 TYR 9 470 PHE 0.028 0.001 PHE 7 481 TRP 0.008 0.001 TRP H 721 HIS 0.022 0.001 HIS 4 625 Details of bonding type rmsd covalent geometry : bond 0.00267 (46622) covalent geometry : angle 0.59361 (63362) SS BOND : bond 0.00756 ( 42) SS BOND : angle 2.03385 ( 84) hydrogen bonds : bond 0.04533 ( 1738) hydrogen bonds : angle 4.52187 ( 4596) link_ALPHA1-2 : bond 0.01009 ( 6) link_ALPHA1-2 : angle 1.99186 ( 18) link_ALPHA1-3 : bond 0.01109 ( 30) link_ALPHA1-3 : angle 1.77262 ( 90) link_ALPHA1-6 : bond 0.00730 ( 30) link_ALPHA1-6 : angle 1.83310 ( 90) link_BETA1-2 : bond 0.00884 ( 6) link_BETA1-2 : angle 4.33285 ( 18) link_BETA1-4 : bond 0.00636 ( 78) link_BETA1-4 : angle 1.61047 ( 234) link_NAG-ASN : bond 0.00432 ( 66) link_NAG-ASN : angle 2.75373 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 450 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8715 (t70) cc_final: 0.8303 (t0) REVERT: A 107 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: D 845 ARG cc_start: 0.7681 (ttt90) cc_final: 0.7103 (ptm160) REVERT: H 670 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: H 792 TRP cc_start: 0.8731 (m-10) cc_final: 0.8510 (m100) REVERT: H 890 ILE cc_start: 0.8424 (mm) cc_final: 0.8160 (mt) REVERT: H 892 GLU cc_start: 0.7160 (tp30) cc_final: 0.6828 (tp30) REVERT: H 954 LEU cc_start: 0.8526 (mm) cc_final: 0.8263 (mm) REVERT: E 83 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7614 (mt) REVERT: E 97 LYS cc_start: 0.8077 (tppt) cc_final: 0.7271 (tppt) REVERT: C 198 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: C 314 HIS cc_start: 0.5958 (m90) cc_final: 0.5306 (m90) REVERT: C 363 TRP cc_start: 0.7233 (m-10) cc_final: 0.6856 (m-10) REVERT: C 547 ASP cc_start: 0.7050 (m-30) cc_final: 0.6824 (t0) REVERT: G 278 LYS cc_start: 0.8134 (tttt) cc_final: 0.7753 (mttm) REVERT: G 556 ASN cc_start: 0.5680 (OUTLIER) cc_final: 0.5301 (t0) REVERT: K 528 TYR cc_start: 0.7340 (t80) cc_final: 0.7132 (t80) REVERT: K 540 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.7324 (mmm-85) REVERT: B 98 ASP cc_start: 0.8713 (t70) cc_final: 0.8299 (t0) REVERT: B 107 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: 0 845 ARG cc_start: 0.7679 (ttt90) cc_final: 0.7102 (ptm160) REVERT: 3 670 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7261 (mt0) REVERT: 3 792 TRP cc_start: 0.8720 (m-10) cc_final: 0.8507 (m100) REVERT: 3 890 ILE cc_start: 0.8423 (mm) cc_final: 0.8158 (mt) REVERT: 3 892 GLU cc_start: 0.7162 (tp30) cc_final: 0.6828 (tp30) REVERT: 3 954 LEU cc_start: 0.8522 (mm) cc_final: 0.8258 (mm) REVERT: 5 83 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7615 (mt) REVERT: 5 97 LYS cc_start: 0.8079 (tppt) cc_final: 0.7273 (tppt) REVERT: 7 172 MET cc_start: 0.8491 (mtt) cc_final: 0.8199 (mtt) REVERT: 7 198 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: 7 314 HIS cc_start: 0.5970 (m90) cc_final: 0.5317 (m90) REVERT: 7 363 TRP cc_start: 0.7246 (m-10) cc_final: 0.6871 (m-10) REVERT: 7 547 ASP cc_start: 0.7065 (m-30) cc_final: 0.6831 (t0) REVERT: 8 278 LYS cc_start: 0.8162 (tttt) cc_final: 0.7777 (mttm) REVERT: 8 556 ASN cc_start: 0.5671 (OUTLIER) cc_final: 0.5290 (t0) REVERT: 9 528 TYR cc_start: 0.7349 (t80) cc_final: 0.7134 (t80) REVERT: 9 540 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.7321 (mmm-85) outliers start: 124 outliers final: 88 residues processed: 547 average time/residue: 0.2266 time to fit residues: 212.6787 Evaluate side-chains 533 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 435 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 905 ASP Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 627 ILE Chi-restraints excluded: chain H residue 628 SER Chi-restraints excluded: chain H residue 670 GLN Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 771 CYS Chi-restraints excluded: chain H residue 801 VAL Chi-restraints excluded: chain H residue 831 THR Chi-restraints excluded: chain H residue 906 ILE Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 740 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 803 VAL Chi-restraints excluded: chain L residue 831 THR Chi-restraints excluded: chain L residue 836 THR Chi-restraints excluded: chain L residue 918 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 86 CYS Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 268 ASN Chi-restraints excluded: chain K residue 318 CYS Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain 0 residue 753 VAL Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 831 THR Chi-restraints excluded: chain 0 residue 905 ASP Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 3 residue 591 VAL Chi-restraints excluded: chain 3 residue 627 ILE Chi-restraints excluded: chain 3 residue 628 SER Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 771 CYS Chi-restraints excluded: chain 3 residue 801 VAL Chi-restraints excluded: chain 3 residue 831 THR Chi-restraints excluded: chain 3 residue 906 ILE Chi-restraints excluded: chain 4 residue 625 HIS Chi-restraints excluded: chain 4 residue 739 VAL Chi-restraints excluded: chain 4 residue 740 THR Chi-restraints excluded: chain 4 residue 753 VAL Chi-restraints excluded: chain 4 residue 803 VAL Chi-restraints excluded: chain 4 residue 831 THR Chi-restraints excluded: chain 4 residue 836 THR Chi-restraints excluded: chain 4 residue 918 LEU Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 86 CYS Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 151 TYR Chi-restraints excluded: chain 7 residue 185 THR Chi-restraints excluded: chain 7 residue 198 GLU Chi-restraints excluded: chain 7 residue 271 SER Chi-restraints excluded: chain 7 residue 348 THR Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 386 SER Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 487 ILE Chi-restraints excluded: chain 8 residue 521 SER Chi-restraints excluded: chain 8 residue 556 ASN Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 268 ASN Chi-restraints excluded: chain 9 residue 318 CYS Chi-restraints excluded: chain 9 residue 329 ILE Chi-restraints excluded: chain 9 residue 344 LEU Chi-restraints excluded: chain 9 residue 483 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 84 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 227 optimal weight: 0.1980 chunk 171 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 478 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 496 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 374 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 722 ASN D 863 GLN ** H 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 625 HIS K 268 ASN 0 722 ASN 0 863 GLN ** 3 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 268 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.160354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.125552 restraints weight = 71706.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122703 restraints weight = 75510.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124442 restraints weight = 69166.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125411 restraints weight = 45122.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125511 restraints weight = 42310.198| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.7210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 46880 Z= 0.112 Angle : 0.614 10.875 64094 Z= 0.288 Chirality : 0.043 0.275 7800 Planarity : 0.004 0.052 7572 Dihedral : 8.603 80.548 10696 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.22 % Allowed : 17.58 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.12), residues: 5196 helix: 1.94 (0.13), residues: 1704 sheet: -0.33 (0.19), residues: 692 loop : -0.84 (0.12), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 269 TYR 0.021 0.001 TYR K 470 PHE 0.030 0.001 PHE 7 481 TRP 0.009 0.001 TRP G 287 HIS 0.032 0.001 HIS 4 625 Details of bonding type rmsd covalent geometry : bond 0.00238 (46622) covalent geometry : angle 0.57411 (63362) SS BOND : bond 0.00841 ( 42) SS BOND : angle 1.79392 ( 84) hydrogen bonds : bond 0.04088 ( 1738) hydrogen bonds : angle 4.38394 ( 4596) link_ALPHA1-2 : bond 0.01031 ( 6) link_ALPHA1-2 : angle 1.90417 ( 18) link_ALPHA1-3 : bond 0.01102 ( 30) link_ALPHA1-3 : angle 1.73146 ( 90) link_ALPHA1-6 : bond 0.00759 ( 30) link_ALPHA1-6 : angle 1.79031 ( 90) link_BETA1-2 : bond 0.00906 ( 6) link_BETA1-2 : angle 4.25431 ( 18) link_BETA1-4 : bond 0.00616 ( 78) link_BETA1-4 : angle 1.54243 ( 234) link_NAG-ASN : bond 0.00425 ( 66) link_NAG-ASN : angle 2.75542 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 465 time to evaluate : 1.323 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 98 ASP cc_start: 0.8694 (t70) cc_final: 0.8255 (t0) REVERT: A 107 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.5375 (m-30) REVERT: D 845 ARG cc_start: 0.7621 (ttt90) cc_final: 0.7067 (ptm160) REVERT: H 670 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: H 863 GLN cc_start: 0.7372 (mm-40) cc_final: 0.6472 (tp40) REVERT: H 890 ILE cc_start: 0.8380 (mm) cc_final: 0.8116 (mt) REVERT: H 892 GLU cc_start: 0.7109 (tp30) cc_final: 0.6798 (tp30) REVERT: H 954 LEU cc_start: 0.8565 (mm) cc_final: 0.8302 (mm) REVERT: E 83 LEU cc_start: 0.7916 (tt) cc_final: 0.7535 (mt) REVERT: E 97 LYS cc_start: 0.7971 (tppt) cc_final: 0.7296 (tppt) REVERT: C 198 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7361 (tt0) REVERT: C 251 LEU cc_start: 0.8210 (tp) cc_final: 0.7944 (tt) REVERT: C 314 HIS cc_start: 0.5886 (m90) cc_final: 0.5316 (m90) REVERT: C 321 GLN cc_start: 0.8044 (mt0) cc_final: 0.7778 (mt0) REVERT: C 363 TRP cc_start: 0.7182 (m-10) cc_final: 0.6816 (m-10) REVERT: G 278 LYS cc_start: 0.8143 (tttt) cc_final: 0.7833 (mttm) REVERT: G 556 ASN cc_start: 0.5623 (OUTLIER) cc_final: 0.5327 (t0) REVERT: B 98 ASP cc_start: 0.8691 (t70) cc_final: 0.8253 (t0) REVERT: B 107 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.5373 (m-30) REVERT: 0 845 ARG cc_start: 0.7620 (ttt90) cc_final: 0.7065 (ptm160) REVERT: 3 670 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: 3 863 GLN cc_start: 0.7367 (mm-40) cc_final: 0.6471 (tp40) REVERT: 3 890 ILE cc_start: 0.8386 (mm) cc_final: 0.8121 (mt) REVERT: 3 892 GLU cc_start: 0.7096 (tp30) cc_final: 0.6788 (tp30) REVERT: 3 954 LEU cc_start: 0.8561 (mm) cc_final: 0.8296 (mm) REVERT: 5 83 LEU cc_start: 0.7914 (tt) cc_final: 0.7535 (mt) REVERT: 5 97 LYS cc_start: 0.7969 (tppt) cc_final: 0.7288 (tppt) REVERT: 7 172 MET cc_start: 0.8476 (mtt) cc_final: 0.8196 (mtt) REVERT: 7 198 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: 7 251 LEU cc_start: 0.8213 (tp) cc_final: 0.7950 (tt) REVERT: 7 314 HIS cc_start: 0.5891 (m90) cc_final: 0.5321 (m90) REVERT: 7 321 GLN cc_start: 0.8046 (mt0) cc_final: 0.7788 (mt0) REVERT: 7 363 TRP cc_start: 0.7197 (m-10) cc_final: 0.6826 (m-10) REVERT: 8 278 LYS cc_start: 0.8140 (tttt) cc_final: 0.7830 (mttm) REVERT: 8 556 ASN cc_start: 0.5619 (OUTLIER) cc_final: 0.5321 (t0) outliers start: 106 outliers final: 91 residues processed: 551 average time/residue: 0.2016 time to fit residues: 190.1928 Evaluate side-chains 538 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 439 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 905 ASP Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain H residue 627 ILE Chi-restraints excluded: chain H residue 628 SER Chi-restraints excluded: chain H residue 670 GLN Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 771 CYS Chi-restraints excluded: chain H residue 801 VAL Chi-restraints excluded: chain H residue 831 THR Chi-restraints excluded: chain H residue 906 ILE Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 803 VAL Chi-restraints excluded: chain L residue 831 THR Chi-restraints excluded: chain L residue 836 THR Chi-restraints excluded: chain L residue 918 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 318 CYS Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 435 CYS Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain 0 residue 753 VAL Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 810 SER Chi-restraints excluded: chain 0 residue 831 THR Chi-restraints excluded: chain 0 residue 841 LEU Chi-restraints excluded: chain 0 residue 905 ASP Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 3 residue 627 ILE Chi-restraints excluded: chain 3 residue 628 SER Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 771 CYS Chi-restraints excluded: chain 3 residue 801 VAL Chi-restraints excluded: chain 3 residue 831 THR Chi-restraints excluded: chain 3 residue 906 ILE Chi-restraints excluded: chain 4 residue 627 ILE Chi-restraints excluded: chain 4 residue 739 VAL Chi-restraints excluded: chain 4 residue 753 VAL Chi-restraints excluded: chain 4 residue 803 VAL Chi-restraints excluded: chain 4 residue 831 THR Chi-restraints excluded: chain 4 residue 836 THR Chi-restraints excluded: chain 4 residue 918 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 151 TYR Chi-restraints excluded: chain 7 residue 185 THR Chi-restraints excluded: chain 7 residue 198 GLU Chi-restraints excluded: chain 7 residue 271 SER Chi-restraints excluded: chain 7 residue 348 THR Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 7 residue 449 CYS Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 300 SER Chi-restraints excluded: chain 8 residue 386 SER Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 487 ILE Chi-restraints excluded: chain 8 residue 521 SER Chi-restraints excluded: chain 8 residue 556 ASN Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 198 GLU Chi-restraints excluded: chain 9 residue 318 CYS Chi-restraints excluded: chain 9 residue 329 ILE Chi-restraints excluded: chain 9 residue 344 LEU Chi-restraints excluded: chain 9 residue 435 CYS Chi-restraints excluded: chain 9 residue 483 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 27 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 chunk 285 optimal weight: 1.9990 chunk 502 optimal weight: 8.9990 chunk 349 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 299 optimal weight: 10.0000 chunk 474 optimal weight: 8.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 863 GLN ** H 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 728 HIS K 268 ASN 0 863 GLN 3 615 HIS 3 728 HIS 4 625 HIS 9 268 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.160340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125694 restraints weight = 71401.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122387 restraints weight = 70814.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124775 restraints weight = 68271.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124675 restraints weight = 45264.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125410 restraints weight = 41547.516| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 46880 Z= 0.112 Angle : 0.600 9.558 64094 Z= 0.282 Chirality : 0.043 0.273 7800 Planarity : 0.004 0.050 7572 Dihedral : 8.292 78.612 10696 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.24 % Allowed : 17.58 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.12), residues: 5196 helix: 2.06 (0.13), residues: 1700 sheet: -0.30 (0.19), residues: 716 loop : -0.78 (0.12), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 865 TYR 0.020 0.001 TYR 9 470 PHE 0.030 0.001 PHE C 481 TRP 0.008 0.001 TRP 8 287 HIS 0.010 0.001 HIS 4 625 Details of bonding type rmsd covalent geometry : bond 0.00242 (46622) covalent geometry : angle 0.56153 (63362) SS BOND : bond 0.00814 ( 42) SS BOND : angle 1.68594 ( 84) hydrogen bonds : bond 0.03933 ( 1738) hydrogen bonds : angle 4.31902 ( 4596) link_ALPHA1-2 : bond 0.00997 ( 6) link_ALPHA1-2 : angle 1.87993 ( 18) link_ALPHA1-3 : bond 0.01074 ( 30) link_ALPHA1-3 : angle 1.73655 ( 90) link_ALPHA1-6 : bond 0.00775 ( 30) link_ALPHA1-6 : angle 1.77283 ( 90) link_BETA1-2 : bond 0.00890 ( 6) link_BETA1-2 : angle 4.26262 ( 18) link_BETA1-4 : bond 0.00599 ( 78) link_BETA1-4 : angle 1.51358 ( 234) link_NAG-ASN : bond 0.00454 ( 66) link_NAG-ASN : angle 2.65614 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 448 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8758 (t70) cc_final: 0.8339 (t0) REVERT: A 107 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.5333 (m-30) REVERT: D 845 ARG cc_start: 0.7622 (ttt90) cc_final: 0.7104 (ptm160) REVERT: H 670 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: H 863 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6451 (tp40) REVERT: H 890 ILE cc_start: 0.8341 (mm) cc_final: 0.8049 (mt) REVERT: H 892 GLU cc_start: 0.7179 (tp30) cc_final: 0.6830 (tp30) REVERT: H 954 LEU cc_start: 0.8512 (mm) cc_final: 0.8253 (mm) REVERT: E 83 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7518 (mt) REVERT: E 97 LYS cc_start: 0.7990 (tppt) cc_final: 0.7284 (tppt) REVERT: C 251 LEU cc_start: 0.8138 (tp) cc_final: 0.7849 (tt) REVERT: C 314 HIS cc_start: 0.5945 (m90) cc_final: 0.5416 (m90) REVERT: C 363 TRP cc_start: 0.7225 (m-10) cc_final: 0.6810 (m-10) REVERT: G 278 LYS cc_start: 0.8195 (tttt) cc_final: 0.7833 (mttm) REVERT: G 283 ARG cc_start: 0.5217 (mmt180) cc_final: 0.4908 (mmm160) REVERT: G 556 ASN cc_start: 0.5641 (OUTLIER) cc_final: 0.5337 (t0) REVERT: B 98 ASP cc_start: 0.8753 (t70) cc_final: 0.8333 (t0) REVERT: B 107 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.5336 (m-30) REVERT: 0 845 ARG cc_start: 0.7621 (ttt90) cc_final: 0.7099 (ptm160) REVERT: 3 670 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: 3 863 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6455 (tp40) REVERT: 3 890 ILE cc_start: 0.8347 (mm) cc_final: 0.8055 (mt) REVERT: 3 892 GLU cc_start: 0.7168 (tp30) cc_final: 0.6822 (tp30) REVERT: 3 954 LEU cc_start: 0.8506 (mm) cc_final: 0.8248 (mm) REVERT: 5 83 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7519 (mt) REVERT: 5 94 GLN cc_start: 0.8371 (tp40) cc_final: 0.8168 (tp40) REVERT: 5 97 LYS cc_start: 0.7987 (tppt) cc_final: 0.7282 (tppt) REVERT: 7 172 MET cc_start: 0.8474 (mtt) cc_final: 0.8192 (mtt) REVERT: 7 251 LEU cc_start: 0.8140 (tp) cc_final: 0.7852 (tt) REVERT: 7 314 HIS cc_start: 0.5951 (m90) cc_final: 0.5429 (m90) REVERT: 7 363 TRP cc_start: 0.7243 (m-10) cc_final: 0.6827 (m-10) REVERT: 8 278 LYS cc_start: 0.8191 (tttt) cc_final: 0.7837 (mttm) REVERT: 8 283 ARG cc_start: 0.5214 (mmt180) cc_final: 0.4913 (mmm160) REVERT: 8 556 ASN cc_start: 0.5637 (OUTLIER) cc_final: 0.5329 (t0) outliers start: 107 outliers final: 88 residues processed: 533 average time/residue: 0.1796 time to fit residues: 165.0824 Evaluate side-chains 534 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 438 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 627 ILE Chi-restraints excluded: chain H residue 670 GLN Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 771 CYS Chi-restraints excluded: chain H residue 801 VAL Chi-restraints excluded: chain H residue 831 THR Chi-restraints excluded: chain H residue 906 ILE Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 803 VAL Chi-restraints excluded: chain L residue 831 THR Chi-restraints excluded: chain L residue 836 THR Chi-restraints excluded: chain L residue 918 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 268 ASN Chi-restraints excluded: chain K residue 318 CYS Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 435 CYS Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain 0 residue 753 VAL Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 810 SER Chi-restraints excluded: chain 0 residue 831 THR Chi-restraints excluded: chain 0 residue 841 LEU Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 3 residue 591 VAL Chi-restraints excluded: chain 3 residue 627 ILE Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 771 CYS Chi-restraints excluded: chain 3 residue 801 VAL Chi-restraints excluded: chain 3 residue 831 THR Chi-restraints excluded: chain 3 residue 906 ILE Chi-restraints excluded: chain 4 residue 739 VAL Chi-restraints excluded: chain 4 residue 803 VAL Chi-restraints excluded: chain 4 residue 831 THR Chi-restraints excluded: chain 4 residue 836 THR Chi-restraints excluded: chain 4 residue 918 LEU Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 151 TYR Chi-restraints excluded: chain 7 residue 185 THR Chi-restraints excluded: chain 7 residue 271 SER Chi-restraints excluded: chain 7 residue 348 THR Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 7 residue 449 CYS Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 300 SER Chi-restraints excluded: chain 8 residue 386 SER Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 487 ILE Chi-restraints excluded: chain 8 residue 521 SER Chi-restraints excluded: chain 8 residue 556 ASN Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 198 GLU Chi-restraints excluded: chain 9 residue 268 ASN Chi-restraints excluded: chain 9 residue 318 CYS Chi-restraints excluded: chain 9 residue 329 ILE Chi-restraints excluded: chain 9 residue 344 LEU Chi-restraints excluded: chain 9 residue 435 CYS Chi-restraints excluded: chain 9 residue 483 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 401 optimal weight: 2.9990 chunk 440 optimal weight: 4.9990 chunk 414 optimal weight: 6.9990 chunk 360 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 chunk 361 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 ASN 9 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124999 restraints weight = 71919.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121659 restraints weight = 76276.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123477 restraints weight = 69022.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124773 restraints weight = 45416.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125029 restraints weight = 41651.563| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 46880 Z= 0.126 Angle : 0.618 11.401 64094 Z= 0.291 Chirality : 0.043 0.274 7800 Planarity : 0.004 0.056 7572 Dihedral : 8.252 78.168 10696 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.07 % Allowed : 17.77 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.12), residues: 5196 helix: 2.03 (0.13), residues: 1704 sheet: -0.38 (0.19), residues: 720 loop : -0.77 (0.12), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 9 269 TYR 0.019 0.001 TYR K 470 PHE 0.031 0.001 PHE 7 481 TRP 0.008 0.001 TRP A 95 HIS 0.015 0.001 HIS K 314 Details of bonding type rmsd covalent geometry : bond 0.00287 (46622) covalent geometry : angle 0.58097 (63362) SS BOND : bond 0.00795 ( 42) SS BOND : angle 1.73028 ( 84) hydrogen bonds : bond 0.04082 ( 1738) hydrogen bonds : angle 4.34898 ( 4596) link_ALPHA1-2 : bond 0.00950 ( 6) link_ALPHA1-2 : angle 1.88317 ( 18) link_ALPHA1-3 : bond 0.01078 ( 30) link_ALPHA1-3 : angle 1.76567 ( 90) link_ALPHA1-6 : bond 0.00773 ( 30) link_ALPHA1-6 : angle 1.79000 ( 90) link_BETA1-2 : bond 0.00875 ( 6) link_BETA1-2 : angle 4.31667 ( 18) link_BETA1-4 : bond 0.00616 ( 78) link_BETA1-4 : angle 1.51520 ( 234) link_NAG-ASN : bond 0.00402 ( 66) link_NAG-ASN : angle 2.62688 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10392 Ramachandran restraints generated. 5196 Oldfield, 0 Emsley, 5196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 446 time to evaluate : 1.100 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 98 ASP cc_start: 0.8775 (t70) cc_final: 0.8352 (t0) REVERT: A 107 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.5359 (m-30) REVERT: D 845 ARG cc_start: 0.7644 (ttt90) cc_final: 0.7165 (ptm160) REVERT: H 863 GLN cc_start: 0.7393 (mm-40) cc_final: 0.6477 (tp40) REVERT: H 890 ILE cc_start: 0.8360 (mm) cc_final: 0.8076 (mt) REVERT: H 892 GLU cc_start: 0.7186 (tp30) cc_final: 0.6839 (tp30) REVERT: H 954 LEU cc_start: 0.8556 (mm) cc_final: 0.8308 (mm) REVERT: L 633 MET cc_start: 0.7360 (mmm) cc_final: 0.7045 (mmt) REVERT: E 83 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7522 (mt) REVERT: E 97 LYS cc_start: 0.7949 (tppt) cc_final: 0.7266 (tppt) REVERT: C 198 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: C 251 LEU cc_start: 0.8141 (tp) cc_final: 0.7867 (tt) REVERT: C 314 HIS cc_start: 0.5943 (m90) cc_final: 0.5415 (m90) REVERT: C 321 GLN cc_start: 0.8114 (mt0) cc_final: 0.7849 (mt0) REVERT: C 363 TRP cc_start: 0.7231 (m-10) cc_final: 0.6829 (m-10) REVERT: G 278 LYS cc_start: 0.8189 (tttt) cc_final: 0.7852 (mttm) REVERT: G 283 ARG cc_start: 0.5195 (mmt180) cc_final: 0.4924 (mmm160) REVERT: G 556 ASN cc_start: 0.5636 (OUTLIER) cc_final: 0.5356 (t0) REVERT: K 211 GLU cc_start: 0.7517 (tp30) cc_final: 0.6885 (tp30) REVERT: B 98 ASP cc_start: 0.8772 (t70) cc_final: 0.8347 (t0) REVERT: B 107 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.5362 (m-30) REVERT: 0 845 ARG cc_start: 0.7642 (ttt90) cc_final: 0.7160 (ptm160) REVERT: 3 863 GLN cc_start: 0.7387 (mm-40) cc_final: 0.6470 (tp40) REVERT: 3 890 ILE cc_start: 0.8367 (mm) cc_final: 0.8083 (mt) REVERT: 3 892 GLU cc_start: 0.7176 (tp30) cc_final: 0.6832 (tp30) REVERT: 3 954 LEU cc_start: 0.8556 (mm) cc_final: 0.8306 (mm) REVERT: 4 633 MET cc_start: 0.7369 (mmm) cc_final: 0.7053 (mmt) REVERT: 5 83 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7519 (mt) REVERT: 5 97 LYS cc_start: 0.7955 (tppt) cc_final: 0.7218 (tppt) REVERT: 7 172 MET cc_start: 0.8503 (mtt) cc_final: 0.8207 (mtt) REVERT: 7 198 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: 7 251 LEU cc_start: 0.8142 (tp) cc_final: 0.7866 (tt) REVERT: 7 314 HIS cc_start: 0.5957 (m90) cc_final: 0.5427 (m90) REVERT: 7 321 GLN cc_start: 0.8120 (mt0) cc_final: 0.7863 (mt0) REVERT: 7 363 TRP cc_start: 0.7249 (m-10) cc_final: 0.6846 (m-10) REVERT: 8 278 LYS cc_start: 0.8089 (tttt) cc_final: 0.7781 (mttm) REVERT: 8 283 ARG cc_start: 0.5197 (mmt180) cc_final: 0.4923 (mmm160) REVERT: 8 556 ASN cc_start: 0.5633 (OUTLIER) cc_final: 0.5349 (t0) REVERT: 9 211 GLU cc_start: 0.7522 (tp30) cc_final: 0.6900 (tp30) outliers start: 99 outliers final: 86 residues processed: 527 average time/residue: 0.1714 time to fit residues: 154.5845 Evaluate side-chains 529 residues out of total 4772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 435 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 753 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain J residue 134 VAL Chi-restraints excluded: chain H residue 591 VAL Chi-restraints excluded: chain H residue 627 ILE Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 771 CYS Chi-restraints excluded: chain H residue 801 VAL Chi-restraints excluded: chain H residue 831 THR Chi-restraints excluded: chain H residue 906 ILE Chi-restraints excluded: chain L residue 739 VAL Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 803 VAL Chi-restraints excluded: chain L residue 812 LEU Chi-restraints excluded: chain L residue 831 THR Chi-restraints excluded: chain L residue 918 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 404 CYS Chi-restraints excluded: chain C residue 449 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 399 LEU Chi-restraints excluded: chain G residue 487 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 556 ASN Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 151 TYR Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 318 CYS Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 483 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain 0 residue 753 VAL Chi-restraints excluded: chain 0 residue 803 VAL Chi-restraints excluded: chain 0 residue 831 THR Chi-restraints excluded: chain 0 residue 841 LEU Chi-restraints excluded: chain 2 residue 134 VAL Chi-restraints excluded: chain 3 residue 591 VAL Chi-restraints excluded: chain 3 residue 627 ILE Chi-restraints excluded: chain 3 residue 695 SER Chi-restraints excluded: chain 3 residue 771 CYS Chi-restraints excluded: chain 3 residue 801 VAL Chi-restraints excluded: chain 3 residue 831 THR Chi-restraints excluded: chain 3 residue 906 ILE Chi-restraints excluded: chain 4 residue 739 VAL Chi-restraints excluded: chain 4 residue 753 VAL Chi-restraints excluded: chain 4 residue 803 VAL Chi-restraints excluded: chain 4 residue 812 LEU Chi-restraints excluded: chain 4 residue 831 THR Chi-restraints excluded: chain 4 residue 918 LEU Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 5 residue 105 VAL Chi-restraints excluded: chain 7 residue 134 VAL Chi-restraints excluded: chain 7 residue 151 TYR Chi-restraints excluded: chain 7 residue 185 THR Chi-restraints excluded: chain 7 residue 198 GLU Chi-restraints excluded: chain 7 residue 271 SER Chi-restraints excluded: chain 7 residue 348 THR Chi-restraints excluded: chain 7 residue 404 CYS Chi-restraints excluded: chain 7 residue 449 CYS Chi-restraints excluded: chain 8 residue 134 VAL Chi-restraints excluded: chain 8 residue 151 TYR Chi-restraints excluded: chain 8 residue 300 SER Chi-restraints excluded: chain 8 residue 375 ILE Chi-restraints excluded: chain 8 residue 386 SER Chi-restraints excluded: chain 8 residue 399 LEU Chi-restraints excluded: chain 8 residue 487 ILE Chi-restraints excluded: chain 8 residue 521 SER Chi-restraints excluded: chain 8 residue 556 ASN Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain 9 residue 151 TYR Chi-restraints excluded: chain 9 residue 198 GLU Chi-restraints excluded: chain 9 residue 318 CYS Chi-restraints excluded: chain 9 residue 329 ILE Chi-restraints excluded: chain 9 residue 344 LEU Chi-restraints excluded: chain 9 residue 483 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 191 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 159 optimal weight: 0.0470 chunk 236 optimal weight: 0.5980 chunk 371 optimal weight: 0.8980 chunk 309 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 335 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 390 optimal weight: 20.0000 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.124664 restraints weight = 71481.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121705 restraints weight = 71440.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123293 restraints weight = 69806.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123728 restraints weight = 45221.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126300 restraints weight = 41886.216| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 46880 Z= 0.125 Angle : 0.614 10.172 64094 Z= 0.289 Chirality : 0.043 0.272 7800 Planarity : 0.004 0.057 7572 Dihedral : 8.118 77.117 10696 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.18 % Allowed : 17.64 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.12), residues: 5196 helix: 2.04 (0.13), residues: 1706 sheet: -0.40 (0.19), residues: 720 loop : -0.76 (0.12), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 865 TYR 0.019 0.001 TYR 9 470 PHE 0.030 0.001 PHE 7 481 TRP 0.011 0.001 TRP G 287 HIS 0.007 0.001 HIS K 314 Details of bonding type rmsd covalent geometry : bond 0.00283 (46622) covalent geometry : angle 0.57779 (63362) SS BOND : bond 0.00832 ( 42) SS BOND : angle 1.70103 ( 84) hydrogen bonds : bond 0.04104 ( 1738) hydrogen bonds : angle 4.34019 ( 4596) link_ALPHA1-2 : bond 0.00940 ( 6) link_ALPHA1-2 : angle 1.83581 ( 18) link_ALPHA1-3 : bond 0.01037 ( 30) link_ALPHA1-3 : angle 1.74583 ( 90) link_ALPHA1-6 : bond 0.00785 ( 30) link_ALPHA1-6 : angle 1.76588 ( 90) link_BETA1-2 : bond 0.00877 ( 6) link_BETA1-2 : angle 4.30109 ( 18) link_BETA1-4 : bond 0.00615 ( 78) link_BETA1-4 : angle 1.51468 ( 234) link_NAG-ASN : bond 0.00395 ( 66) link_NAG-ASN : angle 2.57011 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7229.47 seconds wall clock time: 125 minutes 35.25 seconds (7535.25 seconds total)