Starting phenix.real_space_refine on Sat Dec 28 05:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qx4_18700/12_2024/8qx4_18700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qx4_18700/12_2024/8qx4_18700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qx4_18700/12_2024/8qx4_18700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qx4_18700/12_2024/8qx4_18700.map" model { file = "/net/cci-nas-00/data/ceres_data/8qx4_18700/12_2024/8qx4_18700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qx4_18700/12_2024/8qx4_18700.cif" } resolution = 2.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 160 5.16 5 C 32800 2.51 5 N 7040 2.21 5 O 11960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 51960 Number of models: 1 Model: "" Number of chains: 140 Chain: "H" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "C" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "E" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "F" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "G" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "I" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "J" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "K" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "L" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "M" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "N" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "O" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "P" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "Q" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "R" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "S" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "T" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2206 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain: "U" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "Z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "i" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "j" Number of atoms: 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: "k" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "l" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "m" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "n" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "s" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "x" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "z" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "4" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "5" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "6" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "7" 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: "8" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "9" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "AA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "BA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "CA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "DA" 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: "EA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "FA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "GA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "HA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "IA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "JA" 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: "KA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "LA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "MA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "NA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "OA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "PA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "QA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "RA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "SA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "TA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "UA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "VA" 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: "WA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "XA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "YA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "ZA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "aA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "bA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "cA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "dA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "eA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "fA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "gA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "hA" 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: "iA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "jA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "kA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "lA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "mA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "nA" 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: "oA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "pA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "qA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "rA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "sA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "tA" 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: "uA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "vA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "wA" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "xA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "yA" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "zA" 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: "0A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "1A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "2A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "3A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "4A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "5A" 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: "6A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "7A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "8A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "9A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "AB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "BB" 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: "CB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "DB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "EB" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "FB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "GB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "HB" 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: "IB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "JB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "KB" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 2, 'YZT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "LB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "MB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "NB" 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: "OB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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: "PB" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BGC': 1, 'MAN': 2, 'NAG': 2, 'YZT': 1} 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 Time building chain proxies: 21.90, per 1000 atoms: 0.42 Number of scatterers: 51960 At special positions: 0 Unit cell: (164.971, 159.997, 227.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 160 16.00 O 11960 8.00 N 7040 7.00 C 32800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ?1-3 " NAG 0 2 " - " YZT 0 3 " " NAG 2 2 " - " YZT 2 3 " " NAG 3 2 " - " YZT 3 3 " " NAG 4 2 " - " YZT 4 3 " " NAG 5 2 " - " YZT 5 3 " " NAG 6 2 " - " YZT 6 3 " " NAG 8 2 " - " YZT 8 3 " " NAG 9 2 " - " YZT 9 3 " " NAG U 2 " - " YZT U 3 " " NAG V 2 " - " YZT V 3 " " NAG W 2 " - " YZT W 3 " " NAG Y 2 " - " YZT Y 3 " " NAG Z 2 " - " YZT Z 3 " " NAG a 2 " - " YZT a 3 " " NAG b 2 " - " YZT b 3 " " NAG c 2 " - " YZT c 3 " " NAG e 2 " - " YZT e 3 " " NAG f 2 " - " YZT f 3 " " NAG g 2 " - " YZT g 3 " " NAG h 2 " - " YZT h 3 " " NAG i 2 " - " YZT i 3 " " NAG k 2 " - " YZT k 3 " " NAG l 2 " - " YZT l 3 " " NAG m 2 " - " YZT m 3 " " NAG n 2 " - " YZT n 3 " " NAG o 2 " - " YZT o 3 " " NAG q 2 " - " YZT q 3 " " NAG r 2 " - " YZT r 3 " " NAG s 2 " - " YZT s 3 " " NAG t 2 " - " YZT t 3 " " NAG u 2 " - " YZT u 3 " " NAG w 2 " - " YZT w 3 " " NAG x 2 " - " YZT x 3 " " NAG y 2 " - " YZT y 3 " " NAG z 2 " - " YZT z 3 " " NAG0A 2 " - " YZT0A 3 " " NAG1A 2 " - " YZT1A 3 " " NAG2A 2 " - " YZT2A 3 " " NAG3A 2 " - " YZT3A 3 " " NAG4A 2 " - " YZT4A 3 " " NAG6A 2 " - " YZT6A 3 " " NAG7A 2 " - " YZT7A 3 " " NAG8A 2 " - " YZT8A 3 " " NAG9A 2 " - " YZT9A 3 " " NAGAA 2 " - " YZTAA 3 " " NAGAB 2 " - " YZTAB 3 " " NAGBA 2 " - " YZTBA 3 " " NAGCA 2 " - " YZTCA 3 " " NAGCB 2 " - " YZTCB 3 " " NAGDB 2 " - " YZTDB 3 " " NAGEA 2 " - " YZTEA 3 " " NAGEB 2 " - " YZTEB 3 " " NAGFA 2 " - " YZTFA 3 " " NAGFB 2 " - " YZTFB 3 " " NAGGA 2 " - " YZTGA 3 " " NAGGB 2 " - " YZTGB 3 " " NAGHA 2 " - " YZTHA 3 " " NAGIA 2 " - " YZTIA 3 " " NAGIB 2 " - " YZTIB 3 " " NAGJB 2 " - " YZTJB 3 " " NAGKA 2 " - " YZTKA 3 " " NAGKB 2 " - " YZTKB 3 " " NAGLA 2 " - " YZTLA 3 " " NAGLB 2 " - " YZTLB 3 " " NAGMA 2 " - " YZTMA 3 " " NAGMB 2 " - " YZTMB 3 " " NAGNA 2 " - " YZTNA 3 " " NAGOA 2 " - " YZTOA 3 " " NAGOB 2 " - " YZTOB 3 " " NAGPB 2 " - " YZTPB 3 " " NAGQA 2 " - " YZTQA 3 " " NAGRA 2 " - " YZTRA 3 " " NAGSA 2 " - " YZTSA 3 " " NAGTA 2 " - " YZTTA 3 " " NAGUA 2 " - " YZTUA 3 " " NAGWA 2 " - " YZTWA 3 " " NAGXA 2 " - " YZTXA 3 " " NAGYA 2 " - " YZTYA 3 " " NAGZA 2 " - " YZTZA 3 " " NAGaA 2 " - " YZTaA 3 " " NAGcA 2 " - " YZTcA 3 " " NAGdA 2 " - " YZTdA 3 " " NAGeA 2 " - " YZTeA 3 " " NAGfA 2 " - " YZTfA 3 " " NAGgA 2 " - " YZTgA 3 " " NAGiA 2 " - " YZTiA 3 " " NAGjA 2 " - " YZTjA 3 " " NAGkA 2 " - " YZTkA 3 " " NAGlA 2 " - " YZTlA 3 " " NAGmA 2 " - " YZTmA 3 " " NAGoA 2 " - " YZToA 3 " " NAGpA 2 " - " YZTpA 3 " " NAGqA 2 " - " YZTqA 3 " " NAGrA 2 " - " YZTrA 3 " " NAGsA 2 " - " YZTsA 3 " " NAGuA 2 " - " YZTuA 3 " " NAGvA 2 " - " YZTvA 3 " " NAGwA 2 " - " YZTwA 3 " " NAGxA 2 " - " YZTxA 3 " " NAGyA 2 " - " YZTyA 3 " ALPHA1-4 " NAG 0 2 " - " MAN 0 5 " " NAG 2 2 " - " MAN 2 5 " " NAG 3 2 " - " MAN 3 5 " " NAG 4 2 " - " MAN 4 4 " " NAG 5 2 " - " MAN 5 5 " " NAG 6 2 " - " MAN 6 5 " " NAG 8 2 " - " MAN 8 5 " " NAG 9 2 " - " MAN 9 5 " " NAG U 2 " - " MAN U 4 " " NAG V 2 " - " MAN V 5 " " NAG W 2 " - " MAN W 5 " " NAG Y 2 " - " MAN Y 5 " " NAG Z 2 " - " MAN Z 5 " " NAG a 2 " - " MAN a 4 " " NAG b 2 " - " MAN b 5 " " NAG c 2 " - " MAN c 5 " " NAG e 2 " - " MAN e 5 " " NAG f 2 " - " MAN f 5 " " NAG g 2 " - " MAN g 4 " " NAG h 2 " - " MAN h 5 " " NAG i 2 " - " MAN i 5 " " NAG k 2 " - " MAN k 5 " " NAG l 2 " - " MAN l 5 " " NAG m 2 " - " MAN m 4 " " NAG n 2 " - " MAN n 5 " " NAG o 2 " - " MAN o 5 " " NAG q 2 " - " MAN q 5 " " NAG r 2 " - " MAN r 5 " " NAG s 2 " - " MAN s 4 " " NAG t 2 " - " MAN t 5 " " NAG u 2 " - " MAN u 5 " " NAG w 2 " - " MAN w 5 " " NAG x 2 " - " MAN x 5 " " NAG y 2 " - " MAN y 4 " " NAG z 2 " - " MAN z 5 " " NAG0A 2 " - " MAN0A 5 " " NAG1A 2 " - " MAN1A 5 " " NAG2A 2 " - " MAN2A 4 " " NAG3A 2 " - " MAN3A 5 " " NAG4A 2 " - " MAN4A 5 " " NAG6A 2 " - " MAN6A 5 " " NAG7A 2 " - " MAN7A 5 " " NAG8A 2 " - " MAN8A 4 " " NAG9A 2 " - " MAN9A 5 " " NAGAA 2 " - " MANAA 4 " " NAGAB 2 " - " MANAB 5 " " NAGBA 2 " - " MANBA 5 " " NAGCA 2 " - " MANCA 5 " " NAGCB 2 " - " MANCB 5 " " NAGDB 2 " - " MANDB 5 " " NAGEA 2 " - " MANEA 5 " " NAGEB 2 " - " MANEB 4 " " NAGFA 2 " - " MANFA 5 " " NAGFB 2 " - " MANFB 5 " " NAGGA 2 " - " MANGA 4 " " NAGGB 2 " - " MANGB 5 " " NAGHA 2 " - " MANHA 5 " " NAGIA 2 " - " MANIA 5 " " NAGIB 2 " - " MANIB 5 " " NAGJB 2 " - " MANJB 5 " " NAGKA 2 " - " MANKA 5 " " NAGKB 2 " - " MANKB 4 " " NAGLA 2 " - " MANLA 5 " " NAGLB 2 " - " MANLB 5 " " NAGMA 2 " - " MANMA 4 " " NAGMB 2 " - " MANMB 5 " " NAGNA 2 " - " MANNA 5 " " NAGOA 2 " - " MANOA 5 " " NAGOB 2 " - " MANOB 5 " " NAGPB 2 " - " MANPB 5 " " NAGQA 2 " - " MANQA 5 " " NAGRA 2 " - " MANRA 5 " " NAGSA 2 " - " MANSA 4 " " NAGTA 2 " - " MANTA 5 " " NAGUA 2 " - " MANUA 5 " " NAGWA 2 " - " MANWA 5 " " NAGXA 2 " - " MANXA 5 " " NAGYA 2 " - " MANYA 4 " " NAGZA 2 " - " MANZA 5 " " NAGaA 2 " - " MANaA 5 " " NAGcA 2 " - " MANcA 5 " " NAGdA 2 " - " MANdA 5 " " NAGeA 2 " - " MANeA 4 " " NAGfA 2 " - " MANfA 5 " " NAGgA 2 " - " MANgA 5 " " NAGiA 2 " - " MANiA 5 " " NAGjA 2 " - " MANjA 5 " " NAGkA 2 " - " MANkA 4 " " NAGlA 2 " - " MANlA 5 " " NAGmA 2 " - " MANmA 5 " " NAGoA 2 " - " MANoA 5 " " NAGpA 2 " - " MANpA 5 " " NAGqA 2 " - " MANqA 4 " " NAGrA 2 " - " MANrA 5 " " NAGsA 2 " - " MANsA 5 " " NAGuA 2 " - " MANuA 5 " " NAGvA 2 " - " MANvA 5 " " NAGwA 2 " - " MANwA 4 " " NAGxA 2 " - " MANxA 5 " " NAGyA 2 " - " MANyA 5 " ALPHA1-6 " NAG 0 2 " - " MAN 0 6 " " NAG 2 2 " - " MAN 2 6 " " NAG 3 2 " - " MAN 3 6 " " NAG 4 2 " - " MAN 4 5 " " NAG 5 2 " - " MAN 5 6 " " NAG 6 2 " - " MAN 6 6 " " NAG 8 2 " - " MAN 8 6 " " NAG 9 2 " - " MAN 9 6 " " NAG U 2 " - " MAN U 5 " " NAG V 2 " - " MAN V 6 " " NAG W 2 " - " MAN W 6 " " NAG Y 2 " - " MAN Y 6 " " NAG Z 2 " - " MAN Z 6 " " NAG a 2 " - " MAN a 5 " " NAG b 2 " - " MAN b 6 " " NAG c 2 " - " MAN c 6 " " NAG e 2 " - " MAN e 6 " " NAG f 2 " - " MAN f 6 " " NAG g 2 " - " MAN g 5 " " NAG h 2 " - " MAN h 6 " " NAG i 2 " - " MAN i 6 " " NAG k 2 " - " MAN k 6 " " NAG l 2 " - " MAN l 6 " " NAG m 2 " - " MAN m 5 " " NAG n 2 " - " MAN n 6 " " NAG o 2 " - " MAN o 6 " " NAG q 2 " - " MAN q 6 " " NAG r 2 " - " MAN r 6 " " NAG s 2 " - " MAN s 5 " " NAG t 2 " - " MAN t 6 " " NAG u 2 " - " MAN u 6 " " NAG w 2 " - " MAN w 6 " " NAG x 2 " - " MAN x 6 " " NAG y 2 " - " MAN y 5 " " NAG z 2 " - " MAN z 6 " " NAG0A 2 " - " MAN0A 6 " " NAG1A 2 " - " MAN1A 6 " " NAG2A 2 " - " MAN2A 5 " " NAG3A 2 " - " MAN3A 6 " " NAG4A 2 " - " MAN4A 6 " " NAG6A 2 " - " MAN6A 6 " " NAG7A 2 " - " MAN7A 6 " " NAG8A 2 " - " MAN8A 5 " " NAG9A 2 " - " MAN9A 6 " " NAGAA 2 " - " MANAA 5 " " NAGAB 2 " - " MANAB 6 " " NAGBA 2 " - " MANBA 6 " " NAGCA 2 " - " MANCA 6 " " NAGCB 2 " - " MANCB 6 " " NAGDB 2 " - " MANDB 6 " " NAGEA 2 " - " MANEA 6 " " NAGEB 2 " - " MANEB 5 " " NAGFA 2 " - " MANFA 6 " " NAGFB 2 " - " MANFB 6 " " NAGGA 2 " - " MANGA 5 " " NAGGB 2 " - " MANGB 6 " " NAGHA 2 " - " MANHA 6 " " NAGIA 2 " - " MANIA 6 " " NAGIB 2 " - " MANIB 6 " " NAGJB 2 " - " MANJB 6 " " NAGKA 2 " - " MANKA 6 " " NAGKB 2 " - " MANKB 5 " " NAGLA 2 " - " MANLA 6 " " NAGLB 2 " - " MANLB 6 " " NAGMA 2 " - " MANMA 5 " " NAGMB 2 " - " MANMB 6 " " NAGNA 2 " - " MANNA 6 " " NAGOA 2 " - " MANOA 6 " " NAGOB 2 " - " MANOB 6 " " NAGPB 2 " - " MANPB 6 " " NAGQA 2 " - " MANQA 6 " " NAGRA 2 " - " MANRA 6 " " NAGSA 2 " - " MANSA 5 " " NAGTA 2 " - " MANTA 6 " " NAGUA 2 " - " MANUA 6 " " NAGWA 2 " - " MANWA 6 " " NAGXA 2 " - " MANXA 6 " " NAGYA 2 " - " MANYA 5 " " NAGZA 2 " - " MANZA 6 " " NAGaA 2 " - " MANaA 6 " " NAGcA 2 " - " MANcA 6 " " NAGdA 2 " - " MANdA 6 " " NAGeA 2 " - " MANeA 5 " " NAGfA 2 " - " MANfA 6 " " NAGgA 2 " - " MANgA 6 " " NAGiA 2 " - " MANiA 6 " " NAGjA 2 " - " MANjA 6 " " NAGkA 2 " - " MANkA 5 " " NAGlA 2 " - " MANlA 6 " " NAGmA 2 " - " MANmA 6 " " NAGoA 2 " - " MANoA 6 " " NAGpA 2 " - " MANpA 6 " " NAGqA 2 " - " MANqA 5 " " NAGrA 2 " - " MANrA 6 " " NAGsA 2 " - " MANsA 6 " " NAGuA 2 " - " MANuA 6 " " NAGvA 2 " - " MANvA 6 " " NAGwA 2 " - " MANwA 5 " " NAGxA 2 " - " MANxA 6 " " NAGyA 2 " - " MANyA 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " YZT 0 3 " - " BGC 0 4 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " YZT 2 3 " - " BGC 2 4 " " NAG 3 1 " - " NAG 3 2 " " YZT 3 3 " - " BGC 3 4 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " YZT 5 3 " - " BGC 5 4 " " NAG 6 1 " - " NAG 6 2 " " YZT 6 3 " - " BGC 6 4 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " YZT 8 3 " - " BGC 8 4 " " NAG 9 1 " - " NAG 9 2 " " YZT 9 3 " - " BGC 9 4 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " YZT V 3 " - " BGC V 4 " " NAG W 1 " - " NAG W 2 " " YZT W 3 " - " BGC W 4 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " YZT Y 3 " - " BGC Y 4 " " NAG Z 1 " - " NAG Z 2 " " YZT Z 3 " - " BGC Z 4 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " YZT b 3 " - " BGC b 4 " " NAG c 1 " - " NAG c 2 " " YZT c 3 " - " BGC c 4 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " YZT e 3 " - " BGC e 4 " " NAG f 1 " - " NAG f 2 " " YZT f 3 " - " BGC f 4 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " YZT h 3 " - " BGC h 4 " " NAG i 1 " - " NAG i 2 " " YZT i 3 " - " BGC i 4 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " YZT k 3 " - " BGC k 4 " " NAG l 1 " - " NAG l 2 " " YZT l 3 " - " BGC l 4 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " YZT n 3 " - " BGC n 4 " " NAG o 1 " - " NAG o 2 " " YZT o 3 " - " BGC o 4 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " YZT q 3 " - " BGC q 4 " " NAG r 1 " - " NAG r 2 " " YZT r 3 " - " BGC r 4 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " YZT t 3 " - " BGC t 4 " " NAG u 1 " - " NAG u 2 " " YZT u 3 " - " BGC u 4 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " YZT w 3 " - " BGC w 4 " " NAG x 1 " - " NAG x 2 " " YZT x 3 " - " BGC x 4 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " YZT z 3 " - " BGC z 4 " " NAG0A 1 " - " NAG0A 2 " " YZT0A 3 " - " BGC0A 4 " " NAG1A 1 " - " NAG1A 2 " " YZT1A 3 " - " BGC1A 4 " " NAG2A 1 " - " NAG2A 2 " " NAG3A 1 " - " NAG3A 2 " " YZT3A 3 " - " BGC3A 4 " " NAG4A 1 " - " NAG4A 2 " " YZT4A 3 " - " BGC4A 4 " " NAG5A 1 " - " NAG5A 2 " " NAG6A 1 " - " NAG6A 2 " " YZT6A 3 " - " BGC6A 4 " " NAG7A 1 " - " NAG7A 2 " " YZT7A 3 " - " BGC7A 4 " " NAG8A 1 " - " NAG8A 2 " " NAG9A 1 " - " NAG9A 2 " " YZT9A 3 " - " BGC9A 4 " " NAGAA 1 " - " NAGAA 2 " " NAGAB 1 " - " NAGAB 2 " " YZTAB 3 " - " BGCAB 4 " " NAGBA 1 " - " NAGBA 2 " " YZTBA 3 " - " BGCBA 4 " " NAGBB 1 " - " NAGBB 2 " " NAGCA 1 " - " NAGCA 2 " " YZTCA 3 " - " BGCCA 4 " " NAGCB 1 " - " NAGCB 2 " " YZTCB 3 " - " BGCCB 4 " " NAGDA 1 " - " NAGDA 2 " " NAGDB 1 " - " NAGDB 2 " " YZTDB 3 " - " BGCDB 4 " " NAGEA 1 " - " NAGEA 2 " " YZTEA 3 " - " BGCEA 4 " " NAGEB 1 " - " NAGEB 2 " " NAGFA 1 " - " NAGFA 2 " " YZTFA 3 " - " BGCFA 4 " " NAGFB 1 " - " NAGFB 2 " " YZTFB 3 " - " BGCFB 4 " " NAGGA 1 " - " NAGGA 2 " " NAGGB 1 " - " NAGGB 2 " " YZTGB 3 " - " BGCGB 4 " " NAGHA 1 " - " NAGHA 2 " " YZTHA 3 " - " BGCHA 4 " " NAGHB 1 " - " NAGHB 2 " " NAGIA 1 " - " NAGIA 2 " " YZTIA 3 " - " BGCIA 4 " " NAGIB 1 " - " NAGIB 2 " " YZTIB 3 " - " BGCIB 4 " " NAGJA 1 " - " NAGJA 2 " " NAGJB 1 " - " NAGJB 2 " " YZTJB 3 " - " BGCJB 4 " " NAGKA 1 " - " NAGKA 2 " " YZTKA 3 " - " BGCKA 4 " " NAGKB 1 " - " NAGKB 2 " " NAGLA 1 " - " NAGLA 2 " " YZTLA 3 " - " BGCLA 4 " " NAGLB 1 " - " NAGLB 2 " " YZTLB 3 " - " BGCLB 4 " " NAGMA 1 " - " NAGMA 2 " " NAGMB 1 " - " NAGMB 2 " " YZTMB 3 " - " BGCMB 4 " " NAGNA 1 " - " NAGNA 2 " " YZTNA 3 " - " BGCNA 4 " " NAGNB 1 " - " NAGNB 2 " " NAGOA 1 " - " NAGOA 2 " " YZTOA 3 " - " BGCOA 4 " " NAGOB 1 " - " NAGOB 2 " " YZTOB 3 " - " BGCOB 4 " " NAGPA 1 " - " NAGPA 2 " " NAGPB 1 " - " NAGPB 2 " " YZTPB 3 " - " BGCPB 4 " " NAGQA 1 " - " NAGQA 2 " " YZTQA 3 " - " BGCQA 4 " " NAGRA 1 " - " NAGRA 2 " " YZTRA 3 " - " BGCRA 4 " " NAGSA 1 " - " NAGSA 2 " " NAGTA 1 " - " NAGTA 2 " " YZTTA 3 " - " BGCTA 4 " " NAGUA 1 " - " NAGUA 2 " " YZTUA 3 " - " BGCUA 4 " " NAGVA 1 " - " NAGVA 2 " " NAGWA 1 " - " NAGWA 2 " " YZTWA 3 " - " BGCWA 4 " " NAGXA 1 " - " NAGXA 2 " " YZTXA 3 " - " BGCXA 4 " " NAGYA 1 " - " NAGYA 2 " " NAGZA 1 " - " NAGZA 2 " " YZTZA 3 " - " BGCZA 4 " " NAGaA 1 " - " NAGaA 2 " " YZTaA 3 " - " BGCaA 4 " " NAGbA 1 " - " NAGbA 2 " " NAGcA 1 " - " NAGcA 2 " " YZTcA 3 " - " BGCcA 4 " " NAGdA 1 " - " NAGdA 2 " " YZTdA 3 " - " BGCdA 4 " " NAGeA 1 " - " NAGeA 2 " " NAGfA 1 " - " NAGfA 2 " " YZTfA 3 " - " BGCfA 4 " " NAGgA 1 " - " NAGgA 2 " " YZTgA 3 " - " BGCgA 4 " " NAGhA 1 " - " NAGhA 2 " " NAGiA 1 " - " NAGiA 2 " " YZTiA 3 " - " BGCiA 4 " " NAGjA 1 " - " NAGjA 2 " " YZTjA 3 " - " BGCjA 4 " " NAGkA 1 " - " NAGkA 2 " " NAGlA 1 " - " NAGlA 2 " " YZTlA 3 " - " BGClA 4 " " NAGmA 1 " - " NAGmA 2 " " YZTmA 3 " - " BGCmA 4 " " NAGnA 1 " - " NAGnA 2 " " NAGoA 1 " - " NAGoA 2 " " YZToA 3 " - " BGCoA 4 " " NAGpA 1 " - " NAGpA 2 " " YZTpA 3 " - " BGCpA 4 " " NAGqA 1 " - " NAGqA 2 " " NAGrA 1 " - " NAGrA 2 " " YZTrA 3 " - " BGCrA 4 " " NAGsA 1 " - " NAGsA 2 " " YZTsA 3 " - " BGCsA 4 " " NAGtA 1 " - " NAGtA 2 " " NAGuA 1 " - " NAGuA 2 " " YZTuA 3 " - " BGCuA 4 " " NAGvA 1 " - " NAGvA 2 " " YZTvA 3 " - " BGCvA 4 " " NAGwA 1 " - " NAGwA 2 " " NAGxA 1 " - " NAGxA 2 " " YZTxA 3 " - " BGCxA 4 " " NAGyA 1 " - " NAGyA 2 " " YZTyA 3 " - " BGCyA 4 " " NAGzA 1 " - " NAGzA 2 " NAG-ASN " NAG 0 1 " - " ASN E 195 " " NAG 1 1 " - " ASN E 214 " " NAG 2 1 " - " ASN E 218 " " NAG 3 1 " - " ASN E 229 " " NAG 4 1 " - " ASN F 145 " " NAG 5 1 " - " ASN F 173 " " NAG 6 1 " - " ASN F 195 " " NAG 7 1 " - " ASN F 214 " " NAG 8 1 " - " ASN F 218 " " NAG 9 1 " - " ASN F 229 " " NAG U 1 " - " ASN H 145 " " NAG V 1 " - " ASN H 173 " " NAG W 1 " - " ASN H 195 " " NAG X 1 " - " ASN H 214 " " NAG Y 1 " - " ASN H 218 " " NAG Z 1 " - " ASN H 229 " " NAG a 1 " - " ASN A 145 " " NAG b 1 " - " ASN A 173 " " NAG c 1 " - " ASN A 195 " " NAG d 1 " - " ASN A 214 " " NAG e 1 " - " ASN A 218 " " NAG f 1 " - " ASN A 229 " " NAG g 1 " - " ASN B 145 " " NAG h 1 " - " ASN B 173 " " NAG i 1 " - " ASN B 195 " " NAG j 1 " - " ASN B 214 " " NAG k 1 " - " ASN B 218 " " NAG l 1 " - " ASN B 229 " " NAG m 1 " - " ASN C 145 " " NAG n 1 " - " ASN C 173 " " NAG o 1 " - " ASN C 195 " " NAG p 1 " - " ASN C 214 " " NAG q 1 " - " ASN C 218 " " NAG r 1 " - " ASN C 229 " " NAG s 1 " - " ASN D 145 " " NAG t 1 " - " ASN D 173 " " NAG u 1 " - " ASN D 195 " " NAG v 1 " - " ASN D 214 " " NAG w 1 " - " ASN D 218 " " NAG x 1 " - " ASN D 229 " " NAG y 1 " - " ASN E 145 " " NAG z 1 " - " ASN E 173 " " NAG0A 1 " - " ASN P 218 " " NAG1A 1 " - " ASN P 229 " " NAG2A 1 " - " ASN Q 145 " " NAG3A 1 " - " ASN Q 173 " " NAG4A 1 " - " ASN Q 195 " " NAG5A 1 " - " ASN Q 214 " " NAG6A 1 " - " ASN Q 218 " " NAG7A 1 " - " ASN Q 229 " " NAG8A 1 " - " ASN R 145 " " NAG9A 1 " - " ASN R 173 " " NAGAA 1 " - " ASN G 145 " " NAGAB 1 " - " ASN R 195 " " NAGBA 1 " - " ASN G 173 " " NAGBB 1 " - " ASN R 214 " " NAGCA 1 " - " ASN G 195 " " NAGCB 1 " - " ASN R 218 " " NAGDA 1 " - " ASN G 214 " " NAGDB 1 " - " ASN R 229 " " NAGEA 1 " - " ASN G 218 " " NAGEB 1 " - " ASN S 145 " " NAGFA 1 " - " ASN G 229 " " NAGFB 1 " - " ASN S 173 " " NAGGA 1 " - " ASN I 145 " " NAGGB 1 " - " ASN S 195 " " NAGHA 1 " - " ASN I 173 " " NAGHB 1 " - " ASN S 214 " " NAGIA 1 " - " ASN I 195 " " NAGIB 1 " - " ASN S 218 " " NAGJA 1 " - " ASN I 214 " " NAGJB 1 " - " ASN S 229 " " NAGKA 1 " - " ASN I 218 " " NAGKB 1 " - " ASN T 145 " " NAGLA 1 " - " ASN I 229 " " NAGLB 1 " - " ASN T 173 " " NAGMA 1 " - " ASN J 145 " " NAGMB 1 " - " ASN T 195 " " NAGNA 1 " - " ASN J 173 " " NAGNB 1 " - " ASN T 214 " " NAGOA 1 " - " ASN J 195 " " NAGOB 1 " - " ASN T 218 " " NAGPA 1 " - " ASN J 214 " " NAGPB 1 " - " ASN T 229 " " NAGQA 1 " - " ASN J 218 " " NAGRA 1 " - " ASN J 229 " " NAGSA 1 " - " ASN K 145 " " NAGTA 1 " - " ASN K 173 " " NAGUA 1 " - " ASN K 195 " " NAGVA 1 " - " ASN K 214 " " NAGWA 1 " - " ASN K 218 " " NAGXA 1 " - " ASN K 229 " " NAGYA 1 " - " ASN L 145 " " NAGZA 1 " - " ASN L 173 " " NAGaA 1 " - " ASN L 195 " " NAGbA 1 " - " ASN L 214 " " NAGcA 1 " - " ASN L 218 " " NAGdA 1 " - " ASN L 229 " " NAGeA 1 " - " ASN M 145 " " NAGfA 1 " - " ASN M 173 " " NAGgA 1 " - " ASN M 195 " " NAGhA 1 " - " ASN M 214 " " NAGiA 1 " - " ASN M 218 " " NAGjA 1 " - " ASN M 229 " " NAGkA 1 " - " ASN N 145 " " NAGlA 1 " - " ASN N 173 " " NAGmA 1 " - " ASN N 195 " " NAGnA 1 " - " ASN N 214 " " NAGoA 1 " - " ASN N 218 " " NAGpA 1 " - " ASN N 229 " " NAGqA 1 " - " ASN O 145 " " NAGrA 1 " - " ASN O 173 " " NAGsA 1 " - " ASN O 195 " " NAGtA 1 " - " ASN O 214 " " NAGuA 1 " - " ASN O 218 " " NAGvA 1 " - " ASN O 229 " " NAGwA 1 " - " ASN P 145 " " NAGxA 1 " - " ASN P 173 " " NAGyA 1 " - " ASN P 195 " " NAGzA 1 " - " ASN P 214 " Time building additional restraints: 17.40 Conformation dependent library (CDL) restraints added in 4.5 seconds 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10880 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 140 sheets defined 31.8% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'H' and resid 12 through 59 removed outlier: 4.207A pdb=" N ASP H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 92 No H-bonds generated for 'chain 'H' and resid 90 through 92' Processing helix chain 'H' and resid 109 through 112 Processing helix chain 'H' and resid 124 through 126 No H-bonds generated for 'chain 'H' and resid 124 through 126' Processing helix chain 'H' and resid 127 through 131 Processing helix chain 'H' and resid 164 through 182 Processing helix chain 'H' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) Proline residue: H 203 - end of helix removed outlier: 3.853A pdb=" N ASN H 207 " --> pdb=" O TRP H 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 59 removed outlier: 3.678A pdb=" N THR A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 109 through 112 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 164 through 182 Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.632A pdb=" N ALA A 200 " --> pdb=" O SER A 197 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.850A pdb=" N ASN A 207 " --> pdb=" O TRP A 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 59 removed outlier: 3.679A pdb=" N THR B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 164 through 182 Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA B 200 " --> pdb=" O SER B 197 " (cutoff:3.500A) Proline residue: B 203 - end of helix removed outlier: 3.851A pdb=" N ASN B 207 " --> pdb=" O TRP B 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 59 removed outlier: 3.679A pdb=" N THR C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA C 18 " --> pdb=" O GLY C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 109 through 112 Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 164 through 182 Processing helix chain 'C' and resid 196 through 207 removed outlier: 3.631A pdb=" N ALA C 200 " --> pdb=" O SER C 197 " (cutoff:3.500A) Proline residue: C 203 - end of helix removed outlier: 3.850A pdb=" N ASN C 207 " --> pdb=" O TRP C 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA D 18 " --> pdb=" O GLY D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 109 through 112 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 164 through 182 Processing helix chain 'D' and resid 196 through 207 removed outlier: 3.631A pdb=" N ALA D 200 " --> pdb=" O SER D 197 " (cutoff:3.500A) Proline residue: D 203 - end of helix removed outlier: 3.853A pdb=" N ASN D 207 " --> pdb=" O TRP D 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA E 18 " --> pdb=" O GLY E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 109 through 112 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 164 through 182 Processing helix chain 'E' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA E 200 " --> pdb=" O SER E 197 " (cutoff:3.500A) Proline residue: E 203 - end of helix removed outlier: 3.853A pdb=" N ASN E 207 " --> pdb=" O TRP E 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 59 removed outlier: 3.678A pdb=" N THR F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA F 18 " --> pdb=" O GLY F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'F' and resid 109 through 112 Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 164 through 182 Processing helix chain 'F' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA F 200 " --> pdb=" O SER F 197 " (cutoff:3.500A) Proline residue: F 203 - end of helix removed outlier: 3.853A pdb=" N ASN F 207 " --> pdb=" O TRP F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 59 removed outlier: 3.678A pdb=" N THR G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 92 No H-bonds generated for 'chain 'G' and resid 90 through 92' Processing helix chain 'G' and resid 109 through 112 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'G' and resid 164 through 182 Processing helix chain 'G' and resid 196 through 207 removed outlier: 3.631A pdb=" N ALA G 200 " --> pdb=" O SER G 197 " (cutoff:3.500A) Proline residue: G 203 - end of helix removed outlier: 3.855A pdb=" N ASN G 207 " --> pdb=" O TRP G 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 59 removed outlier: 3.678A pdb=" N THR I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA I 18 " --> pdb=" O GLY I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 92 No H-bonds generated for 'chain 'I' and resid 90 through 92' Processing helix chain 'I' and resid 109 through 112 Processing helix chain 'I' and resid 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 127 through 131 Processing helix chain 'I' and resid 164 through 182 Processing helix chain 'I' and resid 196 through 207 removed outlier: 3.631A pdb=" N ALA I 200 " --> pdb=" O SER I 197 " (cutoff:3.500A) Proline residue: I 203 - end of helix removed outlier: 3.854A pdb=" N ASN I 207 " --> pdb=" O TRP I 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALA J 18 " --> pdb=" O GLY J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 92 No H-bonds generated for 'chain 'J' and resid 90 through 92' Processing helix chain 'J' and resid 109 through 112 Processing helix chain 'J' and resid 124 through 126 No H-bonds generated for 'chain 'J' and resid 124 through 126' Processing helix chain 'J' and resid 127 through 131 Processing helix chain 'J' and resid 164 through 182 Processing helix chain 'J' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA J 200 " --> pdb=" O SER J 197 " (cutoff:3.500A) Proline residue: J 203 - end of helix removed outlier: 3.853A pdb=" N ASN J 207 " --> pdb=" O TRP J 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA K 18 " --> pdb=" O GLY K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 109 through 112 Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 127 through 131 Processing helix chain 'K' and resid 164 through 182 Processing helix chain 'K' and resid 196 through 207 removed outlier: 3.631A pdb=" N ALA K 200 " --> pdb=" O SER K 197 " (cutoff:3.500A) Proline residue: K 203 - end of helix removed outlier: 3.853A pdb=" N ASN K 207 " --> pdb=" O TRP K 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 92 No H-bonds generated for 'chain 'L' and resid 90 through 92' Processing helix chain 'L' and resid 109 through 112 Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'L' and resid 164 through 182 Processing helix chain 'L' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA L 200 " --> pdb=" O SER L 197 " (cutoff:3.500A) Proline residue: L 203 - end of helix removed outlier: 3.854A pdb=" N ASN L 207 " --> pdb=" O TRP L 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA M 18 " --> pdb=" O GLY M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 109 through 112 Processing helix chain 'M' and resid 124 through 126 No H-bonds generated for 'chain 'M' and resid 124 through 126' Processing helix chain 'M' and resid 127 through 131 Processing helix chain 'M' and resid 164 through 182 Processing helix chain 'M' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA M 200 " --> pdb=" O SER M 197 " (cutoff:3.500A) Proline residue: M 203 - end of helix removed outlier: 3.853A pdb=" N ASN M 207 " --> pdb=" O TRP M 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 92 No H-bonds generated for 'chain 'N' and resid 90 through 92' Processing helix chain 'N' and resid 109 through 112 Processing helix chain 'N' and resid 124 through 126 No H-bonds generated for 'chain 'N' and resid 124 through 126' Processing helix chain 'N' and resid 127 through 131 Processing helix chain 'N' and resid 164 through 182 Processing helix chain 'N' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA N 200 " --> pdb=" O SER N 197 " (cutoff:3.500A) Proline residue: N 203 - end of helix removed outlier: 3.854A pdb=" N ASN N 207 " --> pdb=" O TRP N 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA O 18 " --> pdb=" O GLY O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 92 No H-bonds generated for 'chain 'O' and resid 90 through 92' Processing helix chain 'O' and resid 109 through 112 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 127 through 131 Processing helix chain 'O' and resid 164 through 182 Processing helix chain 'O' and resid 196 through 207 removed outlier: 3.631A pdb=" N ALA O 200 " --> pdb=" O SER O 197 " (cutoff:3.500A) Proline residue: O 203 - end of helix removed outlier: 3.853A pdb=" N ASN O 207 " --> pdb=" O TRP O 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 59 removed outlier: 3.676A pdb=" N THR P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA P 18 " --> pdb=" O GLY P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 109 through 112 Processing helix chain 'P' and resid 124 through 126 No H-bonds generated for 'chain 'P' and resid 124 through 126' Processing helix chain 'P' and resid 127 through 131 Processing helix chain 'P' and resid 164 through 182 Processing helix chain 'P' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA P 200 " --> pdb=" O SER P 197 " (cutoff:3.500A) Proline residue: P 203 - end of helix removed outlier: 3.853A pdb=" N ASN P 207 " --> pdb=" O TRP P 204 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 59 removed outlier: 3.676A pdb=" N THR Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA Q 18 " --> pdb=" O GLY Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 92 No H-bonds generated for 'chain 'Q' and resid 90 through 92' Processing helix chain 'Q' and resid 109 through 112 Processing helix chain 'Q' and resid 124 through 126 No H-bonds generated for 'chain 'Q' and resid 124 through 126' Processing helix chain 'Q' and resid 127 through 131 Processing helix chain 'Q' and resid 164 through 182 Processing helix chain 'Q' and resid 196 through 207 removed outlier: 3.631A pdb=" N ALA Q 200 " --> pdb=" O SER Q 197 " (cutoff:3.500A) Proline residue: Q 203 - end of helix removed outlier: 3.853A pdb=" N ASN Q 207 " --> pdb=" O TRP Q 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 59 removed outlier: 3.678A pdb=" N THR R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA R 18 " --> pdb=" O GLY R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 92 No H-bonds generated for 'chain 'R' and resid 90 through 92' Processing helix chain 'R' and resid 109 through 112 Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'R' and resid 127 through 131 Processing helix chain 'R' and resid 164 through 182 Processing helix chain 'R' and resid 196 through 207 removed outlier: 3.630A pdb=" N ALA R 200 " --> pdb=" O SER R 197 " (cutoff:3.500A) Proline residue: R 203 - end of helix removed outlier: 3.854A pdb=" N ASN R 207 " --> pdb=" O TRP R 204 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 59 removed outlier: 3.677A pdb=" N THR S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA S 18 " --> pdb=" O GLY S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 92 No H-bonds generated for 'chain 'S' and resid 90 through 92' Processing helix chain 'S' and resid 109 through 112 Processing helix chain 'S' and resid 124 through 126 No H-bonds generated for 'chain 'S' and resid 124 through 126' Processing helix chain 'S' and resid 127 through 131 Processing helix chain 'S' and resid 164 through 182 Processing helix chain 'S' and resid 196 through 207 removed outlier: 3.631A pdb=" N ALA S 200 " --> pdb=" O SER S 197 " (cutoff:3.500A) Proline residue: S 203 - end of helix removed outlier: 3.853A pdb=" N ASN S 207 " --> pdb=" O TRP S 204 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 59 removed outlier: 3.676A pdb=" N THR T 17 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA T 18 " --> pdb=" O GLY T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 92 No H-bonds generated for 'chain 'T' and resid 90 through 92' Processing helix chain 'T' and resid 109 through 112 Processing helix chain 'T' and resid 124 through 126 No H-bonds generated for 'chain 'T' and resid 124 through 126' Processing helix chain 'T' and resid 127 through 131 Processing helix chain 'T' and resid 164 through 182 Processing helix chain 'T' and resid 196 through 207 removed outlier: 3.629A pdb=" N ALA T 200 " --> pdb=" O SER T 197 " (cutoff:3.500A) Proline residue: T 203 - end of helix removed outlier: 3.852A pdb=" N ASN T 207 " --> pdb=" O TRP T 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.479A pdb=" N VAL H 254 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR H 235 " --> pdb=" O GLN H 120 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER H 122 " --> pdb=" O THR H 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 63 Processing sheet with id=AA3, first strand: chain 'H' and resid 95 through 96 Processing sheet with id=AA4, first strand: chain 'H' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU H 273 " --> pdb=" O ILE H 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 136 through 139 Processing sheet with id=AA6, first strand: chain 'H' and resid 149 through 154 Processing sheet with id=AA7, first strand: chain 'H' and resid 190 through 193 Processing sheet with id=AA8, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.479A pdb=" N VAL A 254 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR A 235 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER A 122 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AB1, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AB2, first strand: chain 'A' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU A 273 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 139 Processing sheet with id=AB4, first strand: chain 'A' and resid 149 through 154 Processing sheet with id=AB5, first strand: chain 'A' and resid 190 through 193 Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 63 removed outlier: 6.479A pdb=" N VAL B 254 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR B 235 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B 122 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 61 through 63 Processing sheet with id=AB8, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain 'B' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU B 273 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 139 Processing sheet with id=AC2, first strand: chain 'B' and resid 149 through 154 Processing sheet with id=AC3, first strand: chain 'B' and resid 190 through 193 Processing sheet with id=AC4, first strand: chain 'C' and resid 61 through 63 removed outlier: 6.480A pdb=" N VAL C 254 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR C 235 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER C 122 " --> pdb=" O THR C 235 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 61 through 63 Processing sheet with id=AC6, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=AC7, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.523A pdb=" N GLU C 273 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 139 Processing sheet with id=AC9, first strand: chain 'C' and resid 149 through 154 Processing sheet with id=AD1, first strand: chain 'C' and resid 190 through 193 Processing sheet with id=AD2, first strand: chain 'D' and resid 61 through 63 removed outlier: 6.480A pdb=" N VAL D 254 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR D 235 " --> pdb=" O GLN D 120 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER D 122 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 61 through 63 Processing sheet with id=AD4, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=AD5, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU D 273 " --> pdb=" O ILE D 293 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 136 through 139 Processing sheet with id=AD7, first strand: chain 'D' and resid 149 through 154 Processing sheet with id=AD8, first strand: chain 'D' and resid 190 through 193 Processing sheet with id=AD9, first strand: chain 'E' and resid 61 through 63 removed outlier: 6.479A pdb=" N VAL E 254 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR E 235 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER E 122 " --> pdb=" O THR E 235 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 61 through 63 Processing sheet with id=AE2, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=AE3, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU E 273 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 136 through 139 Processing sheet with id=AE5, first strand: chain 'E' and resid 149 through 154 Processing sheet with id=AE6, first strand: chain 'E' and resid 190 through 193 Processing sheet with id=AE7, first strand: chain 'F' and resid 61 through 63 removed outlier: 6.479A pdb=" N VAL F 254 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR F 235 " --> pdb=" O GLN F 120 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER F 122 " --> pdb=" O THR F 235 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 61 through 63 Processing sheet with id=AE9, first strand: chain 'F' and resid 95 through 96 Processing sheet with id=AF1, first strand: chain 'F' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU F 273 " --> pdb=" O ILE F 293 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 136 through 139 Processing sheet with id=AF3, first strand: chain 'F' and resid 149 through 154 Processing sheet with id=AF4, first strand: chain 'F' and resid 190 through 193 Processing sheet with id=AF5, first strand: chain 'G' and resid 61 through 63 removed outlier: 6.478A pdb=" N VAL G 254 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR G 235 " --> pdb=" O GLN G 120 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER G 122 " --> pdb=" O THR G 235 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 61 through 63 Processing sheet with id=AF7, first strand: chain 'G' and resid 95 through 96 Processing sheet with id=AF8, first strand: chain 'G' and resid 113 through 115 removed outlier: 3.523A pdb=" N GLU G 273 " --> pdb=" O ILE G 293 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 136 through 139 Processing sheet with id=AG1, first strand: chain 'G' and resid 149 through 154 Processing sheet with id=AG2, first strand: chain 'G' and resid 190 through 193 Processing sheet with id=AG3, first strand: chain 'I' and resid 61 through 63 removed outlier: 6.479A pdb=" N VAL I 254 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR I 235 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER I 122 " --> pdb=" O THR I 235 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 61 through 63 Processing sheet with id=AG5, first strand: chain 'I' and resid 95 through 96 Processing sheet with id=AG6, first strand: chain 'I' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU I 273 " --> pdb=" O ILE I 293 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 136 through 139 Processing sheet with id=AG8, first strand: chain 'I' and resid 149 through 154 Processing sheet with id=AG9, first strand: chain 'I' and resid 190 through 193 Processing sheet with id=AH1, first strand: chain 'J' and resid 61 through 63 removed outlier: 6.478A pdb=" N VAL J 254 " --> pdb=" O VAL J 238 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR J 235 " --> pdb=" O GLN J 120 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER J 122 " --> pdb=" O THR J 235 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 61 through 63 Processing sheet with id=AH3, first strand: chain 'J' and resid 95 through 96 Processing sheet with id=AH4, first strand: chain 'J' and resid 113 through 115 removed outlier: 3.523A pdb=" N GLU J 273 " --> pdb=" O ILE J 293 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 136 through 139 Processing sheet with id=AH6, first strand: chain 'J' and resid 149 through 154 Processing sheet with id=AH7, first strand: chain 'J' and resid 190 through 193 Processing sheet with id=AH8, first strand: chain 'K' and resid 61 through 63 removed outlier: 6.479A pdb=" N VAL K 254 " --> pdb=" O VAL K 238 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR K 235 " --> pdb=" O GLN K 120 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER K 122 " --> pdb=" O THR K 235 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 61 through 63 Processing sheet with id=AI1, first strand: chain 'K' and resid 95 through 96 Processing sheet with id=AI2, first strand: chain 'K' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU K 273 " --> pdb=" O ILE K 293 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 136 through 139 Processing sheet with id=AI4, first strand: chain 'K' and resid 149 through 154 Processing sheet with id=AI5, first strand: chain 'K' and resid 190 through 193 Processing sheet with id=AI6, first strand: chain 'L' and resid 61 through 63 removed outlier: 6.480A pdb=" N VAL L 254 " --> pdb=" O VAL L 238 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR L 235 " --> pdb=" O GLN L 120 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER L 122 " --> pdb=" O THR L 235 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 61 through 63 Processing sheet with id=AI8, first strand: chain 'L' and resid 95 through 96 Processing sheet with id=AI9, first strand: chain 'L' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU L 273 " --> pdb=" O ILE L 293 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 136 through 139 Processing sheet with id=AJ2, first strand: chain 'L' and resid 149 through 154 Processing sheet with id=AJ3, first strand: chain 'L' and resid 190 through 193 Processing sheet with id=AJ4, first strand: chain 'M' and resid 61 through 63 removed outlier: 6.480A pdb=" N VAL M 254 " --> pdb=" O VAL M 238 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR M 235 " --> pdb=" O GLN M 120 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER M 122 " --> pdb=" O THR M 235 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'M' and resid 61 through 63 Processing sheet with id=AJ6, first strand: chain 'M' and resid 95 through 96 Processing sheet with id=AJ7, first strand: chain 'M' and resid 113 through 115 removed outlier: 3.522A pdb=" N GLU M 273 " --> pdb=" O ILE M 293 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 136 through 139 Processing sheet with id=AJ9, first strand: chain 'M' and resid 149 through 154 Processing sheet with id=AK1, first strand: chain 'M' and resid 190 through 193 Processing sheet with id=AK2, first strand: chain 'N' and resid 61 through 63 removed outlier: 6.481A pdb=" N VAL N 254 " --> pdb=" O VAL N 238 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR N 235 " --> pdb=" O GLN N 120 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER N 122 " --> pdb=" O THR N 235 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'N' and resid 61 through 63 Processing sheet with id=AK4, first strand: chain 'N' and resid 95 through 96 Processing sheet with id=AK5, first strand: chain 'N' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU N 273 " --> pdb=" O ILE N 293 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 136 through 139 Processing sheet with id=AK7, first strand: chain 'N' and resid 149 through 154 Processing sheet with id=AK8, first strand: chain 'N' and resid 190 through 193 Processing sheet with id=AK9, first strand: chain 'O' and resid 61 through 63 removed outlier: 6.482A pdb=" N VAL O 254 " --> pdb=" O VAL O 238 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR O 235 " --> pdb=" O GLN O 120 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER O 122 " --> pdb=" O THR O 235 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'O' and resid 61 through 63 Processing sheet with id=AL2, first strand: chain 'O' and resid 95 through 96 Processing sheet with id=AL3, first strand: chain 'O' and resid 113 through 115 removed outlier: 3.523A pdb=" N GLU O 273 " --> pdb=" O ILE O 293 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'O' and resid 136 through 139 Processing sheet with id=AL5, first strand: chain 'O' and resid 149 through 154 Processing sheet with id=AL6, first strand: chain 'O' and resid 190 through 193 Processing sheet with id=AL7, first strand: chain 'P' and resid 61 through 63 removed outlier: 6.483A pdb=" N VAL P 254 " --> pdb=" O VAL P 238 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR P 235 " --> pdb=" O GLN P 120 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER P 122 " --> pdb=" O THR P 235 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'P' and resid 61 through 63 Processing sheet with id=AL9, first strand: chain 'P' and resid 95 through 96 Processing sheet with id=AM1, first strand: chain 'P' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU P 273 " --> pdb=" O ILE P 293 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'P' and resid 136 through 139 Processing sheet with id=AM3, first strand: chain 'P' and resid 149 through 154 Processing sheet with id=AM4, first strand: chain 'P' and resid 190 through 193 Processing sheet with id=AM5, first strand: chain 'Q' and resid 61 through 63 removed outlier: 6.483A pdb=" N VAL Q 254 " --> pdb=" O VAL Q 238 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR Q 235 " --> pdb=" O GLN Q 120 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER Q 122 " --> pdb=" O THR Q 235 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'Q' and resid 61 through 63 Processing sheet with id=AM7, first strand: chain 'Q' and resid 95 through 96 Processing sheet with id=AM8, first strand: chain 'Q' and resid 113 through 115 removed outlier: 3.523A pdb=" N GLU Q 273 " --> pdb=" O ILE Q 293 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'Q' and resid 136 through 139 Processing sheet with id=AN1, first strand: chain 'Q' and resid 149 through 154 Processing sheet with id=AN2, first strand: chain 'Q' and resid 190 through 193 Processing sheet with id=AN3, first strand: chain 'R' and resid 61 through 63 removed outlier: 6.484A pdb=" N VAL R 254 " --> pdb=" O VAL R 238 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR R 235 " --> pdb=" O GLN R 120 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER R 122 " --> pdb=" O THR R 235 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'R' and resid 61 through 63 Processing sheet with id=AN5, first strand: chain 'R' and resid 95 through 96 Processing sheet with id=AN6, first strand: chain 'R' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU R 273 " --> pdb=" O ILE R 293 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'R' and resid 136 through 139 Processing sheet with id=AN8, first strand: chain 'R' and resid 149 through 154 Processing sheet with id=AN9, first strand: chain 'R' and resid 190 through 193 Processing sheet with id=AO1, first strand: chain 'S' and resid 61 through 63 removed outlier: 6.484A pdb=" N VAL S 254 " --> pdb=" O VAL S 238 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR S 235 " --> pdb=" O GLN S 120 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER S 122 " --> pdb=" O THR S 235 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'S' and resid 61 through 63 Processing sheet with id=AO3, first strand: chain 'S' and resid 95 through 96 Processing sheet with id=AO4, first strand: chain 'S' and resid 113 through 115 removed outlier: 3.524A pdb=" N GLU S 273 " --> pdb=" O ILE S 293 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'S' and resid 136 through 139 Processing sheet with id=AO6, first strand: chain 'S' and resid 149 through 154 Processing sheet with id=AO7, first strand: chain 'S' and resid 190 through 193 Processing sheet with id=AO8, first strand: chain 'T' and resid 61 through 63 removed outlier: 6.485A pdb=" N VAL T 254 " --> pdb=" O VAL T 238 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR T 235 " --> pdb=" O GLN T 120 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER T 122 " --> pdb=" O THR T 235 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'T' and resid 61 through 63 Processing sheet with id=AP1, first strand: chain 'T' and resid 95 through 96 Processing sheet with id=AP2, first strand: chain 'T' and resid 113 through 115 removed outlier: 3.525A pdb=" N GLU T 273 " --> pdb=" O ILE T 293 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'T' and resid 136 through 139 Processing sheet with id=AP4, first strand: chain 'T' and resid 149 through 154 Processing sheet with id=AP5, first strand: chain 'T' and resid 190 through 193 2600 hydrogen bonds defined for protein. 6780 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: 19.88 Time building geometry restraints manager: 18.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8339 1.34 - 1.46: 16682 1.46 - 1.58: 27699 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 52940 Sorted by residual: bond pdb=" S6 YZTXA 3 " pdb="O2S6 YZTXA 3 " ideal model delta sigma weight residual 1.477 1.554 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" S6 YZTRA 3 " pdb="O2S6 YZTRA 3 " ideal model delta sigma weight residual 1.477 1.554 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" S6 YZTFA 3 " pdb="O2S6 YZTFA 3 " ideal model delta sigma weight residual 1.477 1.554 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" S6 YZT 3 3 " pdb="O2S6 YZT 3 3 " ideal model delta sigma weight residual 1.477 1.553 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" S6 YZT r 3 " pdb="O2S6 YZT r 3 " ideal model delta sigma weight residual 1.477 1.553 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 52935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 59930 1.91 - 3.81: 11215 3.81 - 5.72: 1343 5.72 - 7.63: 112 7.63 - 9.54: 80 Bond angle restraints: 72680 Sorted by residual: angle pdb=" C ASN L 229 " pdb=" CA ASN L 229 " pdb=" CB ASN L 229 " ideal model delta sigma weight residual 110.86 101.32 9.54 1.65e+00 3.67e-01 3.34e+01 angle pdb=" C ASN G 229 " pdb=" CA ASN G 229 " pdb=" CB ASN G 229 " ideal model delta sigma weight residual 110.86 101.36 9.50 1.65e+00 3.67e-01 3.32e+01 angle pdb=" C ASN D 229 " pdb=" CA ASN D 229 " pdb=" CB ASN D 229 " ideal model delta sigma weight residual 110.86 101.36 9.50 1.65e+00 3.67e-01 3.31e+01 angle pdb=" C ASN J 229 " pdb=" CA ASN J 229 " pdb=" CB ASN J 229 " ideal model delta sigma weight residual 110.86 101.37 9.49 1.65e+00 3.67e-01 3.31e+01 angle pdb=" C ASN B 229 " pdb=" CA ASN B 229 " pdb=" CB ASN B 229 " ideal model delta sigma weight residual 110.86 101.37 9.49 1.65e+00 3.67e-01 3.31e+01 ... (remaining 72675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 37156 25.98 - 51.97: 978 51.97 - 77.95: 522 77.95 - 103.93: 204 103.93 - 129.91: 80 Dihedral angle restraints: 38940 sinusoidal: 21840 harmonic: 17100 Sorted by residual: dihedral pdb=" CA ALA K 266 " pdb=" C ALA K 266 " pdb=" N THR K 267 " pdb=" CA THR K 267 " ideal model delta harmonic sigma weight residual -180.00 -154.32 -25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ALA M 266 " pdb=" C ALA M 266 " pdb=" N THR M 267 " pdb=" CA THR M 267 " ideal model delta harmonic sigma weight residual -180.00 -154.33 -25.67 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ALA D 266 " pdb=" C ALA D 266 " pdb=" N THR D 267 " pdb=" CA THR D 267 " ideal model delta harmonic sigma weight residual 180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 38937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 8293 0.131 - 0.262: 1954 0.262 - 0.393: 228 0.393 - 0.523: 34 0.523 - 0.654: 51 Chirality restraints: 10560 Sorted by residual: chirality pdb=" C1 MANiA 5 " pdb=" O4 NAGiA 2 " pdb=" C2 MANiA 5 " pdb=" O5 MANiA 5 " both_signs ideal model delta sigma weight residual False 2.40 1.87 0.53 2.00e-02 2.50e+03 6.98e+02 chirality pdb=" C1 MANEA 5 " pdb=" O4 NAGEA 2 " pdb=" C2 MANEA 5 " pdb=" O5 MANEA 5 " both_signs ideal model delta sigma weight residual False 2.40 1.87 0.53 2.00e-02 2.50e+03 6.95e+02 chirality pdb=" C1 MANoA 5 " pdb=" O4 NAGoA 2 " pdb=" C2 MANoA 5 " pdb=" O5 MANoA 5 " both_signs ideal model delta sigma weight residual False 2.40 1.87 0.53 2.00e-02 2.50e+03 6.94e+02 ... (remaining 10557 not shown) Planarity restraints: 8080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAGOB 1 " -0.060 2.00e-02 2.50e+03 4.93e-02 3.04e+01 pdb=" C7 NAGOB 1 " 0.018 2.00e-02 2.50e+03 pdb=" C8 NAGOB 1 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAGOB 1 " 0.078 2.00e-02 2.50e+03 pdb=" O7 NAGOB 1 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG6A 1 " 0.059 2.00e-02 2.50e+03 4.89e-02 2.99e+01 pdb=" C7 NAG6A 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG6A 1 " 0.046 2.00e-02 2.50e+03 pdb=" N2 NAG6A 1 " -0.077 2.00e-02 2.50e+03 pdb=" O7 NAG6A 1 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAGCB 1 " 0.059 2.00e-02 2.50e+03 4.88e-02 2.98e+01 pdb=" C7 NAGCB 1 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAGCB 1 " 0.046 2.00e-02 2.50e+03 pdb=" N2 NAGCB 1 " -0.077 2.00e-02 2.50e+03 pdb=" O7 NAGCB 1 " -0.010 2.00e-02 2.50e+03 ... (remaining 8077 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 20913 2.90 - 3.40: 47677 3.40 - 3.90: 90225 3.90 - 4.40: 99423 4.40 - 4.90: 169209 Nonbonded interactions: 427447 Sorted by model distance: nonbonded pdb=" C3 NAGmA 2 " pdb=" O5 YZTmA 3 " model vdw 2.404 2.776 nonbonded pdb=" C3 NAGAB 2 " pdb=" O5 YZTAB 3 " model vdw 2.404 2.776 nonbonded pdb=" C3 NAGyA 2 " pdb=" O5 YZTyA 3 " model vdw 2.404 2.776 nonbonded pdb=" C3 NAG i 2 " pdb=" O5 YZT i 3 " model vdw 2.404 2.776 nonbonded pdb=" C3 NAGsA 2 " pdb=" O5 YZTsA 3 " model vdw 2.404 2.776 ... (remaining 427442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '0A' selection = chain '1A' selection = chain '2' selection = chain '3' selection = chain '3A' selection = chain '4A' selection = chain '5' selection = chain '6' selection = chain '6A' selection = chain '7A' selection = chain '8' selection = chain '9' selection = chain '9A' selection = chain 'AB' selection = chain 'BA' selection = chain 'CA' selection = chain 'CB' selection = chain 'DB' selection = chain 'EA' selection = chain 'FA' selection = chain 'FB' selection = chain 'GB' selection = chain 'HA' selection = chain 'IA' selection = chain 'IB' selection = chain 'JB' selection = chain 'KA' selection = chain 'LA' selection = chain 'LB' selection = chain 'MB' selection = chain 'NA' selection = chain 'OA' selection = chain 'OB' selection = chain 'PB' selection = chain 'QA' selection = chain 'RA' selection = chain 'TA' selection = chain 'UA' selection = chain 'V' selection = chain 'W' selection = chain 'WA' selection = chain 'XA' selection = chain 'Y' selection = chain 'Z' selection = chain 'ZA' selection = chain 'aA' selection = chain 'b' selection = chain 'c' selection = chain 'cA' selection = chain 'dA' selection = chain 'e' selection = chain 'f' selection = chain 'fA' selection = chain 'gA' selection = chain 'h' selection = chain 'i' selection = chain 'iA' selection = chain 'jA' selection = chain 'k' selection = chain 'l' selection = chain 'lA' selection = chain 'mA' selection = chain 'n' selection = chain 'o' selection = chain 'oA' selection = chain 'pA' selection = chain 'q' selection = chain 'r' selection = chain 'rA' selection = chain 'sA' selection = chain 't' selection = chain 'u' selection = chain 'uA' selection = chain 'vA' selection = chain 'w' selection = chain 'x' selection = chain 'xA' selection = chain 'yA' selection = chain 'z' } ncs_group { reference = chain '1' selection = chain '5A' selection = chain '7' selection = chain 'BB' selection = chain 'DA' selection = chain 'HB' selection = chain 'JA' selection = chain 'NB' selection = chain 'PA' selection = chain 'VA' selection = chain 'X' selection = chain 'bA' selection = chain 'd' selection = chain 'hA' selection = chain 'j' selection = chain 'nA' selection = chain 'p' selection = chain 'tA' selection = chain 'v' selection = chain 'zA' } ncs_group { reference = chain '2A' selection = chain '4' selection = chain '8A' selection = chain 'AA' selection = chain 'EB' selection = chain 'GA' selection = chain 'KB' selection = chain 'MA' selection = chain 'SA' selection = chain 'U' selection = chain 'YA' selection = chain 'a' selection = chain 'eA' selection = chain 'g' selection = chain 'kA' selection = chain 'm' selection = chain 'qA' selection = chain 's' selection = chain 'wA' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 1.530 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 95.130 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.930 Set refine NCS operators: 0.010 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:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 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 : 0.011 0.077 52940 Z= 0.640 Angle : 1.484 9.536 72680 Z= 0.868 Chirality : 0.120 0.654 10560 Planarity : 0.007 0.049 7960 Dihedral : 16.913 129.914 28060 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.40 % Allowed : 2.02 % Favored : 97.57 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.10), residues: 5820 helix: 0.31 (0.11), residues: 1420 sheet: 0.83 (0.12), residues: 1540 loop : -0.10 (0.11), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.008 TRP N 81 PHE 0.020 0.004 PHE I 234 TYR 0.050 0.009 TYR B 83 ARG 0.002 0.001 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 637 time to evaluate : 4.020 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: H 179 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8243 (mt-10) REVERT: A 179 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8529 (mt-10) REVERT: D 179 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8408 (mt-10) REVERT: F 179 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8205 (mt-10) REVERT: I 96 ASP cc_start: 0.8260 (t0) cc_final: 0.8049 (t0) REVERT: K 96 ASP cc_start: 0.8348 (t0) cc_final: 0.8146 (t0) REVERT: L 96 ASP cc_start: 0.8343 (t0) cc_final: 0.8122 (t0) REVERT: M 179 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8381 (mt-10) REVERT: N 96 ASP cc_start: 0.8275 (t0) cc_final: 0.8045 (t0) REVERT: O 291 GLN cc_start: 0.8680 (mp10) cc_final: 0.8442 (mp10) REVERT: P 96 ASP cc_start: 0.8297 (t0) cc_final: 0.7874 (t0) REVERT: P 136 GLN cc_start: 0.8706 (pt0) cc_final: 0.8463 (pt0) REVERT: Q 179 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8555 (mt-10) REVERT: Q 273 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7759 (mt-10) REVERT: R 136 GLN cc_start: 0.8724 (pt0) cc_final: 0.8490 (pt0) REVERT: R 179 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8563 (mt-10) REVERT: R 273 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7736 (mt-10) REVERT: R 291 GLN cc_start: 0.8732 (mp10) cc_final: 0.8476 (mp10) REVERT: S 136 GLN cc_start: 0.8662 (pt0) cc_final: 0.8459 (pt0) REVERT: S 179 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8740 (mt-10) REVERT: S 273 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7580 (mt-10) REVERT: T 130 GLN cc_start: 0.9124 (mt0) cc_final: 0.8827 (mt0) REVERT: T 136 GLN cc_start: 0.8701 (pt0) cc_final: 0.8303 (pt0) REVERT: T 179 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8680 (mt-10) outliers start: 20 outliers final: 19 residues processed: 657 average time/residue: 1.3737 time to fit residues: 1124.9165 Evaluate side-chains 374 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 355 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 173 ASN Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain E residue 173 ASN Chi-restraints excluded: chain F residue 173 ASN Chi-restraints excluded: chain G residue 173 ASN Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain J residue 173 ASN Chi-restraints excluded: chain K residue 173 ASN Chi-restraints excluded: chain L residue 173 ASN Chi-restraints excluded: chain M residue 173 ASN Chi-restraints excluded: chain N residue 173 ASN Chi-restraints excluded: chain O residue 173 ASN Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain Q residue 173 ASN Chi-restraints excluded: chain R residue 173 ASN Chi-restraints excluded: chain S residue 173 ASN Chi-restraints excluded: chain T residue 173 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 489 optimal weight: 3.9990 chunk 439 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 296 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 454 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 276 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 526 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 ASN H 136 GLN H 178 GLN ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 GLN A 157 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 136 GLN C 291 GLN D 136 GLN D 291 GLN E 44 GLN E 66 ASN E 130 GLN E 136 GLN F 44 GLN G 44 GLN G 130 GLN G 136 GLN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN J 66 ASN J 136 GLN K 44 GLN L 136 GLN L 291 GLN Q 133 ASN Q 178 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN S 44 GLN S 157 GLN T 178 GLN T 271 GLN ** T 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 52940 Z= 0.274 Angle : 0.733 10.231 72680 Z= 0.345 Chirality : 0.047 0.195 10560 Planarity : 0.004 0.031 7960 Dihedral : 14.188 109.519 18858 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.52 % Allowed : 4.27 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.10), residues: 5820 helix: 2.58 (0.13), residues: 1440 sheet: 1.19 (0.13), residues: 1500 loop : 0.24 (0.11), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 81 PHE 0.012 0.001 PHE L 211 TYR 0.025 0.002 TYR J 33 ARG 0.002 0.001 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 402 time to evaluate : 3.893 Fit side-chains REVERT: A 54 GLU cc_start: 0.8614 (pp20) cc_final: 0.8392 (pp20) REVERT: S 273 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7814 (mt-10) REVERT: T 133 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8125 (t0) outliers start: 75 outliers final: 45 residues processed: 456 average time/residue: 1.1767 time to fit residues: 691.5583 Evaluate side-chains 374 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 328 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 133 ASN Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 280 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 292 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 438 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 527 optimal weight: 7.9990 chunk 570 optimal weight: 5.9990 chunk 469 optimal weight: 8.9990 chunk 523 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 423 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN I 291 GLN J 66 ASN N 66 ASN O 133 ASN P 133 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 52940 Z= 0.275 Angle : 0.681 9.590 72680 Z= 0.318 Chirality : 0.046 0.218 10560 Planarity : 0.003 0.038 7960 Dihedral : 13.833 108.195 18820 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.78 % Allowed : 5.36 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.11), residues: 5820 helix: 2.95 (0.13), residues: 1440 sheet: 1.11 (0.13), residues: 1520 loop : 0.29 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 81 PHE 0.012 0.002 PHE J 211 TYR 0.024 0.002 TYR J 33 ARG 0.001 0.000 ARG R 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 387 time to evaluate : 3.863 Fit side-chains revert: symmetry clash REVERT: B 19 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8811 (pp) REVERT: S 273 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7836 (mt-10) REVERT: T 133 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8173 (t0) outliers start: 88 outliers final: 33 residues processed: 443 average time/residue: 1.2084 time to fit residues: 687.1385 Evaluate side-chains 378 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 343 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 273 GLU Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 273 GLU Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 133 ASN Chi-restraints excluded: chain T residue 135 VAL Chi-restraints excluded: chain T residue 273 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 521 optimal weight: 20.0000 chunk 396 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 58 optimal weight: 40.0000 chunk 251 optimal weight: 10.0000 chunk 354 optimal weight: 0.9990 chunk 529 optimal weight: 6.9990 chunk 560 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 501 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 52940 Z= 0.234 Angle : 0.663 9.823 72680 Z= 0.305 Chirality : 0.045 0.203 10560 Planarity : 0.003 0.032 7960 Dihedral : 13.197 103.942 18820 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.90 % Allowed : 5.75 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.11), residues: 5820 helix: 3.00 (0.13), residues: 1440 sheet: 1.03 (0.13), residues: 1520 loop : 0.30 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 81 PHE 0.011 0.001 PHE J 211 TYR 0.023 0.001 TYR J 33 ARG 0.001 0.000 ARG T 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 369 time to evaluate : 3.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 THR cc_start: 0.9281 (m) cc_final: 0.9079 (p) REVERT: E 54 GLU cc_start: 0.8476 (pp20) cc_final: 0.8254 (tm-30) REVERT: S 273 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7852 (mt-10) REVERT: T 133 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8195 (t0) outliers start: 94 outliers final: 51 residues processed: 434 average time/residue: 1.2033 time to fit residues: 671.9122 Evaluate side-chains 401 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 133 ASN Chi-restraints excluded: chain T residue 135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 466 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 417 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 478 optimal weight: 20.0000 chunk 387 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 286 optimal weight: 2.9990 chunk 503 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 66 ASN K 51 ASN P 51 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 52940 Z= 0.211 Angle : 0.654 9.810 72680 Z= 0.299 Chirality : 0.044 0.198 10560 Planarity : 0.003 0.032 7960 Dihedral : 12.912 102.578 18820 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.58 % Allowed : 6.62 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.11), residues: 5820 helix: 3.03 (0.13), residues: 1440 sheet: 0.96 (0.13), residues: 1520 loop : 0.30 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 81 PHE 0.012 0.001 PHE F 211 TYR 0.022 0.001 TYR J 33 ARG 0.001 0.000 ARG T 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 368 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8753 (pp) REVERT: C 268 ASN cc_start: 0.8290 (p0) cc_final: 0.8017 (p0) REVERT: E 54 GLU cc_start: 0.8477 (pp20) cc_final: 0.8246 (tm-30) REVERT: N 164 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8962 (p0) REVERT: S 273 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7899 (mt-10) outliers start: 78 outliers final: 53 residues processed: 422 average time/residue: 1.2629 time to fit residues: 679.5023 Evaluate side-chains 403 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 348 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 268 ASN Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 268 ASN Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 273 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 135 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 188 optimal weight: 9.9990 chunk 504 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 561 optimal weight: 0.9990 chunk 465 optimal weight: 5.9990 chunk 259 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 294 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 157 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 52940 Z= 0.165 Angle : 0.642 9.972 72680 Z= 0.290 Chirality : 0.043 0.180 10560 Planarity : 0.003 0.032 7960 Dihedral : 12.422 99.370 18820 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.48 % Allowed : 7.37 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.11), residues: 5820 helix: 3.10 (0.13), residues: 1440 sheet: 0.93 (0.13), residues: 1520 loop : 0.31 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 81 PHE 0.012 0.001 PHE F 211 TYR 0.020 0.001 TYR Q 33 ARG 0.001 0.000 ARG T 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 373 time to evaluate : 3.912 Fit side-chains revert: symmetry clash REVERT: B 19 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8766 (pp) REVERT: J 273 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: P 16 ASP cc_start: 0.8447 (p0) cc_final: 0.8213 (m-30) REVERT: S 273 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7940 (mt-10) outliers start: 73 outliers final: 48 residues processed: 425 average time/residue: 1.2519 time to fit residues: 679.9313 Evaluate side-chains 403 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 353 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 135 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 541 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 319 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 chunk 317 optimal weight: 7.9990 chunk 472 optimal weight: 3.9990 chunk 313 optimal weight: 0.0040 chunk 559 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 340 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN M 51 ASN O 51 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 52940 Z= 0.276 Angle : 0.672 9.881 72680 Z= 0.310 Chirality : 0.045 0.212 10560 Planarity : 0.003 0.031 7960 Dihedral : 12.335 101.747 18820 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.60 % Allowed : 7.59 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.11), residues: 5820 helix: 3.06 (0.13), residues: 1440 sheet: 0.91 (0.13), residues: 1520 loop : 0.30 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 81 PHE 0.011 0.001 PHE M 211 TYR 0.024 0.001 TYR J 33 ARG 0.001 0.000 ARG T 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 355 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8768 (pp) REVERT: N 164 ASP cc_start: 0.9202 (OUTLIER) cc_final: 0.8976 (p0) REVERT: P 16 ASP cc_start: 0.8535 (p0) cc_final: 0.8251 (m-30) REVERT: S 273 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7891 (mt-10) outliers start: 79 outliers final: 58 residues processed: 413 average time/residue: 1.2895 time to fit residues: 675.8670 Evaluate side-chains 404 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 344 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 268 ASN Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 273 GLU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 135 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 345 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 439 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 52940 Z= 0.343 Angle : 0.694 9.912 72680 Z= 0.326 Chirality : 0.046 0.246 10560 Planarity : 0.003 0.033 7960 Dihedral : 12.320 104.628 18820 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.48 % Allowed : 8.18 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.11), residues: 5820 helix: 2.94 (0.13), residues: 1440 sheet: 0.89 (0.13), residues: 1520 loop : 0.29 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 PHE 0.010 0.001 PHE M 211 TYR 0.031 0.002 TYR K 73 ARG 0.001 0.000 ARG M 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 351 time to evaluate : 4.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8678 (pp) REVERT: N 164 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.9015 (p0) REVERT: P 16 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8338 (m-30) REVERT: S 273 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8011 (mt-10) outliers start: 73 outliers final: 57 residues processed: 404 average time/residue: 1.2936 time to fit residues: 662.9214 Evaluate side-chains 399 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 3.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 273 GLU Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 273 GLU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 135 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 508 optimal weight: 9.9990 chunk 535 optimal weight: 20.0000 chunk 488 optimal weight: 6.9990 chunk 520 optimal weight: 0.0870 chunk 313 optimal weight: 0.6980 chunk 226 optimal weight: 0.0570 chunk 409 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 470 optimal weight: 0.9990 chunk 492 optimal weight: 7.9990 chunk 519 optimal weight: 7.9990 overall best weight: 1.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 52940 Z= 0.161 Angle : 0.643 14.065 72680 Z= 0.296 Chirality : 0.043 0.212 10560 Planarity : 0.003 0.033 7960 Dihedral : 11.986 99.783 18820 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.19 % Allowed : 8.50 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.11), residues: 5820 helix: 3.02 (0.13), residues: 1440 sheet: 0.92 (0.13), residues: 1520 loop : 0.31 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 81 PHE 0.011 0.001 PHE J 211 TYR 0.020 0.001 TYR Q 33 ARG 0.001 0.000 ARG T 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 360 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8760 (mmt) cc_final: 0.8301 (mmm) REVERT: B 19 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8758 (pp) REVERT: N 16 ASP cc_start: 0.8444 (p0) cc_final: 0.8062 (m-30) REVERT: Q 16 ASP cc_start: 0.8563 (p0) cc_final: 0.8108 (m-30) REVERT: S 273 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7933 (mt-10) outliers start: 59 outliers final: 45 residues processed: 405 average time/residue: 1.2940 time to fit residues: 668.5818 Evaluate side-chains 394 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 348 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 342 optimal weight: 8.9990 chunk 550 optimal weight: 0.4980 chunk 336 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 382 optimal weight: 10.0000 chunk 577 optimal weight: 30.0000 chunk 531 optimal weight: 20.0000 chunk 460 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 355 optimal weight: 9.9990 chunk 282 optimal weight: 6.9990 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 52940 Z= 0.319 Angle : 0.680 10.605 72680 Z= 0.320 Chirality : 0.045 0.229 10560 Planarity : 0.003 0.038 7960 Dihedral : 11.998 102.526 18820 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.07 % Allowed : 8.83 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.11), residues: 5820 helix: 2.95 (0.13), residues: 1440 sheet: 0.92 (0.13), residues: 1520 loop : 0.29 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 81 PHE 0.011 0.001 PHE M 211 TYR 0.024 0.001 TYR J 33 ARG 0.001 0.000 ARG M 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8755 (pp) REVERT: N 164 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8991 (p0) REVERT: S 273 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8006 (mt-10) outliers start: 53 outliers final: 49 residues processed: 382 average time/residue: 1.3437 time to fit residues: 648.1590 Evaluate side-chains 386 residues out of total 4940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 335 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 280 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 268 ASN Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 280 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 280 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 280 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain P residue 280 THR Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 135 VAL Chi-restraints excluded: chain Q residue 280 THR Chi-restraints excluded: chain R residue 16 ASP Chi-restraints excluded: chain R residue 85 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 280 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 280 THR Chi-restraints excluded: chain T residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 365 optimal weight: 5.9990 chunk 490 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 460 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 473 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.097919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061725 restraints weight = 100907.758| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.84 r_work: 0.2779 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 52940 Z= 0.225 Angle : 0.648 9.819 72680 Z= 0.302 Chirality : 0.044 0.222 10560 Planarity : 0.003 0.047 7960 Dihedral : 11.881 100.909 18820 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.09 % Allowed : 8.72 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.11), residues: 5820 helix: 2.95 (0.13), residues: 1440 sheet: 0.90 (0.13), residues: 1520 loop : 0.28 (0.12), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 PHE 0.011 0.001 PHE J 211 TYR 0.022 0.001 TYR J 33 ARG 0.001 0.000 ARG M 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14025.55 seconds wall clock time: 246 minutes 45.17 seconds (14805.17 seconds total)